bluuebunny/crossref_metadata_2025_split huggingface dataset:
POINT PATTERN ANALYSIS OF THE SPATIAL PROXIMITY OF RESIDENCES PRIOR TO DIAGNOSIS OF PERSONS WITH HODGKIN'S DISEASE
Authors: ROSS ANDREW , DAVIS SCOTT 
Published: February 2017

Abstract
There is some evidence to suggest that the etiology of Hodgkin's disease includes an infectious component One approach to investigating this possibility is a formal assessment of the geographic and temporal variation in the incidence of the disease. The present study was designed to better evaluate space-time patterns of residence prior to diagnosis of persons with Hodgkln's disease. Lifetime residential histories were obtained from 279 incident cases of Hodgkin's disease diagnosed between 1974 and 1982 in a defined population in northwestern Washington State, and a similar number of population controls matched to the cases by age, sex, and socioeconomic status. A method of point pattern analysis was modified for use in this context to compare the spatial proximity of case residences to that expected under the null assumption of no difference between the spatial pattern of case and control residences. Analyses were applied within temporal groupings of residences specified a priori assuming 1) no specified latency, 2) four different 5-year latent intervals, and 3) three age at exposure intervals. Assuming no latency, there is no evidence that case residences are more or less clustered than would be expected by chance. Assuming latent intervals of up to 15 years prior to diagnosis, case residences are less clustered than expected, particularly among those who developed Hodgkin's disease after the age of 40 years. In contrast, there is suggestive evidence that persons diagnosed with Hodgkin's disease after age 40 years lived closer together than expected as young children and teenagers. These results illustrate the need to focus such analyses on specific time intervals defined a priori to most likely represent periods of greatest etiologic relevance. To the extent that these findings are not the result of some unknown artifact of the method itself, they may serve to focus additional attention on childhood environment as a particularly important period in the etiology of this disease. Furthermore, the analytic method employed may be useful in identifying space-time clustering using population-based data in other etiologic settings
TOXIC TORT LITIGATION: MEDICAL AND SCIENTIFIC PRINCIPLES IN CAUSATION
Authors: HENDERSON THOMAS W. 
Published: February 2017

Abstract
A definition and an explanation of the legal standard for imposition of legal liability in a toxic tort case are set forth. The focus is on how expert witnesses utilize the applicable medical and scientific data in order to provide opinion evidence of the causal relation between exposure to a toxic substance and disease in an individual case. The author concludes that policy considerations are present in both the legal standard and the basis for establishing a cause and effect relation.
Pregnancy following discontinuation of a calcium channel blocker in the male partner
Authors: Hershlag Avner , Cooper George W. , Benoff Susan 
Published: February 2017

Abstract
The fertility potential of human sperm populations can be assessed by the presence of head-directed mannose ligand receptors (mannose-specific lectin) and the occurrence of spontaneous acrosome reactions after incubation under capacitating conditions in vitro. We have reported previously on the interaction between anti-hypertensive medications and their effects on these parameters of male fertility potential. In this report we document the effects of cessation of calcium ion channel blocker medication on male fertility. Motile spermatozoa from a 30 year old infertile patient on a calcium ion channel blocker as anti-hypertensive treatment had subnormal expression of mannose-specific lectin and did not exhibit spontaneous acrosome reactions. Three months following discontinuation of the medications, complete recovery of both the expression of head-directed mannose ligand receptors and the acrosome reaction was documented, though sperm motility and morphology remained unchanged. The couple had 2 years of infertility and previously failed to conceive through seven cycles of Pergonal/intra-uterine insemination. Conception occurred on the second Pergonal/intra-uterine insemination cycle after the husband discontinued calcium ion channel blocker medication. Calcium ion channel blockers may adversely affect sperm fertilizing potential. Discontinuation of such medications enhances the chances for conception.
Is Democracy the Right System? Collaborative Approaches to Building an Engaged RDM Community
Authors: Teperek Marta , Higman Rosie , Kingsley Danny 
Published: January 2017

AbstractWhen developing new products, tools or services, one always need to think about the end users to ensure a wide-spread adoption. While this applies equally to services developed at higher education institutions, sometimes these services are driven by policies and not by needs of end users. This policy-driven approach can prove challenging for building effective community engagement. The initial development of Research Data Management support services at the University of Cambridge was policy-driven and subsequently failed in the first instance to engage the community of researchers for whom these services were created.In this practice paper we will describe the initial approach undertaken at Cambridge when developing RDM services, the results of this approach and lessons learnt. We will then provide an overview of alternative, democratic strategies employed and their positive effects on community engagement. We will summarise by performing a cost-benefit analysis of the two approaches. This paper might be a useful case study for any institutions aiming to develop central support services for researchers, with conclusions applicable to the wide sector, and extending beyond Research Data Management services.
Deep Recurrent Neural Network for Protein Function Prediction from Sequence
Authors: Liu Xueliang Leon 
Published: January 2017

AbstractAs high-throughput biological sequencing becomes faster and cheaper, the need to extract useful information from sequencing becomes ever more paramount, often limited by low-throughput experimental characterizations. For proteins, accurate prediction of their functions directly from their primary amino-acid sequences has been a long standing challenge. Here, machine learning using artificial recurrent neural networks (RNN) was applied towards classification of protein function directly from primary sequence without sequence alignment, heuristic scoring or feature engineering. The RNN models containing long-short-term-memory (LSTM) units trained on public, annotated datasets from UniProt achieved high performance for in-class prediction of four important protein functions tested, particularly compared to other machine learning algorithms using sequence-derived protein features. RNN models were used also for out-of-class predictions of phylogenetically distinct protein families with similar functions, including proteins of the CRISPR-associated nuclease, ferritin-like iron storage and cytochrome P450 families. Applying the trained RNN models on the partially unannotated UniRef100 database predicted not only candidates validated by existing annotations but also currently unannotated sequences. Some RNN predictions for the ferritin-like iron sequestering function were experimentally validated, even though their sequences differ significantly from known, characterized proteins and from each other and cannot be easily predicted using popular bioinformatics methods. As sequencing and experimental characterization data increases rapidly, the machine-learning approach based on RNN could be useful for discovery and prediction of homologues for a wide range of protein functions.
Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas
Authors: Faria N. R. , Quick J. , Morales I. , Thézé J. , Jesus J.G. , Giovanetti M. , Kraemer M. U. G. , Hill S. C. , Black A. , da Costa A. C. , Franco L.C. , Silva S. P. , Wu C.-H. , Raghwani J. , Cauchemez S. , du Plessis L. , Verotti M. P. , de Oliveira W. K. , Carmo E. H. , Coelho G. E. , Santelli A. C. F. S. , Vinhal L. C. , Henriques C. M. , Simpson J. T. , Loose M. , Andersen K. G. , Grubaugh N. D. , Somasekar S. , Chiu C. Y. , Muñoz-Medina J. E. , Gonzalez-Bonilla C. R. , Arias C. F. , Lewis-Ximenez L. L. , Baylis S.A. , Chieppe A. O. , Aguiar S. F. , Fernandes C. A. , Lemos P. S. , Nascimento B. L. S. , Monteiro H. A. O. , Siqueira I. C. , de Queiroz M. G. , de Souza T. R. , Bezerra J. F. , Lemos M. R. , Pereira G. F. , Loudal D. , Moura L. C. , Dhalia R. , França R. F. , Magalhães T. , Marques E. T. , Jaenisch T. , Wallau G. L. , de Lima M. C. , Nascimento V. , de Cerqueira E. M. , de Lima M. M. , Mascarenhas D. L. , Moura Neto J. P. , Levin A. S. , Tozetto-Mendoza T. R. , Fonseca S. N. , Mendes-Correa M. C. , Milagres F.P. , Segurado A. , Holmes E. C. , Rambaut A. , Bedford T. , Nunes M. R. T. , Sabino E. C. , Alcantara L. C. J. , Loman N. , Pybus O. G. 
Published: February 2017

Zika virus (ZIKV) transmission in the Americas was first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (>200,000 by 24 Dec 20162) as well as the greatest number of cases associated with microcephaly and other birth defects (2,366 confirmed cases by 31 Dec 20162). Following the initial detection of ZIKV in Brazil, 47 countries and territories in the Americas have reported local ZIKV transmission, with 24 of these reporting ZIKV-associated severe disease3. Yet the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of such information for interpreting past and future trends in reported microcephaly. To address this we generated 54 complete or partial ZIKV genomes, mostly from Brazil, and report data generated by the ZiBRA project – a mobile genomics lab that travelled across Northeast (NE) Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Joint analyses of viral genomes with ecological and epidemiological data estimate that ZIKV epidemic was present in NE Brazil by March 2014 and likely disseminated from there, both nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. NE Brazil’s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus’ basic reproduction number.One Sentence SummaryVirus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.
Integrative analysis reveals genomic and epigenomic signatures of super-enhancers and its constituents
Authors: Khan Aziz , Zhang Xuegong 
Published: February 2017

AbstractBackgroundSuper-enhancers are clusters of transcriptional enhancers densely occupied by the Mediators, transcription factors and chromatin regulators. They control the expression of cell identity genes and disease associated genes. Current studies demonstrated the possibility of multiple factors with important roles in super-enhancer formation; however, a systematic analysis to assess the relative importance of chromatin and sequence signatures of super-enhancers and their constituents remain unclear.ResultsHere, we integrated diverse types of genomic and epigenomic datasets to identify key signatures of super-enhancers and their constituents and to investigate their relative importance. Through computational modelling, we found that Cdk8, Cdk9 and Smad3 as new key features of super-enhancers along with many known features such as H3K27ac. Comprehensive analysis of these features in embryonic stem cells and pro-B cells revealed their role in the super-enhancer formation and cellular identity. We also observed that super-enhancers are significantly GC-rich in contrast with typical enhancers. Further, we observed significant correlation among many cofactors at the constituents of super-enhancers.ConclusionsOur analysis and ranking of super-enhancer signatures can serve as a resource to further characterize and understand the formation of super-enhancers. Our observations are consistent with a cooperative or synergistic model underlying the interaction of super-enhancers and their constituents with numerous factors.
Demographic variability and heterogeneity among individuals within and among clonal bacteria strains
Authors: Jouvet Lionel , Rodríguez-Rojas Alexandro , Steiner Ulrich K. 
Published: February 2017

AbstractIdentifying what drives individual heterogeneity has been of long interest to ecologists, evolutionary biologists and biodemographers, because only such identification provides deeper understanding of ecological and evolutionary population dynamics. In natural populations one is challenged to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction is dominating at about 82-88%, over the 12-18% genetically (adaptive fixed) driven differences. The genetic differences among the clonal strains still lead to substantial variability in population growth rates (fitness), but, as well understood based on foundational work in population genetics, the within strain neutral variability slows adaptive change, by enhancing genetic drift, and lowering overall population growth. We also revealed a surprising diversity in senescence patterns among the clonal strains, which indicates diverse underlying cell-intrinsic processes that shape these demographic patterns. Such diversity is surprising since all cells belong to the same bacteria species, E. coli, and still exhibit patterns such as classical senescence, non-senescence, or negative senescence. We end by discussing whether similar levels of non-genetic variability might be detected in other systems and close by stating the open questions how such heterogeneity is maintained, how it has evolved, and whether it is adaptive.Data depositionThe processed image analysis data, R code, as well as the Leslie matrices will be archived at Dryad.org.
Dynamic species classification of microorganisms across time, abiotic and biotic environments — a sliding window approach
Authors: Pennekamp Frank , Griffiths Jason I. , Fronhofer Emanuel A. , Garnier Aurélie , Seymour Mathew , Altermatt Florian , Petchey Owen L. 
Published: February 2017

Summary1. Technological advances have greatly simplified to take and analyze digital images and videos, and ecologists increasingly use these techniques for trait, behavioral and taxonomic analyses. The development of techniques to automate biological measurements from the environment opens up new possibilities to infer species numbers, observe presence/absence patterns and recognize individuals based on audio-visual information.2. Streams of quantitative data, such as temporal species abundances, are processed by machine learning (ML) algorithms into meaningful information. Machine learning approaches learn to distinguish classes (e.g., species) from observed quantitative features (phenotypes), and in-turn predict the distinguished classes in subsequent observations. However, in biological systems, the environment changes, often driving phenotypic changes in behaviour and morphology.3. Here we describe a framework for classifying species under dynamic biotic and abiotic conditions using a novel sliding window approach. We train a random forest classifier on subsets of the data, covering restricted temporal, biotic and abiotic ranges (i.e. windows). We test our approach by applying the classification framework to experimental microbial communities where results were validated against manual classification. Individuals from one to six ciliate species were monitored over hundreds of generations in dozens of different species combinations and over a temperature gradient. We describe the steps of our classification pipeline and systematically explore the effects of the abiotic and biotic environments as well as temporal effects on classification success.4. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, because phenotypic differences driven by environmental change could be captured in the learning algorithm. Importantly, automatic classification showed comparable success compared to manual identifications.5. Our framework allows for reliable classification even in dynamic environmental contexts, and may help to improve long-term monitoring of species from environmental samples. It therefore has application in disciplines with automatic enumeration and phenotyping of organisms such as eco-toxicology, ecology and evolutionary ecology, and broad-scale environmental monitoring.
Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis
Authors: Sutherland Ben J. G. , Rico Ciro , Audet Céline , Bernatchez Louis 
Published: February 2017

ABSTRACTWhole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e. heterochiasmy), which is also poorly understood. Family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have non-homologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook CharrSalvelinus fontinalisand compare sex chromosome identities across the lineage (eight species, four genera). Although non-homology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify QTL for 21 unique growth, reproductive and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.
Informing service responses to co-occurring complex needs
Authors: Stathopoulos Mary , Jenkinson Rebecca 
Published: February 2017

Purpose
The sexual assault and alcohol and other drug (AOD) sectors have much in common in the context of clients presenting with histories of abuse and trauma. The Establishing the Connection project aimed to improve understanding of the complex intersections between sexual victimisation and AOD use, and to build the capacity of the sexual assault and AOD sectors in Victoria, Australia, to respond more effectively to the needs of affected individuals. The paper aims to discuss these issues.

Design/methodology/approach
Establishing the Connection involved a detailed literature review; face-to-face semi-structured interviews and an online quantitative survey with key stakeholders from the AOD and sexual assault sectors; and a cross-sector forum to bring together the practice knowledge and needs of both sectors.

Findings
Most practitioners and clinicians were aware of the interrelationship between sexual victimisation and AOD use, but many lacked access to resources, formal referral processes and pathways, or information about how the other sector worked – all tools which would assist them to respond to clients with complex co-occurring issues. Participants expressed enthusiasm for greater cross-sector communication and collaboration, but emphasised the need for sophisticated governance and resourcing responses from peak bodies and government departments.

Originality/value
The new knowledge generated by this research resulted in the development of shared practice guidelines to guide practice towards the identification, assessment, response and referral of clients with co-occurring sexual victimisation and AOD use issues. The authors hope that the momentum and goodwill built between the two sectors will be harnessed by policy to drive further collaborative partnerships into the future.
The LMRDA. Another labor law that benefits firms?
Authors: Abraham Steven E. 
Published: February 2017

PurposeThis paper aims to examine the impact of the Labor Management Reporting and Disclosure Act (LMRDA). It is expected that returns would have increased in response to the law’s passage, as it imposed a number of restrictions on unionsvis-à-vismanagement and instituted many rules regulating unions’ internal affairs.Design/methodology/approachThis paper uses event study methodology, which examines the impact of the law’s passage on the shareholder returns to the firms likely to have been affected by the law. Three different samples are used. Shareholder returns are examined on critical dates associated with the passage of the law to assess whether it benefited the firms in the samples.FindingsShareholder returns to firms expected to have been affected by the LMRDA fell in comparison to their competitors’ returns, indicating that the law was viewed by investors as being beneficial for firms. Presumably, the restrictions the law placed on unions were judged to be more important by investors than the improvement in unions’ image that might have resulted from the law, indicating that the law benefitted firms.Originality/valueThis is the first paper that has examined the impact of the LMRDA empirically to assess its impact on firms.