bluuebunny/crossref_metadata_2025_split huggingface dataset:
“If the Problem Persists, Come Back To See Me … .”—An Empirical Study of Clinical Negligence Cases Against General Practitioners
Authors: Heywood Rob 
Published: September 2018

Abstract
The law of negligence, as it applies to General Practitioners (GPs), is underexplored in the literature. There has been no substantial research undertaken that has penetrated deeper into claims that have actually reached court in order to analyse judicial reasoning pertaining to both breach of duty and causation. Given the increased pressures that GPs now face, these are important questions to consider. It is against this backdrop that this article seeks to present the findings of an empirical investigation into a number of reported clinical negligence claims brought against GPs. This analysis provides an original contribution to the developing academic discussion surrounding the changing nature of the doctor–patient relationship, and how it has come to be viewed in the eyes of the law. It also assesses the extent to which judges have become more receptive to protecting patient rights through the law of negligence, engaging in the expanding discourse concerning judicial deference to medical decision-making. It is argued that judges should sometimes show a greater propensity to question expert medical testimony in support of GPs, because some of the issues GPs typically face are less complex than in other clinical negligence cases involving technical areas of medicine, and that causation does not appear to be such a key factor in defeating patient claims. The work also provides useful guidance for GPs and their advisers in respect of where liability is most likely to be founded and how behaviour can be modified accordingly to reduce the chances of being sued.
NGC 1052-DF2 and modified gravity (MOG) without dark matter
Authors: Moffat J W , Toth V T 
Published: September 2018

ABSTRACT
We model the velocity dispersion of the ultradiffuse galaxy NGC 1052-DF2 using Newtonian gravity and modified gravity (MOG). The velocity dispersion predicted by MOG is higher than the Newtonian gravity prediction, but it is fully consistent with the observed velocity dispersion that is obtained from the motion of 10 globular clusters (GCs).
Price and Size Discovery in Financial Markets: Evidence from the U.S. Treasury Securities Market
Authors: Fleming Michael J , Nguyen Giang 
Published: September 2018

AbstractWe study the workup protocol, an important size discovery mechanism in the U.S. Treasury market. We find that workup order flow shocks explain 6%–8% of the variation of returns on benchmark notes and, across maturities, 10% of the variation of the yield curve level factor. Information related to proprietary client order flow is more likely to show up in workup trades, whereas information derived from public announcements tends to come through preworkup trades. Our findings highlight how the nature of information affects the trade-off between speed and execution price when informed traders choose between the lit and workup channels.Received May 3, 2017; Editorial decision August 1, 2018 by Editor Thierry Foucault. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online. Internet Appendix tables are numbered with “IA” prefix.
Standing on the Shoulders of Giants: The Effect of Passive Investors on Activism
Authors: Appel Ian R , Gormley Todd A , Keim Donald B 
Published: September 2018

Abstract
We analyze whether the growing importance of passive investors has influenced the campaigns, tactics, and successes of activists. We find activists are more likely to seek board representation when a larger share of the target company’s stock is held by passively managed mutual funds. Furthermore, higher passive ownership is associated with increased use of proxy fights, settlements, and a higher likelihood the activist achieves board representation or the sale of the targeted company. Our findings suggest that the recent growth of passive institutional investors mitigates free-rider problems and facilitates activists’ ability to engage in costly, value-enhancing forms of monitoring.
Received September 28, 2016; editorial decision August 18, 2018 by Editor Andrew Karolyi.
AN ASSESSMENT OF RADIATION EXPOSURE DOSES IN PATIENTS UNDERGOING PRIMARY PERCUTANEOUS CORONARY INTERVENTION BASED ON ANGIOGRAPHIC RECORDS
Authors: Maghbool M , Hosseini M A 
Published: September 2018

Abstract
The stochastic and non-stochastic (deterministic) effects of radiation dose in patients undergoing primary percutaneous coronary intervention (PPCI) have been investigated using data recorded by an angiographic monitoring system. A total of 132 patients with acute myocardial infarction referred to the angiography department of Vali-Asr hospital, Fasa, Iran, during the second half of 2016 were recruited. Quantities like dose–area product (DAP), total air kerma (Ka,r) and fluoroscopy time (FT) were calculated and converted into effective dose (ED) and peak skin dose (PSD). The values for Ka,r, DAP and FT equaled 80 399.20 ± 63 312 mGy cm2, 1392.80 ± 1155.373 mGy and 524.11 ± 423.057 s, respectively, which were within the ranges reported in previous studies. After considering standard dose thresholds for Ka,r and PSD, it was revealed that only a small portion of patients had reached these thresholds and exceeded them (<3%). Moreover, ED < 20 mSv for the majority of patients was fairly consistent with results from a recent research in eight Belgian hospitals. It was shown that angiographic records are reliable for assessing radiation dose in patients.
Twenty years of ‘Law and Finance’: time to take law seriously
Authors: Schnyder Gerhard , Siems Mathias , Aguilera Ruth V 
Published: September 2018

AbstractThis ‘state of the art’ essay provides a comprehensive discussion of the Law and Finance School (LFS) literature. We show that the first two decades of the LFS have focused on empirically investigating the question ‘does law matter?’ Yet, despite the centrality of law to the LFS, it is based on an incoherent theory of law, which leads to shortcomings in the conceptualization and empirical testing of its hypotheses. We also observe that, rather than addressing this deficiency, the LFS has moved its focus to the contentious concept of ‘legal origin’. We argue that the LFS needs to take law more seriously by returning to its initial focus on the substance of legal rules and by addressing the theoretical question ‘how does law matter?’ We propose venues for future research to develop a solid theoretical framework that would put the empirical investigation of law’s impact on economic outcomes on a more solid footing.
Identifying Changes to RNA Editome in Major Depressive Disorder
Authors: Hasan Saam , Robbani Shahriyar Mahdi , Afroze Tamanna , Ahsan Giasuddin , Hossain Muhammad Maqsud 
Published: September 2018

AbstractMajor Depressive Disorder (MDD) is one of the most significant psychiatric disorders in the world today. Its incidence is widespread in society and its heavy adverse impact on the quality of life is well documented. Previously genetic studies on MDD had identified a hereditary component of the disease as well as crediting RNA editing with a role in its development. The later due to an overexpression of a heavily edited isoform of the Serotonin 2c receptor. Here we used publicly available RNA sequence data from suicide patients diagnosed with MDD as well as controls for identifying RNA editing sites unique to MDD. After variant calling and several steps of filtering, we identified 142 unique RNA editing sites in the MDD patients. These included intronic, downstream, UTR3 and exonic edits. The latter comprising several amino acid changes in the encoded protein. The genes implicated to be uniquely edited in MDD included the aforementioned and previously implicated Serotonin 2c receptor, others involved in functions that play roles in depression and suicide such as Cannabinoid Receptor 1, Frizzled Class 3 Receptor, Neuroligin 3 and others.
Localization of balanced chromosome translocation breakpoints by long-read sequencing on the Oxford Nanopore platform
Authors: Hu Liang , Liang Fan , Cheng Dehua , Zhang Zhiyuan , Yu Guoliang , Zha Jianjun , Wang Yang , Wang Feng , Tan Yueqiu , Wang Depeng , Wang Kai , Lin Ge 
Published: September 2018

AbstractStructural variants (SVs) in genomes, including translocations, inversions, insertions, deletions and duplications, remain difficult to be detected reliably by traditional genomic technologies. In particular, balanced translocations and inversions cannot be detected by microarrays since they do not alter chromosome copy numbers; they cannot be reliably detected by short-read sequencing either, since many breakpoints are located within repetitive regions of the genome that are unmappable by short reads. However, the detection and the precise localization of breakpoints at the nucleotide level are important to study the genetic causes in patients carrying balanced translocations or inversions. Long-read sequencing techniques, such as the Oxford Nanopore Technology (ONT), may detect these SVs in a more direct, efficient and accurate manner. In this study, we applied whole-genome long-read sequencing on the Oxford Nanopore GridION sequencer to detect the breakpoints from 6 carriers of balanced translocations and one carrier of inversion, where SVs had initially been detected by karyotyping at the chromosome level. The results showed that all the balanced translocations were detected with ∼10X coverage and were consistent with the karyotyping results. PCR and Sanger sequencing confirmed 8 of the 14 breakpoints to single base resolution, yet other breakpoints cannot be refined to single-base due to their localization at highly repetitive regions or pericentromeric regions, or due to the possible presence of local deletions/duplications. Our results indicate that low-coverage whole-genome sequencing is an ideal tool for the precise localization of most translocation breakpoints and may provide haplotype information on the breakpoint-linked SNPs, which may be widely applied in SV detection, therapeutic monitoring, assisted reproduction technology (ART) and preimplantation genetic diagnosis (PGD).
Drilling down hotspots of intraspecific diversity to bring them into on-ground conservation of threatened species
Authors: Zampiglia Mauro , Bisconti Roberta , Maiorano Luigi , Aloise Gaetano , Siclari Antonino , Pellegrino Francesco , Martino Giuseppe , Pezzarossa Alice , Chiocchio Andrea , Martino Chiara , Nascetti Giuseppe , Canestrelli Daniele 
Published: September 2018

AbstractUnprecedented rates of biodiversity loss rise the urgency for preserving species ability to cope with ongoing global changes. An approach in this direction is to target intra-specific hotspots of genetic diversity as conservation priorities. However, these hotspots are often identified by sampling at a spatial resolution too coarse to be useful in practical management of threatened species, hindering the long-appealed dialog between conservation stakeholders and conservation genetic researchers. Here, we investigated the spatial and temporal variation in species presence, genetic diversity, as well as potential risk factors, within a previously identified hotspot of genetic diversity for the endangered Apennine yellow bellied toad Bombina pachypus. Our results show that this hotspot is neither a geographically homogeneous nor a temporally stable unit. Over a time-window spanning 10-40 years since previous assessments, B. pachypus populations declined in large portions of its hotspot, and their genetic diversity levels decreased. Considering the demographic trend, genetic and epidemiological data, and models of current and future climatic suitability, populations at the extreme south of the hotspot area still qualify for urgent in-situ conservation actions, whereas northern populations would be better managed through a mix of in-situ and ex-situ actions. Our results emphasize that identifying hotspot of genetic diversity, albeit essential step, does not suffice to warrant on-ground conservation of threatened species. Hotspots should be analysed at finer geographic and temporal scales, to provide conservation stakeholders with key knowledge to best define conservation priorities, and to optimize resource allocation to alternative management practices.
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Authors: Bushmanova Elena , Antipov Dmitry , Lapidus Alla , Prjibelski Andrey D. 
Published: September 2018

AbstractSummaryPossibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
Authors: Jammali Safa , Aguilar Jean-David , Kuitche Esaie , Ouangraoua Aïda 
Published: September 2018

AbstractMotivationThe inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. Spliced alignment that consists in aligning a spliced cDNA sequence against an unspliced genomic sequence, constitutes a promising, yet unexplored approach for the identification of splicing orthology relationships. Existing spliced alignment algorithms do not exploit the information on the splicing structure of the input sequences, namely the exon structure of the cDNA sequence and the exon-intron structure of the genomic sequences. Yet, this information is often available for coding DNA sequences (CDS) and gene sequences annotated in databases, and it can help improve the accuracy of the computed spliced alignments. To address this issue, we introduce a new spliced alignment problem and a method called SplicedFamAlign (SFA) for computing the alignment of a spliced CDS against a gene sequence while accounting for the splicing structures of the input sequences, and then the inference of transcript splicing orthology groups in a gene family based on spliced alignments.ResultsThe experimental results show that SFA outperforms existing spliced alignment methods in terms of accuracy and execution time for CDS-to-gene alignment. We also show that the performance of SFA remains high for various levels of sequence similarity between input sequences, thanks to accounting for the splicing structure of the input sequences. It is important to notice that unlike all current spliced alignment methods that are meant for cDNA-to-genome alignments and can be used for CDS-to-gene alignments, SFA is the first method specifically designed for CDS-to-gene alignments. We show its usefulness for the comparison of genes and transcripts within a gene family for the purpose of analyzing splicing orthologies. It can also be used for gene structure annotation and alternative splicing analyses.AvailabilitySplicedFamAlign was implemented in Python. Source code is freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlignContactsafa.jammali@usherbrooke.ca
Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast
Authors: Heppenheimer Elizabeth , Brzeski Kristin E. , Wooten Ron , Waddell Will , Rutledge Linda Y. , Chamberlain Michael J. , Stahler Daniel R. , Hinton Joseph W. , vonHoldt Bridgett M. 
Published: September 2018

AbstractRediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the Gulf Coast region since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7,000 SNPs in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.
VAPiD: a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
Authors: Shean Ryan C. , Makhsous Negar , Stoddard Graham D. , Lin Michelle J. , Greninger Alexander L. 
Published: September 2018

AbstractBackgroundWith sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available.GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.ResultsWe present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1-4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems.ConclusionsWe have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found athttps://github.com/rcs333/VAPiD.
Meteorin-like (Metrnl) adipomyokine improves glucose tolerance in type 2 diabetes via AMPK pathway
Authors: Lee Jung Ok , Lee Hye Jeong , Lee Yong Woo , Han Jeong Ah , Kang Min Ju , Moon Jiyoung , Shin Min-Jeong , Lee Ho Jun , Chung Ji Hyung , Lee Jin-Seok , Son Chang-Gue , Song Kwon-Ho , Kim Tae Woo , Lee Eun-Soo , Kim Hong min , Chung Choon Hee , Ngoei Kevin R.W. , Ling Naomi X.Y. , Oakhill Jonathan S. , Galic Sandra , Murray-Segal Lisa , Kemp Bruce E. , Kim Kyoung Min , Lim Soo , Kim Hyeon Soo 
Published: September 2018

AbstractMeteorin-like (metrnl) is a recently identified adipomyokine that has beneficial effects on glucose metabolism. However, its underlying mechanism of action is not completely understood. In this study, we have shown that a level of metrnl increase in vitro under electrical-pulse-stimulation (EPS) and in vivo in exercise mice, suggesting that metrnl is an exercise-induced myokine. In addition, metrnl increases glucose uptake through the calcium-dependent AMPK pathway. Metrnl also increases the phosphorylation of HDAC5, a transcriptional repressor of GLUT4, in an AMPK-dependent manner. Phosphorylated HDAC5 interacts with 14-3-3 proteins and sequesters them in the cytoplasm, resulting in the activation of GLUT4 transcription. The intraperitoneal injection of recombinant metrnl improves glucose tolerance in mice with high fat-induced obesity or type 2 diabetes (db/db), but this is not seen in AMPK β1β2 muscle-specific null mice (AMPK β1β2 MKO). In conclusion, we have demonstrated that metrnl induces beneficial effects on glucose metabolism via AMPK and is a promising therapeutic candidate for glucose-related diseases such as type 2 diabetes.
Penetrance and pleiotropy of polygenic risk scores for schizophrenia in 106,160 patients across four healthcare systems
Authors: Zheutlin Amanda B , Dennis Jessica , Linnér Richard Karlsson , Moscati Arden , Restrepo Nicole , Straub Peter , Ruderfer Douglas , Castro Victor M , Chen Chia-Yen , Ge Tian , Huckins Laura M , Charney Alexander , Lester Kirchner H , Stahl Eli A , Chabris Christopher F , Davis Lea K , Smoller Jordan W 
Published: September 2018

AbstractOBJECTIVEIndividuals at high risk for schizophrenia may benefit from early intervention but few validated risk predictors are available. Genetic profiling is one approach to risk stratification that has been extensively validated in research cohorts, but its utility in clinical settings remains largely unexplored. Moreover, the broad health consequences of a high genetic risk of schizophrenia are poorly understood, despite being relevant to treatment decisions.METHODWe used electronic health records for 106,160 patients from four healthcare systems to evaluate the penetrance and pleiotropy of genetic risk for schizophrenia. Polygenic risk scores (PRSs) for schizophrenia were calculated from summary statistics and tested for association with 1359 disease categories, including schizophrenia and psychosis, in phenome-wide association studies. Effects were combined through meta-analysis across sites.RESULTSPRSs were robustly associated with schizophrenia (odds ratio per standard deviation increase in PRS=1.55 [95% confidence interval (CI), 1.4-1.7], p=4.48 x 10-16) and patients in the highest risk decile of the PRS distribution had up to 4.6-fold increased odds of schizophrenia compared to those in the bottom decile (95% CI, 2.9-7.3, p=1.37 x 10-10). PRSs were also positively associated with a range of other phenotypes, including anxiety, mood, substance use, neurological, and personality disorders, as well as suicidal behavior, memory loss, and urinary syndromes; they were inversely related to obesity.CONCLUSIONSWe demonstrate that an available measure of genetic risk for schizophrenia is robustly associated with schizophrenia in healthcare settings and has pleiotropic effects on related psychiatric disorders as well as other medical syndromes. Our results provide an initial indication of the opportunities and limitations that may arise with the future application of PRS testing in healthcare systems.