bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing Legislative Deferral
Authors: Parent Jonathan F. 
Published: March 2018

AbstractThe legislative deferral hypothesis posits that elected policy makers, anxious to avoid the political repercussions of taking clear positions on controversial issues, will actively seek to involve the judiciary in resolving these disputes. This study seeks to further test the legislative deferral theory by considering its applicability to the state level. What is revealed from an examination of the development of abortion policy in New York is that, despite the controversial nature of the issue, lawmakers did not seem to attempt to involve the courts in its resolution, and virtually no policy was created by the state’s judicial branch. I propose an alternative explanation for judicial noninvolvement, borrowing from path-dependence theory, that emphasizes the importance of the initial location of policy change and the issue frames that first took hold around this issue.
A novel computational approach for drug repurposing using systems biology
Authors: Peyvandipour Azam , Saberian Nafiseh , Shafi Adib , Donato Michele , Draghici Sorin 
Published: March 2018

AbstractMotivationIdentification of novel therapeutic effects for existing US Food and Drug Administration (FDA)-approved drugs, drug repurposing, is an approach aimed to dramatically shorten the drug discovery process, which is costly, slow and risky. Several computational approaches use transcriptional data to find potential repurposing candidates. The main hypothesis of such approaches is that if gene expression signature of a particular drug is opposite to the gene expression signature of a disease, that drug may have a potential therapeutic effect on the disease. However, this may not be optimal since it fails to consider the different roles of genes and their dependencies at the system level.ResultsWe propose a systems biology approach to discover novel therapeutic roles for established drugs that addresses some of the issues in the current approaches. To do so, we use publicly available drug and disease data to build a drug-disease network by considering all interactions between drug targets and disease-related genes in the context of all known signaling pathways. This network is integrated with gene-expression measurements to identify drugs with new desired therapeutic effects based on a system-level analysis method. We compare the proposed approach with the drug repurposing approach proposed by Sirota et al. on four human diseases: idiopathic pulmonary fibrosis, non-small cell lung cancer, prostate cancer and breast cancer. We evaluate the proposed approach based on its ability to re-discover drugs that are already FDA-approved for a given disease.Availability and implementationThe R package DrugDiseaseNet is under review for publication in Bioconductor and is available at https://github.com/azampvd/DrugDiseaseNet.Supplementary informationSupplementary data are available at Bioinformatics online.
ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data
Authors: Brink Benedikt G , Meskas Justin , Brinkman Ryan R 
Published: March 2018

Abstract

Motivation
Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20 000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high-throughput.

Results
ddPCRclust is an R package for automated analysis of data from Bio-Rad’s droplet digital PCR systems (QX100 and QX200). It can automatically analyze and visualize multiplexed ddPCR experiments with up to four targets per reaction. Results are on par with manual analysis, but only take minutes to compute instead of hours. The accompanying Shiny app ddPCRvis provides easy access to the functionalities of ddPCRclust through a web-browser based GUI.

Availability and implementation
R package: https://github.com/bgbrink/ddPCRclust; Interface: https://github.com/bgbrink/ddPCRvis/; Web: https://bibiserv.cebitec.uni-bielefeld.de/ddPCRvis/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exploiting and assessing multi-source data for supervised biomedical named entity recognition
Authors: Galea Dieter , Laponogov Ivan , Veselkov Kirill 
Published: March 2018

AbstractMotivationRecognition of biomedical entities from scientific text is a critical component of natural language processing and automated information extraction platforms. Modern named entity recognition approaches rely heavily on supervised machine learning techniques, which are critically dependent on annotated training corpora. These approaches have been shown to perform well when trained and tested on the same source. However, in such scenario, the performance and evaluation of these models may be optimistic, as such models may not necessarily generalize to independent corpora, resulting in potential non-optimal entity recognition for large-scale tagging of widely diverse articles in databases such as PubMed.ResultsHere we aggregated published corpora for the recognition of biomolecular entities (such as genes, RNA, proteins, variants, drugs and metabolites), identified entity class overlap and performed leave-corpus-out cross validation strategy to test the efficiency of existing models. We demonstrate that accuracies of models trained on individual corpora decrease substantially for recognition of the same biomolecular entity classes in independent corpora. This behavior is possibly due to limited generalizability of entity-class-related features captured by individual corpora (model ‘overtraining’) which we investigated further at the orthographic level, as well as potential annotation standard differences. We show that the combined use of multi-source training corpora results in overall more generalizable models for named entity recognition, while achieving comparable individual performance. By performing learning-curve-based power analysis we further identified that performance is often not limited by the quantity of the annotated data.Availability and implementationCompiled primary and secondary sources of the aggregated corpora are available on: https://github.com/dterg/biomedical_corpora/wiki and https://bitbucket.org/iAnalytica/bioner.Supplementary informationSupplementary data are available at Bioinformatics online.
Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum
Authors: Takahagi Kotaro , Inoue Komaki , Shimizu Minami , Uehara-Yamaguchi Yukiko , Onda Yoshihiko , Mochida Keiichi 
Published: March 2018

Abstract

Background
Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition.

Results
We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the 3 Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of approximately 26% and approximately 38% of the homoeolog groups in B. hybridum changed toward nonadditive expression and nonancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggest that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum.

Conclusions
Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
Manipulation of successive crystalline transformations to control electron transfer and switchable functions
Authors: Jiao Cheng-Qi , Jiang Wen-Jing , Meng Yin-Shan , Wen Wen , Zhao Liang , Wang Jun-Li , Hu Ji-Xiang , Gurzadyan Gagik G , Duan Chun-Ying , Liu Tao 
Published: March 2018

ABSTRACT
Electron transfer in solid is crucial to switchable magnetic, electrical, optical and mechanical properties. However, it is a formidable challenge to control electron-transfer behaviors via manipulation of crystalline phases, especially through dynamic crystalline transformation. Herein, three crystalline phases of an {Fe2Co2} compound were obtained via enhancement of intermolecular π···π interactions inducing successive single-crystal-to-single-crystal transformations, from solvated 1·2CH3OH·4H2O, to desolvated 1 and its polymorph 1a accompanying electron transfer. 1·2CH3OH·4H2O showed thermally induced reversible intermetallic electron transfer in mother liquor. No electron-transfer behavior was observed in 1. 1a showed reversible intermetallic electron transfer upon thermal treatment or alternative irradiation with 808- and 532-nm lasers at cryogenic temperatures. The electron-transfer behaviors significantly change the magnetic and optical properties, providing a strategy to realize different electron-transfer behaviors and switchable functions via π···π interactions manipulated dynamic crystalline transformation.
Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)
Authors: Taylor Peter J , Macdonald Angus , Goodman Steven M , Kearney Teresa , Cotterill Fenton P D , Stoffberg Sam , Monadjem Ara , Schoeman M Corrie , Guyton Jennifer , Naskrecki Piotr , Richards Leigh R 
Published: March 2018

AbstractExamination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
Simulation-Based Assessment of Critical Care “Front-Line” Providers*
Authors: Boyle Walter A. , Murray David J. , Beyatte Mary Beth , Knittel Justin G. , Kerby Paul W. , Woodhouse Julie , Boulet John R. 
Published: March 2018

Objectives:
Develop a standardized simulation method to assess clinical skills of ICU providers.

Design:
Simulation assessment.

Setting:
Simulation laboratory.

Subjects:
Residents, Critical Care Medicine fellows, acute care nurse practitioner students.

Interventions:
Performance scoring in scenarios from multiple Critical Care Medicine competency domains.

Measurements and Main Results:
Three-hundred eighty-four performances by 48 participants were scored using checklists (% correct) and holistic “global” ratings (1 [unprepared] to 9 [expert]). One-hundred eighty were scored by two raters. Mean checklist and global scores (± sd) ranged from 65.0% (± 16.3%) to 84.5% (± 17.3%) and 4.7 (± 1.4) to 7.2 (± 1.2). Checklist and global scores for Critical Care Medicine fellows and senior acute care nurse practitioner students (Experienced group, n = 26) were significantly higher than those for the Novice acute care nurse practitioner students (Novice group, n = 14) (75.6% ± 15.6% vs 68.8% ± 21.0% and 6.1 ± 1.6 vs 5.4 ± 1.5, respectively; p < 0.05). Residents (Intermediate group, n = 8) scored between the two (75.4% ± 18.3% and 5.7 ± 1.7). 38.5% of the Experienced group scored in the top quartile for mean global score, compared with 12.5% of the Intermediate and 7.1% of the Novice groups. Conversely, 50% of the Novice group scored in the lower quartile (< 5.3), compared with 37.5% of the Intermediate and 11.5% of the Experienced groups. Psychometric analyses yielded discrimination values greater than 0.3 for most scenarios and reliability for the eight-scenario assessments of 0.51 and 0.60, with interrater reliability of 0.71 and 0.75, for checklist and global scoring, respectively.

Conclusions:
The simulation assessments yielded reasonably reliable measures of Critical Care Medicine decision-making skills. Despite a wide range of performance, those with more ICU training and experience performed better, providing evidence to support the validity of the scores. Simulation-based assessments may ultimately prove useful to determine readiness to assume decision-making roles in the ICU.
Comparison of Antivenom Dosing Strategies for Rattlesnake Envenomation
Authors: Spyres Meghan B. , Skolnik Aaron B. , Moore Elizabeth C. , Gerkin Richard D. , Padilla-Jones Angela , Ruha Anne-Michelle 
Published: March 2018

Objectives:
This study compares maintenance with clinical- and laboratory-triggered (as-needed [PRN]) antivenom dosing strategies with regard to patient-centered outcomes after rattlesnake envenomation.

Design:
This is a retrospective cohort study of adult rattlesnake envenomations treated at a regional toxicology center. Data on demographics, envenomation details, antivenom administration, length of stay, and laboratory and clinical outcomes were compared between the PRN and maintenance groups. Primary outcomes were hospital length of stay and total antivenom used, with a hypothesis of no difference between the two dosing strategies.

Setting:
A single regional toxicology center

Patients:
Three-hundred ten adult patients envenomated by rattlesnakes between 2007 and 2014 were included. Patients were excluded if no antivenom was administered or for receiving an antivenom other than Crofab (BTG International, West Conshohocken, PA).

Interventions:
This is a retrospective study of rattlesnake envenomations treated with and without maintenance antivenom dosing.

Main Results:
One-hundred forty-eight in the maintenance group and 162 in the PRN group were included. There was no difference in demographics or baseline envenomation severity or hemotoxicity (32.7% vs 40.5%; respectively; p = 0.158) between the two groups. Comparing the PRN with the maintenance group, less antivenom was used (8 [interquartile range, 6–12] vs 16 [interquartile range, 12–18] vials, respectively; p < 0.001), and hospital length of stay was shorter (27 hr [interquartile range, 20–44 hr] vs 34 hr [interquartile range, 24–43 hr], respectively; p = 0.014). There were no differences in follow-up outcomes of readmission, retreatment, or bleeding and surgical complications.

Conclusions:
Hospital length of stay was shorter, and less antivenom was used in patients receiving a PRN antivenom dosing strategy after rattlesnake envenomation.
Understanding Patients’ Experiences of Diagnosis and Treatment of Advanced Colorectal Cancer in a Safety-Net Hospital System: A Qualitative Study
Authors: Leal Isabel M. , Kao Lillian S. , Karanjawala Burzeen , Escamilla Richard J. , Ko Tien C. , Millas Stefanos G. 
Published: March 2018

BACKGROUND:
Greater understanding of barriers to screening of colorectal cancer among lower socioeconomic, particularly Hispanic, patients is needed to improve disparities in care.

OBJECTIVE:
This study aimed to explore patients’ perceptions and experiences of care seeking for colorectal cancer to identify barriers to early diagnosis and treatment.

DESIGN:
This explorative qualitative study was conducted as a focused ethnography of patients diagnosed with advanced-stage colorectal cancer.

SETTINGS:
This study was conducted at an urban safety-net hospital.

PARTICIPANTS:
Thirty lower-income, primarily minority, patients diagnosed with stage III and IV colorectal cancer without prior colorectal cancer screening were selected.

MAIN OUTCOME MEASURES:
The primary outcomes measured were participants’ perceptions and experiences of colorectal cancer and barriers they faced in seeking diagnosis and treatment

RESULTS:
Data analysis yielded 4 themes consistently influencing participants’ decisions to seek diagnosis and treatment: 1) limited resources for accessing care (structural barriers, including economic, health care and health educational resources); 2) (mis)understanding of symptoms by patients; misdiagnosis of symptoms, by physicians; 3) beliefs about illness and health, such as relying on faith, or self-care when symptoms developed; and 4) reactions to illness, including maintenance of masculinity, confusing interactions with physicians, embarrassment, and fear. These 4 themes describe factors on the structural, health care system, provider and patient level, that interact to make engaging in prevention foreign among this population, thus limiting early detection and treatment of colorectal cancer.

LIMITATIONS:
This study was limited by selection bias and the lack of generalizability.

CONCLUSION:
Improving screening rates among lower-income populations requires addressing barriers across the multiple levels, structural, personal, health care system, that patients encounter in seeking care for colorectal cancer. Acknowledging the complex, multilevel influences impacting patient health care choices and behaviors allows for the development of culturally tailored interventions, and educational, financial, and community resources to decrease disparities in cancer screening and care and improve outcomes for these at-risk patients. See Video Abstract at http://links.lww.com/DCR/A473.
Biological Effects From Low Doses and Dose Rates of Ionizing Radiation: Science in the Service of Protecting Humans, a Synopsis
Authors: Feinendegen Ludwig E. , Cuttler Jerry M. 
Published: March 2018

Abstract
There is considerable controversy regarding risk of health detriment after low-level exposure to ionizing radiation. This stems in part from a sort of distance between radiation biologists, epidemiologists, and radiation protection professionals, as well as regulatory institutions. Also, there is a lack of overview of the relevant data and their origins regarding health risks at low doses of ionizing radiation. This feeds seriously into a somewhat hazy fear of ionizing radiation that besets large portions of the public. The current synopsis aims at presenting a holistic view in a concise yet comprehensive manner in order to help people understand the full extent of inputs into attempting to relate low-dose radiation exposure to health risk. It emerges again that different approaches must be found for optimal radiation protection replacing the use of the linear no-threshold (LNT) model.
pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Authors: Ulgen Ege , Ozisik Ozan , Sezerman Osman Ugur 
Published: March 2018

AbstractSummaryPathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies gene sets that form active subnetworks in a protein-protein interaction network using a list of genes provided by the user. It then performs pathway enrichment analyses on the identified gene sets. Further, using the R package pathview, it maps the user data on the enriched pathways and renders pathway diagrams with the mapped genes. Because many of the enriched pathways are usually biologically related, pathfindR also offers functionality to cluster these pathways and identify representative pathways in the clusters. PathfindR is built as a stand-alone package but it can easily be integrated with other tools, such as differential expression/methylation analysis tools, for building fully automated pipelines. In this article, an overview of pathfindR is provided and an example application on a rheumatoid arthritis dataset is presented and discussed.AvailabilityThe package is freely available under MIT license at:https://github.com/egeulgen/pathfindR
Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing
Authors: Baldi Sandro , Krebs Stefan , Blum Helmut , Becker Peter B. 
Published: March 2018

AbstractThe nature of chromatin as regular succession of nucleosomes has gained iconic status. However, since most nucleosomes in metazoans are poorly positioned it is unknown to which extent the bulk genomic nucleosome repeat length (NRL) reflects the regularity and spacing of nucleosome arrays at individual loci. We describe a new approach to map nucleosome array regularity and spacing through sequencing oligonucleosome-derived DNA by Illumina sequencing as well as emergent nanopore-technology. This revealed modulation of array regularity and NRL depending on functional chromatin states independently of nucleosome phasing and even in unmappable regions. We also found that nucleosome arrays downstream of silent promoters are considerably more regular than those downstream of highly expressed ones, despite more extensive nucleosome phasing of the latter. Our approach is generally applicable and provides an important parameter of chromatin organisation that so far had been missing.