bluuebunny/crossref_metadata_2025_split huggingface dataset:
myChEMBL: a virtual machine implementation of open data and cheminformatics tools
Authors: Ochoa Rodrigo , Davies Mark , Papadatos George , Atkinson Francis , Overington John P. 
Published: November 2013

Abstract
Summary: myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications.
Availability and implementation: The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.
Contact: jpo@ebi.ac.uk
A novel splicing outcome reveals more than 2000 new mammalian protein isoforms
Authors: Wilson Laurence O. W. , Spriggs Andrew , Taylor Jennifer M. , Fahrer Aude M. 
Published: November 2013

Abstract
Motivation: We have recently characterized an instance of alternative splicing that differs from the canonical gene transcript by deletion of a length of sequence not divisible by three, but where translation can be rescued by an alternative start codon. This results in a predicted protein in which the amino terminus differs markedly in sequence from the known protein product(s), as it is translated from an alternative reading frame. Automated pipelines have annotated thousands of splice variants but have overlooked these protein isoforms, leading to them being underrepresented in current databases.
Results: Here we describe 1849 human and 733 mouse transcripts that can be transcribed from an alternate ATG. Of these, &gt;80% have not been annotated previously. Those conserved between human and mouse genomes (and hence under likely evolutionary selection) are identified. We provide mass spectroscopy evidence for translation of selected transcripts. Of the described splice variants, only one has previously been studied in detail and converted the encoded protein from an activator of cell-function to a suppressor, demonstrating that these splice variants can result in profound functional change. We investigate the potential functional effects of this splicing using a variety of bioinformatic tools. The 2582 variants we describe are involved in a wide variety of biological processes, and therefore open many new avenues of research.
Contact: aude.fahrer@anu.edu.au
Supplementary Inforation: Supplementary data are available at Bioinformatics online.
Identification of transcription factors for drug-associated gene modules and biomedical implications
Authors: Xiong Min , Li Bin , Zhu Qiang , Wang Yun-Xing , Zhang Hong-Yu 
Published: November 2013

Abstract
Motivation: One of the major findings in systems biomedicine is that both pathogenesis of diseases and drug mode of action have a module basis. However, the transcription factors (TFs) regulating the modules remain largely unknown.
Results: In this study, by using biclustering approach FABIA (factor analysis for bicluster acquisition), we generate 49 modules for gene expression profiles on 1309 agent treatments. These modules are of biological relevance in terms of functional enrichment, drug–drug interactions and 3D proximity in chromatins. By using the information of drug targets (some of which are TFs) and biological regulation, the links between 28 modules and 12 specific TFs, such as estrogen receptors (ERs), nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma, can be established. Some of the links are supported by 3D transcriptional regulation data [derived from ChIA-PET (chromatin interaction analysis using paired-end tags) experiments] and drug mode of action as well. The relationships between modules and TFs provide new clues to interpreting biological regulation mechanisms, in particular, the lipid metabolism regulation by ERα. In addition, the links between natural products (e.g. polyphenols) and their associated modules and TFs are helpful to elucidate their polypharmacological effects in terms of activating specific TFs, such as ERs, nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma.
Contact: zhy630@mail.hzau.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
The production of strong, broad He ii emission after the tidal disruption of a main-sequence star by a supermassive black hole
Authors: Gaskell C. Martin , Rojas Lobos P. Andrea 
Published: November 2013

Abstract
The tidal disruption event (TDE) PS1-10jh lacked strong Balmer lines but showed strong, broad He ii emission both before maximum light and for at least eight months thereafter. Gezari et al. interpreted this as evidence for the disruption of a rare hydrogen-deficient star. However, Guillochon et al. have argued instead that the disrupted star was a normal main-sequence star and that the strength of the He ii emission compared with the Balmer lines is a result the emission being similar to the broad-line region (BLR) of an active galactic nucleus (AGN), but lacking the outer, lower ionization BLR gas. We show that the profile of He ii λ4686 in PS1-10jh is similar to the blueshifted profiles of high-ionization lines in AGNs. We find an He ii λ4686/Hα ratio for PS1-10jh of ∼3.7. We show that both the high-velocity gas of the inner BLR of normal AGNs and the spectra of Type II-P supernovae right after shock break out also produce very high He ii λ4686/Hα ratios. A high He ii λ4686/Hα ratio can thus be produced with a solar H/He abundance ratio. We demonstrate from photoionization modelling that the estimated He ii λ4686/Hα ratio can be produced with a BLR truncated before the He++ Strömgren length if the density is ∼1011 cm−3. The similarity of the He ii λ4686 emission in PS1-10jh to the emission from the inner BLRs of AGNs supports the idea that the emission after a TDE event is similar to that of normal AGNs.
Adaptation of theHaloarcula hispanicaCRISPR-Cas system to a purified virus strictly requires a priming process
Authors: Li Ming , Wang Rui , Zhao Dahe , Xiang Hua 
Published: November 2013

AbstractThe clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system mediates adaptive immunity against foreign nucleic acids in prokaryotes. However, efficient adaptation of a native CRISPR to purified viruses has only been observed for the type II-A system from a Streptococcus thermophilus industry strain, and rarely reported for laboratory strains. Here, we provide a second native system showing efficient adaptation. Infected by a newly isolated virus HHPV-2, Haloarcula hispanica type I-B CRISPR system acquired spacers discriminatively from viral sequences. Unexpectedly, in addition to Cas1, Cas2 and Cas4, this process also requires Cas3 and at least partial Cascade proteins, which are involved in interference and/or CRISPR RNA maturation. Intriguingly, a preexisting spacer partially matching a viral sequence is also required, and spacer acquisition from upstream and downstream sequences of its target sequence (i.e. priming protospacer) shows different strand bias. These evidences strongly indicate that adaptation in this system strictly requires a priming process. This requirement, if validated also true for other CRISPR systems as implied by our bioinformatic analysis, may help to explain failures to observe efficient adaptation to purified viruses in many laboratory strains, and the discrimination mechanism at the adaptation level that has confused scientists for years.
Effects of Various Modes of Mechanical Ventilation in Normal Rats
Authors: Pecchiari Matteo , Monaco Ario , Koutsoukou Antonia , Valle Patrizia Della , Gentile Guendalina , D’Angelo Edgardo 
Published: November 2013

Abstract

Background:
Recent studies in healthy mice and rats have reported that positive pressure ventilation delivered with physiological tidal volumes at normal end-expiratory volume worsens lung mechanics and induces cytokine release, thus suggesting that detrimental effects are due to positive pressure ventilation per se. The aim of this study in healthy animals is to assess whether these adverse outcomes depend on the mode of mechanical ventilation.

Methods:
Rats were subjected to 4 h of spontaneous, positive pressure, and whole-body or thorax-only negative pressure ventilation (N = 8 per group). In all instances the ventilatory pattern was that of spontaneous breathing. Lung mechanics, cytokines concentration in serum and broncho–alveolar lavage fluid, lung wet-to-dry ratio, and histology were assessed. Values from eight animals euthanized shortly after anesthesia served as control.

Results:
No evidence of mechanical ventilation–dependent lung injury was found in terms of lung mechanics, histology, or wet-to-dry ratio. Relative to control, cytokine levels and recruitment of polymorphonuclear leucocytes increased slightly, and to the same extent with spontaneous, positive pressure, and whole-body negative pressure ventilation. Thorax-only negative pressure ventilation caused marked chest and lung distortion, reversible increase of lung elastance, and higher polymorphonuclear leucocyte count and cytokine levels.

Conclusion:
Both positive and negative pressure ventilation performed with tidal volumes and timing of spontaneous, quiet breathing neither elicit an inflammatory response nor cause morpho-functional alterations in normal animals, thus supporting the notion of the presence of a critical volume threshold above which acute lung injury ensues. Distortion of lung parenchyma can induce an inflammatory response, even in the absence of volotrauma.
Long Allele Designations at D2S1338 and D19S433 Loci as Influenced by Various Multiplex STR Kits
Authors: Dell'Ariccia‐Carmon Aviva , Raziel Aliza , Oz Carla , Berdugo Reouven , Zamir Ashira 
Published: November 2013

AbstractEuropean forensic laboratories are replacing the STR multiplex kits with the new generation 16/17 STR kits. This study examines the influence of the new generation kits and the new Applied Biosystems 3500xL Genetic Analyzer on the designation of long D2S1338 and D19S433 off‐ladder alleles. Different allele calls were obtained using the new NGM™ (Applied Biosystems) and PowerPlex® ESI™ (Promega) kits compared with AmpFℓSTR® SGM Plus™ kit (Applied Biosystems). Sequence analysis was used to determine accurate allele designation. The new multiplex kits and the 3500xL Genetic Analyzer improved accuracy of long allele designations. DNA databases worldwide include countless profiles obtained by previous kits. Discrepancies between the new and former technologies may cause failure to detect hits. Discordance is expected due to primer sequence differences between various kits. An additional discordance, occurring in long alleles, independent of primer sequence is reported in this study.
An Empirical Study of Rape in the Context of Multiple Murder
Authors: DeLisi Matt 
Published: November 2013

AbstractIn recent years, multiple homicide offending has received increased research attention from criminologists; however, there is mixed evidence about the role of rape toward the perpetration of multiple murder. Drawing on criminal career data from a nonprobability sample of 618 confined male homicide offenders selected from eight U.S. states, the current study examines the role of rape as a predictor of multiple homicide offending. Bivariate analyses indicated a significant association between rape and murder charges. Multivariate path regression models indicated that rape had a significant and robust association with multiple murder. This relationship withstood the confounding effects of kidnapping, prior prison confinement, and prior murder, rape, and kidnapping. These results provide evidence that rape potentially serves as a gateway to multiple murder for some serious offenders. Suggestions for future research are proffered.
Antimicrobial susceptibilities of Mycoplasma isolated from bovine mastitis in Japan
Authors: Kawai Kazuhiro , Higuchi Hidetoshi , Iwano Hidetomo , Iwakuma Akihiro , Onda Ken , Sato Reiichiro , Hayashi Tomohito , Nagahata Hajime , Oshida Toshio 
Published: November 2013

AbstractMycoplasma spp. are highly contagious pathogens and intramammary Mycoplasma infection is a serious issue for the dairy industry. As there is no effective vaccine for Mycoplasma infection, control depends on good husbandry and chemo‐antibiotic therapy. In this study, antimicrobial susceptibility of Mycoplasma strains recently isolated from cases of bovine mastitis in Japan was evaluated by minimum inhibitory concentration (MIC). All Mycoplasma bovis strains were sensitive to pirlimycin, danofloxacin and enrofloxacin, but not kanamycin, oxytetracycline, tilmicosin or tylosin. M. californicum and M. bovigenitalium strains were sensitive to pirlimycin, danofloxacin, enrofloxacin, oxytetracycline, tilmicosin and tylosin, but not to kanamycin. This is the first report to describe the MIC of major antimicrobial agents for Mycoplasma species isolated from bovine mastitis in Japan.
Relationships of neonatal plasma oxytocin with the behavioral characteristics of cattle introduced into a novel environment
Authors: Yayou Ken‐ichi , Ito Shuichi , Yamamoto Naoyuki 
Published: November 2013

AbstractTo examine the influence of postnatal oxytocin (OXT) on behavioral development, we examined individual variations in basal OXT and suckling‐induced changes in OXT, and their relationship with emotional traits during development. Blood OXT were measured in 20 Holstein heifer calves at 1 (wk1), 2 (wk2), and 6 weeks of age (wk6). The relationships of OXT variables with principal component scores in the open‐field tests at wk2 and 2 months and the number of flinch, step and kick responses during first artificial insemination and machine milking were analyzed. The basal OXT showed individual variability and significantly correlated (wk1 vs. wk2: r = 0.753, P < 0.001; wk1 vs. wk6: r = 0.499, P < 0.05; wk2 vs. wk6: r = 0.476, P < 0.05). The personality traits reflecting a response in the form of escape from novel environments in the open‐field test at wk2 were inversely correlated with basal OXT at wk1 (rs = −0.640, P < 0.01) and wk2 (rs = −0.447, P < 0.05). However, none of the behavioral variables after 2 months correlated with OXT. These findings suggest that, postnatal OXT might be related to behavioral characteristics in novel environments only during the early stages of life.
Predictors of distress associated with psychotic‐like anomalous experiences in clinical and non‐clinical populations
Authors: Brett Caroline , Heriot‐Maitland Charles , McGuire Philip , Peters Emmanuelle 
Published: November 2013

ObjectivesPsychotic‐like anomalous experiences are not inherently distressing, nor do they inevitably lead to clinical conditions. However, distress is an important predictor of onset and relapse in psychosis, and a primary indicator of problematic mental health. This study aimed to identify factors that predict distress across three groups with anomalous experiences.Design and methodsThis study used a cross‐sectional design. Participants in ‘Diagnosed’ (n = 35), ‘At Risk’ (n = 20), and ‘Undiagnosed’ (n = 36) groups completed the Appraisals of Anomalous Experiences Interview (AANEX; Brett et al., 2007, Br. J. Psychiatry, 191, s23), which taps anomalies experienced, appraisals, and other psychological and contextual variables. A series of ordinal logistic regression analyses was conducted to investigate which variables predicted anomaly‐related distress.ResultsPredictors of higher distress were anomalous states characterized by changes in awareness and cognitive functioning (rather than more typical positive symptoms), appraisals of experiences as caused by ‘other people’, and greater attempted control over experiences. Predictors of lower distress were ‘spiritual’ appraisals, greater perceived social support/understanding, greater perceived controllability, and reacting with a ‘neutral response’.ConclusionsWhile psychotic‐like experiences themselves are not necessarily distressing, appraisals and responses to anomalies do predict distress, as do factors relating to the social context. This adds support to the cognitive‐behavioural models, and continuum models, of positive psychotic symptoms.Practitioner points

The findings suggest that distress is reduced by developing normalizing and validating contexts in which psychotic experiences can be accepted, understood, and shared.

Recommendation for delivering therapies that promote reappraising and/or accepting psychotic experiences, rather than attempting to control them.

The findings reinforce the ‘continuum model’ of psychosis to help cultivate less stigmatizing, and more normalizing, views of psychotic experiences.

A limitation is that the samples recruited cannot be assumed to be representative of all people experiencing psychotic‐like anomalies.

A further limitation is that a small number of AANEX items did not achieve satisfactory inter‐rater agreement.
A clinical evaluation of a sensor to detect blockage due to crystalline biofilm formation on indwelling urinary catheters
Authors: Long Adele , Edwards Julia , Thompson Richard , Lewis Debbie A. , Timoney Anthony G. 
Published: November 2013

ObjectiveTo test the performance and acceptability of an early warning sensor to predict encrustation and blockage of long‐term indwelling urinary catheters.Patients and MethodsIn all, 17 long‐term indwelling catheter users, 15 ‘blockers’ and two ‘non‐blockers’ (controls) were recruited; 11 participants were followed prospectively until catheter change, three withdrew early and three did not start.Two sensors were placed in series between the catheter and the urine bag at catheter change. The sensor nearest the bag was changed at the same time as the bag change (weekly); the sensor nearest the catheter remained in situ for the duration of the catheter's life.Bacteriology and pH determinations were performed on urine samples at each bag, sensor and catheter change. The colour of the sensors was recorded daily. On removal, each sensor and the catheter were examined for visible evidence of encrustation and blockage.Participants were asked to keep a daily diary to record colour change and any other relevant observations and to complete a psychosocial impact of assistive devices tool at the end of the study. Participants and carers/healthcare professionals (when involved in urine bag or catheter change) were asked to complete a questionnaire about the sensor.ResultsUrease‐producing bacteria were isolated from seven of the 14 patients (including early withdrawals; P. mirabilis in four, Morganella or Providencia in three).In six of the seven patients the sensors turned blue‐black; two of these were early withdrawals, two went to planned catheter change (one of these was recruited as a ‘non‐blocker’) and three had catheter blockage.The number of days of catheterisation before blockage was 22, 23 and 25 days, and the sensor changed colour within 24–48 h after insertion.The urine mean (range) pH of the sensors that turned blue‐black was 7.6 (5.5–9.0) and of the sensors that remained yellow 6.1 (5.1–7.5).The sensor was generally well‐received and was positive in the psychosocial assessment.ConclusionsThe sensor is a useful indicator of urine pH and of the conditions that lead to catheter blockage.It may be particularly useful for new indwelling catheter users.To be a universally acceptable predictor of catheter blockage, the time from sensor colour change to blockage needs to be reduced.
Efficacy of methylprednisolone pulse therapy for acute relapse in Japanese patients with multiple sclerosis and neuromyelitis optica: A multicenter retrospective analysis – 1. Whole group analysis
Authors: Kira Jun‐ichi , Yamasaki Ryo , Yoshimura Satoshi , Fukazawa Toshiyuki , Yokoyama Kazumasa , Fujihara Kazuo , Ogino Mieko , Yokota Takanori , Miyamoto Katsuichi , Niino Masaaki , Nomura Kyoichi , Tomioka Ryo , Tanaka Masami , Kawachi Izumi , Ohashi Takashi , Kaida Kenichi , Matsui Makoto , Nakatsuji Yuji , Ochi Hirofumi , Fukaura Hikoaki , Kanda Takashi , Nagaishi Akiko , Togo Kanae , Mizusawa Hidehiro , Kawano Yuji 
Published: November 2013

AbstractObjectivesThere has been no large‐scale study of methylprednisolone pulse therapy in Asian patients with multiple sclerosis (MS) or neuromyelitis optica (NMO), despite it being widely used for acute relapse. We aimed to clarify treatment response of MS and NMO patients to methylprednisolone pulse therapy and post‐pulse oral corticosteroids in real clinical practice in a multicenter study in Japan.MethodsInvestigators at 28 institutions collected changes in neurological symptoms/signs and Expanded Disability Status Scale (EDSS) scores before and within 1 week of completion of methylprednisolone pulse therapy carried out in 2010, and after post‐pulse oral corticosteroids therapy, by retrospective review of medical records.ResultsIn 345 patients (95.1% of all registered patients), 457 series of methylprednisolone pulse therapy were carried out for treatment of acute relapse. EDSS scores improved by 0.8 ± 1.1 (mean ± SD) after the first course. The second and third courses also produced sufficient improvements (by 0.7 and 0.6, respectively), but much smaller improvements were observed thereafter. The target neurological symptoms and signs improved in 79.5% of patients. Improvement rates were 5–20% lower after a course of pulse therapy than after a series of pulse therapy. A half dose (500 mg/day) produced less improvement than a standard dose (1000 mg/day; 65.9 vs 79.5%). During post‐pulse oral corticosteroid therapy, EDSS scores decreased by 0.6 ± 0.9. No significant adverse effects were observed.ConclusionsMethylprednisolone pulse therapy is beneficial in nearly 80% of Japanese MS and NMO patients, and EDSS score improvements after therapy are compatible with those in Western MS patients.
Policy transfer, social pedagogy and children's residential care in England
Authors: Berridge David 
Published: November 2013

AbstractMuch concern has been expressed about the quality of care and poor outcomes for looked‐after children (‘children in care’) in England, especially regarding residential homes. This paper builds on a recent evaluation of the piloting of the continental European model of social pedagogy (SP) in English residential care. It does three things: it considers the theoretical social policy literature on policy transfer and its implications; discusses European residential care for children and the discipline of SP; and reflects on these debates and the situation of children's residential care in England. The paper concludes that there are some major hurdles to a widespread implementation of SP in England. This particularly concerns the differing social, professional and political context of children's residential services across neighbouring countries.