The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage

Abstract: BACKGROUND G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds.

Abstract: Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes.

Abstract: The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo.

Abstract: RESULTS We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase.

Abstract: Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1.

Abstract: Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively.

Abstract: In general, G4 motifs were underrepresented in genes.

Abstract: However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites.

Abstract: CONCLUSIONS In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.


Wnt7a signaling promotes dendritic spine growth and synaptic strength through Ca²⁺/Calmodulin-dependent protein kinase II.

Abstract: The balance between excitatory and inhibitory synapses is crucial for normal brain function.

Abstract: Wnt proteins stimulate synapse formation by increasing synaptic assembly.

Abstract: However, it is unclear whether Wnt signaling differentially regulates the formation of excitatory and inhibitory synapses.

Abstract: Here, we demonstrate that Wnt7a preferentially stimulates excitatory synapse formation and function.

Abstract: In hippocampal neurons, Wnt7a increases the number of excitatory synapses, whereas inhibitory synapses are unaffected.

Abstract: Wnt7a or postsynaptic expression of Dishevelled-1 (Dvl1), a core Wnt signaling component, increases the frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs), but not miniature inhibitory postsynaptic currents (mIPSCs).

Abstract: Wnt7a increases the density and maturity of dendritic spines, whereas Wnt7a-Dvl1-deficient mice exhibit defects in spine morphogenesis and mossy fiber-CA3 synaptic transmission in the hippocampus.

Abstract: Using a postsynaptic reporter for Ca(2+)/Calmodulin-dependent protein kinase II (CaMKII) activity, we demonstrate that Wnt7a rapidly activates CaMKII in spines.

Abstract: Importantly, CaMKII inhibition abolishes the effects of Wnt7a on spine growth and excitatory synaptic strength.

Abstract: These data indicate that Wnt7a signaling is critical to regulate spine growth and synaptic strength through the local activation of CaMKII at dendritic spines.

Abstract: Therefore, aberrant Wnt7a signaling may contribute to neurological disorders in which excitatory signaling is disrupted.


Bitter taste receptors and α-gustducin regulate the secretion of ghrelin with functional effects on food intake and gastric emptying.

Abstract: Ghrelin is a hunger hormone with gastroprokinetic properties but the factors controlling ghrelin secretion from the stomach are unknown.

Abstract: Bitter taste receptors (T2R) and the gustatory G proteins, α-gustducin (gust) and α-transducin, are expressed in the gut and are involved in the chemosensation of nutrients.

Abstract: This study aimed to investigate whether T2R-agonists affect (i) ghrelin release via α-gustducin and (ii) food intake and gastric emptying via the release of ghrelin.

Abstract: The mouse stomach contains two ghrelin cell populations: cells containing octanoyl and desoctanoyl ghrelin, which were colocalized with α-gustducin and α-transducin, and cells staining for desoctanoyl ghrelin.

Abstract: Gavage of T2R-agonists increased plasma octanoyl ghrelin levels in WT mice but the effect was partially blunted in gust(-/-) mice.

Abstract: Intragastric administration of T2R-agonists increased food intake during the first 30 min in WT but not in gust(-/-) and ghrelin receptor knockout mice.

Abstract: This increase was accompanied by an increase in the mRNA expression of agouti-related peptide in the hypothalamus of WT but not of gust(-/-) mice.

Abstract: The temporary increase in food intake was followed by a prolonged decrease (next 4 h), which correlated with an inhibition of gastric emptying.

Abstract: The delay in emptying, which was partially counteracted by ghrelin, was not mediated by cholecystokinin and GLP-1 but involved a direct inhibitory effect of T2R-agonists on gastric contractility.

Abstract: This study is unique in providing functional evidence that activation of bitter taste receptors stimulates ghrelin secretion.

Abstract: Modulation of endogenous ghrelin levels by tastants may provide novel therapeutic applications for the treatment of weight -and gastrointestinal motility disorders.


Ca2+-permeable AMPA receptors regulate growth of human glioblastoma via Akt activation.

Abstract: Evidence has been accumulated that glioblastoma cells release and exploit glutamate for proliferation and migration by autocrine or paracrine loops through Ca2+-permeable AMPA-type glutamate receptors.

Abstract: Here, we show that Ca2+ signaling mediated by AMPA receptor regulates the growth and motility of glioblastoma cells via activation of Akt.

Abstract: Ca2+ supplied through Ca2+-permeable AMPA receptor phosphorylated Akt at Ser-473, thereby facilitating proliferation and mobility.

Abstract: A dominant-negative form of Akt inhibited cell proliferation and migration accelerated by overexpression of Ca2+-permeable AMPA receptor.

Abstract: In contrast, introduction of a constitutively active form of Akt rescued tumor cells from apoptosis induced by the conversion of Ca2+-permeable AMPA receptor to Ca2+-impermeable receptors by the delivery of GluR2 cDNA.

Abstract: Therefore, Akt functions as downstream effectors for Ca2+-signaling mediated by AMPA receptor in glioblastoma cells.

Abstract: The activation of the glutamate-AMPA receptor-Akt pathway may contribute to the high degree of anaplasia and invasive growth of human glioblastoma.

Abstract: This novel pathway might give an alternative therapeutic target.


The Extracellular Surface of the GLP-1 Receptor Is a Molecular Trigger for Biased Agonism

Abstract: Ligand-directed signal bias offers opportunities for sculpting molecular events, with the promise of better, safer therapeutics.

Abstract: Critical to the exploitation of signal bias is an understanding of the molecular events coupling ligand binding to intracellular signaling.

Abstract: Activation of class B G protein-coupled receptors is driven by interaction of the peptide N terminus with the receptor core.

Abstract: To understand how this drives signaling, we have used advanced analytical methods that enable separation of effects on pathway-specific signaling from those that modify agonist affinity and mapped the functional consequence of receptor modification onto three-dimensional models of a receptor-ligand complex.

Abstract: This yields molecular insights into the initiation of receptor activation and the mechanistic basis for biased agonism.

Abstract: Our data reveal that peptide agonists can engage different elements of the receptor extracellular face to achieve effector coupling and biased signaling providing a foundation for rational design of biased agonists.


A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells

Abstract: CD8 tissue-resident memory T (TRM) cells provide efficient local control of viral infection, but the role of CD4 TRM is less clear.

Abstract: Here, by using parabiotic mice, we show that a preexisting pool of CD4 TRM cells in the genital mucosa was required for full protection from a lethal herpes simplex virus 2 (HSV-2) infection.

Abstract: Chemokines secreted by a local network of macrophages maintained vaginal CD4 TRM in memory lymphocyte clusters (MLCs), independently of circulating memory T cells.

Abstract: CD4 TRM cells within the MLCs were enriched in clones that expanded in response to HSV-2.

Abstract: Our results highlight the need for vaccine strategies that enable establishment of TRM cells for protection from a sexually transmitted virus and provide insights as to how such a pool might be established.


Influence of smoking and plasma factors on patency of femoropopliteal vein grafts.

Abstract: OBJECTIVE To determine the effects of smoking, plasma lipids, lipoproteins, apolipoproteins, and fibrinogen on the patency of saphenous vein femoropopliteal bypass grafts at one year.

Abstract: DESIGN Prospective study of patients with saphenous vein femoropopliteal bypass grafts entered into a multicentre trial.

Abstract: SETTING Surgical wards, outpatient clinics, and home visits coordinated by two tertiary referral centres in London and Birmingham.

Abstract: PATIENTS 157 Patients (mean age 66.6 (SD 8.2) years), 113 with patent grafts and 44 with occluded grafts one year after bypass.

Abstract: MAIN OUTCOME MEASURE Cumulative percentage patency at one year.

Abstract: RESULTS Markers for smoking (blood carboxyhaemoglobin concentration (p less than 0.05) and plasma thiocyanate concentration (p less than 0.01) and plasma concentrations of fibrinogen (p less than 0.001) and apolipoproteins AI (p less than 0.04) and (a) (p less than 0.05) were significantly higher in patients with occluded grafts.

Abstract: Serum cholesterol concentrations were significantly higher in patients with grafts that remained patent one year after bypass (p less than 0.005).

Abstract: Analysis of the smoking markers indicated that a quarter of patients (40) were untruthful in their claims to have stopped smoking.

Abstract: Based on smoking markers, patency of grafts in smokers was significantly lower at one year by life table analysis than in non-smokers (63% v 84%, p less than 0.02).

Abstract: Patency was significantly higher by life table analysis in patients with a plasma fibrinogen concentration below the median than in those with a concentration above (90% v 57%, p less than 0.0002).

Abstract: Surprisingly, increased plasma low density lipoprotein cholesterol concentration was significantly associated with improved patency at one year (85%) at values above the median compared with patency (only 68%) at values in the lower half of the range (p less than 0.02).

Abstract: CONCLUSIONS Plasma fibrinogen concentration was the most important variable predicting graft occlusion, followed by smoking markers.

Abstract: A more forceful approach is needed to stop patients smoking; therapeutic measures to improve patency of vein grafts should focus on decreasing plasma fibrinogen concentration rather than serum cholesterol concentration.


No effect of dietary fat on short-term weight gain in mice treated with atypical antipsychotic drugs

Abstract: Rationale:Atypical antipsychotic drugs (AAD) induce significant weight gain in female C57BL/6J mice.

Abstract: The effect of dietary fat on weight gain and serum lipids in this model is unknown.

Abstract: Objectives:

Abstract: Test the hypothesis that the obesigenic effects of these drugs are greater in the presence of a high-fat diet.

Abstract: Methods:Female C57BL/6J mice were treated with atypical antipsychotics for 3 weeks and fed either a low-fat or high-fat diet (4.6 vs 15.6% fat by wt).

Abstract: Food intake (FI), body weight (BW), body composition, and serum lipids were measured during treatment with optimized doses of olanzapine, quetiapine, and risperidone.

Abstract: Energy intake (EI) and feed efficiency (FE) were calculated.

Abstract: Group differences in change were analyzed via repeated measures analysis of variance (ANOVA).

Abstract: Serum lipid concentrations, EI and FE were compared using two-way ANOVA.Results:AAD-treated mice gained significantly more weight than controls after 3 weeks (P<0.001).

Abstract: Treatment and diet had significant effects on FI and EI over time (P<0.001).

Abstract: AAD-treated mice had significantly higher FE than controls (P<0.05); however, there was no significant drug by diet interaction (P=0.65).

Abstract: Risperidone low-fat mice gained significantly more absolute fat mass than placebo low-fat mice (P<0.05).

Abstract: All treatment groups, except quetiapine low-fat and olanzapine high-fat, gained significantly more absolute lean mass than placebo controls (P<0.05).

Abstract: Cholesterol levels were significantly lower in quetiapine and risperidone than placebo (P<0.05).

Abstract: Risperidone low-fat mice had significantly higher triglyceride levels than placebo and risperidone high-fat mice (P<0.05).Conclusions:A high-fat diet does not increase AAD-induced BW gain in female mice during a 3-week treatment period.


The role of free radicals in cold injuries.

Abstract: Cold injury is a tissue trauma produced by exposure to freezing temperatures and even brief exposure to a severely cold and windy environment.

Abstract: Rewarming of frozen tissue is associated with blood reperfusion and the simultaneous generation of free oxygen radicals.

Abstract: In this review is discussed the current understanding of the mechanism of action of free oxygen radicals as related to cold injury during rewarming.

Abstract: Decreased energy stores during ischaemia lead to the accumulation of adenine nucleotides and liberation of free fatty acids due to the breakdown of lipid membranes.

Abstract: On rewarming, free fatty acids are metabolized via cyclo-oxygenase and adenine nucleotides are metabolized via the xanthine oxidase pathway.

Abstract: These may be the source of free oxygen radicals.

Abstract: Leukocytes may also play a major role in the pathogenesis of cold injury.

Abstract: Oxygen radical scavengers, such as superoxide dismutase and catalase, may help to reduce the cold induced injury but their action is limited due to the inability readily to cross the plasma membrane.

Abstract: Lipid soluble antioxidants are likely to be more effective scavengers because of their presence in membranes where peroxidative reactions can be arrested.


SIRT1 deacetylase in SF1 neurons protects against metabolic imbalance.

Abstract: Chronic feeding on high-calorie diets causes obesity and type 2 diabetes mellitus (T2DM), illnesses that affect hundreds of millions.

Abstract: Thus, understanding the pathways protecting against diet-induced metabolic imbalance is of paramount medical importance.

Abstract: Here, we show that mice lacking SIRT1 in steroidogenic factor 1 (SF1) neurons are hypersensitive to dietary obesity owing to maladaptive energy expenditure.

Abstract: Also, mutant mice have increased susceptibility to developing dietary T2DM due to insulin resistance in skeletal muscle.

Abstract: Mechanistically, these aberrations arise, in part, from impaired metabolic actions of the neuropeptide orexin-A and the hormone leptin.

Abstract: Conversely, mice overexpressing SIRT1 in SF1 neurons are more resistant to diet-induced obesity and insulin resistance due to increased energy expenditure and enhanced skeletal muscle insulin sensitivity.

Abstract: Our results unveil important protective roles of SIRT1 in SF1 neurons against dietary metabolic imbalance.


mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells.

Abstract: Despite the recent identification of the transcriptional regulatory circuitry involving SOX2, NANOG, and OCT-4, the intracellular signaling networks that control pluripotency of human embryonic stem cells (hESCs) remain largely undefined.

Abstract: Here, we demonstrate an essential role for the serine/threonine protein kinase mammalian target of rapamycin (mTOR) in regulating hESC long-term undifferentiated growth.

Abstract: Inhibition of mTOR impairs pluripotency, prevents cell proliferation, and enhances mesoderm and endoderm activities in hESCs.

Abstract: At the molecular level, mTOR integrates signals from extrinsic pluripotency-supporting factors and represses the transcriptional activities of a subset of developmental and growth-inhibitory genes, as revealed by genome-wide microarray analyses.

Abstract: Repression of the developmental genes by mTOR is necessary for the maintenance of hESC pluripotency.

Abstract: These results uncover a novel signaling mechanism by which mTOR controls fate decisions in hESCs.

Abstract: Our findings may contribute to effective strategies for tissue repair and regeneration.


Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion

Abstract: Stromal fibroblasts can contribute to tumor invasion through the release of matrix metalloproteinases (MMPs).

Abstract: Population studies have suggested that single nucleotide polymorphisms (SNPs) in MMP genes influence levels of expression and may be associated with breast cancer risk and with disease progression.

Abstract: This study directly examined the impact of MMP SNP genotype on the ability of host fibroblasts to promote tumor cell invasion.

Abstract: Primary breast fibroblasts were isolated from patients with (n = 13) or without (n = 19) breast cancer, and their ability to promote breast cancer cell invasion was measured in in vitro invasion assays.

Abstract: Fibroblast invasion-promoting capacity (IPC) was analyzed in relation to donor type (tumor or non-tumor patient), MMP-1, MMP-3, and MMP-9 SNP genotype and MMP activity using independent samples t test and analysis of variance.

Abstract: All statistical tests were two-sided.

Abstract: Tumor-derived fibroblasts promoted higher levels of invasion than normal fibroblasts (p = 0.041).

Abstract: When IPC was related to genotype, higher levels of IPC were generated by tumor fibroblasts with the high-expressing MMP-3 5A/5A genotype compared with the 5A/6A and 6A/6A genotypes (p = 0.05 and 0.07, respectively), and this was associated with enhanced MMP-3 release.

Abstract: The functional importance of MMP-3 was demonstrated by enhanced invasion in the presence of recombinant MMP-3, whereas reduction occurred in the presence of a specific MMP-3 inhibitor.

Abstract: An inverse relationship was demonstrated between fibroblast IPC and the high-expressing MMP-1 genotype (p = 0.031), but no relationship was seen with MMP-9 SNP status.

Abstract: In contrast, normal fibroblasts showed no variation in IPC in relation to MMP genotype, with MMP-3 5A/5A fibroblasts exhibiting significantly lower levels of IPC than their tumor-derived counterparts (p = 0.04).

Abstract: This study has shown that tumor-derived fibroblasts exhibit higher levels of IPC than normal fibroblasts and that the MMP-3 5A/5A genotype contributes to this through enhanced MMP-3 release.

Abstract: Despite a high-expressing genotype, normal fibroblasts do not exhibit higher IPC or enhanced MMP release.

Abstract: This suggests that more complex changes occur in tumor-derived fibroblasts, enabling full expression of the MMP SNP genotype and these possibly are epigenetic in nature.

Abstract: The results do suggest that, in women with breast cancer, a high-expressing MMP-3 genotype may promote tumor progression more effectively.


Hallmarks of Cancer: The Next Generation

Abstract: The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors.

Abstract: The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease.

Abstract: They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis.

Abstract: Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions.

Abstract: Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list-reprogramming of energy metabolism and evading immune destruction.

Abstract: In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the "tumor microenvironment.

Abstract: Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer.


BCR/ABL oncogenic kinase promotes unfaithful repair of the reactive oxygen species-dependent DNA double-strand breaks.

Abstract: The oncogenic BCR/ABL tyrosine kinase induces constitutive DNA damage in Philadelphia chromosome (Ph)-positive leukemia cells.

Abstract: We find that BCR/ABL-induced reactive oxygen species (ROSs) cause chronic oxidative DNA damage resulting in double-strand breaks (DSBs) in S and G(2)/M cell cycle phases.

Abstract: These lesions are repaired by BCR/ABL-stimulated homologous recombination repair (HRR) and nonhomologous end-joining (NHEJ) mechanisms.

Abstract: A high mutation rate is detected in HRR products in BCR/ABL-positive cells, but not in the normal counterparts.

Abstract: In addition, large deletions are found in NHEJ products exclusively in BCR/ABL cells.

Abstract: We propose that the following series of events may contribute to genomic instability of Ph-positive leukemias: BCR/ABL --> ROSs --> oxidative DNA damage --> DSBs in proliferating cells --> unfaithful HRR and NHEJ repair.


Cancer risks attributable to low doses of ionizing radiation: assessing what we really know.

Abstract: High doses of ionizing radiation clearly produce deleterious consequences in humans, including, but not exclusively, cancer induction.

Abstract: At very low radiation doses the situation is much less clear, but the risks of low-dose radiation are of societal importance in relation to issues as varied as screening tests for cancer, the future of nuclear power, occupational radiation exposure, frequent-flyer risks, manned space exploration, and radiological terrorism.

Abstract: We review the difficulties involved in quantifying the risks of low-dose radiation and address two specific questions.

Abstract: First, what is the lowest dose of x- or gamma-radiation for which good evidence exists of increased cancer risks in humans?

Abstract: The epidemiological data suggest that it is approximately 10-50 mSv for an acute exposure and approximately 50-100 mSv for a protracted exposure.

Abstract: Second, what is the most appropriate way to extrapolate such cancer risk estimates to still lower doses?

Abstract: Given that it is supported by experimentally grounded, quantifiable, biophysical arguments, a linear extrapolation of cancer risks from intermediate to very low doses currently appears to be the most appropriate methodology.

Abstract: This linearity assumption is not necessarily the most conservative approach, and it is likely that it will result in an underestimate of some radiation-induced cancer risks and an overestimate of others.


Laparoscopic uterosacral nerve ablation for alleviating chronic pelvic pain: a randomized controlled trial.

Abstract: CONTEXT Chronic pelvic pain is a common condition with a major effect on health-related quality of life, work productivity, and health care use.

Abstract: Operative interruption of nerve trunks in the uterosacral ligaments by laparoscopic uterosacral nerve ablation (LUNA) is a treatment option for patients with chronic pelvic pain.

Abstract: OBJECTIVE To assess the effectiveness of LUNA in patients with chronic pelvic pain.

Abstract: DESIGN, SETTING, AND PARTICIPANTS Randomized controlled trial of 487 women with chronic pelvic pain lasting longer than 6 months without or with minimal endometriosis, adhesions, or pelvic inflammatory disease, who were recruited to the study by consultant gynecological surgeons from 18 UK hospitals between February 1998 and December 2005.

Abstract: Follow-up was conducted by questionnaires mailed at 3 and 6 months and at 1, 2, 3, and 5 years.

Abstract: INTERVENTION Bilateral LUNA or laparoscopy without pelvic denervation (no LUNA); participants were blinded to the treatment allocation.

Abstract: MAIN OUTCOME MEASURES

Abstract: The primary outcome was pain, which was assessed by a visual analogue scale.

Abstract: Data concerning the 3 types of pain (noncyclical pain, dysmenorrhea, and dyspareunia) were analyzed separately as was the worst pain level experienced from any of these 3 types of pain.

Abstract: The secondary outcome was health-related quality of life, which was measured using a generic instrument (EuroQoL EQ-5D and EQ-VAS).

Abstract: RESULTS After a median follow-up of 69 months, there were no significant differences reported on the visual analogue pain scales for the worst pain (mean difference between the LUNA group and the no LUNA group, -0.04 cm [95% confidence interval {CI}, -0.33 to 0.25 cm]; P = .80), noncyclical pain (-0.11 cm [95% CI, -0.50 to 0.29 cm]; P = .60), dysmenorrhea (-0.09 cm [95% CI, -0.49 to 0.30 cm]; P = .60), or dyspareunia (0.18 cm [95% CI, -0.22 to 0.62 cm]; P = .40).

Abstract: No differences were observed between the LUNA group and the no LUNA group for quality of life.

Abstract: CONCLUSION Among women with chronic pelvic pain, LUNA did not result in improvements in pain, dysmenorrhea, dyspareunia, or quality of life compared with laparoscopy without pelvic denervation.

Abstract: TRIAL REGISTRATION controlled-trials.com Identifier: ISRCTN41196151.


Identification of bone and liver metastases from breast cancer by measurement of plasma alkaline phosphatase isoenzyme activity.

Abstract: Plasma alkaline phosphatase isoenzyme activities were determined in patients with breast cancer to diagnose and monitor bone and liver metastases.

Abstract: Bone alkaline phosphatase activity was increased in 21 of 50 patients (42%) with radiologically confirmed bone metastases, while total alkaline phosphatase activity was increased in only 10 of 50 (20%); liver alkaline phosphatase activity was raised in 12 of 25 patients (48%) with liver metastases.

Abstract: All patients with liver metastases had bone metastases.

Abstract: Bone alkaline phosphatase activity was significantly higher in patients with symptomatic bone disease.

Abstract: Isoenzyme determination provided additional information that would have changed patient management in five of 20 patients who were monitored serially.

Abstract: Measurement of alkaline phosphatase isoenzyme activity, though less sensitive than imaging procedures, can assist in screening for, and in early detection of, a high proportion of bone and liver metastases, and can provide useful objective evidence of their response to treatment.


Recommendations on how to ensure the safety and effectiveness of biosimilars in Latin America: a point of view

Abstract: The use of biotechnology-derived medicines has significantly increased in recent decades.

Abstract: Although biosimilars undergo rigorous characterization as well as clinical studies to document their safety and effectiveness, they are highly complex molecules and small changes in the purification and production process of a biosimilar can have major implications in its safety and effectiveness profile.

Abstract: In Latin America, regulatory authorities have begun to establish well-described and standardized pathways that permit a biosimilar to gain commercial licensure.

Abstract: In order to be certain that a biosimilar reaches its potential in ordinary clinical use, an intensive post-licensing monitoring system must be established since it is the only means to ascertain the true similarity between the original biologic and its biosimilar.

Abstract: Pharmacovigilance allows national authorities to determine a drug's performance in the marketplace.

Abstract: An effective tracking and pharmacovigilance system for biological medicines has many steps and processes.

Abstract: To aid policy makers in Latin American in addressing the many issues surrounding the establishment of an effective pharmacovigilance system, the Americas Health Foundation convened a group of experts to discuss the topic and develop recommendations for implementation.

Abstract: The group discussed current challenges and gaps in pharmacovigilance in Latin America, paying close attention to the major issues associated with traceability and pharmacovigilance of biosimilars following their approval.

Abstract: The recommendations developed should enable countries to accurately document the safety and performance of a biosimilar as experienced by patients under real-life conditions and have a significant impact on the successful implementation of pharmacovigilance of biosimilars throughout the region.


Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast

Abstract: A yeast strain lacking Met4p, the primary transcriptional regulator of the sulfur assimilation pathway, cannot synthesize methionine.

Abstract: This apparently simple auxotroph did not grow well in rich media containing excess methionine, forming small colonies on yeast extract/peptone/dextrose plates.

Abstract: Faster-growing large colonies were abundant when overnight cultures were plated, suggesting that spontaneous suppressors of the growth defect arise with high frequency.

Abstract: To identify the suppressor mutations, we used genome-wide single-nucleotide polymorphism and standard genetic analyses.

Abstract: The most common suppressors were loss-of-function mutations in OPI1, encoding a transcriptional repressor of phospholipid metabolism.

Abstract: Using a new system that allows rapid and specific degradation of Met4p, we could study the dynamic expression of all genes following loss of Met4p.

Abstract: Experiments using this system with and without Opi1p showed that Met4 activates and Opi1p represses genes that maintain levels of S-adenosylmethionine (SAM), the substrate for most methyltransferase reactions.

Abstract: Cells lacking Met4p grow normally when either SAM is added to the media or one of the SAM synthetase genes is overexpressed.

Abstract: SAM is used as a methyl donor in three Opi1p-regulated reactions to create the abundant membrane phospholipid, phosphatidylcholine.

Abstract: Our results show that rapidly growing cells require significant methylation, likely for the biosynthesis of phospholipids.


Glossary of reference terms for alternative test methods and their validation.

Abstract: This glossary was developed to provide technical references to support work in the field of the alternatives to animal testing.

Abstract: It was compiled from various existing reference documents coming from different sources and is meant to be a point of reference on alternatives to animal testing.

Abstract: Giving the ever-increasing number of alternative test methods and approaches being developed over the last decades, a combination, revision, and harmonization of earlier published collections of terms used in the validation of such methods is required.

Abstract: The need to update previous glossary efforts came from the acknowledgement that new words have emerged with the development of new approaches, while others have become obsolete, and the meaning of some terms has partially changed over time.

Abstract: With this glossary we intend to provide guidance on issues related to the validation of new or updated testing methods consistent with current approaches.

Abstract: Moreover, because of new developments and technologies, a glossary needs to be a living, constantly updated document.

Abstract: An Internet-based version based on this compilation may be found at http://altweb.jhsph.edu/, allowing the addition of new material.


Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators.

Abstract: Combinatorial transcription factor (TF) interactions control cellular phenotypes and, therefore, underpin stem cell formation, maintenance, and differentiation.

Abstract: Here, we report the genome-wide binding patterns and combinatorial interactions for ten key regulators of blood stem/progenitor cells (SCL/TAL1, LYL1, LMO2, GATA2, RUNX1, MEIS1, PU.1, ERG, FLI-1, and GFI1B), thus providing the most comprehensive TF data set for any adult stem/progenitor cell type to date.

Abstract: Genome-wide computational analysis of complex binding patterns, followed by functional validation, revealed the following: first, a previously unrecognized combinatorial interaction between a heptad of TFs (SCL, LYL1, LMO2, GATA2, RUNX1, ERG, and FLI-1).

Abstract: Second, we implicate direct protein-protein interactions between four key regulators (RUNX1, GATA2, SCL, and ERG) in stabilizing complex binding to DNA.

Abstract: Third, Runx1(+/-)::Gata2(+/-) compound heterozygous mice are not viable with severe hematopoietic defects at midgestation.

Abstract: Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells.


Influence of CYP2D6 Polymorphisms on Serum Levels of Tamoxifen Metabolites in Spanish Women with Breast Cancer

Abstract: BACKGROUND Estrogen receptor-positive breast cancer tumors depend on estrogen signaling for their growth and replication and can be treated by anti-estrogen therapy with tamoxifen.

Abstract: Polymorphisms of the CYP2D6 and CYP2C19 genes are associated with an impaired response to tamoxifen.

Abstract: The study objective was to investigate the impact of genetic polymorphisms in CYP2D6 and CYP2C19 on the pharmacokinetics of tamoxifen and its metabolites in Spanish women with estrogen receptor-positive breast cancer who were candidates for tamoxifen therapy.

Abstract: METHODS We studied 90 women with estrogen receptor-positive breast cancer, using the AmpliChip CYP450 test to determine CYP2D6 and CYP2C19 gene variants.

Abstract: Plasma levels of tamoxifen and its metabolites were quantified by high-performance liquid chromatography.

Abstract: RESULTS The CYP2D6 phenotype was extensive metabolizer in 80%, intermediate metabolizer in 12.2%, ultra-rapid metabolizer in 2.2%, and poor metabolizer in 5.6% of patients, and the allele frequency was 35.0% for allele (*)1, 21.0% for *2, and 18.9% for *4.

Abstract: All poor metabolizers in this series were *4/*4, and their endoxifen and 4-hydroxy tamoxifen levels were 25% lower than those of extensive metabolizers.

Abstract: CYP2C19*2 allele, which has been related to breast cancer outcomes, was detected in 15.6% of the studied alleles.

Abstract: CONCLUSION CYP2D6*4/*4 genotype was inversely associated with 4-hydroxy tamoxifen and endoxifen levels.

Abstract: According to these results, CYP2D6 and CYP2C19 genotyping appears advisable before the prescription of tamoxifen therapy.


Role of tumor associated macrophages in tumor angiogenesis and lymphangiogenesis

Abstract: Tumor angiogenesis is an essential process for supplying rapidly growing malignant tissues with essential nutrients and oxygen.

Abstract: An angiogenic switch allows tumor cells to survive and grow, and provides them access to vasculature resulting in metastatic disease.

Abstract: Monocyte-derived macrophages recruited and reprogrammed by tumor cells serve as a major source of angiogenic factors boosting the angiogenic switch.

Abstract: Tumor endothelium releases angiopoietin-2 and further facilitates recruitment of TIE2 receptor expressing monocytes (TEM) into tumor sites.

Abstract: Tumor-associated macrophages (TAM) sense hypoxia in avascular areas of tumors, and react by production of angiogenic factors such as VEGFA.

Abstract: VEGFA stimulates chemotaxis of endothelial cells (EC) and macrophages.

Abstract: In some tumors, TAM appeared to be a major source of MMP9.

Abstract: Elevated expression of MMP9 by TAM mediates extracellular matrix (ECM) degradation and the release of bioactive VEGFA.

Abstract: Other angiogenic factors released by TAM include basic fibroblast growth factor (bFGF), thymidine phosphorylase (TP), urokinase-type plasminogen activator (uPA), and adrenomedullin (ADM).

Abstract: The same factors used by macrophages for the induction of angiogenesis [like vascular endothelial growth factor A (VEGF-A) and MMP9] support lymphangiogenesis.

Abstract: TAM can express LYVE-1, one of the established markers of lymphatic endothelium.

Abstract: TAM support tumor lymphangiogenesis not only by secretion of pro-lymphangiogenic factors but also by trans-differentiation into lymphatic EC.

Abstract: New pro-angiogenic factor YKL-40 belongs to a family of mammalian chitinase-like proteins (CLP) that act as cytokines or growth factors.

Abstract: Human CLP family comprises YKL-40, YKL-39, and SI-CLP.

Abstract: Production of all three CLP in macrophages is antagonistically regulated by cytokines.

Abstract: It was recently established that YKL-40 induces angiogenesis in vitro and in animal tumor models.

Abstract: YKL-40-neutralizing monoclonal antibody blocks tumor angiogenesis and progression.

Abstract: The role of YKL-39 and SI-CLP in tumor angiogenesis and lymphangiogenesis remains to be investigated.


The HIV Treatment Gap: Estimates of the Financial Resources Needed versus Available for Scale-Up of Antiretroviral Therapy in 97 Countries from 2015 to 2020

Abstract: BACKGROUND The World Health Organization (WHO) released revised guidelines in 2015 recommending that all people living with HIV, regardless of CD4 count, initiate antiretroviral therapy (ART) upon diagnosis.

Abstract: However, few studies have projected the global resources needed for rapid scale-up of ART.

Abstract: Under the Health Policy Project, we conducted modeling analyses for 97 countries to estimate eligibility for and numbers on ART from 2015 to 2020, along with the facility-level financial resources required.

Abstract: We compared the estimated financial requirements to estimated funding available.

Abstract: METHODS AND FINDINGS Current coverage levels and future need for treatment were based on country-specific epidemiological and demographic data.

Abstract: Simulated annual numbers of individuals on treatment were derived from three scenarios: (1) continuation of countries' current policies of eligibility for ART, (2) universal adoption of aspects of the WHO 2013 eligibility guidelines, and (3) expanded eligibility as per the WHO 2015 guidelines and meeting the Joint United Nations Programme on HIV/AIDS "90-90-90" ART targets.

Abstract: We modeled uncertainty in the annual resource requirements for antiretroviral drugs, laboratory tests, and facility-level personnel and overhead.

Abstract: We estimate that 25.7 (95% CI 25.5, 26.0) million adults and 1.57 (95% CI 1.55, 1.60) million children could receive ART by 2020 if countries maintain current eligibility plans and increase coverage based on historical rates, which may be ambitious.

Abstract: If countries uniformly adopt aspects of the WHO 2013 guidelines, 26.5 (95% CI 26.0 27.0) million adults and 1.53 (95% CI 1.52, 1.55) million children could be on ART by 2020.

Abstract: Under the 90-90-90 scenario, 30.4 (95% CI 30.1, 30.7) million adults and 1.68 (95% CI 1.63, 1.73) million children could receive treatment by 2020.

Abstract: The facility-level financial resources needed for scaling up ART in these countries from 2015 to 2020 are estimated to be US$45.8 (95% CI 45.4, 46.2) billion under the current scenario, US$48.7 (95% CI 47.8, 49.6) billion under the WHO 2013 scenario, and US$52.5 (95% CI 51.4, 53.6) billion under the 90-90-90 scenario.

Abstract: After projecting recent external and domestic funding trends, the estimated 6-y financing gap ranges from US$19.8 billion to US$25.0 billion, depending on the costing scenario and the U.S. President's Emergency Plan for AIDS Relief contribution level, with the gap for ART commodities alone ranging from US$14.0 to US$16.8 billion.

Abstract: The study is limited by excluding above-facility and other costs essential to ART service delivery and by the availability and quality of country- and region-specific data.

Abstract: CONCLUSIONS The projected number of people receiving ART across three scenarios suggests that countries are unlikely to meet the 90-90-90 treatment target (81% of people living with HIV on ART by 2020) unless they adopt a test-and-offer approach and increase ART coverage.

Abstract: Our results suggest that future resource needs for ART scale-up are smaller than stated elsewhere but still significantly threaten the sustainability of the global HIV response without additional resource mobilization from domestic or innovative financing sources or efficiency gains.

Abstract: As the world moves towards adopting the WHO 2015 guidelines, advances in technology, including the introduction of lower-cost, highly effective antiretroviral regimens, whose value are assessed here, may prove to be "game changers" that allow more people to be on ART with the resources available.


Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo.

Abstract: A number of proteins and drugs have been implicated in the process of transcriptional elongation by RNA polymerase (Pol) II, but the factors that govern the elongation rate (nucleotide additions per min) and processivity (nucleotide additions per initiation event) in vivo are poorly understood.

Abstract: Here, we show that a mutation in the Rpb2 subunit of Pol II reduces both the elongation rate and processivity in vivo.

Abstract: In contrast, none of the putative elongation factors tested affect the elongation rate, although mutations in the THO complex and in Spt4 significantly reduce processivity.

Abstract: The drugs 6-azauracil and mycophenolic acid reduce both the elongation rate and processivity, and this processivity defect is aggravated by mutations in Spt4, TFIIS, and CTDK-1.

Abstract: Our results suggest that, in vivo, a reduced rate of Pol II elongation leads to premature dissociation along the chromatin template and that Pol II processivity can be uncoupled from elongation rate.


Neurite sprouting and synapse deterioration in the aging Caenorhabditis elegans nervous system.

Abstract: Caenorhabditis elegans is a powerful model for analysis of the conserved mechanisms that modulate healthy aging.

Abstract: In the aging nematode nervous system, neuronal death and/or detectable loss of processes are not readily apparent, but because dendrite restructuring and loss of synaptic integrity are hypothesized to contribute to human brain decline and dysfunction, we combined fluorescence microscopy and electron microscopy (EM) to screen at high resolution for nervous system changes.

Abstract: We report two major components of morphological change in the aging C. elegans nervous system: (1) accumulation of novel outgrowths from specific neurons, and (2) physical decline in synaptic integrity.

Abstract: Novel outgrowth phenotypes, including branching from the main dendrite or new growth from somata, appear at a high frequency in some aging neurons, but not all.

Abstract: Mitochondria are often associated with age-associated branch sites.

Abstract: Lowered insulin signaling confers some maintenance of ALM and PLM neuron structural integrity into old age, and both DAF-16/FOXO and heat shock factor transcription factor HSF-1 exert neuroprotective functions.

Abstract: hsf-1 can act cell autonomously in this capacity.

Abstract: EM evaluation in synapse-rich regions reveals a striking decline in synaptic vesicle numbers and a diminution of presynaptic density size.

Abstract: Interestingly, old animals that maintain locomotory prowess exhibit less synaptic decline than same-age decrepit animals, suggesting that synaptic integrity correlates with locomotory healthspan.

Abstract: Our data reveal similarities between the aging C. elegans nervous system and mammalian brain, suggesting conserved neuronal responses to age.

Abstract: Dissection of neuronal aging mechanisms in C. elegans may thus influence the development of brain healthspan-extending therapies.


Determinants of adolescent physical activity and inactivity patterns.

Abstract: OBJECTIVES Despite recognition of the important influence of environmental determinants on physical activity patterns, minimal empirical research has been done to assess the impact of environmental/contextual determinants of physical activity.

Abstract: This article aims to investigate environmental and sociodemographic determinants of physical activity and inactivity patterns among subpopulations of US adolescents.

Abstract: We define environmental determinants as modifiable factors in the physical environment that impose a direct influence on the opportunity to engage in physical activity.

Abstract: The present research examines environmental and sociodemographic determinants of physical activity and inactivity with the implication that these findings can point toward societal-level intervention strategies for increasing physical activity and decreasing inactivity among adolescents.

Abstract: STUDY DESIGN AND METHODOLOGY The study population consists of nationally representative data from the 1996 National Longitudinal Study of Adolescent Health on 17 766 US adolescents enrolled in US middle and high schools (including 3933 non-Hispanic blacks, 3148 Hispanics, and 1337 Asians).

Abstract: Hours/week of inactivity (TV/video viewing and video/computer games) and times/week of moderate to vigorous physical activity were collected by questionnaire.

Abstract: Outcome variables were moderate to vigorous physical activity and inactivity, which were broken into categories (physical activity: 0-2 times/week, 3-4 times/week, and >/=5 times/week; inactivity: 0-10 hours/week, 11-24 hours/week, and >/=25 hours/week).

Abstract: Sociodemographic and environmental correlates of physical activity and inactivity were used as exposure and control variables and included sex, age, urban residence, participation in school physical education program, use of community recreation center, total reported incidents of serious crime in neighborhood, socioeconomic status, ethnicity, generation of residence in the United States, presence of mother/father in household, pregnancy status, work status, in-school status, region, and month of interview.

Abstract: Logistic regression models of high versus low and medium physical activity and inactivity were used to investigate sex and ethnic interactions in relation to environmental and sociodemographic factors to examine evidence for the potential impact of physical education and recreation programs and sociodemographic factors on physical activity and inactivity patterns.

Abstract: RESULTS Moderate to vigorous physical activity was lower and inactivity higher for non-Hispanic black and Hispanic adolescents.

Abstract: Participation in school physical education programs was considerably low for these adolescents and decreased with age.

Abstract: Participation in daily school physical education (PE) program classes (adjusted odds ratio [AOR]: 2.21; confidence interval [CI]: 1.82-2.68) and use of a community recreation center (AOR: 1.75; CI: 1.56-1.96) were associated with an increased likelihood of engaging in high level moderate to vigorous physical activity.

Abstract: Maternal education was inversely associated with high inactivity patterns; for example, having a mother with a graduate or professional degree was associated with an AOR of.61 (CI:.48-.76) for high inactivity.

Abstract: High family income was associated with increased moderate to vigorous physical activity (AOR: 1.43; CI: 1.22-1.67) and decreased inactivity (AOR:.70; CI:.59-.82).

Abstract: High neighborhood serious crime level was associated with a decreased likelihood of falling in the highest category of moderate to vigorous physical activity (AOR:.77; CI:.66-.91).

Abstract: CONCLUSIONS These results show important associations between modifiable environmental factors, such as participation in school PE and community recreation programs, with activity patterns of adolescents.

Abstract: Despite the marked and significant impact of participation in school PE programs on physical activity patterns of US adolescents, few adolescents participated in such school PE programs; only 21.3% of all adolescents


Suicide prevention strategies: a systematic review.

Abstract: CONTEXT In 2002, an estimated 877,000 lives were lost worldwide through suicide.

Abstract: Some developed nations have implemented national suicide prevention plans.

Abstract: Although these plans generally propose multiple interventions, their effectiveness is rarely evaluated.

Abstract: OBJECTIVES To examine evidence for the effectiveness of specific suicide-preventive interventions and to make recommendations for future prevention programs and research.

Abstract: DATA SOURCES AND STUDY SELECTION Relevant publications were identified via electronic searches of MEDLINE, the Cochrane Library, and PsychINFO databases using multiple search terms related to suicide prevention.

Abstract: Studies, published between 1966 and June 2005, included those that evaluated preventative interventions in major domains; education and awareness for the general public and for professionals; screening tools for at-risk individuals; treatment of psychiatric disorders; restricting access to lethal means; and responsible media reporting of suicide.

Abstract: DATA EXTRACTION Data were extracted on primary outcomes of interest: suicidal behavior (completion, attempt, ideation), intermediary or secondary outcomes (treatment seeking, identification of at-risk individuals, antidepressant prescription/use rates, referrals), or both.

Abstract: Experts from 15 countries reviewed all studies.

Abstract: Included articles were those that reported on completed and attempted suicide and suicidal ideation; or, where applicable, intermediate outcomes, including help-seeking behavior, identification of at-risk individuals, entry into treatment, and antidepressant prescription rates.

Abstract: We included 3 major types of studies for which the research question was clearly defined: systematic reviews and meta-analyses (n = 10); quantitative studies, either randomized controlled trials (n = 18) or cohort studies (n = 24); and ecological, or population- based studies (n = 41).

Abstract: Heterogeneity of study populations and methodology did not permit formal meta-analysis; thus, a narrative synthesis is presented.

Abstract: DATA SYNTHESIS Education of physicians and restricting access to lethal means were found to prevent suicide.

Abstract: Other methods including public education, screening programs, and media education need more testing.

Abstract: CONCLUSIONS Physician education in depression recognition and treatment and restricting access to lethal methods reduce suicide rates.

Abstract: Other interventions need more evidence of efficacy.

Abstract: Ascertaining which components of suicide prevention programs are effective in reducing rates of suicide and suicide attempt is essential in order to optimize use of limited resources.


Oxidative damage of DNA confers resistance to cytosolic nuclease TREX1 degradation and potentiates STING-dependent immune sensing.

Abstract: Immune sensing of DNA is critical for antiviral immunity but can also trigger autoimmune diseases such as lupus erythematosus (LE).

Abstract: Here we have provided evidence for the involvement of a damage-associated DNA modification in the detection of cytosolic DNA.

Abstract: The oxidized base 8-hydroxyguanosine (8-OHG), a marker of oxidative damage in DNA, potentiated cytosolic immune recognition by decreasing its susceptibility to 3' repair exonuclease 1 (TREX1)-mediated degradation.

Abstract: Oxidizative modifications arose physiologically in pathogen DNA during lysosomal reactive oxygen species (ROS) exposure, as well as in neutrophil extracellular trap (NET) DNA during the oxidative burst.

Abstract: 8-OHG was also abundant in UV-exposed skin lesions of LE patients and colocalized with type I interferon (IFN).

Abstract: Injection of oxidized DNA in the skin of lupus-prone mice induced lesions that closely matched respective lesions in patients.

Abstract: Thus, oxidized DNA represents a prototypic damage-associated molecular pattern (DAMP) with important implications for infection, sterile inflammation, and autoimmunity.


IL-18 induction of osteopontin mediates cardiac fibrosis and diastolic dysfunction in mice.

Abstract: Osteopontin (OPN), a key component of the extracellular matrix, is associated with the fibrotic process during tissue remodeling.

Abstract: OPN and the cytokine interleukin (IL)-18 have been shown to be overexpressed in an array of human cardiac pathologies.

Abstract: In the present study, we determined the role of IL-18 in the regulation of cardiac OPN expression and the subsequent interstitial fibrosis and diastolic dysfunction.

Abstract: We demonstrated parallel increases in IL-18, OPN expression, and interstitial fibrosis in murine models of left ventricular pressure and volume overload.

Abstract: Exogenous recombinant (r)IL-18 administered for 2 wk increased cardiac OPN expression, interstitial fibrosis, and diastolic dysfunction.

Abstract: Stimulation of the T helper (Th)1 lymphocyte phenotype with a selective toll-like receptor (TLR)9 agonist induced cardiac IL-18 and OPN expression, which was associated with increased cardiac fibrillar collagen concentrations and interstitial fibrosis resulting in diastolic dysfunction.

Abstract: rIL-18 induced OPN expression and protein levels in primary of cardiac fibroblast cultures.

Abstract: Conditioned media from TLR9-stimulated T lymphocyte cultures induced IL-18 and OPN expression in cardiac fibroblasts, while blockade of the IL-18 receptor with a neutralizing antibody abolished the increase in OPN expression.

Abstract: Furthermore, a mutation in the transcriptional factor interferon regulatory factor (IRF)1 or IRF1 small interfering RNA (siRNA) resulted in the decreased expression of IL-18 and OPN in cardiac fibroblasts.

Abstract: With pressure overload, IRF1-mutant mice showed downregulation of IL-18 and OPN expression in cardiac tissue, reduced cardiac fibrotic development, and increased left ventricular function compared with wild type.

Abstract: These results provide direct evidence that the induction of IL-18 regulates OPN-mediated cardiac fibrosis and diastolic dysfunction.


Hematopoietic stem cell: self-renewal versus differentiation.

Abstract: The mammalian blood system, containing more than 10 distinct mature cell types, stands on one specific cell type, hematopoietic stem cell (HSC).

Abstract: Within the system, only HSCs possess the ability of both multipotency and self-renewal.

Abstract: Multipotency is the ability to differentiate into all functional blood cells.

Abstract: Self-renewal is the ability to give rise to HSC itself without differentiation.

Abstract: Since mature blood cells (MBCs) are predominantly short-lived, HSCs continuously provide more differentiated progenitors while properly maintaining the HSC pool size throughout life by precisely balancing self-renewal and differentiation.

Abstract: Thus, understanding the mechanisms of self-renewal and differentiation of HSC has been a central issue.

Abstract: In this review, we focus on the hierarchical structure of the hematopoietic system, the current understanding of microenvironment and molecular cues regulating self-renewal and differentiation of adult HSCs, and the currently emerging systems approaches to understand HSC biology.


RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Abstract: BACKGROUND RNA-Seq is revolutionizing the way transcript abundances are measured.

Abstract: A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms.

Abstract: This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene.

Abstract: A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments.

Abstract: RESULTS We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.

Abstract: RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data.

Abstract: In contrast to other existing tools, the software does not require a reference genome.

Abstract: Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes.

Abstract: On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome.

Abstract: Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads.

Abstract: On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene.

Abstract: CONCLUSIONS RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data.

Abstract: As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies.

Abstract: In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.


A synthetic Escherichia coli predator–prey ecosystem

Abstract: We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits.

Abstract: Our synthetic ecosystem resembles canonical predator-prey systems in terms of logic and dynamics.

Abstract: The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator.

Abstract: Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats.

Abstract: A simple mathematical model is developed to capture these system dynamics.

Abstract: Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.


Funnel trap for the capture of phlebotomine sand flies (Diptera: Psychodidae) from tree holes.

Abstract: A funnel trap that fitted over holes leading into hollow trees was used to capture adult phlebotomine sand flies, Lutzomyia shannoni Dyar, on Ossabaw Island, Chatham County, Ga. These insects rested in hollow trees during the day and were collected by funnel traps as they egressed from the tree holes at night.

Abstract: The trap is lightweight, durable, inexpensive, waterproof, and selective.

Abstract: Using this trap, greater than 100 healthy L. shannoni ++were captured per night by a single investigator during July and August 1988 when adult flies were abundant on the island.


Cystine/glutamate exchange regulates metabotropic glutamate receptor presynaptic inhibition of excitatory transmission and vulnerability to cocaine seeking.

Abstract: Withdrawal from chronic cocaine reduces extracellular glutamate levels in the nucleus accumbens by decreasing cystine/glutamate exchange (xc-).

Abstract: Activating xc- with N-acetylcysteine restores extracellular glutamate and prevents cocaine-induced drug seeking.

Abstract: It was hypothesized that the activation of xc- prevents drug seeking by increasing glutamatergic tone on presynaptic group II metabotropic glutamate receptors (mGluR2/3) and thereby inhibiting excitatory transmission.

Abstract: In the first experiment, the capacity of glutamate derived from xc- to regulate excitatory transmission via mGluR2/3 was determined.

Abstract: Physiological levels of cystine (100-300 nm) were restored to acute tissue slices from the nucleus accumbens or prefrontal cortex.

Abstract: Cystine increased glutamate efflux and decreased miniature EPSC (mEPSC) and spontaneous EPSC (sEPSC) frequency as well as evoked EPSC amplitude.

Abstract: These effects of cystine were presynaptic, because there was no change in mEPSC or sEPSC amplitude, and an increase in the evoked EPSC paired-pulse facilitation ratio.

Abstract: The cystine-induced reduction in EPSCs was reversed by blocking either xc- or mGluR2/3.

Abstract: In the second experiment, blocking mGluR2/3 prevented the ability of N-acetylcystine to inhibit the reinstatement of drug seeking in rats trained to self-administer cocaine.

Abstract: These data demonstrate that nonsynaptic glutamate derived from xc- modulates synaptic glutamate release and thereby regulates cocaine-induced drug seeking.


Survival analysis: time-dependent effects and time-varying risk factors.

Abstract: In traditional Kaplan-Meier or Cox regression analysis, usually a risk factor measured at baseline is related to mortality thereafter.

Abstract: During follow-up, however, things may change: either the effect of a fixed baseline risk factor may vary over time, resulting in a weakening or strengthening of associations over time, or the risk factor itself may vary over time.

Abstract: In this paper, short-term versus long-term effects (so-called time-dependent effects) of a fixed baseline risk factor are addressed.

Abstract: An example is presented showing that underweight is a strong risk factor for mortality in dialysis patients, especially in the short run.

Abstract: In contrast, overweight is a risk factor for mortality, which is stronger in the long run than in the short run.

Abstract: In addition, the analysis of how time-varying risk factors (so-called time-dependent risk factors) are related to mortality is demonstrated by paying attention to the pitfall of adjusting for sequelae.

Abstract: The proper analysis of effects over time should be driven by a clear research question.

Abstract: Both kinds of research questions, that is those of time-dependent effects as well those of time-dependent risk factors, can be analyzed with time-dependent Cox regression analysis.

Abstract: It will be shown that using time-dependent risk factors usually implies focusing on short-term effects only.


Control of interneuron dendritic growth through NRG1/erbB4-mediated kalirin-7 disinhibition

Abstract: Neuregulin 1 (NRG1) is a secreted trophic factor that activates the postsynaptic erbB4 receptor tyrosine kinase.

Abstract: Both NRG1 and erbB4 have been repeatedly associated with schizophrenia, but their downstream targets are not well characterized.

Abstract: ErbB4 is highly abundant in interneurons, and NRG1-mediated erbB4 activation has been shown to modulate interneuron function, but the role for NRG1-erbB4 signaling in regulating interneuron dendritic growth is not well understood.

Abstract: Here we show that NRG1/erbB4 promote the growth of dendrites in mature interneurons through kalirin, a major dendritic Rac1-GEF.

Abstract: Recent studies have shown associations of the KALRN gene with schizophrenia.

Abstract: Our data point to an essential role of phosphorylation in kalirin-7's C terminus as the critical site for these effects.

Abstract: As reduced interneuron dendrite length occurs in schizophrenia, understanding how NRG1-erbB4 signaling modulates interneuron dendritic morphogenesis might shed light on disease-related alterations in cortical circuits.


Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia.

Abstract: BACKGROUND In patients with acute myeloid leukemia (AML), the presence or absence of recurrent cytogenetic aberrations is used to identify the appropriate therapy.

Abstract: However, the current classification system does not fully reflect the molecular heterogeneity of the disease, and treatment stratification is difficult, especially for patients with intermediate-risk AML with a normal karyotype.

Abstract: METHODS We used complementary-DNA microarrays to determine the levels of gene expression in peripheral-blood samples or bone marrow samples from 116 adults with AML (including 45 with a normal karyotype).

Abstract: We used unsupervised hierarchical clustering analysis to identify molecular subgroups with distinct gene-expression signatures.

Abstract: Using a training set of samples from 59 patients, we applied a novel supervised learning algorithm to devise a gene-expression-based clinical-outcome predictor, which we then tested using an independent validation group comprising the 57 remaining patients.

Abstract: RESULTS Unsupervised analysis identified new molecular subtypes of AML, including two prognostically relevant subgroups in AML with a normal karyotype.

Abstract: Using the supervised learning algorithm, we constructed an optimal 133-gene clinical-outcome predictor, which accurately predicted overall survival among patients in the independent validation group (P=0.006), including the subgroup of patients with AML with a normal karyotype (P=0.046).

Abstract: In multivariate analysis, the gene-expression predictor was a strong independent prognostic factor (odds ratio, 8.8; 95 percent confidence interval, 2.6 to 29.3; P<0.001).

Abstract: CONCLUSIONS The use of gene-expression profiling improves the molecular classification of adult AML.


Perspectives on public health workforce research.

Abstract: The Centers for Disease Control and Prevention Office of Workforce and Career Development is committed to developing a competent, sustainable, and diverse public health workforce through evidence-based training, career and leadership development, and strategic workforce planning to improve population health outcomes.

Abstract: This article reviews the previous efforts in identifying priorities of public health workforce research, which are summarized as eight major research themes.

Abstract: We outline a strategic framework for public health workforce research that includes six functional areas (ie, definition and standards, data, methodology, evaluation, policy, and dissemination and translation).

Abstract: To conceptualize and prioritize development of an actionable public health research agenda, we constructed a matrix of key challenges in workforce analysis by public health workforce categories.

Abstract: Extensive reviews were conducted to identify valuable methods, models, and approaches to public health workforce research.

Abstract: We explore new tools and approaches for addressing priority areas for public health workforce and career development research and assess how tools from multiple disciplines of social sciences can guide the development of a research framework for advancing public health workforce research and policy.


Gene targeting using zinc finger nucleases

Abstract: The ability to achieve site-specific manipulation of the mammalian genome has widespread implications for basic and applied research.

Abstract: Gene targeting is a process in which a DNA molecule introduced into a cell replaces the corresponding chromosomal segment by homologous recombination, and thus presents a precise way to manipulate the genome.

Abstract: In the past, the application of gene targeting to mammalian cells has been limited by its low efficiency.

Abstract: Zinc finger nucleases (ZFNs) show promise in improving the efficiency of gene targeting by introducing DNA double-strand breaks in target genes, which then stimulate the cell's endogenous homologous recombination machinery.

Abstract: Recent results have shown that ZFNs can be used to create targeting frequencies of up to 20% in a human disease-causing gene.

Abstract: Future work will be needed to translate these in vitro findings to in vivo applications and to determine whether zinc finger nucleases create undesired genomic instability.


relative expression results in real-time

Abstract: Real-time reverse transcription followed by polymerase chain reaction (RT-PCR) is the most suitable method for the detection and quantification of mRNA.

Abstract: It offers high sensitivity, good reproducibility and a wide quantification range.

Abstract: Today, relative expression is increasingly used, where the expression of a target gene is standardised by a non-regulated reference gene.

Abstract: Several mathematical algorithms have been developed to compute an expression ratio, based on real-time PCR efficiency and the crossing point deviation of an unknown sample versus a control.

Abstract: But all published equations and available models for the calculation of relative expression ratio allow only for the determination of a single transcription difference between one control and one sample.

Abstract: Therefore a new software tool was established, named REST (relative expression software tool), which compares two groups, with up to 16 data points in a sample and 16 in a control group, for reference and up to four target genes.

Abstract: The mathematical model used is based on the PCR efficiencies and the mean crossing point deviation between the sample and control group.

Abstract: Subsequently, the expression ratio results of the four investigated transcripts are tested for significance by a randomisation test.

Abstract: Herein, development and application of REST is explained and the usefulness of relative expression in real-time PCR using REST is discussed.

Abstract: The latest software version of REST and examples for the correct use can be downloaded at http://www.wzw.tum.de/gene-quantification/.


Pain attacks in non-complicated and complicated gallstone disease have a characteristic pattern and are accompanied by dyspepsia in most patients: the results of a prospective study.

Abstract: OBJECTIVE The cardinal indication for surgical treatment of gallstones is pain attacks.

Abstract: However, following cholecystectomy, 20% of patients remain symptomatic.

Abstract: It is unclear to what extent post-cholecystectomy symptoms can be ascribed to persistence of preoperative symptoms or to new pathology.

Abstract: The pain and digestive pattern in gallstone patients has not been defined in a recent setting with ultrasonography as the diagnostic method.

Abstract: The aim of this study was to characterize a pain pattern that is typical for gallstone disease and to describe the extent of associated dyspepsia.

Abstract: MATERIAL AND METHODS A total of 220 patients with symptomatic gallstone disease including complicated disease (acute cholecystitis and common bile duct stones) were interviewed using detailed questionnaires to disclose pain patterns and symptoms of indigestion.

Abstract: RESULTS All patients had pain in the right upper quadrant (RUQ) including the upper midline epigastrium.

Abstract: The pain was localized to the right subcostal area in 20% and to the upper epigastrium in 14%, and in the rest (66%) it was more evenly distributed.

Abstract: An area of maximal pain could be defined in 90%.

Abstract: Maximal pain was located under the costal arch in 51% of patients and in the epigastrium in 41%, but in 3% behind the sternum and in 5% in the back.

Abstract: The pain was referred to the back in 63% of the patients.

Abstract: The mean visual analogue scale (VAS) score was very high: 90 mm on a 0-100 scale.

Abstract: A pattern of incipient or low-grade warning pain with a subsequent relatively steady state until subsiding in the same fashion was present in 90% of the patients.

Abstract: An urge to walk around was experienced by 71%.

Abstract: Pain attacks usually occurred in the late evening or at night (77%), with 85% of the attacks lasting for more than one hour and almost never less than half an hour.

Abstract: Sixty-six percent of the patients were intolerant to at least one kind of food, but only 48% to fatty foods.

Abstract: Symptoms of functional indigestion (gastroesophageal reflux, dyspepsia or irritable bowel symptoms) were seen in the vast majority in association with attacks.

Abstract: CONCLUSIONS Gallstone-associated pain follows a certain pattern in the majority of patients.

Abstract: The pain is located in a defined area with a point of maximum intensity, is usually referred, and occurs mainly at night with duration of more than one hour.

Abstract: The majority of patients experience functional indigestion, mainly of the reflux type or dyspepsia.


Prevalence and cardiovascular disease correlates of low cardiorespiratory fitness in adolescents and adults.

Abstract: CONTEXT Population surveys indicate that physical activity levels are low in the United States.

Abstract: One consequence of inactivity, low cardiorespiratory fitness, is an established risk factor for cardiovascular disease (CVD) morbidity and mortality, but the prevalence of cardiorespiratory fitness has not been quantified in representative US population samples.

Abstract: OBJECTIVES To describe the prevalence of low fitness in the US population aged 12 through 49 years and to relate low fitness to CVD risk factors in this population.

Abstract: DESIGN, SETTING, AND PARTICIPANTS Inception cohort study using data from the cross-sectional nationally representative National Health and Nutrition Examination Survey 1999-2002.

Abstract: Participants were adolescents (aged 12-19 years; n = 3110) and adults (aged 20-49 years; n = 2205) free from previously diagnosed CVD who underwent submaximal graded exercise treadmill testing to achieve at least 75% to 90% of their age-predicted maximum heart rate.

Abstract: Maximal oxygen consumption (VO2max) was estimated by measuring the heart rate response to reference levels of submaximal work.

Abstract: MAIN OUTCOME MEASURES Low fitness defined using percentile cut points of estimated VO2max from existing external referent populations; anthropometric and other CVD risk factors measured according to standard methods.

Abstract: RESULTS Low fitness was identified in 33.6% of adolescents (approximately 7.5 million US adolescents) and 13.9% of adults (approximately 8.5 million US adults); the prevalence was similar in adolescent females (34.4%) and males (32.9%) (P = .40) but was higher in adult females (16.2%) than in males (11.8%) (P = .03).

Abstract: Non-Hispanic blacks and Mexican Americans were less fit than non-Hispanic whites.

Abstract: In all age-sex groups, body mass index and waist circumference were inversely associated with fitness; age- and race-adjusted odds ratios of overweight or obesity (body mass index > or =25) ranged from 2.1 to 3.7 (P<.01 for all), comparing persons with low fitness with those with moderate or high fitness.

Abstract: Total cholesterol levels and systolic blood pressure were higher and levels of high-density lipoprotein cholesterol were lower among participants with low vs high fitness.

Abstract: CONCLUSION Low fitness in adolescents and adults is common in the US population and is associated with an increased prevalence of CVD risk factors.


In situ regulation of DC subsets and T cells mediates tumor regression in mice.

Abstract: Vaccines are largely ineffective for patients with established cancer, as advanced disease requires potent and sustained activation of CD8(+) cytotoxic T lymphocytes (CTLs) to kill tumor cells and clear the disease.

Abstract: Recent studies have found that subsets of dendritic cells (DCs) specialize in antigen cross-presentation and in the production of cytokines, which regulate both CTLs and T regulatory (Treg) cells that shut down effector T cell responses.

Abstract: Here, we addressed the hypothesis that coordinated regulation of a DC network, and plasmacytoid DCs (pDCs) and CD8(+) DCs in particular, could enhance host immunity in mice.

Abstract: We used functionalized biomaterials incorporating various combinations of an inflammatory cytokine, immune danger signal, and tumor lysates to control the activation and localization of host DC populations in situ.

Abstract: The numbers of pDCs and CD8(+) DCs, and the endogenous production of interleukin-12, all correlated strongly with the magnitude of protective antitumor immunity and the generation of potent CD8(+) CTLs.

Abstract: Vaccination by this method maintained local and systemic CTL responses for extended periods while inhibiting FoxP3 Treg activity during antigen clearance, resulting in complete regression of distant and established melanoma tumors.

Abstract: The efficacy of this vaccine as a monotherapy against large invasive tumors may be a result of the local activity of pDCs and CD8(+) DCs induced by persistent danger and antigen signaling at the vaccine site.

Abstract: These results indicate that a critical pattern of DC subsets correlates with the evolution of therapeutic antitumor responses and provide a template for future vaccine design.


VEGF inhibits tumor cell invasion and mesenchymal transition through a MET/VEGFR2 complex.

Abstract: Inhibition of VEGF signaling leads to a proinvasive phenotype in mouse models of glioblastoma multiforme (GBM) and in a subset of GBM patients treated with bevacizumab.

Abstract: Here, we demonstrate that vascular endothelial growth factor (VEGF) directly and negatively regulates tumor cell invasion through enhanced recruitment of the protein tyrosine phosphatase 1B (PTP1B) to a MET/VEGFR2 heterocomplex, thereby suppressing HGF-dependent MET phosphorylation and tumor cell migration.

Abstract: Consequently, VEGF blockade restores and increases MET activity in GBM cells in a hypoxia-independent manner, while inducing a program reminiscent of epithelial-to-mesenchymal transition highlighted by a T-cadherin to N-cadherin switch and enhanced mesenchymal features.

Abstract: Inhibition of MET in GBM mouse models blocks mesenchymal transition and invasion provoked by VEGF ablation, resulting in substantial survival benefit.


Interaction between Oct3/4 and Cdx2 Determines Trophectoderm Differentiation

Abstract: Trophectoderm (TE), the first differentiated cell lineage of mammalian embryogenesis, forms the placenta, a structure unique to mammalian development.

Abstract: The differentiation of TE is a hallmark event in early mammalian development, but molecular mechanisms underlying this first differentiation event remain obscure.

Abstract: Embryonic stem (ES) cells can be induced to differentiate into the TE lineage by forced repression of the POU-family transcription factor, Oct3/4.

Abstract: We show here that this event can be mimicked by overexpression of Caudal-related homeobox 2 (Cdx2), which is sufficient to generate proper trophoblast stem (TS) cells.

Abstract: Cdx2 is dispensable for trophectoderm differentiation induced by Oct3/4 repression but essential for TS cell self-renewal.

Abstract: In preimplantation embryos, Cdx2 is initially coexpressed with Oct3/4 and they form a complex for the reciprocal repression of their target genes in ES cells.

Abstract: This suggests that reciprocal inhibition between lineage-specific transcription factors might be involved in the first differentiation event of mammalian development.


SSEA-1 is an enrichment marker for tumor-initiating cells in human glioblastoma.

Abstract: CD133+ populations of human glioblastoma multiforme (GBM) cells are reportedly enriched for tumor stem cells (TSCs) or tumor-initiating cells (TICs).

Abstract: Approximately 40% of freshly isolated GBM specimens, however, do not contain CD133+ tumor cells, raising the possibility that CD133 may not be a universal enrichment marker for GBM TSCs/TICs.

Abstract: Here we demonstrate that stage-specific embryonic antigen 1(SSEA-1/LeX)+ GBM cells fulfill the functional criteria for TSC/TIC, since (1) SSEA-1+ cells are highly tumorigenic in vivo, unlike SSEA-1- cells; (2) SSEA-1+ cells can give rise to both SSEA-1+ and SSEA-1- cells, thereby establishing a cellular hierarchy; and (3) SSEA-1+ cells have self-renewal and multilineage differentiation potentials.

Abstract: A distinct subpopulation of SSEA-1+ cells was present in all but one of the primary GBMs examined (n = 24), and most CD133+ tumor cells were also SSEA-1+, suggesting that SSEA-1 may be a general TSC/TIC enrichment marker in human GBMs.


Temporal regulation of topoisomerase IV activity in E. coli.

Abstract: We isolated a mutant allele of dnaX, encoding the tau and gamma subunits of the DNA polymerase III holoenzyme, that causes extreme cell filamentation but does not affect either cell growth or DNA replication.

Abstract: This phenotype results from a defect in daughter chromosome decatenation during rapid growth.

Abstract: In these cells, ParC, one subunit of topoisomerase IV, no longer associated with the replication factory, as occurs in wild-type cells, and was instead distributed uniformly on the nucleoid; the distribution of ParE, the other subunit of topoisomerase IV, was unaffected.

Abstract: In addition, the majority of topoisomerase IV activity in synchronized cell populations was restricted to late in the cell cycle, when replication was essentially complete.

Abstract: These observations suggest that topoisomerase IV activity in vivo might be dependent on release of ParC from the replication factory.


Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.

Abstract: BACKGROUND Molecularly targeted agents have been reported to have anti-tumour activity for patients whose tumours harbour the matching molecular alteration.

Abstract: These results have led to increased off-label use of molecularly targeted agents on the basis of identified molecular alterations.

Abstract: We assessed the efficacy of several molecularly targeted agents marketed in France, which were chosen on the basis of tumour molecular profiling but used outside their indications, in patients with advanced cancer for whom standard-of-care therapy had failed.

Abstract: METHODS The open-label, randomised, controlled phase 2 SHIVA trial was done at eight French academic centres.

Abstract: We included adult patients with any kind of metastatic solid tumour refractory to standard of care, provided they had an Eastern Cooperative Oncology Group performance status of 0 or 1, disease that was accessible for a biopsy or resection of a metastatic site, and at least one measurable lesion.

Abstract: The molecular profile of each patient's tumour was established with a mandatory biopsy of a metastatic tumour and large-scale genomic testing.

Abstract: We only included patients for whom a molecular alteration was identified within one of three molecular pathways (hormone receptor, PI3K/AKT/mTOR, RAF/MEK), which could be matched to one of ten regimens including 11 available molecularly targeted agents (erlotinib, lapatinib plus trastuzumab, sorafenib, imatinib, dasatinib, vemurafenib, everolimus, abiraterone, letrozole, tamoxifen).

Abstract: We randomly assigned these patients (1:1) to receive a matched molecularly targeted agent (experimental group) or treatment at physician's choice (control group) by central block randomisation (blocks of size six).

Abstract: Randomisation was done centrally with a web-based response system and was stratified according to the Royal Marsden Hospital prognostic score (0 or 1 vs 2 or 3) and the altered molecular pathway.

Abstract: Clinicians and patients were not masked to treatment allocation.

Abstract: Treatments in both groups were given in accordance with the approved product information and standard practice protocols at each institution and were continued until evidence of disease progression.

Abstract: The primary endpoint was progression-free survival in the intention-to-treat population, which was not assessed by independent central review.

Abstract: We assessed safety in any patients who received at least one dose of their assigned treatment.

Abstract: This trial is registered with ClinicalTrials.gov, number NCT01771458.

Abstract: FINDINGS Between Oct 4, 2012, and July 11, 2014, we screened 741 patients with any tumour type.

Abstract: 293 (40%) patients had at least one molecular alteration matching one of the 10 available regimens.

Abstract: At the time of data cutoff, Jan 20, 2015, 195 (26%) patients had been randomly assigned, with 99 in the experimental group and 96 in the control group.

Abstract: All patients in the experimental group started treatment, as did 92 in the control group.

Abstract: Two patients in the control group received a molecularly targeted agent: both were included in their assigned group for efficacy analyses, the patient who received an agent that was allowed in the experimental group was included in the experimental group for the purposes of safety analyses, while the other patient, who received a molecularly targeted agent and chemotherapy, was kept in the control group for safety analyses.

Abstract: Median follow-up was 11·3 months (IQR 5·8-11·6) in the experimental group and 11·3 months (8·1-11·6) in the control group at the time of the primary analysis of progression-free survival.

Abstract: Median progression-free survival was 2·3 months (95% CI 1·7-3·8) in the experimental group versus 2·0 months (1·8-2·1) in the control group (hazard ratio 0·88, 95% CI 0·65-1·19, p=0·41).

Abstract: In the safety population, 43 (43%) of 100 patients treated with a molecularly targeted agent and 32 (35%) of 91 patients treated with cytotoxic chemotherapy had grade 3-4 adverse events (p=0·30).

Abstract: INTERPRETATION The use of molecularly targeted agents outside their indications does not improve progression-free survival compared with treatment at physician's choice in heavily pretreated patients with cancer.

Abstract: Off-label use of molecularly targeted agents should be discouraged, but enrolment in clinical trials should be encouraged to assess predictive biomarkers of efficacy.


CRTC2 (TORC2) contributes to the transcriptional response to fasting in the liver but is not required for the maintenance of glucose homeostasis.

Abstract: The liver contributes to glucose homeostasis by promoting either storage or production of glucose, depending on the physiological state.

Abstract: The cAMP response element-binding protein (CREB) is a principal regulator of genes involved in coordinating the hepatic response to fasting, but its mechanism of gene activation remains controversial.

Abstract: We derived CRTC2 (CREB-regulated transcription coactivator 2, previously TORC2)-deficient mice to assess the contribution of this cofactor to hepatic glucose metabolism in vivo.

Abstract: CRTC2 mutant hepatocytes showed reduced glucose production in response to glucagon, which correlated with decreased CREB binding to several gluconeogenic genes.

Abstract: However, despite attenuated expression of CREB target genes, including PEPCK, G6Pase, and PGC-1alpha, no hypoglycemia was observed in mutant mice.

Abstract: Collectively, these results provide genetic evidence supporting a role for CRTC2 in the transcriptional response to fasting, but indicate only a limited contribution of this cofactor to the maintenance of glucose homeostasis.


Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

Abstract: BACKGROUND Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern.

Abstract: Despite this, little is known about polar bear species history.

Abstract: Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.

Abstract: RESULTS We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges.

Abstract: Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia.

Abstract: In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.

Abstract: CONCLUSIONS The reconstructed matrilineal history of brown and polar bears has two striking features.

Abstract: First, it is punctuated by dramatic and discrete climate-driven dispersal events.

Abstract: Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint.

Abstract: In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline.

Abstract: This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.


FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation

Abstract: FBW7 (F-box and WD repeat domain-containing 7) is the substrate recognition component of an evolutionary conserved SCF (complex of SKP1, CUL1 and F-box protein)-type ubiquitin ligase.

Abstract: SCFFBW7 degrades several proto-oncogenes that function in cellular growth and division pathways, including MYC, cyclin E, Notch and JUN.

Abstract: FBW7 is also a tumour suppressor, the regulatory network of which is perturbed in many human malignancies.

Abstract: Numerous cancer-associated mutations in FBW7 and its substrates have been identified, and loss of FBW7 function causes chromosomal instability and tumorigenesis.

Abstract: This Review focuses on structural and functional aspects of FBW7 and its role in the development of cancer.


Hypoglycemic episodes and risk of dementia in older patients with type 2 diabetes mellitus.

Abstract: CONTEXT Although acute hypoglycemia may be associated with cognitive impairment in children with type 1 diabetes, no studies to date have evaluated whether hypoglycemia is a risk factor for dementia in older patients with type 2 diabetes.

Abstract: OBJECTIVE To determine if hypoglycemic episodes severe enough to require hospitalization are associated with an increased risk of dementia in a population of older patients with type 2 diabetes followed up for 27 years.

Abstract: DESIGN, SETTING, AND PATIENTS A longitudinal cohort study from 1980-2007 of 16,667 patients with a mean age of 65 years and type 2 diabetes who are members of an integrated health care delivery system in northern California.

Abstract: MAIN OUTCOME MEASURE Hypoglycemic events from 1980-2002 were collected and reviewed using hospital discharge and emergency department diagnoses.

Abstract: Cohort members with no prior diagnoses of dementia, mild cognitive impairment, or general memory complaints as of January 1, 2003, were followed up for a dementia diagnosis through January 15, 2007.

Abstract: Dementia risk was examined using Cox proportional hazard regression models, adjusted for age, sex, race/ethnicity, education, body mass index, duration of diabetes, 7-year mean glycated hemoglobin, diabetes treatment, duration of insulin use, hyperlipidemia, hypertension, cardiovascular disease, stroke, transient cerebral ischemia, and end-stage renal disease.

Abstract: RESULTS At least 1 episode of hypoglycemia was diagnosed in 1465 patients (8.8%) and dementia was diagnosed in 1822 patients (11%) during follow-up; 250 patients had both dementia and at least 1 episode of hypoglycemia (16.95%).

Abstract: Compared with patients with no hypoglycemia, patients with single or multiple episodes had a graded increase in risk with fully adjusted hazard ratios (HRs): for 1 episode (HR, 1.26; 95% confidence interval [CI], 1.10-1.49); 2 episodes (HR, 1.80; 95% CI, 1.37-2.36); and 3 or more episodes (HR, 1.94; 95% CI, 1.42-2.64).

Abstract: The attributable risk of dementia between individuals with and without a history of hypoglycemia was 2.39% per year (95% CI, 1.72%-3.01%).

Abstract: Results were not attenuated when medical utilization rates, length of health plan membership, or time since initial diabetes diagnosis were added to the model.

Abstract: When examining emergency department admissions for hypoglycemia for association with risk of dementia (535 episodes), results were similar (compared with patients with 0 episodes) with fully adjusted HRs: for 1 episode (HR, 1.42; 95% CI, 1.12-1.78) and for 2 or more episodes (HR, 2.36; 95% CI, 1.57-3.55).

Abstract: CONCLUSIONS Among older patients with type 2 diabetes, a history of severe hypoglycemic episodes was associated with a greater risk of dementia.

Abstract: Whether minor hypoglycemic episodes increase risk of dementia is unknown.


Defective mast cell effector functions in mice lacking the CRACM1 pore subunit of store-operated calcium release–activated calcium channels

Abstract: CRACM1 (also called Orai1) constitutes the pore subunit of store-operated calcium release–activated calcium channels.

Abstract: A point mutation in the gene encoding CRACM1 is associated with severe combined immunodeficiency disease in humans.

Abstract: Here we generated CRACM1-deficient mice in which β-galactosidase activity 'reported' CRACM1 expression.

Abstract: CRACM1-deficient mice were smaller in size.

Abstract: Mast cells derived from CRACM1-deficient mice showed grossly defective degranulation and cytokine secretion, and the allergic reactions elicited in vivo were inhibited in CRACM1-deficient mice.

Abstract: We detected robust CRACM1 expression in skeletal muscles and some regions of the brain, heart and kidney but not in the lymphoid regions of thymus and spleen.

Abstract: In contrast, we found CRACM2 expression to be much higher in mouse T cells.

Abstract: In agreement with those findings, the store-operated calcium influx and development and proliferation of CRACM1-deficient T cells was unaffected.

Abstract: Thus, CRACM1 is crucial in mouse mast cell effector function, but mouse T cell calcium release–activated calcium channels are functional in the absence of CRACM1.


MicroRNA-7: A miRNA with expanding roles in development and disease.

Abstract: MicroRNAs (miRNAs) are a family of short, non-coding RNA molecules (∼22nt) involved in post-transcriptional control of gene expression.

Abstract: They act via base-pairing with mRNA transcripts that harbour target sequences, resulting in accelerated mRNA decay and/or translational attenuation.

Abstract: Given miRNAs mediate the expression of molecules involved in many aspects of normal cell development and functioning, it is not surprising that aberrant miRNA expression is closely associated with many human diseases.

Abstract: Their pivotal role in driving a range of normal cellular physiology as well as pathological processes has established miRNAs as potential therapeutics, as well as potential diagnostic and prognostic tools in human health.

Abstract: MicroRNA-7 (miR-7) is a highly conserved miRNA which displays restricted spatiotemporal expression during development and in maturity.

Abstract: In humans and mice, mature miR-7 is generated from three different genes, illustrating unexpected redundancy and also the importance of this miRNA in regulating key cellular processes.

Abstract: In this review we examine the expanding role of miR-7 in the context of health, with emphasis on organ differentiation and development, as well as in various mammalian diseases, particularly of the brain, heart, endocrine pancreas and skin, as well as in cancer.

Abstract: The more we learn about miR-7, the more we realise the complexity of its regulation and potential functional application both from a biomarker and therapeutic perspective.


Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology.

Abstract: Down syndrome (DS) is the most frequent cause of human congenital mental retardation.

Abstract: Cognitive deficits in DS result from perturbations of normal cellular processes both during development and in adult tissues, but the mechanisms underlying DS etiology remain poorly understood.

Abstract: To assess the ability of induced pluripotent stem cells (iPSCs) to model DS phenotypes, as a prototypical complex human disease, we generated bona fide DS and wild-type (WT) nonviral iPSCs by episomal reprogramming.

Abstract: DS iPSCs selectively overexpressed chromosome 21 genes, consistent with gene dosage, which was associated with deregulation of thousands of genes throughout the genome.

Abstract: DS and WT iPSCs were neurally converted at >95% efficiency and had remarkably similar lineage potency, differentiation kinetics, proliferation, and axon extension at early time points.

Abstract: However, at later time points DS cultures showed a twofold bias toward glial lineages.

Abstract: Moreover, DS neural cultures were up to two times more sensitive to oxidative stress-induced apoptosis, and this could be prevented by the antioxidant N-acetylcysteine.

Abstract: Our results reveal a striking complexity in the genetic alterations caused by trisomy 21 that are likely to underlie DS developmental phenotypes, and indicate a central role for defective early glial development in establishing developmental defects in DS brains.

Abstract: Furthermore, oxidative stress sensitivity is likely to contribute to the accelerated neurodegeneration seen in DS, and we provide proof of concept for screening corrective therapeutics using DS iPSCs and their derivatives.

Abstract: Nonviral DS iPSCs can therefore model features of complex human disease in vitro and provide a renewable and ethically unencumbered discovery platform.