bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compensatory Reserve Index: Performance of A Novel Monitoring Technology to Identify the Bleeding Trauma Patient
Authors: Johnson Michael C. , Alarhayem Abdul , Convertino Victor , Carter Robert , Chung Kevin , Stewart Ronald , Myers John , Dent Daniel , Liao Lilian , Cestero Ramon , Nicholson Susannah , Muir Mark , Schwacha Martin , Wampler David , DeRosa Mark , Eastridge Brian 
Published: August 2017

ABSTRACT

Introduction:
Hemorrhage is one of the most substantial causes of death after traumatic injury. Standard measures, including systolic blood pressure (SBP), are poor surrogate indicators of physiologic compromise until compensatory mechanisms have been overwhelmed. Compensatory Reserve Index (CRI) is a novel monitoring technology with the ability to assess physiologic reserve. We hypothesized CRI would be a better predictor of physiologic compromise secondary to hemorrhage than traditional vital signs.

Methods:
A prospective observational study of 89 subjects meeting trauma center activation criteria at a single level I trauma center was conducted from October 2015 to February 2016. Data collected included demographics, SBP, heart rate, and requirement for hemorrhage-associated, life-saving intervention (LSI) (i.e., operation or angiography for hemorrhage, local or tourniquet control of external bleeding, and transfusion >2 units PRBC). Receiver-operator characteristic (ROC) curves were formulated and appropriate thresholds were calculated to compare relative value of the metrics for predictive modeling.

Results:
For predicting hemorrhage-related LSI, CRI demonstrated a sensitivity of 83% and a negative predictive value (NPV) of 91% as compared with SBP with a sensitivity to detect hemorrhage of 26% (P < 0.05) and an NPV of 78%. ROC curves generated from admission CRI and SBP measures demonstrated values of 0.83 and 0.62, respectively. CRI identified significant hemorrhage requiring potentially life-saving therapy more reliably than SBP (P < 0.05).

Conclusion:
The CRI device demonstrated superior capacity over systolic blood pressure in predicting the need for posttraumatic hemorrhage intervention in the acute resuscitation phase after injury.
Should Benzodiazepines and Anticonvulsants Be Used During Electroconvulsive Therapy?
Authors: Tang Victor M. , Pasricha Akash N. , Blumberger Daniel M. , Voineskos Daphne , Pasricha Suvercha , Mulsant Benoit H. , Daskalakis Zafiris J. 
Published: August 2017

Objective
This study aims to investigate the clinical effects of benzodiazepines or anticonvulsant use during a course of electroconvulsive therapy (ECT).

Method
A case report study of a patient who received ECT with and without concomitant flurazepam and pregabalin is presented. The literature on the use of benzodiazepines and anticonvulsants during ECT is reviewed.

Results
A woman with treatment resistant depression received a course of ECT while taking flurazepam and pregabalin, but seizures were of short duration and symptomatic improvement was minimal. After discontinuation of flurazepam and pregabalin, a course of right unilateral ultrabrief ECT was associated with adequate seizures and remission of depression and suicidal ideation. Our literature review suggests that benzodiazepines decrease seizure duration, but most evidence shows no association with increased seizure threshold. One prospective RCT and 3 large retrospective studies found that benzodiazepines compromise the efficacy of unilateral but not bilateral ECT. Regarding anticonvulsants, several studies had varied and contradictory results on their effect on seizure duration and seizure threshold. Of the 2 large retrospective studies and 3 RCTs, only 1 retrospective study showed that anticonvulsants decrease the efficacy of ECT.

Conclusions
Judicious assessment of all medications used in combination with ECT is recommended. Overall, published studies suggest that benzodiazepines and anticonvulsants impact the clinical outcomes of ECT less than what would be expected given their pharmacologic effects. However, there are significant gaps in the literature, including a lack of study on suprathreshold stimulation of right unilateral ECT and the possibility of a greater effect with higher medication doses.
Causes and consequences of adult sex ratio imbalance in a historical U.S. population
Authors: Schacht Ryan , Smith Ken R. 
Published: August 2017

The responsiveness of individuals to partner availability has been well-documented across the literature. However, there is disagreement regarding the direction of the consequences of sex ratio imbalance. Specifically, does an excess of males or females promote male–male mating competition? In an attempt to clarify the role of the adult sex ratio (ASR) on behaviour, here we evaluate both competing and complimentary expectations derived from theory across the social and biological sciences. We use data drawn from a historical, nineteenth century population in North America and target several life-history traits thought to be affected by partner availability: age at first birth, relationship status, completed fertility and longevity. Furthermore, we assess the role of various contributors to a population's ASR. We find that both the contributors to and consequences of sex ratio imbalance vary over time. Our results largely support predictions of greater male pairbond commitment and lesser male mating effort, as well as elevated bargaining power of women in response to female scarcity. After reviewing our findings, and others from across the literature, we highlight the need to adjust predictions in response to ASR imbalance by the: (i) culturally mediated mating arena, (ii) variable role of demographic inputs across time and place, (iii) constraints to behavioural outcomes across populations, and (iv) ability and accuracy of individuals to assess partner availability.This article is part of the themed issue ‘Adult sex ratios and reproductive strategies: a critical re-examination of sex differences in human and animal societies’.
Adult sex ratios and their implications for cooperative breeding in birds
Authors: Komdeur Jan , Székely Tamás , Long Xiaoyan , Kingma Sjouke A. 
Published: August 2017

Cooperative breeding is a form of breeding system where in addition to a core breeding pair, one or more usually non-breeding individuals provide offspring care. Cooperative breeding is widespread in birds, but its origin and maintenance in contemporary populations are debated. Although deviations in adult sex ratio (ASR, the proportion of males in the adult population) have been hypothesized to influence the occurrence of cooperative breeding because of the resulting surplus of one sex and limited availability of breeding partners, this hypothesis has not been tested across a wide range of taxa. By using data from 188 bird species and phylogenetically controlled analyses, we show that cooperatively breeding species have more male-biased ASRs than non-cooperative species. Importantly, ASR predicts helper sex ratio: in species with more male-biased ASR, helper sex ratio is also more male biased. We also show that offspring sex ratios do not predict ASRs, so that the skewed ASRs emerge during the period when individuals aim to obtain a breeding position or later during adulthood. In line with this result, we found that ASR (among both cooperatively and non-cooperatively breeding species) is inversely related to sex bias in dispersal distance, suggesting that the cost of dispersal is more severe for the further-dispersing sex. As females usually disperse further in birds, this explains the generally male-biased ASR, and in combination with benefits of philopatry for males, this probably explains why ASR is more biased in cooperatively breeding species. Taken together, our results suggest that a sex bias in helping in cooperatively breeding species relates to biased ASRs. We propose that this relationship is driven by sex-specific costs and benefits of dispersal and helping, as well as other demographic factors. Future phylogenetic comparative and experimental work is needed to establish how this relationship emerges.This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Social determinants of adult sex ratios and racial/ethnic disparities in transmission of HIV and other sexually transmitted infections in the USA
Authors: Pouget Enrique Rodriguez 
Published: August 2017

In Black population centres in the USA, adult sex ratios (ASRs) are strongly female-biased primarily due to high male incarceration and early mortality rates. I explore the system of social determinants that shape these ASRs, and describe their apparent consequences. Evidence suggests that female-biased ASRs play a role, along with racial residential segregation, to increase mixing between core and peripheral members of sexual networks, facilitating transmission of human immunodeficiency virus and other sexually transmitted infections. Unique historical factors underlie Black male incarceration and mortality rates in the USA, making comparisons with other groups or other countries challenging.This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Climate-driven shifts in adult sex ratios via sex reversals: the type of sex determination matters
Authors: Bókony Veronika , Kövér Szilvia , Nemesházi Edina , Liker András , Székely Tamás 
Published: August 2017

Sex reversals whereby individuals of one genetic sex develop the phenotype of the opposite sex occur in ectothermic vertebrates with genetic sex-determination systems that are sensitive to extreme temperatures during sexual differentiation. Recent rises in global temperatures have led researchers to predict that sex reversals will become more common, resulting in the distortion of many populations' sex ratios. However, it is unclear whether susceptibility to climate-driven sex-ratio shifts depends on the type of sex determination that varies across species. First, we show here using individual-based theoretical models that XX/XY (male-heterogametic) and ZZ/ZW (female-heterogametic) sex-determination systems can respond differentially to temperature-induced sex reversals. Interestingly, the impacts of climate warming on adult sex ratio (ASR) depend on the effects of both genotypic and phenotypic sex on survival and reproduction. Second, we analyse the temporal changes of ASR in natural amphibian populations using data from the literature, and find that ASR shifted towards males in ZZ/ZW species over the past 60 years, but did not change significantly in XX/XY species. Our results highlight the fact that we need a better understanding of the interactions between genetic and environmental sex-determining mechanisms to predict the responses of ectotherms to climate change and the associated extinction risks.
This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Reconsolidation-disruption diminishes spontaneous and stress-induced cocaine seeking
Authors: Marc TJ Exton-McGuinness , Mohamed L Drame , Charlotte R Flavell , Jonathan LC Lee 
Published: August 2017

ABSTRACTBACKGROUNDThere has been a recent surge of interest in exploiting the process of reconsolidation to weaken maladaptive memories, in the hope this will drive the next wave of innovation in psychotherapy. Reconsolidation normally functions to stabilise and maintain memories in the long-term, and is critical in enabling memory updating. However, this process can be disrupted pharmacologically to weaken memories, or harnessed to allow destructive interference of a memory trace. Work has already begun to exploit this mechanism to disrupt pavlovian fear memories in the treatment of maladaptive anxiety and threat processing, and additionally being able to target instrumental memories may provide further clinical benefit.METHODSExpanding our rat intravenous (i.v.) self-administration paradigm, we tested whether disruption of instrumental memory reconsolidation with the noncompetitive N-methyl-D-aspartate receptor (NMDAR) antagonist MK-801 could reduce relapse of cocaine seeking in response to stress, drug-priming or presentation of a drug-associated cue.RESULTSSpontaneous responding for i.v. cocaine was reduced by reconsolidation-disruption. Furthermore, responding was not rescued by pharmacologically-induced stress. However, responding was restored following systemic administration of the drug, or presentation of a drug-associated cue.CONCLUSIONSThese data are consistent with hypothesis that there exist multiple ‘routes to relapse’, and suggest that at least some of these routes could be blocked by reconsolidation-disruption. This work provides important proof-of-principle that reconsolidation based therapies are a viable means of reducing the rates of relapse in substance use disorders.
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
Authors: Szedlak Anthony , Sims Spencer , Smith Nicholas , Paternostro Giovanni , Piermarocchi Carlo 
Published: August 2017

AbstractModern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series data sets in the near future, we use the Hopfield model, a recurrent neural network based on spin glasses, to model the dynamics of cell cycle in HeLa (human cervical cancer) andS. cerevisiaecells. We study some of the rich dynamical properties of these cyclic Hopfield systems, including the ability of populations of simulated cells to recreate experimental expression data and the effects of noise on the dynamics. Next, we use a genetic algorithm to identify sets of genes which, when selectively inhibited by local external fields representing gene silencing compounds such as kinase inhibitors, disrupt the encoded cell cycle. We find, for example, that inhibiting the set of four kinasesBRD4,MAPK1,NEK7, andYES1in HeLa cells causes simulated cells to accumulate in the M phase. Finally, we suggest possible improvements and extensions to our model.Author SummaryCell cycle – the process in which a parent cell replicates its DNA and divides into two daughter cells – is an upregulated process in many forms of cancer. Identifying gene inhibition targets to regulate cell cycle is important to the development of effective therapies. Although modern high throughput techniques offer unprecedented resolution of the molecular details of biological processes like cell cycle, analyzing the vast quantities of the resulting experimental data and extracting actionable information remains a formidable task. Here, we create a dynamical model of the process of cell cycle using the Hopfield model (a type of recurrent neural network) and gene expression data from human cervical cancer cells and yeast cells. We find that the model recreates the oscillations observed in experimental data. Tuning the level of noise (representing the inherent randomness in gene expression and regulation) to the “edge of chaos” is crucial for the proper behavior of the system. We then use this model to identify potential gene targets for disrupting the process of cell cycle. This method could be applied to other time series data sets and used to predict the effects of untested targeted perturbations.
dropClust: Efficient clustering of ultra-large scRNA-seq data
Authors: Sinha Debajyoti , Kumar Akhilesh , Kumar Himanshu , Bandyopadhyay Sanghamitra , Sengupta Debarka 
Published: August 2017

ABSTRACTDroplet based single cell transcriptomics has recently enabled parallel screening of tens of thousands of single cells. Clustering methods that scale for such high dimensional data without compromising accuracy are scarce. We exploit Locality Sensitive Hashing, an approximate nearest neighbor search technique to develop ade novoclustering algorithm for large-scale single cell data. On a number of real datasets, dropClust outperformed the existing best practice methods in terms of execution time, clustering accuracy and detectability of minor cell sub-types.
Ants express risk-adjusted sanitary care
Authors: Konrad Matthias , Pull Christopher D. , Seif Katharina , Metzler Sina , Grasse Anna V. , Cremer Sylvia 
Published: August 2017

AbstractBeing cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop micro-infections that do not cause disease, but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent pathogen infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we here tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behaviour. We found that micro-infections contracted during sanitary care had protective or neutral effects upon secondary exposure to the same (homologous) pathogen, but consistently induced high mortality upon super-infection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming yet more antimicrobial disinfection, when caring for nestmates contaminated with heterologous pathogens as compared to homologous ones. By modulating the components of sanitary care in this way, the ants reduced their probability of contracting super-infections of the harmful heterologous pathogens. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history, and to flexibly adjust collective care to individual risk.
The High-resolution Timeline of Expression of Ribosomal Protein Genes in Yeast
Authors: Li Xueling , Chen Gang , Fongang Bernard , Homouz Dirar , Rowicka Maga , Kudlicki Andrzej 
Published: August 2017

AbstractThe yeast ribosome is a complex molecular machine built from four rRNAs and over 70 r-proteins. Ribosome biogenesis involves ordered incorporation of ribosomal proteins, accompanied by and association and dissociation of other proteins specific to different stages of the process. By model-based analysis of temporal profiles of gene expression in a metabolically regulated system, we obtained an accurate, high-resolution estimation of the time of expression of genes coding for proteins involved in ribosome biogenesis. The ribosomal proteins are expressed in a sequence that spans approximately 25-minutes under metabolically regulated conditions. The genes coding for proteins incorporated into the mature ribosome are expressed significantly later than those that are not incorporated, but are otherwise involved in ribosome biogenesis, localization and assembly, rRNA processing and translational initiation. The relative expression time of proteins localized within specified neighborhood is significantly correlated with the distance to the centroid of the mature ribosome: protein localized closer to the center of mass of the entire complex tend to be expressed earlier than the protein localized further from the center. The timeline of gene expression also agrees with the known dependencies between recruitment of specific proteins into the mature ribosome. These findings are consistent in two independent experiments. We have further identified regulatory elements correlated with the time of regulation, including a possible dependence of expression time on the position of the RAP1 binding site within the 5’UTR.
Protein classification using modifiedn-gramandskip-grammodels
Authors: Islam S M Ashiqul , Heil Benjamin J , Kearney Christopher Michel , Baker Erich J 
Published: August 2017

ABSTRACTMotivationClassification by supervised machine learning greatly facilitates the annotation of protein characteristics from their primary sequence. However, the feature generation step in this process requires detailed knowledge of attributes used to classify the proteins. Lack of this knowledge risks the selection of irrelevant features, resulting in a faulty model. In this study, we introduce a means of automating the work-intensive feature generation step via a Natural Language Processing (NLP)-dependent model, using a modified combination of N-Gram and Skip-Gram models (m-NGSG).ResultsA meta-comparison of cross validation accuracy with twelve training datasets from nine different published studies demonstrates a consistent increase in accuracy of m-NGSG when compared to contemporary classification and feature generation models. We expect this model to accelerate the classification of proteins from primary sequence data and increase the accessibility of protein prediction to a broader range of scientists.Availabilitym-NGSG is freely available at Bitbucket:https://bitbucket.org/smislam/mngsg/srcSupplementslink to supplementary documentsContactErich_Baker@baylor.edu
Hidden diversity and macroevolutionary mode ofCaulimoviridaeuncovered by euphyllophyte paleoviruses
Authors: Gong Zhen , Han Guan-Zhu 
Published: August 2017

AbstractFew viruses have been documented in plants outside angiosperms. Endogenous viral elements (paleoviruses) provide ‘molecular fossils’ for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread across angiosperms, but little is known about EPRVs in earlier branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known asCaulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs in the genomes of gymnosperms and ferns. The known angiosperm viruses only constitute a minor part of theCaulimoviridaediversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity ofCaulimoviridae, raising the possibility that many exogenousCaulimoviridaeremain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs define a unique group of repetitive elements and represent major components of euphyllophyte genomes. Phylogenetic analyses reveal an ancient monilophyte origin ofCaulimoviridaeand at least three independent origins ofCaulimoviridaein angiosperms by cross-division transmissions. Our findings uncover the remarkable diversity ofCaulimoviridaeand have important implications in understanding the origin and macroevolution of plant pararetroviruses.