bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropilin-1 regulates the secondary CD8 T cell response to virus infection
Authors: Hwang Ji Young , Sun Yanbo , Carroll Christopher R. , Usherwood Edward J 
Published: April 2019

AbstractNeuropilin-1 plays important roles in axonal guidance in neurons, and in the growth of new blood vessels. There is also a growing appreciation for roles played by neuropilin-1 in the immune response. This molecule is important for the function of regulatory T cells, however roles in other T cell populations have not been identified. Here we show that neuropilin-1 is expressed during the peak of the antiviral CD8 T cell response during murine gammaherpesvirus infection. Using a conditional knockout model, we deleted Nrp1 either before infection, or after CD8 T cell memory had been established. We found deletion of Nrp1 skewed the acute CD8 T cell response toward a memory precursor-like phenotype, however the ensuing resting memory response was similar regardless of Nrp1 expression. Interestingly Nrp1 deletion had differing effects on the recall response depending on the timing of deletion. When deleted before infection, Nrp1 deficiency inhibited the secondary response. Deletion just prior to re-exposure to virus lead to an enhanced secondary response. Interestingly these effects were observed only in mice infected with a persistent strain of murine gammaherpesvirus, and not a non-persistent mutant strain. These data highlight a multifaceted role for neuropilin-1 in memory CD8 T cell differentiation, dependent upon the stage of the T cell response and characteristics of the infectious agent. Several therapeutic anti-cancer therapies focus on inhibition of Nrp1 to restrict tumor growth, so knowledge of how Nrp1 blockade may affect the CD8 T cell response will provide a better understanding of treatment consequences.ImportanceCD8 T cell responses are critical to control both virus infections and tumors. The ability of these cells to persist for long periods of time can result in lifelong immunity, as relatively small populations of cell can expand rapidly to counter re-exposure to the same insult. Understanding the molecules necessary for this rapid secondary expansion is critical if we are to develop therapies that can provide lifelong protection. This report shows an important and complex role for the molecule neuropilin-1 in the secondary response. Several cancer therapies targeting neuropilin-1 are in development, and this work will lead to better understanding of the effect these therapies could have upon the protective CD8 T cell response.
A novel mutant allele uncouples brassinosteroid-dependent and independent functions of BRI1
Authors: Holzwart Eleonore , Glöckner Nina , Höfte Herman , Harter Klaus , Wolf Sebastian 
Published: April 2019

AbstractPlants depend on an array of cell surface receptors to integrate extracellular signals with developmental programs. One of the best-studied receptors is BRASSINOSTEROID INSENSITIVE 1 (BRI1), which upon binding of its hormone ligands forms a complex with shape-complimentary co-receptors and initiates a signal transduction cascade leading to a wide range of responses. BR biosynthetic and receptor mutants have similar growth defects on the macroscopic level, which had initially led to the assumption of a largely linear signalling pathway. However, recent evidence suggests that BR signalling is interconnected with a number of other pathways through a variety of different mechanisms. We recently described that feedback information from the cell wall is integrated at the level of the receptor complex through interaction with RLP44. Moreover, BRI1 is required for a second function of RLP44, the control of procambial cell fate. Here, we report on a BRI1 mutant, bri1cnu4, which differentially affects canonical BR signalling and RLP44 function in the vasculature. While BR signalling is only mildly impaired, bri1cnu4 mutants show ectopic xylem in the position of procambium. Mechanistically, this is explained by an increased association of RLP44 and the mutated BRI1 protein, which prevents the former from acting in vascular cell fate maintenance. Consistent with this, the mild BR response phenotype of bri1cnu4 is a recessive trait, whereas the RLP44-mediated xylem phenotype is semi-dominant. Our results highlight the complexity of plant plasma membrane receptor function and provide a tool to dissect BR signalling-related roles of BRI1 from its non-canonical functions.One sentence summaryA novel mutant allows to dissect brassinosteroid signalling related and non-canonical functions of the receptor-like kinase BRI1.
How many samples are needed to infer truly clonal mutations from heterogenous tumours?
Authors: Opasic Luka , Zhou Da , Werner Benjamin , Dingli David , Traulsen Arne 
Published: April 2019

AbstractBackgroundModern cancer treatment strategies aim to target tumour specific genetic (or epigenetic) alterations. Treatment response improves if these alterations are clonal, i.e. present in all cancer cells within tumours. However, the identification of truly clonal alterations is impaired by the tremendous intra-tumour genetic heterogeneity and unavoidable sampling biases.MethodsHere, we investigate the underlying causes of these spatial sampling biases and how the distribution and sizes of biopsies in sampling protocols can be optimized to minimize such biases.ResultsWe find that in the ideal case, less than a handful of samples can be enough to infer truly clonal mutations. The frequency of the largest sub-clone at diagnosis is the main factor determining the accuracy of truncal mutation estimation in structured tumours. If the first sub-clone is dominating the tumour, higher spatial dispersion of samples and larger sample size can increase the accuracy of the estimation. In such an improved sampling scheme, fewer samples will enable the detection of truly clonal alterations with the same probability.ConclusionsTaking spatial tumour structure into account will decrease the probability to misclassify a sub-clonal mutation as clonal and promises better informed treatment decisions.
Deciphering interaction fingerprints from protein molecular surfaces
Authors: Gainza P , Sverrisson F , Monti F , Rodolà E , Bronstein MM , Correia BE 
Published: April 2019

AbstractPredicting interactions between proteins and other biomolecules purely based on structure is an unsolved problem in biology. A high-level description of protein structure, the molecular surface, displays patterns of chemical and geometric features thatfingerprinta protein’s modes of interactions with other biomolecules. We hypothesize that proteins performing similar interactions may share common fingerprints, independent of their evolutionary history. Fingerprints may be difficult to grasp by visual analysis but could be learned from large-scale datasets. We presentMaSIF, a conceptual framework based on a new geometric deep learning method to capture fingerprints that are important for specific biomolecular interactions. We showcase MaSIF with three prediction challenges: protein pocket-ligand prediction, protein-protein interaction site prediction, and ultrafast scanning of protein surfaces for prediction of protein-protein complexes. We anticipate that our conceptual framework will lead to improvements in our understanding of protein function and design.
Genome-wide developed microsatellites reveal a weak population differentiation in the hoverflyEupeodes corollae(Diptera: Syrphidae) across China
Authors: Liu Meng-Jia , Wang Xiao-qiang , Ma Ling , Cao Li-Jun , Liu Hong-Ling , Pu De-Qiang , Wei Shu-Jun 
Published: April 2019

AbstractThe hoverfly,Eupeodes corollae,is a worldwide natural enemy of aphids and a plant pollinator. To provide insights into the biology of this species, we examined its population genetic structure by obtaining 1.15-GB random genomic sequences using next-generation sequencing and developing genome-wide microsatellite markers. A total of 79,138 microsatellite loci were initially isolated from the genomic sequences; after strict selection and further testing of 40 primer pairs in eight individuals, 24 polymorphic microsatellites with high amplification rates were developed. These microsatellites were used to examine the population genetic structure of 96 individuals from four field populations collected across southern to northern China. The number of alleles per locus ranged from 5 to 13 with an average of 8.75; the observed and expected heterozygosity varied from 0.235 to 0.768 and from 0.333 to 0.785, respectively. Population genetic structure analysis showed weak genetic differentiation among the four geographical populations ofE. corollae, suggesting a high rate of gene flow reflecting likely widespread migration ofE. corollaein China.
Multiple institutional logics and their impact on accounting in higher education
Authors: Conrath-Hargreaves Annemarie , Wüstemann Sonja 
Published: April 2019

PurposeThe purpose of this paper is to explore how an Higher Education Institution’s (HEI) choice of undergoing a voluntary reorganisation, motivated by its own interest of increasing its autonomy, whilst also having to satisfy the government in order to maintain the level of public funding, impacts on the HEI’s accounting.Design/methodology/approachThe paper draws on the institutional logics perspective to present a single case study of a German HEI that chose to be reorganised from a public into a foundation university. Data were obtained using multiple data collection methods.FindingsThe findings suggest that organisational characteristics, which act as filters for institutional logics, play an important role for HEIs’ ability to increase not only theirde jure, but also theirde factoautonomy through self-motivated, rather than government imposed, reform processes.Research limitations/implicationsThe paper is based on a single case study in a country-specific context, limiting the empirical generalisability of the findings.Originality/valueGermany is not only one of the main nations exporting higher education, but its economy has also been recognised for its stability and development over the last decades. Nevertheless, Germany struggles in its transition to become a knowledge-based economy. Yet, research has so far tended to neglect educational reforms in Continental European countries, such as Germany. By addressing this gap in the literature, this paper is among the first to explore how reform processes shape accounting in German HEIs.
Probability of change orders and the effect on cost and schedule for new public school buildings
Authors: Shrestha Pramen P. , Shrestha Kabindra Kumar , Zeleke Haileab B. 
Published: April 2019

Purpose
Change orders (COs) adversely affect the cost and schedule of projects, specifically during the construction phase. COs of 95 new public school building projects contracted by the Clark County School District (CCSD) of Nevada were analyzed to quantify the cost and schedule growth as well as to determine the effect of COs on cost and schedule growth. The paper aims to discuss these issues.

Design/methodology/approach
The data were collected from CCSD through questionnaire survey. Descriptive statistics and statistical tests were conducted to determine the effect of COs on cost and schedule growth.

Findings
It was found that the average amount of COs as well as cost and schedule overruns were 5.9, 3.0 and 7.4 percent, respectively. Statistical tests showed that the amount of COs had an adverse effect on schedule growth; schedule overruns in projects with less than 4 percent COs were significantly lower than projects with more than 4 percent COs. Cost overruns did not significantly differ in those two types of projects. The primary contribution of this study is that it provides the tools and the framework for school district engineers to determine the probability of the occurrence of COs as well as the optimum percentage of COs for a minimum effect on cost and schedule growth of new public school buildings. Probability curves were also developed to determine the likelihood of the occurrence of COs, cost growth and schedule growth in these projects. These findings could be used by school districts to avoid or reduce COs in future projects, minimizing the effect on cost and schedule growth during the construction phase.

Research limitations/implications
The findings and the probabilities curves developed in this study should be used carefully in other cases. These data were specific to the owner, location and types of buildings and generalizing these findings may have negative consequences.

Practical implications
The practical implications are that this study could provide a tool to school building administrators to determine the probability of having COs as well as cost and schedule overruns and the effects of COs on cost and schedule overruns. To the authors’ best knowledge, no other studies of this type have been conducted previously.

Social implications
The social implication of this study is it will help to efficiently use the tax payers’ money while building new school buildings.

Originality/value
This study has collected the hard data of COs, cost and schedule data of CCSD new school building projects. Therefore, the data are from the projects completed by CCSD. So, the paper is written from the original data received from CCSD.
Implicit occupational gender stereotypes: a research among Turkish university students
Authors: Basfirinci Cigdem , Cilingir Uk Zuhal , Karaoglu Sernur , Onbas Kadriye 
Published: April 2019

PurposeThe purpose of this paper is to reveal implicit occupational gender stereotypes for 12 different occupations in Turkey.Design/methodology/approachUsing a sample of 954 Turkish university students, this study aimed to explore which jobs are implicitly perceived to be masculine and which jobs are implicitly perceived to be feminine. The role of the respondents’ sex, the place where they grew up (metropolitan or rural) and the information level about the occupation (job title or job description) on occupational gender stereotypes were also tested. Gender stereotypes were assessed using a hypothetical scenario method, which provides an opportunity to reveal implicit information processing. Chi Square andt-test were used in hypothesis testing.FindingsConsistent with the circumscription and compromise and the social role theory, as expected, the findings of the current study provided additional support about occupational gender stereotypes showing that job titles are strongly effective vehicles to communicate gender stereotypes for Turkish university students.Originality/valueUsing implicit measures of information processing and offering findings from a completely different cultural background (Turkey) constitutes the original contribution of this work.
Evolution of the social structure of hospitality management literature: 1960-2016
Authors: Koseoglu Mehmet Ali 
Published: April 2019

PurposeThis study aims to address how the social structure of the hospitality management field has evolved from 1960 to 2016.Design/methodology/approachThe informal social structure of the hospitality management literature was analyzed by collecting authorship data from seven hospitality management journals. Co-authorship analyses via network analysis were conducted.FindingsAccording to the findings, throughout the history of hospitality management, international collaboration levels are relatively low. Based on social network analysis, the research community is only loosely connected, and the network of the community does not fit with the small-world network theory. Additional findings indicate that researchers in the hospitality management literature are ranked via degree centrality, closeness centrality and betweenness centrality. Cliques, which contain at least five researchers, and core researchers are identified.Practical implicationsThis study helps both scholars and practitioners improve the informal structure of the field. Scholars must generate strong ties to strengthen cross-fertilization in the field; hence, they collaborate with authors who have strong positions in the field. Specifically, this provides a useful performance analysis. To the extent that institutions and individuals are rewarded for publications, this study demonstrates the performance and connectivity of several key researchers in the field. This finding could be interesting to (post)graduate students. Hospitality managers looking for advisors and consultants could benefit from the findings. Additionally, these are beneficial for journal editors, junior researchers and agencies/institutions.Originality/valueAs one of the first study in the field, this research examines the informal social structure of hospitality management literature in seven journals.
Utilising digital media as enabling technologies for effective correctional rehabilitation
Authors: Chan Joyce P.S. , Yeung Jessie H.Y. , Wong Nicholas C.Q. , Tan Richie C.H. , Musa N. 
Published: April 2019

PurposeThe purpose of this paper is to understand how digital media technologies can enhance offender rehabilitation in correctional institutions.Design/methodology/approachA qualitative approach was adopted for this study involving young prisoners who had been incarcerated for at least six months. In total, 16 participants who fulfilled the criteria of listening to at least 30 of the podcasts were eventually selected for face-to-face interview.FindingsThis study focuses on how the radio podcast impacted the rehabilitation process of the 16 young inmates. From data collected through the interviews, three major themes emerged from the study, namely, reflective thinking, increased motivation to change and structured routines. The participants highlighted how these factors are essential in moving them towards successful rehabilitation upon their release.Research limitations/implicationsA convenient sample was used as there was a lack of a more diverse sample to better represent the prison population in Singapore. The number of participants who took part in the study were limited and only young inmates. Thus, the outcome of the research may not be directly applicable to the general prison population. Another issue is that media has short-lived effects and does not encourage persistent learning, it would be prudent to explore other options that can complement the radio podcasts.Originality/valueThe study indicated that the use of digital media technology can effectively aid the rehabilitation of offenders in Singapore. It enhanced work efficiency since fewer resources were required as inmates can have podcast access within their cells. The content of the podcasts complements the overall framework of rehabilitation for young inmates when they are serving their sentences in the institutions.
All‐ceramic single crowns supported by zirconia implants: 5‐year results of a prospective multicenter study
Authors: Spies Benedikt C. , Balmer Marc , Jung Ronald E. , Sailer Irena , Vach Kirstin , Kohal Ralf‐Joachim 
Published: April 2019

AbstractObjectivesTo assess survival/success rates and patient‐reported outcome of zirconia‐based posterior single crowns (SCs) supported by zirconia implants in a prospective two‐center study after five years of observation.Material and methodsForty‐five patients were restored with 45 zirconia implant‐supported posterior SCs composed of zirconia frameworks hand‐layered with a leucite‐reinforced feldspathic ceramic. Survival rates of SCs were assessed and technical success was evaluated according to modified United States Public Health Care (USPHS) criteria. Furthermore, patient‐reported outcome measures (PROMs) were assessed by applying visual analog scales (VAS). Wilcoxon matched‐pairs signed‐rank test, mixed‐effects ordered logistic regression, and linear mixed models were used to evaluate time effects on response variables.ResultsForty patients were available after a mean observation period of 61.0 ± 1.4 months. One SC had to be replaced, resulting in a Kaplan–Meier (KM) survival estimate for the SCs of 97.5 ± 2.47%. Since nine reconstructions showed at least in one category a major deviation from the ideal (five major chippings, four with increased occlusal roughness, one significant crevice, and one pronounced over‐contouring), the KM success estimate was 79.3 ± 5.8%. Incidence of chipping (n = 19) and occlusal roughness (n = 35) was frequent (p < 0.001). All PROMs at prosthetic delivery except for speech (p = 0.139) showed significantly improved VAS scores (81%–94%; p < 0.001) compared to pre‐treatment evaluations. Thereafter, no decrease in satisfaction could be observed until the 5‐year follow‐up (93%–97%).ConclusionVeneered zirconia‐based SCs supported by zirconia implants showed high survival rates and highly satisfied patients' needs. However, significant incidence of technical complications is compromising the clinical long‐term outcome for this indication.
Pleistocene extinctions as drivers of biogeographical patterns on the easternmost Canary Islands
Authors: García‐Verdugo Carlos , Caujapé‐Castells Juli , Illera Juan Carlos , Mairal Mario , Patiño Jairo , Reyes‐Betancort Alfredo , Scholz Stephan 
Published: April 2019

AbstractSubtropical islands are often viewed as refuges where Quaternary climatic shifts driving global episodes of extinction were buffered. Island biodiversity, however, may have been impacted by climatic fluctuations at local scales, particularly in spatially heterogeneous island systems. In this study, we generated a conceptual framework for predicting the potential impact of Pleistocene extinctions on the biogeographical pattern of the Canarian spermatophyte flora, with a focus on the easternmost Canarian islands (ECI). Then, we performed an exhaustive bibliographic revision (270 studies) to examine whether taxonomic, phylogenetic and phylogeographical data support our predictions. Although molecular information is limited for many lineages, the available data suggest that the majority of extant ECI plant taxa may be the result of relatively recent (<1 Ma) dispersal from surrounding insular and mainland areas. Different lines of evidence are compatible with the idea of a Pleistocene period of frequent lineage extirpation on ECI. Extinction may thus have provided new ecological opportunities for recent (re)colonization, with some cases of recent establishment mediated by facilitation. Considering background extinction on ECI, we describe five general patterns of colonization for Canarian plant lineages. In addition to factors related to island ontogeny and long‐distance dispersal, we suggest that Pleistocene extinctions may have significantly contributed to extant biogeographical patterns in the Canarian archipelago, such as the biased distribution ranges of island plants and the low endemic richness on ECI. This new scenario provides testable hypotheses for future studies dealing with the phylogeography, taxonomy and conservation of terrestrial biodiversity on the Canarian islands, and possibly, on other near‐shore islands.