bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age Shock Index is Superior to Shock Index and Modified Shock Index for Predicting Long-Term Prognosis in Acute Myocardial Infarction
Authors: Yu Tongtong , Tian Chunyang , Song Jia , He Dongxu , Sun Zhijun , Sun Zhaoqing 
Published: May 2017

ABSTRACT

Background:
Shock index (SI) has been reported to help us predict adverse prognosis in patients with acute myocardial infarction (AMI) undergoing percutaneous coronary intervention (PCI). However, the prognostic value of age SI and modified shock index (MSI) in AMI undergoing PCI is unknown. Moreover, the prognostic performance of admission age SI is not compared with SI, MSI, and the Global Registry of Acute Coronary Events (GRACE) risk score.

Methods:
One thousand eight hundred sixty-four AMI patients undergoing PCI were analyzed in a retrospective cohort study. Clinical endpoint was all-cause mortality. The predictive performance of new models was assessed by C-statistic, Hosmer–Lemeshow test, Nagelkerke-R2, Brier scores, integrated discrimination improvement (IDI), and net reclassification improvement (NRI).

Results:
Multivariate analysis showed that higher age SI and MSI were both associated with a higher rate of all-cause mortality [age SI: hazard ratios (HR) = 1.025, 95% CI = 1.010–1.040, P = 0.001; MSI: HR = 2.902, 95% CI = 1.180–7.137, P = 0.020]. The prognostic performance of admission age SI was similar to the GRACE systems for predicting all-cause mortality (C-statistic: z = 0.437, P = 0.662; IDI: −0.005, P = 0.474; NRI: −0.028, P = 0.257), but better than admission SI (C-statistic: z = 3.944, P < 0.001; IDI: 0.012, P = 0.016; NRI: 0.472, P < 0.001) and admission MSI (C-statistic: z = 3.214, P = 0.001; IDI: 0.011, P = 0.001; NRI: 0.561, P < 0.001).

Conclusions:

Age SI alone can identify patients at high risk of death in AMI patients undergoing PCI. It is similar to GRACE but better than SI and MSI for predicting all-cause mortality. However, age SI is easier to calculate than GRACE.
A persistent lack of International representation on editorial boards in environmental biology
Authors: Espin Johanna , Palmas Sebastian , Carrasco-Rueda Farah , Riemer Kristina , Allen Pablo E. , Berkebile Nathan , Hecht Kirsten A. , Kastner-Wilcox Kay , Núñez-Regueiro Mauricio M. , Prince Candice , Rios Constanza , Ross Erica , Sangha Bhagatveer , Tyler Tia , Ungvari-Martin Judit , Villegas Mariana , Cataldo Tara T. , Bruna Emilio M. 
Published: May 2017

ABSTRACTThe scholars comprising journal editorial boards play a critical role in defining the trajectory of knowledge in their field. Nevertheless, studies of editorial board composition remain rare, especially those focusing on journals publishing research in the increasingly globalized fields of science, technology, engineering, and math (STEM). Using metrics for quantifying the diversity of ecological communities, we quantified international representation on the 1985-2014 editorial boards of twenty-four environmental biology journals. Over the course of three decades there were 3831 unique scientists based in 70 countries that served as editors. The size of the editorial community increased over time – there were 420% more editors serving in 2014 than in 1985 – as did the number of countries in which editors were based. Nevertheless, editors based outside the ‘Global North’ (the group of economically developed countries with high per capita Gross Domestic Product (GDP) that collectively concentrate most global wealth) were extremely rare. Furthermore, 67.06% of all editors were based in either the USA or UK. Consequently, Geographic Diversity – already low in 1985 – remained unchanged through 2014. We argue that this limited geographic diversity can detrimentally affect the creativity of scholarship published in journals, the progress and direction of research, the composition of the STEM workforce, and the development of science in Latin America, Africa, the Middle East, and much of Asia (i.e., the ‘Global South’).
taxMaps - Ultra-comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
Authors: Corvelo André , Clarke Wayne E. , Robine Nicolas , Zody Michael C. 
Published: May 2017

AbstractHigh-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive and fully scalable taxonomic classification tool, capable of delivering classification accuracy comparable to that of BLASTn, but at up to 3 orders of magnitude less computational cost. taxMaps is freely available for academic and non-commercial research purposes athttps://github.com/nygenome/taxmaps.
Selecting short DNA fragments in plasma improves detection of circulating tumour DNA
Authors: Mouliere Florent , Piskorz Anna M. , Chandrananda Dineika , Moore Elizabeth , Morris James , Smith Christopher G. , Goranova Teodora , Heider Katrin , Mair Richard , Supernat Anna , Gounaris Ioannis , Ros Susana , Wan Jonathan C. M. , Jimenez-Linan Mercedes , Gale Davina , Brindle Kevin , Massie Charles E. , Parkinson Christine A. , Brenton James D. , Rosenfeld Nitzan 
Published: May 2017

Introductory paragraphNon-invasive analysis of cancer genomes using cell-free circulating tumour DNA (ctDNA) is being widely implemented for clinical indications. The sensitivity for detecting the presence of ctDNA and genomic changes in ctDNA is limited by its low concentration compared to cell-free DNA of non-tumour origin. We studied the feasibility for enrichment of ctDNA by size selection, in plasma samples collected before and during chemotherapy treatment in 13 patients with recurrent high-grade serous ovarian cancer. We evaluated the effects using targeted and whole genome sequencing. Selecting DNA fragments between 90-150 bp before analysis yielded enrichment of mutated DNA fraction of up to 11-fold. This allowed identification of adverse copy number alterations, includingMYCamplification, otherwise not observed. Size selection allows detection of tumour alterations masked by non-tumour DNA in plasma and could help overcome sensitivity limitations of liquid biopsy for applications in early diagnosis, detection of minimal residual disease, and genomic profiling.
Effect of initial body orientation on escape probability in prey fish escaping from predators
Authors: Kimura Hibiki , Kawabata Yuuki 
Published: May 2017

AbstractSince the escape response is crucial to survival and hence to the fitness of species, several studies have attempted to elucidate the kinematic and behavioral components of the response that affect evasion outcome. The prey’s body orientation relative to a predator at the onset of the escape response (initial orientation) could affect evasion outcome, because the turn angle and its duration before the initiation of escape locomotion would be smaller when the initial orientation is more away from the predator. We tested this hypothesis by recording the escape responses of juvenile red sea bream (Pagrus major) in response to the predatory scorpion fish (Sebastiscus marmoratus) using a high-speed video camera. Our results show that an increased initial orientation (i.e., more away from the predator) increases escape probability. Our results also indicate that an increase in the initial orientation decreases the turn angle and its duration. The flight initiation distance tends to be small when the initial orientation is away from the predator, suggesting that the prey might have a blind zone of sensory perception. These findings highlight the importance of incorporating initial orientation into both empirical and theoretical studies of the kinematics of predator-prey interactions.Summary statementOur predator-prey experiments reveal that the prey’s initial body orientation relative to a predator affects the prey’s turn angle and its duration, and consequently affects escape probability.
Genetic stratification of depression in UK Biobank suggests a subgroup linked to age of natural menopause
Authors: Howard David M. , Folkersen Lasse , Coleman Jonathan R. I. , Adams Mark J. , Glanville Kylie , Werge Thomas , Hagenaars Saskia P. , Han Buhm , Porteous David , Campbell Archie , Clarke Toni-Kim , Breen Gerome , Sullivan Patrick F. , Wray Naomi R. , Lewis Cathryn M. , McIntosh Andrew M. 
Published: May 2017

AbstractDepression is a common and clinically heterogeneous mental health disorder that is frequently comorbid with other diseases and conditions. Stratification of depression may align sub-diagnoses more closely with their underling aetiology and provide more tractable targets for research and effective treatment. In the current study, we investigated whether genetic data could be used to identify subgroups within people with depression using the UK Biobank. Examination of cross-locus correlations was used to test for evidence of subgroups by examining whether there was clustering of independent genetic variants associated with eleven other complex traits and disorders in people with depression. We found evidence of a subgroup within depression using age of natural menopause variants (P= 1.69 × 10−3) and this effect remained significant in females (P= 1.18 × 10−3), but not males (P= 0.186). However, no evidence for this subgroup (P> 0.05) was found in Generation Scotland, iPSYCH, a UK Biobank replication cohort or the GERA cohort. In the UK Biobank, having depression was also associated with a later age of menopause (beta = 0.34, standard error = 0.06,P= 9.92 × 10−8). A potential age of natural menopause subgroup within depression and the association between depression and a later age of menopause suggests that they partially share a developmental pathway.
The equivalent arc ratio for auditory space
Authors: Brimijoin W. Owen 
Published: May 2017

AbstractThe minimum audible movement angle increases as a function of source azimuth. If listeners do not perceptually compensate for this change in acuity, then sounds rotating around the head should appear to move faster at the front than at the side. We examined whether judgments of relative amounts of acoustic motion depend on signal center angle and found that the azimuth of two signals strongly affects their point of subjective similarity for motion. Signal motion centered at 90° had to be roughly twice as large as motion centered at 0° to be judged as equivalent. This distortion of acoustic space around the listener suggests that the perceived velocity of moving sound sources changes as a function of azimuth around the head. The “equivalent arc ratio,” a mathematical framework based on these results, is used to successfully provide quantitative explanations for previously documented discrepancies in spatial localization, motion perception, and head-to-world coordinate transformations.
Quantitative RNA-seq meta analysis of alternative exon usage in C. elegans
Authors: Tourasse Nicolas , Millet Jonathan R. M. , Dupuy Denis 
Published: May 2017

ABSTRACTAlmost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated.Here we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing reads come from reproducibly detected splicing events, a large fraction of purported junctions are only supported by a very low number of reads. We devised an automated curation method that takes into account the expression level of each gene to discriminate robust splicing events from potential biological noise. We found that rarely used splice sites disproportionately come from highly expressed genes and are significantly less conserved in other nematode genomes than splice sites with a higher usage frequency.Our increased detection power confirmed trans-splicing for at least 84% of C. elegans protein coding genes. The genes for which trans-splicing was not observed are overwhelmingly low expression genes, suggesting that the mechanism is pervasive but not full captured by organism-wide RNA-Seq.We generated annotated gene models including quantitative exon usage information for the entire C. elegans genome. This allows users to visualize at a glance the relative expression of each isoform for their gene of interest.
The unfolded protein response switches from pro-survival to pro-apoptotic to cap the extent of endoplasmic reticulum expansion
Authors: Vitale Milena , Orsi Andrea , Bakunts Anush , Lari Federica , Tadè Laura , Cattaneo Angela , Sitia Roberto , Raimondi Andrea , Bachi Angela , Anken Eelco van 
Published: May 2017

ABSTRACTInsufficient folding capacity of the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) to restore homeostasis. Yet, how the UPR achieves and evaluates ER homeostatic readjustment is poorly understood. In a HeLa cell model we show that, upon a severe proteostatic insult that eclipses the ER chaperone BiP, the UPR transitions from acute full-gear activation to chronic submaximal activation, when BiP is in excess again. As such, the UPR-driven ER expansion is pro-survival, primarily via the UPR transducer ATF6α. Simultaneous abrogation of ER-associated degradation (ERAD) leads to chronic full-gear UPR activation and further ER expansion, but the UPR transducers IRE1α and PERK turn pro-apoptotic. Pro-survivalXBP1mRNA processing by IRE1α is then trumped since unsplicedXBP1mRNA is depleted and IRE1α’s endonuclease activity is unleashed against other RNAs. Thus, the IRE1α/XBP1relay serves as a capacitor of ER expansion that heralds cell death if the expansion is deemed excessive.
Central amygdala CRF pathways in alcohol dependence
Authors: de Guglielmo Giordano , Kallupi Marsida , Pomrenze Matthew B. , Crawford Elena , Simpson Sierra , Schweitzer Paul , Koob George F. , Messing Robert O. , George Olivier 
Published: May 2017

AbstractAlcohol withdrawal activates a neuronal ensemble in the central nucleus of the amygdala (CeA) that is responsible for high levels of uncontrolled alcohol drinking. However, the neuronal phenotypes and circuits controlled by these neurons are unknown. We investigated the cellular identity of this CeA neuronal ensemble and found that most neurons expressed corticotropin-releasing factor (CRF). UsingCrh-Cre transgenic rats combined within vivooptogenetics, we tested the role of CeA CRF neurons and their projections in excessive alcohol self-administration during withdrawal. Rats were injected with AAV-DIO-NpHR-eYFP or AAV-DIO-eYFP and implanted with optical fibers over the CeA. Animals were then exposed to chronic intermittent ethanol vapor to induce alcohol dependence. Inactivation of CeA CRF neurons decreased alcohol drinking in dependent rats to non-dependent levels and completely suppressed activation of the CeA neuronal ensemble (Fos+neurons) during withdrawal. No effects were observed on water or saccharin self-administration. In a second experiment, CeA CRF neurons were infected with AAV-DIO-NpHR-eYFP and optical fibers were implanted into downstream projection regions, including the bed nucleus of the stria terminalis (BNST), lateral hypothalamus (LH), parasubthalamic nucleus (pSTN), substantia innominata (SI), and parabrachial nuclei (PBN). Optogenetic inactivation of CRF terminals in the BNST reduced alcohol drinking and withdrawal signs, whereas inactivation of all other projections had no effect. These results demonstrate that CeA CRF neurons and their projections to the BNST drive excessive alcohol drinking and withdrawal in dependent rats.
Transcriptomic correlates of neuron electrophysiological diversity
Authors: Tripathy Shreejoy J. , Toker Lilah , Li Brenna , Crichlow Cindy-Lee , Tebaykin Dmitry , Ogan Mancarci B. , Pavlidis Paul 
Published: May 2017

AbstractHow neuronal diversity emerges from complex patterns of gene expression remains poorly understood. Here we present an approach to understand electrophysiological diversity through gene expression by integrating transcriptomics with intracellular electrophysiology. Using a brain-wide dataset of 34 neuron types, we identified 420 genes whose expression levels significantly correlated with variability in one or more of 11 electrophysiological parameters. The majority of these correlations were consistent in an independent sample of 12 visual cortex cell types. Many associations reported here have the potential to provide new insights into how neurons generate functional diversity, and correlations of ion channel genes likeGabrdandScn1a(Nav1.1) with resting potential and spiking frequency are consistent with known causal mechanisms. These results suggest that despite the complexity linking gene expression to electrophysiology, there are likely some general principles that govern how individual genes establish phenotypic diversity across very different cell types.
Spindle assembly checkpoint strength is governed by cell size and PAR-mediated cell fate determination inC. elegans
Authors: Gerhold Abigail R. , Poupart Vincent , Labbé Jean-Claude , Maddox Paul S. 
Published: May 2017

AbstractThe spindle assembly checkpoint (SAC) is a conserved mitotic regulator that preserves genome stability. Despite its central role in preserving the fidelity of mitosis, the strength of the SAC varies widely between cell types. How the SAC is adapted to different cellular contexts remains largely unknown. Here we show that both cell size and cell fate impact SAC strength. While smaller cells have a stronger SAC, cells with a germline fate show increased SAC activity relative to their somatic counterparts across all cell sizes. We find that enhanced SAC activity in the germline blastomere P1requires proper specification of cell fate downstream of the conserved PAR polarity proteins, supporting a model in which checkpoint factors are distributed asymmetrically during early germ cell divisions. Our results indicate that size scaling of SAC activity is modulated by cell fate and reveal a novel interaction between asymmetric cell division and the SAC.
Food Webs Over Time: Evaluating the Variability of Degree Distribution on Ecological Networks
Authors: Lopez Daniela N , Camus Patricio A , Valdivia Nelson , Estay Sergio A 
Published: May 2017

AbstractAlthough networks analysis has moved from static to dynamic, ecological networks are still analyzed as time-aggregated units where time-specific interactions are aggregated into one single network. As a result, several questions arise such as what is the functional form of and how variable is the topology of time-specific versus time-aggregated ecological networks? Furthermore, it is yet unknown to what extent the structure of time-aggregated networks is representative of the dynamics of the community. Here, we compared the topology of time-specific and time-aggregated networks by analyzing a set of intertidal networks containing more than 1,000 interactions, and assessed the spatiotemporal dynamics of their degree distributions. By fitting different distribution models, we found that the out-degree distributions of seasonal and time-aggregated networks were best described by an exponential model while the in-degree distributions were best described by a discrete generalized beta model. The degree distributions of the seasonal networks were highly temporally variable and are significantly different from those of time-aggregated networks. We observed that seasonal degree distributions converged toward time-aggregated network distributions after 1.5 years of sampling. Our results highlight the importance of understanding the dynamics of ecological networks, which can show topological characteristics significantly different from those of time-aggregated networks.
Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion
Authors: Briggs Adrian W. , Goldfless Stephen J. , Timberlake Sonia , Belmont Brian J. , Clouser Christopher R. , Koppstein David , Sok Devin , Heiden Jason Vander A. , Tamminen Manu V. , Kleinstein Steven H. , Burton Dennis R. , Church George M. , Vigneault Francois 
Published: May 2017

AbstractTumor-infiltrating lymphocytes (TILs) are critical to anti-cancer immune responses, but their diverse phenotypes and functions remain poorly understood and challenging to study. We therefore developed a single-cell barcoding technology for deep characterization of TILs without the need for cell-sorting or culture. Our emulsion-based method captures full-length, natively paired B-cell and T-cell receptor (BCR and TCR) sequences from lymphocytes among millions of input cells. We validated the method with 3 million B-cells from healthy human blood and 350,000 B-cells from an HIV elite controller, before processing 400,000 cells from an unsorted dissociated ovarian adenocarcinoma and recovering paired BCRs and TCRs from over 11,000 TILs. We then extended the barcoding method to detect DNA-labeled antibodies, allowing ultra-high throughput, simultaneous protein detection and RNA sequencing from single cells.
Inhibitory effect of the urothelium/lamina propria on female porcine urethral contractility & effect of age
Authors: Folasire Oladayo S , Chess‐Williams Russ , Sellers Donna J 
Published: May 2017

SummaryThe urethral uroepithelium has been implicated in urethral sensation and maintenance of continence. However, relatively little is known about the function of the urethral urothelium compared with that of the bladder. The aim of the study was to examine the role of the urothelium/lamina propria on contractility of the porcine urethra, along with the influence of nitric oxide, prostaglandins and ageing. Porcine urethral tissues, intact and denuded of urothelium/lamina propria, were mounted in tissue baths and contractions to noradrenaline, phenylephrine and carbachol obtained. Contractions in the presence of Nώ–nitro‐l‐arginine (100 μmol/L) and indomethacin (10 μmol/L) were examined, along with contractions of tissues from young (6 months) and older (3 years) animals. The urothelium/lamina propria of the urethra significantly inhibited contractions to carbachol, noradrenaline and phenylephrine. This inhibitory effect was not significantly different for the three agonists (58.7±10.3%, 60.4±12.6% and 39.4±12.2% inhibition; n=4‐7), and was also observed when denuded tissues were co‐incubated with a second tissue with intact urothelium/lamina propria (40.6±7.5% inhibition; n=6). Inhibition of nitric oxide and prostaglandin production did not attenuate the inhibitory effect of the urothelium/lamina propria on noradrenaline contractions. In addition, ageing did not alter the inhibitory effect for either phenylephrine contractions (33.9±2.2% vs 41.0±9.7%, young vs older urethral tissues) or noradrenaline contractions (32.9±11.1% vs 53.7±11.0%). In conclusion the urothelium/lamina propria of the urethra has an inhibitory effect on receptor‐mediated urethral contraction. This inhibition is due to the release of a diffusible factor, and the effect is not mediated by nitric oxide or prostaglandins, or affected by age.