bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conceptual and statistical problems with the DEC+J model of founder‐event speciation and its comparison with DEC via model selection
Authors: Ree Richard H. , Sanmartín Isabel 
Published: February 2018

AbstractPhylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal‐extinction‐cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder‐event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder‐event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time‐dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non‐jump events is assigned a free parameter, j, that when maximized precludes the possibility of non‐jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time‐dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time‐dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state‐dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC‐based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
Sleep apnea and type 2 diabetes
Authors: Muraki Isao , Wada Hiroo , Tanigawa Takeshi 
Published: February 2018

AbstractThe aim of the present review was to clarify the association between obstructive sleep apnea (OSA) and type 2 diabetes, and discuss the therapeutic role of continuous positive airway pressure (CPAP) in type 2 diabetes. OSA patients are more likely than non‐OSA populations to develop type 2 diabetes, while more than half of type 2 diabetes patients suffer from OSA. Similar to Western countries, in the East Asian population, the association between these two disorders has also been reported. CPAP is the primary treatment for OSA, but the effect of CPAP on comorbid diabetes has not been established. CPAP improved glucose metabolism determined by the oral glucose tolerance test in OSA patients, and several studies have shown that CPAP improves insulin resistance, particularly in obese populations undergoing long‐term CPAP. Diabetes is associated with other sleep‐related manifestations as well, such as snoring and excessive daytime sleepiness. Snoring is associated with the development of diabetes, and excessive daytime sleepiness appears to modify insulin resistance. Well‐designed studies are required to clarify the therapeutic effect of CPAP on diabetes. As both diabetes and OSA lead to cardiovascular disease, clinicians and healthcare professionals should be aware of the association between diabetes and OSA, and should take CPAP and health‐related behaviors into consideration when treating patients with diabetes and/or OSA.
Assessment of antiplaque effectiveness of chlorhexidine‐soaked gauze compared to chlorhexidine mouth rinse: Randomized clinical trial
Authors: Sparabombe Scilla , Roncati Marisa , Monterubbianesi Riccardo , Catellani Alberto , Manzoli Lamberto , Bambini Fabrizio , Procaccini Maurizio , Putignano Angelo , Orsini Giovanna 
Published: February 2018

AbstractAimThe aim of the present study was to compare the efficacy of a disposable gauze soaked with chlorhexidine and rolled up on the finger vs chlorhexidine mouth rinse (CM) to maintain oral hygiene.MethodsIn this single‐blind, randomized trial, both groups were instructed to brush their teeth and use the 0.12% chlorhexidine intervention twice per day (experimental group: toothbrushing + chlorhexidine‐soaked gauze; control group: toothbrushing + mouth rinse). The main outcome was the change in full mouth plaque index scores from baseline to 2 weeks. Secondary outcomes were the patient's appreciation (visual analog scale) and the bleeding index.ResultsThe final sample consisted of 60 young patients: 31 in the experimental group and 29 in the control group. After 2 weeks, both interventions were effective in reducing plaque index. The percentage of score reduction was 33% in the experimental group and 30% for the controls, with no significant difference between groups. Both interventions reduced the bleeding index, but this reduction was significant only in the experimental group (P < .001).ConclusionsThere is no difference between chlorhexidine‐soaked gauze and CM regarding plaque control. In addition, gauze soaked with chlorhexidine was significantly more effective in reducing the bleeding index score and was appreciated by the patients.
Children's hymn singing in Victorian culture and scholarship
Authors: Clapp‐Itnyre Alisa 
Published: February 2018

AbstractChildren's lives in nineteenth‐century Britain were filled with hymn‐singing, whether at church, school, home, or Sunday schools. Yet this dimension to Victorian culture has rarely been studied either by Hymn Studies or Childhood Studies. This article explores the ways that children's hymns are central to our understanding of hymns and of children, urging crosspollination of these two important disciplines. It will explore ways that hymns empowered children throughout the century, breaking down the perceived child‐adult binary of Victorian society.
Victorian gothic soundscapes
Authors: Schlauraff Kristie A. 
Published: February 2018

AbstractResounding with wails, groans, creaks, thunders, bells, and a score of other unsettling and often unidentifiable sounds, the Victorian gothic emerges against the backdrop of what John M. Picker has called “a period of unprecedented amplification” that necessitated new modes of listening. While critics have increasingly acknowledged the significance of the audible world to Victorian literature, and sound studies has exposed new approaches to addressing the acoustic dimensions of texts, the gothic soundscape remains largely unexamined. This article identifies the shared qualities of the sonic world and Victorian gothic fiction, building on two key definitions of sound to expose how the genre absorbed, manipulated, and leveraged the soundscape to spark terror among characters and readers alike. It then offers an overview of scholarship on the gothic and sound, focusing primarily on the past twenty years. Although a number of critics investigate the role of music in gothic fiction by Ann Radcliffe, Charles Dickens, George Eliot, and Wilkie Collins, among others, few move beyond it to consider the soundscape in its entirety. The final section calls attention to some of the shared keynotes among Victorian gothic texts and suggests possible approaches to more sustained scholarly work on their dynamic soundscapes.
Fungal infections in patients with inflammatory bowel disease: A systematic review
Authors: Stamatiades George A. , Ioannou Petros , Petrikkos George , Tsioutis Constantinos 
Published: February 2018

SummaryBackgroundDespite reports of fungal infections in patients with inflammatory bowel disease (IBD), their clinical and microbiological characteristics remain unknown.ObjectivesThe aim of this systematic review was to examine all available evidence regarding fungal infections in patients with IBD.MethodsSystematic search of PubMed (through 27 May 2017) for studies providing data on clinical, microbiological, treatment and outcome data of fungal infections in patients with IBD. The primary study outcome was to record the most common fungal species in patients with IBD. Secondary outcomes were classified into 3 categories: (i) characteristics of fungal infections; (ii) data on IBD and (iii) treatment and outcomes of fungal infections in patients with IBD.ResultsFourteen studies with data on 1524 patients were included in final analysis. The most common fungal infections in patients with IBD were caused by Candida species (903 infections); the most commonly reported site of Candida infection was the gastrointestinal tract. Available evidence shows that most fungal infections occur within 12 months of IBD treatment and within 6 months when anti‐TNFa agents are used.ConclusionsThis systematic review thoroughly describes fungal infections in patients with IBD and provides important information for the early detection and management of these infections.
Spillover Effects: Immigrant Policing and Government Skepticism in Matters of Health for Latinos
Authors: Cruz Nichols Vanessa , LeBrón Alana M. W. , Pedraza Francisco I. 
Published: February 2018

AbstractTo what extent do people become less trusting of the government under threatening policy contexts? The authors find evidence that Secure Communities, a bureaucratic program that enhances immigrant policing through collaboration between local law and immigration enforcement agencies, spurs mistrust among Latinos but not non‐Latinos. This article focuses on the politics of immigration and health, two issue areas marked by large‐scale bureaucratic developments over the last 50 years. The authors argue that a major consequence of expanding immigrant policing is its trickle‐down effect on how individuals view public institutions charged with the provision of public goods, such as health information. The results indicate that Latinos in locales where immigrant policing is most intense express lower levels of trust in government as a source of health information. Through a policy feedback lens, the findings suggest that the state's deployment of immigrant policing conveys more widespread lessons about the trustworthiness of government.
The Generating Function for the Airy Point Process and a System of Coupled Painlevé II Equations
Authors: Claeys Tom , Doeraene Antoine 
Published: February 2018

AbstractFor a wide class of Hermitian random matrices, the limit distribution of the eigenvalues close to the largest one is governed by the Airy point process. In such ensembles, the limit distribution of the kth largest eigenvalue is given in terms of the Airy kernel Fredholm determinant or in terms of Tracy–Widom formulas involving solutions of the Painlevé II equation. Limit distributions for quantities involving two or more near‐extreme eigenvalues, such as the gap between the kth and the ℓth largest eigenvalue or the sum of the k largest eigenvalues, can be expressed in terms of Fredholm determinants of an Airy kernel with several discontinuities. We establish simple Tracy–Widom type expressions for these Fredholm determinants, which involve solutions to systems of coupled Painlevé II equations, and we investigate the asymptotic behavior of these solutions.
More on Plagiarism in the Social Sciences*
Authors: Stitzel Brandli , Hoover Gary A. , Clark William 
Published: February 2018

AbstractThis research presents the results of a follow‐up survey to journal editors more than a decade after Enders and Hoover (Journal of Economic Literature 42(3):487–93). The original survey asked editors about their definition of plagiarism and known cases. This work investigates what, if anything, has changed in regards to how journal editors react to suspected plagiarism and if the definition of plagiarism has changed. In addition to surveying editors of economics journals, we have surveyed many more editors, including political science, sociology, and others, to contrast differences that might exist. There is great variation within disciplines regarding the appropriate definition of plagiarism or punishments but fairly consistent agreement across disciplines.
Nerve reinnervation and itch behavior in a rat burn wound model
Authors: Saffari Tiam M. , Schüttenhelm Barthold N. , van Neck Johan. W. , Holstege Jan C. 
Published: February 2018

AbstractIn this study, we investigated whether postburn itch in rats, after a full thickness burn, is correlated to the nervous reinnervation of the burn wound area. For this purpose, we determined scratching duration (expressed as second/hour) at 24 hours, 2, 4, 8, and 12 weeks postburn and combined this with immunohistochemistry for protein gene product 9.5 (PGP9.5) to identify all nerve fibers, calcitonin gene related peptide (CGRP) to identify peptidergic fibers, tyrosine hydroxylase (TH) for sympathetic fibers, and growth‐associated protein 43 (GAP‐43) for regrowing fibers. We found a modest, but highly significant, increase in scratching duration of all burn wound rats from 3 to 12 weeks postburn (maximally 63 ± 9.5 second/hour compared to sham 3.1 ± 1.4 second/hour at 9 weeks). At 24 hours postburn, all nerve fibers had disappeared from the burn area. Around 4 weeks postburn PGP 9.5‐ and CGRP‐immunoreactive nerve fibers returned to control levels. TH‐ and GAP‐43‐IR nerve fibers, which we found to be almost completely colocalized, did not regrow. No correlation was found between scratching duration and nervous reinnervation of the skin. The present results suggest that in rat, like in human, burn wound healing will induce increased scratching, which is not correlated to the appearance of nervous reinnervation.
First Report of a Complete Genome Sequence of White spot syndrome virus from India
Authors: Vinaya Kumar K. , Shekhar M. S. , Otta S. K. , Karthic K. , Ashok Kumar J. , Gopikrishna G. , Vijayan K. K. 
Published: February 2018

ABSTRACT

White spot syndrome virus
is a major pathogen of shrimp, causing economic loss to the aquaculture industry. For the first time, a complete
de novo
genome of an Indian isolate of this virus has been deciphered using Illumina and Nanopore sequencing technologies. The genome has 280,591 bp with 442 predicted coding genes.
Complete Genome Sequence of
Escherichia coli
81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug-Resistant Phenotype
Authors: Mutti Michele , Sonnevend Ágnes , Pál Tibor , Junttila Sini , Ekker Heinz , Galik Bence , Gyenesei Attila , Nagy Gábor , Nagy Eszter , Szijártó Valéria 
Published: February 2018

ABSTRACT

The sequence type 131 (ST131)-
H
30 clone is responsible for a significant proportion of multidrug-resistant extraintestinal
Escherichia coli
infections. Recently, the C1-M27 clade of ST131-
H
30, associated with
bla
CTX-M-27
, has emerged. The complete genome sequence of
E. coli
isolate 81009 belonging to this clone, previously used during the development of ST131-specific monoclonal antibodies, is reported here.
Complete Genome Sequence of Lactococcus lactis subsp. lactis G50 with Immunostimulating Activity, Isolated from Napier Grass
Authors: Nakano Kazuma , Minami Maiko , Shinzato Misuzu , Shimoji Makiko , Ashimine Noriko , Shiroma Akino , Ohki Shun , Nakanishi Tetsuhiro , Tamotsu Hinako , Teruya Kuniko , Satou Kazuhito , Moriya Naoko , Kimoto-Nira Hiromi , Kobayashi Miho , Hagi Tatsuro , Nomura Masaru , Suzuki Chise , Hirano Takashi 
Published: February 2018

ABSTRACT

Lactococcus lactis
subsp.
lactis
G50 is a strain with immunostimulating activity, isolated from Napier grass (
Pennisetum purpureum
). We determined the complete genome sequence of this strain using the PacBio RS II platform. The single circular chromosome consists of 2,346,663 bp, with 35.03% G+C content and no plasmids.
Theory of change for the delivery of talking therapies by lay workers to survivors of humanitarian crises in low-income and middle-income countries: protocol of a systematic review
Authors: Ryan Grace Kathryn , Bauer Andreas , Bass Judith K , Eaton Julian 
Published: February 2018

IntroductionThere is a severe shortage of specialist mental healthcare providers in low-income and middle-income countries (LMICs) affected by humanitarian crises. In these settings, talking therapies may be delivered by non-specialists, including lay workers with no tertiary education or formal certification in mental health. This systematic review will synthesise the literature on the implementation and effectiveness of talking therapies delivered by lay workers in LMICs affected by humanitarian crises, in order to develop a Theory of Change (ToC).Methods and analysisQualitative, quantitative and mixed-methods studies assessing the implementation or effectiveness of lay-delivered talking therapies for common mental disorders provided to adult survivors of humanitarian crises in LMICs will be eligible for inclusion. Studies set in high-income countries will be excluded. No restrictions will be applied to language or year of publication. Unpublished studies will be excluded. Seven electronic databases will be searched: MEDLINE, Embase, PsycINFO, PsycEXTRA, Global Health, Cochrane Library and ClinicalTrials.gov. Contents pages of three peer-reviewed journals will be hand-searched. Sources of grey literature will include resource directories of two online mental health networks (MHPSS.net and MHInnovation.net) and expert consultation. Forward and backward citation searches of included studies will be performed. Two reviewers will independently screen studies for inclusion, extract data and assess study quality. A narrative synthesis will be conducted, following established guidelines. A ToC map will be amended iteratively to take into account the review results and guide the synthesis.Ethics and disseminationFindings will be presented in a manuscript for publication in a peer-reviewed journal and disseminated through a coordinated communications strategy targeting knowledge generators, enablers and users.PROSPERO registration numberCRD42017058287.
Surgical efficiency in femtosecond laser cataract surgery compared with phacoemulsification cataract surgery: a case–control study
Authors: Day Alexander C , Smith Phillip R , Tang Hongying Lilian , Aiello Francesco , Hussain Badrul , Maurino Vincenzo , Marshall John , Saleh George M 
Published: February 2018

ObjectivesTo investigate differences in surgical time, the distance the surgical instrument travelled and number of movements required to complete manual phacoemulsification cataract surgery versus femtosecond laser cataract surgery.DesignNon-randomised comparative case series.SettingSingle surgery site, Moorfields Eye Hospital, UK.Participants40 cataract surgeries of 40 patients.InterventionsLaser-assisted and manual phacoemulsification cataract surgery. Laser-assisted surgery cases were performed using the AMO Catalys platform.Primary and secondary outcome measuresComputer vision tracking software PhacoTracking were applied to the recordings to establish the distance the instrument travelled, total number of movements (the number of times an instrument stops and starts moving) and time taken for surgery steps including phacoemulsification, irrigation–aspiration (IA) and overall surgery time. The time taken for laser docking and delivery was not included in the analyses.ResultsData on 19 laser-assisted and 19 manual phacoemulsification surgeries were analysed (two cases were excluded due to insufficient video-recording quality). There were no differences in the number of instrument moves, the distance the instrument travelled or time taken to complete the phacoemulsification stage. However for IA, the number of instrument moves (manual: mean 20 (SD 15) vs laser: mean 38 (SD 22), P=0.008) and time taken (manual: mean 75 s (SD 24) vs laser: mean 108 s (SD 36), P=0.003) were significantly greater for laser cases. For laser versus manual cases overall, there was no difference in number of moves or the distance the instrument travelled, but laser cases took longer (mean 88 s, P=0.049).ConclusionsLaser cataract surgery cases took longer to complete without accounting for the time taken to complete the laser procedure itself. This appears to be in part due to IA requiring more instrument manoeuvres and taking longer to complete. Data from a large randomised series would better elucidate this relationship.
Pulmonary metastasis in rectal cancer: a retrospective study of clinicopathological characteristics of 404 patients in Chinese cohort
Authors: Pan Hong-Da , Zhao Gang , An Qi , Xiao Gang 
Published: February 2018

ObjectivesThis study aim to investigate the incidence, timing and risk factors of metachronous pulmonary recurrence after curative resection in patients with rectal cancer.DesignA retrospective cohort study.SettingThis study was conducted at a tertiary referral cancer hospital.ParticipantsA total of 404 patients with rectal cancer who underwent curative resection from 2007 to 2012 at Beijing Hospital were enrolled in this study.InterventionsThe pattern of recurrence was observed and evaluated.Primary and secondary outcome measuresThe incidence and timing of recurrences by site were calculated, and the risk factors of pulmonary recurrence were analysed.ResultsThe 5-year disease-free survival for the entire cohort was 77.0%. The most common site of recurrence was the lungs, with an incidence of 11.4%, followed by liver. Median interval from rectal surgery to diagnosis of pulmonary recurrence was much longer than that of hepatic recurrence (20 months vs 10 months, P=0.022). Tumour location, pathological tumor-node-metastasis (TNM) stage and positive circumferential resection margin were identified as independent risk factors for pulmonary recurrence. A predictive model based on the number of risk factors identified on multivariate analysis was developed, 5-year pulmonary recurrence-free survival for patients with 0, 1, 2 and 3 risk factors was 100%, 90.4%, 77.3% and 70.0%, respectively (P<0.001).ConclusionsThis study emphasised that the lung was the most common site of metachronous metastasis in patients with rectal cancer who underwent curative surgery. For patients with unfavourable risk profiles, a more intensive surveillance programme that could lead to the early detection of recurrence is strongly needed.