bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of Schmallenberg virus infection in sheep and goats flocks in Germany, 2012–2013
Authors: Helmer Carina , Eibach Regina , Humann‐Ziehank Esther , Tegtmeyer Philip C. , Bürstel Daniela , Mayer Kathrin , Moog Udo , Stauch Sieglinde , Strobel Heinz , Voigt Katja , Sieber Philipp , Greiner Matthias , Ganter Martin 
Published: January 2016

SummarySchmallenberg virus (SBV) is a member of the family Bunyaviridae and mainly affects ruminants. It is transmitted by biting midges, first and foremost Culicoides spp., and causes congenital malformations reflected in arthrogryposis–hydranencephaly (AH) syndrome. The aim of this study was to collect data on the emergence of SBV as a new arthropod‐borne disease introduced into Europe in 2011. Germany was located in the core region of the 2011/2012 epidemic. Following two seroprevalence studies in the north‐west of Germany in 2012, this study focused on the epidemiology and distribution of SBV throughout 130 small ruminant flocks in the whole country. Blood samples were obtained of 30 animals per flock and a SBV‐specific questionnaire was used to collect operating data of the farms. The median within‐herd seroprevalence for all 130 flocks tested was 53.3% with a total range from 0% to 100%. The median within‐herd seroprevalence for goats was 30% [interquartile range (IQR): 40.3%] and 57% for sheep (IQR: 43.3%). Small ruminant flocks kept permanently indoors or housed overnight had a significantly lower seroprevalence than flocks kept permanently outdoors. In addition, this study revealed a significantly lower seroprevalence in the north‐east of Germany. These results show that small ruminants in Germany are still at risk of contracting new SBV infections following incomplete seroconversion of flocks especially in the north‐east of Germany. This might contribute to SBV becoming enzootic in central and northern Europe. Furthermore, the survey revealed that housing animals at least during mating and early pregnancy may reduce the risk of new SBV infections and may thus be an option to reduce losses as long as there is no licensed vaccine available on the German market.
Understanding the canine intestinal microbiota and its modification by pro‐, pre‐ and synbiotics – what is the evidence?
Authors: Schmitz Silke , Suchodolski Jan 
Published: January 2016

AbstractInterest in the composition of the intestinal microbiota and possibilities of its therapeutic modifications has soared over the last decade and more detailed knowledge specific to the canine microbiota at different mucosal sites including the gut is available. Probiotics, prebiotics or their combination (synbiotics) are a way of modifying the intestinal microbiota and exert effects on the host immune response. Probiotics are proposed to exert their beneficial effects through various pathways, for example production of antimicrobial peptides, enhancing growth of favourable endogenous microorganisms, competition for epithelial colonisation sites and immune‐modulatory functions. Despite widespread use of pro‐, pre‐ and synbiotics, scientific evidence of their beneficial effects in different conditions of the dog is scarce. Specific effects of different strains, their combination or their potential side‐effects have not been evaluated sufficiently. In some instances, in vitro results have been promising, but could not be transferred consistently into in vivo situations. Specific canine gastrointestinal (GI) diseases or conditions where probiotics would be beneficial, their most appropriate dosage and application have not been assessed extensively. This review summarises the current knowledge of the intestinal microbiome composition in the dog and evaluates the evidence for probiotic use in canine GI diseases to date. It wishes to provide veterinarians with evidence‐based information on when and why these products could be useful in preventing or treating canine GI conditions. It also outlines knowledge about safety and approval of commercial probiotic products, and the potential use of faecal microbial transplantation, as they are related to the topic of probiotic usage.
Objective review of de novo stand‐alone error correction methods for NGS data
Authors: Alic Andy S. , Ruzafa David , Dopazo Joaquin , Blanquer Ignacio 
Published: January 2016

The sequencing market has increased steadily over the last few years, with different approaches to read DNA information prone to different types of errors. Multiple studies demonstrated the impact of sequencing errors on different applications of next‐generation sequencing (NGS), making error correction a fundamental initial step. Different methods in the literature use different approaches and fit different types of problems. We analyzed 50 methods divided into five main approaches (k‐spectrum, suffix arrays, multiple‐sequence alignment, read clustering, and probabilistic models). They are not published as a part of a suite (stand‐alone), and target raw, unprocessed data without an existing reference genome (de novo). These correctors handle one or more sequencing technologies using the same or different approaches. They face general challenges (sometimes with specific traits for specific technologies) such as repetitive regions, uncalled bases, and ploidy. Even assessing their performance is a challenge in itself because of the approach taken by various authors, the unknown factor (de novo), and the behavior of the third‐party tools employed in the benchmarks. This study aims to help the researcher in the field to advance the field of error correction, the educator to have a brief but comprehensive companion, and the bioinformatician to choose the right tool for the right job. WIREs Comput Mol Sci 2016, 6:111–146. doi: 10.1002/wcms.1239This article is categorized under:

Computer and Information Science > Computer Algorithms and Programming
Regulation and functions of bacterial PNPase
Authors: Briani Federica , Carzaniga Thomas , Dehò Gianni 
Published: January 2016

Polynucleotide phosphorylase (PNPase) is an exoribonuclease that catalyzes the processive phosphorolytic degradation of RNA from the 3′‐end. The enzyme catalyzes also the reverse reaction of polymerization of nucleoside diphosphates that has been implicated in the generation of heteropolymeric tails at the RNA 3′‐end. The enzyme is widely conserved and plays a major role in RNA decay in both Gram‐negative and Gram‐positive bacteria. Moreover, it participates in maturation and quality control of stable RNA. PNPase autoregulates its own expression at post‐transcriptional level through a complex mechanism that involves the endoribonuclease RNase III and translation control. The activity of PNPase is modulated in an intricate and still unclear manner by interactions with small molecules and recruitment in different multiprotein complexes. Not surprisingly, given the wide spectrum of PNPase substrates, PNPase‐defective mutations in different bacterial species have pleiotropic effects and perturb the execution of genetic programs involving drastic changes in global gene expression such as biofilm formation, growth at suboptimal temperatures, and virulence. WIREs RNA 2016, 7:241–258. doi: 10.1002/wrna.1328This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Turnover and Surveillance > Regulation of RNA Stability
Non-monotonic Travelling Wave Fronts in a System of Fractional Flow Equations from Porous Media
Authors: Hönig O. , Zegeling P. A. , Doster F. , Hilfer R. 
Published: January 2016

Abstract
Motivated by observations of saturation overshoot, this article investigates generic classes of smooth travelling wave solutions of a system of two coupled nonlinear parabolic partial differential equations resulting from a flux function of high symmetry. All boundary resp. limit value problems of the travelling wave ansatz, which lead to smooth travelling wave solutions, are systematically explored. A complete, visually and computationally useful representation of the five-dimensional manifold connecting wave velocities and boundary resp. limit data is found by using methods from dynamical systems theory. The travelling waves exhibit monotonic, non-monotonic or plateau-shaped behaviour. Special attention is given to the non-monotonic profiles. The stability of the travelling waves is studied by numerically solving the full system of the partial differential equations with an efficient and accurate adaptive moving grid solver.
Coupling Inward Diffusion and Precipitation Kinetics; the Case of Nitriding Iron-Based Alloys
Authors: Jung Minsu , Meka Sai Ramudu , Rheingans Bastian , Mittemeijer Eric Jan 
Published: January 2016

AbstractA model that describes the inward diffusion of an element I into a solid substrate and the simultaneous precipitation of a compound MyIz, with M as the alloying element initially dissolved in the substrate matrix, is presented for the case of nitriding iron-based alloys. The model was developed by coupling the diffusion kinetics and the precipitation (nucleation and growth) kinetics. Additionally, the role of excess nitrogen and the kinetics of ammonia dissociation at the iron surface were incorporated into this coupled model. The model was successfully applied to the case of nitriding an Fe-2.23 at. pct V alloy; the simulation results are in good agreement with the measured data and allow for detailed understanding of the evolution of the nitride precipitates (volume fraction, number density, and size distribution) as a function of both nitriding time and depth in the specimen. The present model exposed the pronounced effects of the precipitation kinetics, of excess nitrogen, and of the surface-reaction kinetics on the overall nitriding kinetics and demonstrated a striking, nonmonotonous change with time of precipitate particle size at a distinct depth in the specimen.
Blessé médullaire: prise en charge en andrologie
Authors: Soler J. -M. , Mieusset R. 
Published: January 2016

RésuméLes réactions sexuelles sont sous contrôle neurologique. Le traumatisme vertébromédullaire altère l’organisation neurologique et génère un dysfonctionnement sexuel. Les substances pharmacologiques actuelles permettent de rétablir la fonction érectile du blessé médullaire, première étape essentielle à la réorganisation d’une vie sexuelle. Le déclenchement de l’éjaculation est souvent difficile. Les techniques de stimulation périnéale isolées ou associées au traitement pharmacologique favorisent la réalisation d’éjaculation et permettent un recueil et une conservation du sperme. La possibilité d’obtenir une éjaculation au cours des rapports sexuels, chez le blessé médullaire, reste rare et sans véritable solution thérapeutique. Malgré l’altération de la qualité du sperme, les blessés médullaires conservent une possibilité de procréation pour 40 à 60 % des couples. Le recours à des techniques d’assistance médicale à la procréation est souvent nécessaire. La prise en charge des dysfonctionnements sexuels des blessés médullaires doit être intégrée dans un programme de rééducation et de réinsertion.
The Effect(s) of Teen Pregnancy: Reconciling Theory, Methods, and Findings
Authors: Diaz Christina J. , Fiel Jeremy E. 
Published: January 2016

Abstract
Although teenage mothers have lower educational attainment and earnings than women who delay fertility, causal interpretations of this relationship remain controversial. Scholars argue that there are reasons to predict negative, trivial, or even positive effects, and different methodological approaches provide some support for each perspective. We reconcile this ongoing debate by drawing on two heuristics: (1) each methodological strategy emphasizes different women in estimation procedures, and (2) the effects of teenage fertility likely vary in the population. Analyses of the Child and Young Adult Cohorts of the National Longitudinal Survey of Youth (N = 3,661) confirm that teen pregnancy has negative effects on most women’s attainment and earnings. More striking, however, is that effects on college completion and early earnings vary considerably and are most pronounced among those least likely to experience an early pregnancy. Further analyses suggest that teen pregnancy is particularly harmful for those with the brightest socioeconomic prospects and who are least prepared for the transition to motherhood.
Eliciting and measuring betrayal aversion using the BDM mechanism
Authors: Quercia Simone 
Published: January 2016

AbstractBetrayal aversion has been operationalized as the evidence that subjects demand a higher risk premium to take social risks compared to natural risks. This evidence has been first shown by Bohnet and Zeckhauser (J Econ Behav 98:294–310, 2004) using an adaptation of the Becker–DeGroot–Marschak mechanism (BDM, Becker et al. Behav Sci 9:226–232, 1964). We compare their implementation of the BDM mechanism with a new version designed to facilitate subjects’ comprehension. We find that, although the two versions produce different distributions of values, the size of betrayal aversion, measured as an average treatment difference between social and natural risk settings, is not different across the two versions. We further show that our implementation is preferable to use in practice as it reduces substantially subjects’ mistakes and the likelihood of noisy valuations.
An Analysis of Inpatient Rehabilitation Approval Among Private Insurance Carriers at a Cancer Center
Authors: Fu Jack B. , Bianty Josephine R. , Wu Jimin , Ngo‐Huang An , Shin Ki Y. , Bruera Eduardo 
Published: January 2016

AbstractBackgroundAcute inpatient rehabilitation is often used by cancer patients to assist with discharge home and/or preparation for further treatment. Private insurance patients often require approval before transfer to acute inpatient rehabilitation.ObjectiveTo analyze the approval rate of private insurance carriers for acute inpatient cancer rehabilitation.DesignRetrospective analysis.SettingTertiary referral‐based cancer center.PatientsA total of 96 consecutive patients with private insurance who had acute inpatient rehabilitation authorization requests made between April 1, 2014, and September 17, 2014.InterventionPatient cases were assessed by a physiatrist, deemed clinically appropriate for acute inpatient rehabilitation, and submitted to private insurance payers for an approval request.ResultsIn all, 84 of 96 requests (87%) for private insurance authorization for inpatient rehabilitation transfer were approved. Of the 96 cases, 14 cases (14.6%) were initially denied. Nine of 96 (9.4%) progressed to a peer‐to‐peer appeal, of which only 2 of 9 (11.1%) resulted in approval for inpatient rehabilitation transfer (P = .222). The insurance carriers represented were designated as insurance A (46 patients, 48%), insurance B (18 patients, 19%), insurance C (12 patients, 13%), and other insurances (20, 21%). Two of 46 insurance A requests were initially denied, as compared to 7 of 18 for insurance B, 0 of 12 for insurance C, and 4 of 20 for other insurances (P = .001). Patients with insurance B (P = .002, odds ratio = 14) and other insurances (P = .062, odds ratio = 5.50) were more likely to be denied inpatient rehabilitation approval compared to patients with insurance A. No significant difference between mean Functional Independence Measure scores for approved and denied patients were found for transfers (P = .239) and mobility (P = .129), respectively.ConclusionAccess to acute inpatient rehabilitation is unfortunately limited by insurers rather than clinical indicators. Future multicenter studies and universally accepted guidelines regarding inpatient rehabilitation criteria are needed.
Discontinuation of Systematic Surveillance and Contact Precautions for Vancomycin-ResistantEnterococcus(VRE) and Its Impact on the Incidence of VREfaeciumBacteremia in Patients with Hematologic Malignancies
Authors: Almyroudis Nikolaos G. , Osawa Ryosuke , Samonis George , Wetzler M. , Wang Eunice S. , McCarthy Philip L. , Segal Brahm H. 
Published: January 2016

OBJECTIVETo study the effect of discontinuation of systematic surveillance for vancomycin-resistantEnterococcus(VRE) and contact isolation of colonized patients on the incidence of VRE bacteremiaSETTINGA hematology-oncology unit with high prevalence of VRE colonization characterized by predominantly sporadic molecular epidemiologyPARTICIPANTSInpatients with hematologic malignancies and recipients of hematopoietic stem cell transplantationMETHODSThe incidence of VRE bacteremia was measured prospectively during 2 different 3-year time periods; the first during active VRE surveillance and contact precautions and the second after discontinuation of these policies. We assessed the collateral impact of this policy change on the incidence of bacteremia due to methicillin-resistantStaphylococcus aureus(MRSA) andClostridium difficileinfection even though we maintained contact precautions for these organisms. Incidence of infectious events was measured as number of events per 1,000 patients days per month. Time series analysis was used to evaluate trends.RESULTSThe incidence of VRE bacteremia remained stable after discontinuation of VRE surveillance and contact precautions. The incidence of MRSA bacteremia andClostridium difficileinfection for which we continued contact precautions also remained stable. Aggregated antibiotic utilization and nursing hours per patient days were similar between the 2 study periods.CONCLUSIONActive surveillance and contact precautions for VRE colonization did not appear to prevent VRE bacteremia in patients with hematologic malignancies and recipients of hematopoietic stem cell transplantation with high prevalence of VRE characterized by predominantly sporadic molecular epidemiology.Infect. Control Hosp. Epidemiol.2016;37(4):398–403
The timing of worm exclusion in dogs repeatedly infected with the cestode Echinococcus multilocularis
Authors: Kouguchi H. , Irie T. , Matsumoto J. , Nakao R. , Sugano Y. , Oku Y. , Yagi K. 
Published: January 2016

AbstractExperimental Echinococcus multilocularis infection and deworming was repeated three or five times in nine dogs at various re-infection schedules. The mean number of worms decreased more than 91% in dogs with repeated infection, compared to first infection controls (n= 6). The copro-antigen assay and the egg count in the faeces suggested that the worm burden gradually decreased each time the dogs were re-infected. To examine whether such worm exclusion was a non-specific response, five dogs were sequentially infected with the parasite four times and subsequently fed freely for 6 months. Even after the 6-month interval, the five dogs that were infected five times with the parasite were still able largely to exclude the adult worms. The results suggested that the ability of worm exclusion in dogs that developed a resistance did not become rapidly extinct. Observation of the condition of faeces and the excretion of hooks in the faeces of repeatedly infected dogs revealed that the exclusion of worms started at the first week after the re-infection, and it continued during the patent period. Serum antibodies specific to the parasite antigen increased gradually until the third infection and significantly decreased during the 6-month interval. There was little enhancement of serum antibodies after the fifth infection in most dogs, although no clear correlation was observed between the antibody response and the worm burden. These findings suggested the possibility of developing a vaccine.
Differential efficacy of cognitive behavioral therapy and psychodynamic therapy for major depression: a study of prescriptive factors
Authors: Driessen E. , Smits N. , Dekker J. J. M. , Peen J. , Don F. J. , Kool S. , Westra D. , Hendriksen M. , Cuijpers P. , Van H. L. 
Published: January 2016

BackgroundMinimal efficacy differences have been found between cognitive behavioral therapy (CBT) and psychodynamic therapies for depression, but little is known about patient characteristics that might moderate differential treatment effects. We aimed to generate hypotheses regarding such potential prescriptive factors.MethodWe conducted post-hoc model-based recursive partitioning analyses alongside a randomized clinical trial comparing the efficacy of CBT and short-term psychodynamic supportive psychotherapy (SPSP). Severely depressed patients received additional antidepressant medication. We included 233 adults seeking treatment for a major depressive episode in psychiatric outpatient clinics, who completed post-treatment assessment. Post-treatment mean Hamilton Depression Rating Scale scores constituted the main outcome measure.ResultsWhile treatment differences (CBT v. SPSP) were minimal in the total sample of patients (d = 0.04), model-based recursive partitioning indicated differential treatment efficacy in certain subgroups of patients. SPSP was found more efficacious among moderately depressed patients receiving psychotherapy only who showed low baseline co-morbid anxiety levels (d = −0.40) and among severely depressed patients receiving psychotherapy and antidepressant medication who reported a duration of the depressive episode of ⩾1 year (d = −0.31), while CBT was found more efficacious for such patients reporting a duration <1 year (d = 0.83).ConclusionsOur findings are observational and need validation before they can be used to guide treatment selection, but suggest that knowledge of prescriptive factors can help improve the efficacy of psychotherapy for depression. Depressive episode duration and co-morbid anxiety level should be included as stratification variables in future randomized clinical trials comparing CBT and psychodynamic therapy.
Difference without Disagreement: Rethinking Hobbes on “Independency” and Toleration
Authors: Bejan Teresa M. 
Published: January 2016

AbstractIn arguments for a more tolerant Hobbes, Leviathan's endorsement of “Independency” is often Exhibit A; however, the conditionals Hobbes attached have received little attention. These—and the dangers of “contention” and sectarian “affection” they identify—are essential for understanding Hobbes's views on toleration. Together, they express a vision of “difference without disagreement” in which the accommodation of diversity in religious worship and association depends on the suppression of disagreement through sovereign- and self-discipline over speech. This expressly antievangelical ideal of toleration as a civil silence about difference presents a challenge to the more tolerant Hobbes thesis, particularly in its recent “Erastian Independency” guise. It also raises deeper questions about what might be at stake in applying the labels of “intolerant” or “tolerant” to Hobbes today.
Intoxicated Reasons, Rational Feelings: Rethinking the Early Modern English Public Sphere
Authors: Hsueh Vicki 
Published: January 2016

AbstractThis article examines early modern English public houses and related period miscellany—broadside ballads, conduct books, and songs—to more closely investigate the discourses and performances of drinking culture. Drinking culture, I argue, not only had a significant role in shaping the Restoration's civic culture of political participation and the emerging early modern public sphere, but also positioned emotions of pleasure and melancholy as social and political objects of care and cultivation. While the politics of pub culture and intoxication have been well documented by historians and literary scholars of early modern England and eighteenth-century America, much of this discussion has not yet been incorporated into political assessments of the public sphere and its history. Reinserting emotion and intoxication into the emergence of the public sphere helps to flesh out the history of feeling and social ritual in civic engagement.