bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why successful replications across contexts and Operationalizations might not be good for theory building or testing
Authors: Trafimow David 
Published: May 2019

AbstractDespite wide acceptance that replications across operationalizations and contexts is positive for psychology, the present goal is to suggest a more nuanced view that sometimes successful replications can be to the detriment of progress in psychology. The present manuscript distinguishes between replication in two idealized universes. In one such universe, the only difference between original and replication studies is randomness. In the other such universe, there are systematic differences between original and replication studies. Of course, replication in the real universe is subject to both randomness and systematicity. Although it is desirable to maximize, to the extent feasible, the probability of replication in the idealized universe where only random effects differ between original and replication studies; this may or may not be so with respect to systematicity. An important factor that determines the desirability of replications in the context of systematic differences pertains to auxiliary assumptions. A famous crisis in social psychology, with respect to the influence of attitudes on behaviors, illustrates the relevance of auxiliary assumptions in the replication context where there is serious consideration of systematic likeness or unlikeness between original and replication studies.
Plasma amino acid profiles in dogs with inflammatory bowel disease
Authors: Tamura Yu , Ohta Hiroshi , Kagawa Yumiko , Osuga Tatsuyuki , Morishita Keitaro , Sasaki Noboru , Takiguchi Mitsuyoshi 
Published: May 2019

AbstractBackgroundLymphocytic‐plasmacytic enteritis is the common form of idiopathic inflammatory bowel disease (IBD) in dogs. In human IBD, disturbances of amino acid metabolism have been demonstrated to be involved in the pathophysiology of IBD. Therefore, plasma amino acid profile might represent a novel marker of human IBD.ObjectivesTo determine the plasma amino acid profiles of dogs with IBD and its usefulness as a novel marker of IBD in dogs.AnimalsFasting blood plasma was obtained from 10 dogs with IBD and 12 healthy dogs.MethodsAll IBD dogs were prospectively included in this study, and heparinized blood samples were collected. The plasma concentrations of 21 amino acids were determined using the ninhydrin method. The relationships among the plasma amino acid concentrations and plasma C‐reactive protein (CRP) concentration, canine chronic enteropathy clinical activity index (CCECAI), and overall World Small Animal Veterinary Association (WSAVA) score were investigated.ResultsMedian concentration (nmol/mL) of methionine [46.2; range, 30.0‐59.3], proline [119.4; range, 76.7‐189.2], serine [115.1; range, 61.4‐155.9], and tryptophan [17.4; range, 11.9‐56.3]) were significantly lower than in control dogs [62.6; range, 51.0‐83.6, 199.1; range, 132.5‐376.7, 164.3; range, 124.7‐222.9, and 68.3; range, 35.7‐94.8, respectively]. A negative correlation was identified between the plasma serine concentration and CCECAI (r
s = −.67, P = .03), but there were no correlations between plasma amino acid concentrations and CRP concentration or overall WSAVA score.Conclusions and Clinical ImportancePlasma serine concentration might represent a novel maker of IBD in dogs.
Cascading effects of canopy mortality drive long‐term changes in understorey diversity in temperate old‐growth forests of Europe
Authors: Nagel Thomas A. , Iacopetti Giovanni , Javornik Jernej , Rozman Andrej , De Frenne Pieter , Selvi Federico , Verheyen Kris 
Published: May 2019

AbstractQuestionsWe investigated the influence of protracted mortality of a dominant canopy tree (Abies alba) on long‐term understorey dynamics. We ask (a) how tree regeneration and understorey species diversity and composition changed over 32 years; and (b) whether the observed changes were mainly driven by mortality of A. alba.LocationThree old‐growth forest reserves dominated by A. alba and Fagus sylvatica in the Dinaric Mountains of Slovenia.MethodTree layer and understorey regeneration and herbs were surveyed in 147 plots across the three forest reserves in 1983 and 2015. Soils were also sampled in 2015. The study period coincides with a protracted period of increased A. alba mortality in the canopy layer associated with anthropogenic emissions.ResultsBetween 1983 and 2015, the decline in canopy layer A. alba caused a recruitment pulse of F. sylvatica regeneration to the subcanopy tree layer across the three reserves. These changes were accompanied by a significant decline in plot level herb species richness. A model‐based analysis of beta‐diversity revealed significant community convergence during the study period, mainly caused by the loss of rare species. Ellenberg values indicate that these changes were mainly driven by loss of understorey light, while an increase in soil pH may have played a role also.ConclusionsThis observational study suggests that the long‐term decline of A. alba resulted in a cascade of processes — widespread F. sylvatica recruitment that impeded penetration of light to the forest floor, and possibly a change in soil conditions due to the decline of coniferous litter. These changes caused a significant loss of herb diversity and homogenization of the understorey community across the three sites. This study sheds light on the potential cascading consequences triggered by episodes of increased tree mortality resulting from global‐change‐type drivers.
The immune repressor BIR1 contributes to antiviral defense and undergoes transcriptional and post‐transcriptional regulation during viral infections
Authors: Guzmán‐Benito Irene , Donaire Livia , Amorim‐Silva Vítor , Vallarino José G. , Esteban Alicia , Wierzbicki Andrzej T. , Ruiz‐Ferrer Virginia , Llave César 
Published: May 2019

Summary

BIR1 is a receptor‐like kinase that functions as a negative regulator of basal immunity and cell death in Arabidopsis.

Using Arabidopsis thaliana and Tobacco rattle virus (TRV), we investigate the antiviral role of BIR1, the molecular mechanisms of BIR1 gene expression regulation during viral infections, and the effects of BIR1 overexpression on plant immunity and development.

We found that SA acts as a signal molecule for BIR1 activation during infection. Inactivating mutations of BIR1 in the bir1‐1 mutant cause strong antiviral resistance independently of constitutive cell death or SA defense priming. BIR1 overexpression leads to severe developmental defects, cell death and premature death, which correlate with the constitutive activation of plant immune responses.

Our findings suggest that BIR1 acts as a negative regulator of antiviral defense in plants, and indicate that RNA silencing contributes, alone or in conjunction with other regulatory mechanisms, to define a threshold expression for proper BIR1 function beyond which an autoimmune response may occur. This work provides novel mechanistic insights into the regulation of BIR1 homeostasis that may be common for other plant immune components.
Oral presentation of diffuse large B‐cell lymphoma: a rare entity
Authors: Hindocha N. , Nilsson J. 
Published: May 2019

AbstractDiffuse large B‐cell lymphoma (DLBCL) is the second most common non‐epithelial malignant tumour in the oral and maxillofacial region. It can mimic other benign conditions such as dental abscesses and benign tumours. We report a case of DLBCL mimicking a dental abscess. This resulted in delays of several months to correct diagnosis and thereby a poorer prognosis for the patient. Unfortunately, this is not uncommon, and it is therefore imperative that a histological examination is performed in cases where symptoms do not subside after a specific treatment. The earliest possible diagnosis is a critical prognostic factor for DLBCL.
Measurement of transepidermal water loss, stratum corneum hydration and skin surface pH in occupational settings: A review
Authors: Jansen van Rensburg Sané , Franken Anja , Du Plessis Johannes Lodewykus 
Published: May 2019

AbstractBackgroundThe skin provides a permeable barrier which may be impaired in occupational settings. Transepidermal water loss (TEWL), stratum corneum hydration (SCH) and skin surface pH (SSpH) have been used in occupational settings to predict early onset of occupational skin diseases, to measure the effectiveness of prevention strategies for occupational skin diseases, and to assess skin condition during exposure. The aim was to compare the findings, identify shortcomings in the methodology and data reporting and furthermore, to make recommendations for future studies.Materials and MethodsA literature study was conducted on studies published before December 2018 to provide a review on the measurement of TEWL, SCH and SSpH in occupational settings.ResultsTEWL, SCH and SSpH were previously measured in a wide variety of industries. Results between studies were highly variable, due to different study designs and different anatomical positions measured. Not all of the measurement conditions were reported and variations in study objectives led to data being reported and interpreted differently for most studies.ConclusionIncomplete reporting of methodology hinders comparison of bioengineering measurements. No bioengineering method has been proven useful as a predictive tool for occupational skin diseases, however, it is useful in the acute assessment of skin condition. It is recommended that future studies on TEWL, SCH and SSpH adhere to guidelines for occupational settings as far as possible to enable comparison between studies.
Fracturing behaviour of sandstone specimens with a cavity formed by intersecting excavations under compression: Experimental study and numerical modelling
Authors: Wu Hao , Zhao Guoyan , Kulatilake Pinnaduwa H.S.W. , Liang Weizhang , Wang Enjie 
Published: May 2019

AbstractTo investigate the mechanical properties, damage characteristics, and fracturing behaviour of specimens with a cavity formed by intersecting excavations, a series of uniaxial compression tests were conducted incorporating digital image correlation (DIC) and acoustic emission (AE) techniques. PFC2D modelling was conducted to further study the failure modes and crack evolution under biaxial loading. The results showed that the mechanical properties are significantly weakened by the cavity and influenced by its shape. The failure of the specimens containing a cavity under uniaxial compression can be considered as a progressive process of crack initiation, propagation, and coalescence of different cracks with each other, leading to forming macrofractures, which can be visually displayed by the DIC technique. A new method for determining the crack closure stress is proposed, and the crack initiation stress and the crack damage stress of specimens are also obtained by the AE measurements. The failure mode of the intact specimen changed from the tensile–shear failure mode under the uniaxial compression to the shear‐dominated failure mode under the biaxial compression. Failure of the specimens with a cavity is dominated by shear cracks rather than tensile cracks. Under high confining stresses, almost no macrotensile cracks appeared on the roof or floor of the cavity; instead, several spalling fractures were visible on the two sides of the cavity. The fracturing mechanism is well explained by the evolution of the internal stresses in the specimens.
Epidemiology and successful containment of a carbapenem‐resistant Enterobacteriaceae outbreak in a Southern Italian Transplant Institute
Authors: Mularoni Alessandra , Martucci Gennaro , Douradinha Bruno , Campanella Ornella , Hazen Benjamin , Medaglia Alice , Arena Giuseppe , Gruttadauria Salvatore , Tuzzolino Fabio , Arcadipane Antonio , Gioè Santi , Luca Angelo , Conaldi Pier Giulio , Grossi Paolo , Gridelli Bruno 
Published: May 2019

AbstractIntroductionCarbapenem‐resistant enterobacteriaceae (CRE) infections are difficult to treat and pose a serious threat to solid organ transplant (SOT) recipients. At our institute we observed an infection burden in 2012.MethodsIn order to contain the spread of CRE infections, we established a taskforce to implement guidelines suggested by the Centers for Disease Control and Prevention (CDC) for this type of outbreak. Here, we describe the epidemiology of the outbreak in our SOT population, and the effectiveness of such interventions, by comparing levels of CRE hospital‐acquired infection (HAI) pre‐ and post‐task force intervention (from January 2009 to December 2012, and from September 2013 to December 2016, respectively) through a linear regression model.ResultsIn this study, we included 933 patients who underwent a total of 1017 SOT procedures, 286 of whom had a CRE‐positive culture (28.8%), of which 65 (22.7% of CRE positive) developed infection. One‐year mortality post‐SOT was significantly higher in patients with CRE infection. After the taskforce intervention, the CRE HAI rate in SOT showed a significant inverse trend (event rate: −1.28, CI −1.70 to 0.86; P < 0.01).ConclusionIn the paucity of treatment options, the application of CDC measures in our SOT institute contributed significantly to containing CRE infections.
Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data
Authors: Kumar Vikash , Hainaut Matthieu , Delhomme Nicolas , Mannapperuma Chanaka , Immerzeel Peter , Street Nathaniel R. , Henrissat Bernard , Mellerowicz Ewa J. 
Published: May 2019

SummaryCarbohydrate‐active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long‐term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re‐annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high‐resolution RNA‐Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co‐expression network analysis of CAZymes in wood‐forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue‐specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.
Genomics and Genetics of
Streptococcus pneumoniae
Authors: Santoro Francesco , Iannelli Francesco , Pozzi Gianni 
Published: May 2019

ABSTRACT

Ninety years after the discovery of pneumococcal Transformation, and 74 years after the work of Avery and colleagues that identified DNA as the genetic material,
Streptococcus pneumoniae
is still one of the most important model organism to understand Bacterial Genetics and Genomics. In this Chapter special emphasis has been given to Genomics and to Mobile Genetic Elements (the Mobilome) which greatly contribute to the dynamic variation of pneumococcal genomes by horizontal gene transfer. Other topics include molecular mechanisms of Genetic Transformation, Restriction/Modification Systems, Mismatch DNA Repair, and techniques for construction of genetically engineered pneumococcal strains.
The Bacteriophages ofStreptococcus pyogenes
Authors: McShan W. Michael , McCullor Kimberly A. , Nguyen Scott V. 
Published: May 2019

ABSTRACTThe bacteriophages ofStreptococcus pyogenes(group A streptococcus) play a key role in population shaping, genetic transfer, and virulence of this bacterial pathogen. Lytic phages like A25 can alter population distributions through elimination of susceptible serotypes but also serve as key mediators for genetic transfer of virulence genes and antibiotic resistance via generalized transduction. The sequencing of multipleS. pyogenesgenomes has uncovered a large and diverse population of endogenous prophages that are vectors for toxins and other virulence factors and occupy multiple attachment sites in the bacterial genomes. Some of these sites for integration appear to have the potential to alter the bacterial phenotype through gene disruption. Remarkably, the phage-like chromosomal islands (SpyCI), which share many characteristics with endogenous prophages, have evolved to mediate a growth-dependent mutator phenotype while acting as global transcriptional regulators. The diverse population of prophages appears to share a large pool of genetic modules that promotes novel combinations that may help disseminate virulence factors to different subpopulations ofS. pyogenes. The study of the bacteriophages of this pathogen, both lytic and lysogenic, will continue to be an important endeavor for our understanding of howS. pyogenescontinues to be a significant cause of human disease.
Effect of late-life weight change on dementia incidence: a 10-year cohort study using claim data in Korea
Authors: Park Susan , Jeon Soo-Min , Jung Sun-Young , Hwang Jinseub , Kwon Jin-Won 
Published: May 2019

BackgroundThe association between body mass index (BMI) in late-life and dementia risk remains unclear. We investigated the association between BMI changes over a 2-year period and dementia in an elderly Korean population.MethodsWe examined 67 219 participants aged 60–79 years who underwent BMI measurement in 2002/2003 and 2004/2005 as part of the National Health Insurance Service-Health Screening Cohort. Baseline characteristics including BMI, socioeconomic status and cardiometabolic risk factors were measured at baseline (2002/2003). The difference between BMI at baseline and at the next health screening (2004/2005) was used to calculate the BMI change. After 2 years, the incidence of dementia was monitored for a mean 5.3 years from 2008 to 2013. Multivariate HRs for dementia incidence were estimated on the basis of baseline BMI and its changes after adjusting for various other risk factors. A subgroup analysis was conducted to determine the effects of baseline BMI and BMI changes.ResultsWe demonstrated a significant association between late-life BMI changes and dementia in both sexes (men: >−10% HR=1.26, 95% CI 1.08 to 1.46, >+10% HR=1.25, 95% CI 1.08 to 1.45; women: >−10% HR=1.15, 95% CI 1.03 to 1.29, >+10% HR=1.17, 95% CI 1.05 to 1.31). However, the baseline BMI was not associated with dementia, except in underweight men. After stratification based on the baseline BMI, the BMI increase over 2 years was associated with dementia in men with a BMI of <25 kg/m2and women with a BMI of 18.5–25 kg/m2, but not in the obese subgroup in either sex. However, BMI decrease was associated with dementia in those with a BMI of ≥18.5 kg/m2, but not in the underweight subgroup in either sex.ConclusionBoth weight gain and weight loss may be significant risk factors associated with dementia. Continuous weight control and careful monitoring of weight changes are necessary to prevent dementia development.
Prognostic impact of p16 and PD-L1 expression in patients with oropharyngeal squamous cell carcinoma receiving a definitive treatment
Authors: Sato Fumihiko , Ono Takeharu , Kawahara Akihiko , Kawaguchi Toshihiko , Tanaka Hisaichiro , Shimamatsu Kazuhide , Kakuma Tatsuyuki , Akiba Jun , Umeno Hirohito , Yano Hirohisa 
Published: May 2019

AimsLimited information is available regarding the precise differences in the tumour immune microenvironment (TIM) of patients with human papilloma virus (HPV)-associated and non-HPV-associated oropharyngeal squamous cell carcinoma (OPSCC). Here, we retrospectively reviewed 137 patients with OPSCC treated with a definitive treatment to identify molecular relationships in the TIM.Materials and methodsWe used immunohistochemical analysis to assess p16 status, programmed death ligand 1 (PD-L1) level, and/or CD8+tumour-infiltrating lymphocyte (TIL) density, followed by prognostic evaluation of these immune-related parameters.ResultsMultivariate analyses demonstrated that PD-L1 level on immune cells but not on tumour cells or CD8+TIL density was a significant predictive factor of disease-free survival (DFS) and overall survival (OS). Additionally, subgroup analyses demonstrated that patients positive for p16 and PD-L1 expression on immune cells had favourable DFS and OS, whereas patients negative for p16 and PD-L1 expression on immune cells showed worse DFS and OS.ConclusionsWe demonstrated that PD-L1 expression on immune cells but not tumour cells might represent a useful prognostic biomarker in patients with OPSCC receiving a definitive treatment. We propose that a co-assessment of p16 and PD-L1 expression on immune cells would have greater prognostic potential compared with evaluation of each factor alone in patients with OPSCC.
Prevalence of genital and oropharyngeal chlamydia and gonorrhoea among female sex workers in Melbourne, Australia, 2015–2017: need for oropharyngeal testing
Authors: Chow Eric PF , Williamson Deborah A , Fortune Ria , Bradshaw Catriona S , Chen Marcus Y , Fehler Glenda , De Petra Vesna , Howden Benjamin P , Fairley Christopher K 
Published: May 2019

ObjectiveThe Victorian legislation requires sex workers to have quarterly screening for genital chlamydia and gonorrhoea, but screening for oropharyngeal infection is not mandatory in Victoria, Australia. In 2017, oropharyngeal screening for gonorrhoea and chlamydia was added as part of the routine quarterly screening for sex workers attending the Melbourne Sexual Health Centre (MSHC). The aim of this study was to examine the prevalence of oropharyngeal gonorrhoea and chlamydia among female sex workers (FSW).MethodsWe included females who (1) self-identified as sex workers or were attended MSHC for a sex work certificate and (2) had tested for any STI or HIV, between March 2015 and December 2017. The prevalence of HIV, syphilis, chlamydia and gonorrhoea was calculated.ResultsThere were 8538 FSW consultations among 2780 individuals during the study period. There was a twofold increase in genital gonorrhoea (from 0.5% (95% CI 0.3% to 0.9%) to 1.1% (95% CI 0.8% to 1.5%); ptrend=0.047) and a 1.5-fold increase in genital chlamydia (from 2.2% (95% CI 1.6% to 2.8%) to 3.2% (95% CI 2.6% to 3.8%); ptrend=0.031) during the period. Overall, the prevalence of HIV (0.2% (95% CI 0.1% to 0.3%)) and syphilis (0.1% (95% CI 0.0% to 0.2%)) remained low and did not change over time. In 2017, the prevalence of oropharyngeal gonorrhoea was 2.0% (95% CI 1.6% to 2.6%) and oropharyngeal chlamydia was 2.1% (95% CI 1.6% to 2.7%). Among FSW who were tested positive for gonorrhoea and chlamydia, 55% (n=41) and 34% (n=45) only tested positive in the oropharynx but not genital for gonorrhoea and chlamydia, respectively.ConclusionThe prevalence of oropharyngeal gonorrhoea and chlamydia is similar to the prevalence at genital sites and is often independent of genital infection. It is important to test the oropharynx and genital site for chlamydia and gonorrhoea among FSW.