bluuebunny/crossref_metadata_2025_split huggingface dataset:
BarcodingR: an integrated r package for species identification using DNA barcodes
Authors: Zhang Ai‐bing , Hao Meng‐di , Yang Cai‐qing , Shi Zhi‐yong 
Published: October 2016

Summary

Species identification via DNA barcodes has recently become an important and routine task in many biodiversity projects using DNA sequence data.

Here, we present BarcodingR, an integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy‐set, Bayesian and kmer‐based methods, that are not readily available in other packages.

BarcodingR additionally provides new functions for barcode evaluation, barcoding gap analysis, delimitation comparison analysis, species membership analysis and consensus identification.

Comparison with other barcoding methods using 11 empirical data sets indicates that on average, FZKMER (implemented in BarcodingR) and one extant barcoding method BRONX outperform all other methods examined in this study. Two other methods, BP and FZ (both implemented in BarcodingR), present similar performance as SVM and BLOG, respectively, and all display better performance than that of Jrip.

The software of BarcodingR is open source under GNU General Public License and freely available for all major operating systems.
Genetic Loss of Immunoglobulin A Does Not Influence Development of Alcoholic Steatohepatitis in Mice
Authors: Inamine Tatsuo , Yang An‐Ming , Wang Lirui , Lee Kuei‐Chuan , Llorente Cristina , Schnabl Bernd 
Published: October 2016

BackgroundChronic alcohol abuse is associated with intestinal dysbiosis and bacterial translocation. Translocated commensal bacteria contribute to alcoholic liver disease. Secretory immunoglobulin A (IgA) in the intestine binds bacteria and prevents bacterial translocation.MethodsTo investigate the functional role of IgA in ethanol (EtOH)‐induced liver disease in mice, we subjected wild type (WT) and IgA‐deficient littermate mice to Lieber–DeCarli models of chronic EtOH administration and the model of chronic and binge EtOH feeding (the NIAAA model).ResultsChronic EtOH feeding increased systemic levels of IgA, while fecal IgA was reduced in C57BL/6 WT mice. WT and Iga−/− littermate mice showed similar liver injury, steatosis, and inflammation following 4 weeks of EtOH feeding or chronic and binge EtOH feeding. IgA deficiency did not affect intestinal absorption or hepatic metabolism of EtOH. Pretreatment with ampicillin elevated intestinal IgA in WT littermate mice. Despite increased intestinal IgA, WT littermate mice exhibited a similar degree of liver disease compared with Iga−/− mice after 7 weeks of EtOH feeding. Interestingly, bacterial translocation to mesenteric lymph nodes was increased in Iga−/− mice fed an isocaloric diet, but was the same after EtOH feeding relative to WT littermate mice. The absence of intestinal IgA was associated with increased intestinal and plasma IgM in Iga−/− mice after EtOH feeding.ConclusionsOur findings indicate that absence of IgA does not affect the development of alcoholic liver disease in mice. Loss of intestinal IgA is compensated by increased levels of intestinal IgM, which likely limits bacterial translocation after chronic EtOH administration.
Impact of smoking reduced nicotine content cigarettes on sensitivity to cigarette price: further results from a multi‐site clinical trial
Authors: Smith Tracy T. , Cassidy Rachel N. , Tidey Jennifer W. , Luo Xianghua , Le Chap T. , Hatsukami Dorothy K. , Donny Eric C. 
Published: October 2016

AbstractAimsTo assess the impact of a reduction in the nicotine content of cigarettes on estimated consumption of reduced nicotine cigarettes and usual brand cigarettes at a variety of hypothetical prices.DesignDouble‐blind study with participants assigned randomly to receive cigarettes for 6 weeks that were either usual brand or an investigational cigarette with one of five nicotine contents.SettingTen sites across the United States.ParticipantsA total of 839 eligible adult smokers randomized from 2013 to 2014.Intervention and comparatorParticipants received their usual brand or an investigational cigarette with one of five nicotine contents: 15.8 (primary control), 5.2, 2.4, 1.3, or 0.4 mg/g.MeasurementsThe Cigarette Purchase Task was completed at baseline and at the week 6 post‐randomization visit.FindingsCompared with normal nicotine content controls, the lowest nicotine content (0.4 mg/g) reduced the number of study cigarettes participants estimated they would smoke at a range of prices [mean reduction relative to 15.8 mg/g at a price of $4.00/pack: 9.50, 95% confidence interval (CI) = 6.81,12.19]. The lowest nicotine content also reduced the maximum amount of money allocated to study cigarettes and the price at which participants reported they would stop buying study cigarettes [median reduction relative to 15.8 mg/g, 95% CI = $8.21 (4.27,12.15) per day and $0.44 (0.17,0.71) per cigarette, respectively]. A reduction in nicotine content to the lowest level also reduced the maximum amount of money allocated to usual brand cigarettes (median reduction relative to 15.8 mg/g: $4.39 per day, 95% CI = 1.88,6.90).ConclusionsIn current smokers, a reduction in nicotine content may reduce cigarette consumption, reduce the reinforcement value of cigarettes and increase cessation if reduced nicotine content cigarettes were the only cigarette available for purchase.
Squatting Social Centres in a Sicilian City: Liberated Spaces and Urban Protest Actors
Authors: Piazza Gianni 
Published: October 2016

AbstractThe Social Centres in Italy are simultaneously “liberated spaces”, empty and unused large buildings squatted by groups of radical left/antagonist activists to self‐manage social and countercultural activities, and “political contentious places”. They are indeed urban but not only local protest actors, denouncing the scarcity of spaces of sociability outside of commercial circuits, campaigning against market‐oriented urban renewal, property speculation, and on other anti‐capitalistic issues addressed outside the occupied spaces. The long history of Social Centres in Catania, the second largest city of Sicily, is reconstructed and explained through the choices and actions made by the squatters/activists, depending on their political‐ideological orientation, on the one hand; and by the opportunities and constraints of the specific political and socio‐spatial structure, which they had to face, on the other. The Social Centres, CPO Experia, CSOA Guernica, CSA Auro, and more recently CSO Liotru, are the main analysed empirical cases.
Estimation of fetal weight in pregnancies past term
Authors: Eggebø Torbjørn M. , Klefstad Olav A. , Økland Inger , Lindtjørn Elsa , Eik‐Nes Sturla H. , Gjessing Håkon K. 
Published: October 2016

AbstractIntroductionThe aim of the study was to investigate the accuracy of estimating fetal weight with ultrasound in pregnancies past term, using the eSnurra algorithm.Material and methodsIn all, 419 women with pregnancy length of 290 days, attending a specialist consultation at Stavanger University Hospital, Norway, were included in a prospective observational study. Fetal weight was estimated using biparietal diameter (BPD) and abdominal circumference (AC). The algorithm implemented in an electronic calculation (eSnurra) was used to compute estimated fetal weight (EFW). Results were compared with birthweight (BW).ResultsThe mean interval between the ultrasound examination and birth was 2 days (SD 1.4). The median difference between BW and EFW was −6 g (CI −40 to +25 g) and the median percentage error was –0.1% (95% CI −1.0 to 0.6%). The median absolute difference was 190 g (95% CI 170–207 g). The BW was within 10% of EFW in 83% (95% CI 79–87%) of cases and within 15% of EFW in 94% (95% CI 92–96%) of cases. Limits of agreement (95%) were from −553 g to +556 g. Using 5% false‐positive rates, the sensitivity in detecting macrosomic and small for gestational age fetuses was 54% (95% CI 35–72%) and 49% (95% CI 35–63%), respectively.ConclusionThe accuracy of fetal weight estimation was good. Clinicians should be aware of limitations related to prediction at the upper and lower end, and the importance of choosing appropriate cut‐off levels.
Spironolactone use and risk of incident cancers: a retrospective, matched cohort study
Authors: Mackenzie Isla S. , Morant Steven V. , Wei Li , Thompson Alastair M. , MacDonald Thomas M. 
Published: October 2016

AimsSpironolactone is widely used to treat heart failure, hypertension and liver disease with increased usage in recent years. Spironolactone has endocrine effects that could influence cancer risks and historical reports suggest possible links with increased risk of certain types of cancer. The aim of this study was to assess the effect of spironolactone exposure on cancer incidence.MethodsA pharmacoepidemiological propensity score‐matched cohort study was performed to assess the effect of spironolactone exposure on cancer incidence. Cox proportional hazards models were used to analyse time to first diagnosis of each prespecified cancer and hazard ratios for spironolactone exposure are presented. The setting for the study was UK primary care using the Clinical Practice Research Datalink. The participants were 74 272 patients exposed to spironolactone between 1986 and 2013, matched 1:2 with unexposed controls. The prespecified primary outcomes were the first incidence of ovarian, endometrial, pancreatic, colorectal, prostate, renal cell, pharyngeal and thyroid cancers, and myelomonoblastic/‐cytic leukaemias. Secondary outcomes were the remaining 27 types of cancer.ResultsThere was no evidence of an increased risk of any cancer associated with spironolactone use. Spironolactone use was associated with a significantly lower risk of prostate cancer (hazard ratio 0.69; 95% confidence interval 0.60–0.80, P < 0.001).ConclusionsIn this study, spironolactone use was associated with a lower incidence of prostate cancer, the most common cancer in men in the UK. The possible mechanisms and clinical implications merit further investigation.
Patient reported outcome measures in child and adolescent mental health services: associations between clinician demographic characteristics, attitudes and efficacy
Authors: Edbrooke‐Childs Julian , Barry David , Rodriguez Irene Mateos , Papageorgiou Danae , Wolpert Miranda , Schulz Joerg 
Published: October 2016

BackgroundPolicy recommends using patient reported outcome measures (PROMs), yet their use is persistently low. Our aim was to examine the association between PROM use and clinician demographic characteristics, attitudes and efficacy.MethodA sample of N = 109 clinicians completed an online survey.ResultsClinicians who reported higher levels of use of cognitive behaviour or humanistic approaches had higher levels of PROM use than clinicians who reported lower levels of use of these approaches. Clinicians who reported having received training had higher levels of self‐efficacy regarding PROMs than clinicians who reported not having received training, but the effects of training on PROM attitudes and use were not significant. Still, clinicians with more positive attitudes or self‐efficacy regarding PROMs had higher levels of PROM use than clinicians with less positive attitudes or self‐efficacy regarding PROMs.ConclusionClinicians should be supported to have the knowledge, skills and confidence to effectively use PROMs in their clinical practice.
Factors related to genetic testing in adults at risk for Huntington disease: the prospective Huntington at‐risk observational study (PHAROS)
Authors: Quaid K.A. , Eberly S.W. , Kayson‐Rubin E. , Oakes D. , Shoulson I. ,   on behalf of the Huntington Study Group PHAROS Investigators and Coordinators
Published: October 2016

Huntington disease (HD) is a late onset ultimately fatal neurodegenerative disorder caused by a cytosine–adenine–guanine ( CAG) triplet repeat expansion in the Huntingtin gene which was discovered in 1993. The PHAROS study is a unique observational study of 1001 individuals at risk for HD who had not been previously tested for HD and who had no plans to do so. In this cohort, 104 (10%) individuals changed their minds and chose to be tested during the course of the study but outside of the study protocol.Baseline behavioral scores, especially apathy, were more strongly associated with later genetic testing than motor and chorea scores, particularly among subjects with expanded CAG repeat length. In the CAG expanded group, those choosing to be tested were older and had more chorea and higher scores on the behavioral section of the unified Huntington's disease rating scale at baseline than those not choosing to be tested. Following genetic testing, 56% of subjects with CAG < 37 had less depression when compared to prior to testing, but depression generally stayed the same or increased for 64% of subjects in the expanded group. This finding suggests that approaches to testing must continue to be cautious, with appropriate medical, psychological and social support.
Long‐term outcomes of heart transplant recipients with hepatitis C positivity: the data from the U.S. transplant registry
Authors: Stepanova Maria , Locklear Trevor , Rafiq Nila , Mishra Alita , Venkatesan Chapy , Younossi Zobair M. 
Published: October 2016

AbstractBackgroundChronic HCV infection is often considered a contraindication for receiving a heart transplantation.MethodsFrom the Scientific Registry of Transplant Recipients, we selected all adults with and without HCV infection who underwent a single‐organ heart transplantation in 1995‐2013; the mortality status was updated in September 2015.ResultsA total of 32 812 heart transplant recipients were included; N=756 (2.30%) HCV positive. Post‐transplant patients were discharged alive at similar rates regardless of their HCV status (P=.10). Despite this, mortality in HCV+ heart transplant recipients was consistently higher throughout post‐discharge follow‐up (P<.002). In multivariate survival analysis, being HCV+ was independently associated with a higher post‐transplant mortality: adjusted hazard ratio 1.35 (1.16‐1.56), P<.0001. Other predictors of lower post‐transplant survival included being obese at transplant and pre‐transplant history of comorbidities (type 2 diabetes, COPD, hypertension) (all P<.05). No association of HCV infection with graft loss rates or time to graft loss was found (all P>.23).ConclusionChronic hepatitis C infection is associated with a significantly increased post‐transplant mortality in heart transplant recipients. The introduction of new direct‐acting antiviral agents may provide a treatment option for HCV pre‐ or post‐heart transplantation which could have a positive impact on patients' survival.
Open‐Mindedness: An Intellectual Virtue in the Pursuit of Knowledge and Understanding
Authors: Taylor Rebecca M. 
Published: October 2016

AbstractOpen‐mindedness is widely valued as an important intellectual virtue. Definitional debates about open‐mindedness have focused on whether open‐minded believers must possess a particular first‐order attitude toward their beliefs or a second‐order attitude toward themselves as believers, taking it for granted that open‐mindedness is motivated by the pursuit of propositional knowledge. In this article, Rebecca Taylor develops an alternative to knowledge‐centered accounts of open‐mindedness. Drawing on recent work in epistemology that reclaims understanding as a primary epistemic good, Taylor argues for an expanded account of open‐mindedness as an intellectual virtue motivated by the pursuit of both knowledge and understanding. Incorporating understanding allows for a more robust account of open‐mindedness that better accommodates common usage, avoids common criticisms, and better explains the widespread acceptance of open‐mindedness as an important intellectual virtue. Taylor also identifies the connections between open‐mindedness and several other intellectual virtues, including intellectual humility, intellectual courage, and intellectual diligence.
Optogenetic excitation in the ventral tegmental area of glutamatergic or cholinergic inputs from the laterodorsal tegmental area drives reward
Authors: Steidl Stephan , Wang Huiling , Ordonez Marco , Zhang Shiliang , Morales Marisela 
Published: October 2016

AbstractConverging evidence shows that ventral tegmental area (VTA) dopamine neurons receive laterodorsal tegmental nucleus (LDTg) cholinergic and glutamatergic inputs. To test the behavioral consequences of selectively driving the two sources of excitatory LDTg input to the VTA, channelrhodopsin‐2 (ChR2) was expressed in LDTg cholinergic neurons of ChAT::Cre mice (ChAT‐ChR2 mice) or in LDTg glutamatergic neurons of VGluT2::Cre mice (VGluT2‐ChR2 mice). Mice were tested in a 3‐chamber place preference apparatus where entry into a light‐paired chamber resulted in VTA light stimulation of LDTg‐cholinergic or LDTg‐glutamatergic axons for the duration of a chamber stay. ChAT‐ChR2 mice spent more time in the light‐paired chamber and subsequently showed conditioned place preference for the light‐paired chamber in the absence of light. VGluT2‐ChR2 mice, entered the light‐paired chamber significantly more times than a light‐unpaired chamber, but remained in the light‐paired chamber for short time periods and did not show a conditioned place preference. When each entry into the light‐paired chamber resulted in a single train of VTA light stimulation, VGluT2‐ChR2 mice entered the light‐paired chamber significantly more times than the light‐unpaired chamber, but spent approximately equal amounts of time in the two chambers. VTA excitation of LDTg‐glutamatergic inputs may be more important for reinforcement of initial chamber entry while VTA excitation of LDTg‐cholinergic inputs may be more important for the rewarding effects of chamber stays. We suggest that LDTg‐cholinergic and LDTg‐glutamatergic inputs to the VTA each contribute to the net rewarding effects of exciting LDTg axons in the VTA.
Overweight in epilepsy as a risk factor for pregnancy and delivery complications
Authors: Kolstad Eivind , Veiby Gyri , Gilhus Nils Erik , Bjørk Marte 
Published: October 2016

SummaryObjectiveTo investigate whether prepregnancy overweight in women with epilepsy increases their risk for complications during pregnancy and delivery.MethodsThis study is based on The Norwegian Mother and Child Cohort Study (MoBa) linked to the Medical Birth Registry of Norway. A diagnosis of epilepsy was reported in 706 pregnancies. Overweight was defined as body mass index ≥ 25 prepregnancy. Overweight women with epilepsy (n = 259) were compared to normal‐weight women with epilepsy (n = 416), and to women without epilepsy with and without overweight (n = 30,516 and n = 67,977, respectively). The risks of pregnancy and delivery complications were calculated as odds ratios (ORs) with 95% confidence intervals (CIs) adjusted for adverse socioeconomic factors, age, parity, and smoking.ResultsWomen with epilepsy were more often overweight than women without epilepsy (38.4% vs. 31.3%, p < 0.001). The majority of pregnancy and delivery complications were more frequent in overweight women with epilepsy. Compared to overweight women without epilepsy, the risk was increased for cesarean section (OR 1.6, CI 1.2–2.2, p < 0.001), excessive bleeding (OR 1.4, CI 1.0–1.8, p = 0.04), peripartum anxiety and depressive symptoms (OR 1.9, CI 1.3–2.8, p < 0.001), small for gestational age children (OR 2.4, CI 1.2–4.8, p = 0.02), and transfer of the infant to a neonatal ward (OR 1.5, CI 1.1–2.2, p = 0.02). Compared to normal‐weight women with epilepsy, the risk of cesarean section (OR 1.6, CI 1.1–2.3, p < 0.05), gestational hypertension (OR 2.0, CI 1.1–3.5, p < 0.05), preeclampsia (OR 2.3, CI 1.2–4.5, p < 0.05), and transfer of the infant to a neonatal ward (OR 2.2, CI 1.3–3.6, p < 0.01) was increased.SignificancePrepregnancy overweight in combination with epilepsy entails a strong negative effect on risk of complications during pregnancy and delivery. In women with epilepsy and overweight referral to a nutritionist should be considered when an antiepileptic drug is started as well as when pregnancy is planned. These women should be regarded as a high‐risk group.
Tuberculosis caused byMycobacterium bovisinfection in a donkey
Authors: Bryan J. , den Boon P. , McGuirk J. , Madigan G. , Skuce R. , Fogarty U. 
Published: October 2016

SummaryMycobacterial infections are rare in equines.Mycobacterium bovis(M. bovis) is an important zoonotic bacterial pathogen causing disease in a wide range of animal species and sporadically causes severe disseminated disease in horses. This report describes the clinical, gross post‐mortem examination and histopathological findings in a case of disseminatedM. bovisinfection in a donkey which to the authors’ knowledge has not been previously documented in the scientific literature.
2D modelling of inclined intergranular stress corrosion crack paths
Authors: Griggs J , Gamboa E , Lavigne O 
Published: October 2016

AbstractInclined high pH stress corrosion cracking (SCC) is a type of intergranular environmental cracking in gas pipelines, which differs from typical SCC by propagating at an angle from the wall direction. Investigations of Australian and Canadian inclined SCC colonies have not provided a clear indicator of a cause for the abnormal crack growth direction. This paper addresses the possibility of crack tip strain enhanced electrochemistry causing the inclination. Potentiodynamic tests were conducted to quantify the influence of strain on the electrochemistry, and strain was found to increase current density up to 300% in the SCC region. A model was developed that incorporates crack tip strain driven SCC growth, which showed good agreement with field grown cracks, and the aspect ratio of the grains was shown to have an effect on the inclination angle. The results indicate that crack tip strain enhanced electrochemistry is a plausible cause for inclined SCC.
Fracture mechanics modelling of constant and variable amplitude fatigue behaviour of field corroded 7075‐T6511 aluminium
Authors: McMurtrey M.D. , Bae D. , Burns J.T. 
Published: October 2016

AbstractFor ageing airframe structures, a critical challenge for next generation linear elastic fracture mechanics (LEFM) modelling is to predict the effect of corrosion damage on the remaining fatigue life and structural integrity of components. This effort aims to extend a previously developed LEFM modelling approach to field corroded specimens and variable amplitude loading. Iterations of LEFM modelling were performed with different initial flaw sizes and crack growth rate laws and compared to detailed experimental measurements of crack formation and small crack growth. Conservative LEFM‐based lifetime predictions of corroded components were achieved using a corrosion modified‐equivalent initial flaw size along with crack growth rates from a constant Kmax‐decreasing ΔK protocol. The source of the error in each of the LEFM iterations is critiqued to identify the bounds for engineering application.
Divisional Informativeness Gap and Value Creation from Asset Sales
Authors: Desai Chintal A. , Gupta Manu 
Published: October 2016

AbstractNanda and Narayanan (1999) show that the information asymmetry between the managers and market participants regarding divisional cash flows helps explain the value creation on asset sales. Based on their theoretical framework, the divisional informativeness gap hypothesis predicts that the announcement‐period return increases with the difference in cash‐flow informativeness of retained and divested divisions prior to the divestiture. Our results, using industry‐average earnings response coefficient as a proxy for cash‐flow informativeness of a division, support this prediction. The effect is stronger when a conglomerate retains the division with relatively greater growth opportunities.