bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance
Authors: Sweeny Amy R , Lemon Hannah E , Ibrahim Anan , Watt Kathryn A. , Wilson Kenneth , Childs Dylan Z , Nussey Daniel H , Free Andrew , McNally Luke 
Published: November 2020

AbstractNext-generation sequencing (NGS) and meta-barcoding approaches have revolutionized understanding of within-host communities, such as the gut microbiome, in humans and laboratory animals. The application of such approaches in wild animal populations is growing, but there is a disconnect between the widely-applied generalised linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology which is typically applied to meta-barcoding data.Here, we describe and illustrate a novel GLMM-based approach for analysing the taxon-specific sequence read counts derived from standard meta-barcoding data. This approach allows us to decompose the contribution of different drivers of variation in community structure (e.g. year, season, individual host), via interaction terms in the random effects structure of the model. We also show how these models can be used to determine the degree to which specific taxa or taxonomic groups are responsible for variance attributed to different drivers.To illustrate this approach, we applied it to two cross-sectional meta-barcoding data sets from the Soay Sheep population of St. Kilda. The GLMM approach yielded results that were in agreement with more classical approaches from community ecology, showing that variation the gut microbiota community in these sheep was better explained by age group than by season. We were able to quantify the contributions of different sources of variation to community structure, and also to drill down into the model predictions to show that the age effects we observed were principally due to increases in taxa of the phyla Bacteroidetes and declines in taxa of the phyla Firmicutes.Our proposed models offer a powerful new approach to understanding the drivers of variation in estimates of community structure derived from meta-barcoding data. We discuss how our approach could be readily adapted to allow researchers to estimate that contribution of host genotype, environment, and microbial/parasite phylogeny to observed community structure, and thus provide a powerful means to answer emerging questions surrounding the ecological and evolutionary roles of within-host communities.
Drosophilalarval light avoidance is negatively regulated by temperature through two pairs of central brain neurons
Authors: Wang Jie , Zhao Weiqiao , Zhao Qianhui , Zhou Jinrun , Li Xinhang , He Yinhui , Gong Zhefeng 
Published: November 2020

AbstractAnimal’s innate avoidance behavior is crucial for its survival. It subjects to modulation by environmental conditions in addition to the commanding sensorimotor transformation pathway. Although much has been known about the commanding neural basis, relatively less is known about how innate avoidance behavior is shaped by external conditions. Here in this paper, we report thatDrosophilalarvae showed stronger light avoidance at lower temperatures than at higher temperatures. Such negative regulation of light avoidance by temperature was abolished by blocking two pairs of central brain neurons, ACLPR60F09neurons, that were responsive to both light and temperature change, including cooling and warming. ACLPR60F09neurons could be excited bypdf-LaN neurons in the visual pathway. On the downstream side, they could inhibit the CLPNR82B09neurons that command light induced reorientation behavior. Compared with at warm temperature, ACLPR60F09neurons’ response to light was decreased at cool temperature so that the inhibition on CLPNR82B09neurons was relieved and the light induced avoidance was enhanced. Our result proposed a neural mechanism underlying cross-modal modulation of animal innate avoidance behavior.
Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Authors: Dhaka Bhavya , Sabarinathan Radhakrishnan 
Published: November 2020

AbstractMutations in TP53 not only affect its tumour suppressor activity but also exerts oncogenic gain-of-function activity. While the genome-wide mutant p53 binding sites have been identified in cancer cell lines, the chromatin accessibility landscape driven by mutant p53 in primary tumours is unknown. Here, we leveraged the chromatin accessibility data of primary tumours from TCGA to identify differentially accessible regions in mutant p53 tumours compared to wild p53 tumours, especially in breast and colon cancers. We found 1587 lost and 984 gained accessible regions in breast, and 1143 lost and 640 gained regions in colon. However, less than half of those regions in both cancer types contain sequence motifs for wild-type or mutant p53 binding. Whereas, the remaining showed enrichment for master transcriptional regulators, such as FOX-Family TFs and NF-kB in lost and SMAD and KLF TFs in gained regions of breast. In colon, ATF3 and FOS/JUN TFs were enriched in lost, and CDX family TFs and HNF4A in gained regions. By integrating the gene expression data, we identified known and novel target genes regulated by the mutant p53. Together, these results suggest the tissue- and tumour-type specific role of mutant p53 in regulating chromatin structure and gene expression.
BERTMHC: Improves MHC-peptide class II interaction prediction with transformer and multiple instance learning
Authors: Cheng Jun , Bendjama Kaïdre , Rittner Karola , Malone Brandon 
Published: November 2020

AbstractMotivationIncreasingly comprehensive characterisation of cancer associated genetic alteration has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely binding and presentation of peptides by MHC alleles is an important step towards such therapies. Recent data suggest that presentation of both class I and II epitopes is critical for the induction of a sustained effective immune response. However, the prediction performance for MHC class II has been limited compared to class I.ResultsWe present a transformer neural network model which leverages on self-supervised pretraining from a large corpus of protein sequences. We also propose a multiple instance learning (MIL) framework to deconvolve mass spectrometry data where multiple potential MHC alleles may have presented each peptide. We show that pretraining boosted the performance for these tasks. Combining pretraining and the novel MIL approach, our model outperforms state-of-the-art models for both binding and mass spectrometry presentation predictions.AvailabilityOur model is available athttps://github.com/s6juncheng/BERTMHCContactjun.cheng@neclab.eu,brandon.malone@neclab.eu
Examining the factors influencing information poverty in western China
Authors: Mou Xiaobo , Xu Fang 
Published: November 2020

Purpose
The purpose of this study is to explore the factors impacting information poverty in western China and investigate to what extent these determinants contribute to information poverty in these areas.

Design/methodology/approach
Structural equation modeling (SEM) technique was used to analyze 232 valid responses collected from a survey to examine the research model and hypotheses in this study.

Findings
The results indicate that information literacy, information supply and information and communication technologies (ICTs) positively and significantly affect information poverty, while social prejudice and information orientation had no significant effects on information poverty.

Practical implications
Public libraries, government departments and other institutions should pay attention to the significant impact of information literacy, information supply and ICTs on information poverty and formulate corresponding systems and policies to alleviate or reduce information poverty.

Originality/values
In the past, few studies have focused on information poverty in western China and most of the existing research on information poverty adopts qualitative research methods, such as interview, systematic literature review and so on, while quantitative research is rare. In addition, the focus of these research studies was on one or two aspects, and a few of them can systematically study the influencing factors of information poverty. Inspired by the theories of information literacy, social prejudice and information poverty, this study comprehensively used a questionnaire survey and SEM to investigate the influences of information literacy, social prejudice, information supply, information orientation and ICTs on information poverty.
Joint university-industry laboratories through the lens of proximity dimensions: moving beyond geographical proximity
Authors: Mahdad Maral , Minh Thai Thi , Bogers Marcel L.A.M. , Piccaluga Andrea 
Published: November 2020

Purpose
There is little known about investigating the importance of all proximity dimensions simultaneously as a result of geographical proximity on university-industry collaborative innovation. This paper aims to answer the question of how geographically proximate university and industry influence cognitive, social, organizational, institutional and cultural proximity within university-industry joint laboratories and finally, what is the outcome of these interplays on collaborative innovation.

Design/methodology/approach
The study uses an exploratory multiple-case study approach. The results are derived from 53 in-depth, semistructured interviews with laboratory directors and representatives from both the company and the university within 8 joint laboratories of Telecom Italia (TIM). The data collection was carried out in 2014 and 2015. The analysis follows a multi-grounded theory approach and relies on a mix of deductive and inductive reasoning with the final goal of theoretical elaboration.

Findings
This study finds the role of social and cultural proximity at the individual level as a result of geographical proximity as an enabler of collaborative innovation by triggering mutual learning, trust formation and frequent interactions. Cognitive proximity at the interface level could systematically influence collaborative innovation, while organizational and institutional proximity has marginal roles in facilitating collaborative innovation. The qualitative analysis offers a conceptual framework for proximity dimensions and collaborative innovation within university-industry joint laboratories.

Practical implications
The framework not only advances state-of-the-art university-industry collaboration and proximity dimension but also offers guidance for managers in designing collaborative innovation settings between university and industry.

Originality/value
With this study, the paper advances the understanding beyond solely the relationship between proximity and collaboration and shed light on the interplay between geographical proximity and other proximity dimensions in this context, which has received limited scholarly attention.
The effects of service quality and perceived price on revisit intention of patients: the Malaysian context
Authors: Lai Kim Piew , Yee Yen Yuen , Siong Choy Chong 
Published: November 2020

Purpose
This paper aims to investigate the effects of service quality and perceived price (monetary and behavioural price) on the revisit intention of patients to hospitals, as well as the mediating role of perceived price on the relationship between service quality and revisit intention.

Design/methodology/approach
This paper distributes questionnaires to outpatients in three major cities in Malaysia, namely, Penang, Melaka and Johor. Patients who were in the foyer, dispensary area and waiting area were intercepted where their responses were sought. The responses obtained from 400 patients were analysed using the structural equation modelling technique. Besides analysing the path coefficients, this study has examined the common method variance, bias and indirect effects of the relationships.

Findings
The results suggest that patients pay more attention to certain values in their search for the best health-care service and subsequently move on to new values. Pricing is an effective strategy to promote favourable behavioural intentions amongst patients. Better service quality is reflected in the reasonableness of monetary costs incurred by patients in acquiring health-care services. Patients who received poor services will be more likely to compare such services to the medical costs incurred to ascertain the worthiness of the amount paid. In addition, service quality also influences how patients perceive spending their time and efforts (waiting for nurses and physicians, as well as queueing in hospitals) as worthy and vice-versa. Their revisit intention will also be affected by the extent of which they invest their time, energy and efforts to search for relevant information.

Practical implications
The hospitals which desire to charge additional fees should enhance their service quality to reflect price equity. This is imperative in view of the pricing structure which can be relatively complex in subsequent follow-up treatments that may affect the decision of patients on the sources of health-care services.

Originality/value
Given the inevitable increase in medical fees, the perceived price can be a key determinant to the overall judgement patients had in terms of the health-care services received and the time and efforts sacrificed. However, the importance of monetary price and the behavioural price is still relatively unstudied, particularly their influence on revisit intention in the health-care setting.
In or out? – the CFTC explains when virtual currencies come within its jurisdiction
Authors: Nathan Daniel , Mathews Nikiforos 
Published: November 2020

Purpose
To summarize and explain the U.S. Commodity Futures Trading Commission’s (CFTC’s) guidance regarding whether cryptocurrency is subject to CFTC jurisdiction.

Design/methodology/approach
The article reviews the CFTC’s March 24, 2020 final interpretive guidance, summarizes the history of the agency’s jurisdiction over leveraged, margined or financed retail transactions, and relates it to the CFTC’s guidance and judicial decisions regarding cryptocurrency.

Findings
We found that the CFTC, in carrying out its leadership role related to developments in the fintech industry, had provided clarity about its jurisdiction over cryptocurrency. The CFTC defines virtual currency as a “commodity,” even if intangible, and finds that many transactions in virtual currency satisfy the exception to the CFTC’s jurisdiction over leveraged retail commodity transactions because “delivery” can be said to occur within 28 days.

Originality/value
The article provides a useful summary of an important pronouncement from the CFTC in a manner that is readily understandable and relatable to industry participants and legal practitioners in this field.
China’s new fund custodian rules
Authors: Yang Melody (Fan) 
Published: November 2020

Purpose
To explain the key amendments to China’s rules governing fund custody business and highlight the implications for private fund managers.

Design/methodology/approach
The article analyses, from the perspective of private fund managers, the key amendments to the rules governing fund the custody business in China in terms of custody of fund assets, the fund settlement and clearing process, valuation, disclosure and reports, investment supervision, review of distributions and governance.

Findings
The revised rules governing the fund custody business allow private fund managers to use their global custodian in China locally and leave room for managers and custodians to agree on their responsibilities and risk allocation in the fund contract.

Originality/value
The article offers practical guidance on how private fund managers may contractually allocate responsibilities and risks between themselves and fund custodians in the fund contract.
Managing conflicting objectives of social enterprises
Authors: Eiselein Philippe , Dentchev Nikolay A. 
Published: November 2020

Purpose
Most strategies for managing conflicts between social and commercial objectives of social enterprises are discussed either at the individual or at the team level of analysis. This paper aims to argue in favor of taking into account both levels of analysis at the same time. It furthermore aims to unravel how management strategies at the individual and the team level reinforce one another.

Design/methodology/approach
This study adopts the theoretical lenses of personal values (at the individual level of analysis) and stewardship (at the team level). The authors have conducted 23 semi-structured interviews across three Belgian social enterprises. Primary data collection was complemented with secondary data of 12 annual reports and 314 newspaper articles. The variety of cases and the richness of primary and secondary data proved useful to elaborate on the mechanisms of managing conflicting objectives.

Findings
This paper highlights four bridging mechanisms that facilitate the mitigation of conflict between social and commercial objectives, i.e. fit of values, agile structure, partnerships and communications. It also shows how these mechanisms reinforce each other at the individual and team levels of analysis and thus form an iterative process for managing the conflicting objectives of social entrepreneurs.

Originality/value
This paper contributes by bringing the level of analysis on managing conflicting objectives at the intersection of the individual and team performance. It argues that social entrepreneurs should target both individuals and teams at the same time, to manage effectively conflicting objectives. The four mechanisms create an alignment and reflection iterative process for managing conflicting objectives.
The relationship between corporate identity and university loyalty: The moderating effect of brand identification in managing an institutional crisis
Authors: Cachón‐Rodríguez Gabriel , Prado‐Román Camilo , Blanco‐González Alicia 
Published: November 2020

AbstractThe objective of this paper is to analyse the relationship between corporate identity and loyalty in a public institution of higher education in an institutional crisis context. Moreover, the aim is to study the possible moderating effect that brand identification can have on this relationship. The information required to conduct the empirical analysis was obtained from an online survey. Data processing was carried out using the PLS‐SEM technique. The results obtained show that in an institutional crisis context, corporate identity influences university loyalty positively and significantly. However, it is detected that brand identification moderates the relationship between corporate identity and loyalty positively and significantly in an institutional crisis situation. In addition, we also observe that this moderating effect is greater in students than in graduates. It is considered a useful contribution, as it is one of the first studies in which the proposed relationships are analysed in an institutional crisis context. In addition, there is a concern about investigating the possible existence of the moderating role exerted by brand identification and if there are significant differences between students and graduates in this moderating effect. Significant practical implications arise from the results of this work, which can be particularly useful for managers of the type of organizations analysed.
Multipartite symbioses in fungus‐growing termites (Blattodea: Termitidae, Macrotermitinae) for the degradation of lignocellulose
Authors: Ahmad Farhan , Yang Gui‐Ying , Liang Shi‐You , Zhou Qi‐Huan , Gaal Hassan Ahmed , Mo Jian‐Chu 
Published: November 2020

AbstractFungus‐growing termites are among the most successful herbivorous animals and improve crop productivity and soil fertility. A range of symbiotic organisms can be found inside their nests. However, interactions of termites with these symbionts are poorly understood. This review provides detailed information on the role of multipartite symbioses (between termitophiles, termites, fungi, and bacteria) in fungus‐growing termites for lignocellulose degradation. The specific functions of each component in the symbiotic system are also discussed. Based on previous studies, we argue that the enzymatic contribution from the host, fungus, and bacteria greatly facilitates the decomposition of complex polysaccharide plant materials. The host–termitophile interaction protects the termite nest from natural enemies and maintains the stability of the microenvironment inside the colony.
Cingulate Cortex Structural Alterations in Substance Use Disorder Psychiatric Inpatients
Authors: Oh Hyuntaek , Gosnell Savannah , Nguyen Tien , Tran Tiffany , Kosten Thomas R. , Salas Ramiro 
Published: November 2020

Background and ObjectivesSubstance use disorder (SUD) includes maladaptive patterns of substance use despite negative consequences. Previous structural neuroimaging studies showed some structural alterations in SUD, but it remains unknown whether these alterations are specifically associated with SUD or common comorbidities. This study attempts to validate the findings of structural differences between SUD, healthy controls (HC), and psychiatric controls (PC).MethodsWe used HC (N = 86) matched for demographics, and PC (N = 86) matched for demographics and psychiatric diagnoses to a group of SUD patients (N = 86). We assessed the group differences of subcortical volumes, cortical volumes, thickness, and surface areas between SUD and HC. We then analyzed the group differences between SUD and PC within regions showing differences between SUD and HC.ResultsSUD had smaller left nucleus accumbens, right thalamus, right hippocampus, left caudal anterior cingulate cortex (ACC) volume, and larger right caudal ACC volume, and right caudal ACC, right caudal middle frontal gyrus (MFG), and right posterior cingulate cortex (PCC) surface than HC. Increased right caudal ACC volume and right PCC surface in SUD were the only findings when compared with PC. Several areas showed thickness alterations between SUD and HC, but none survived multiple comparisons vs PC.Discussion and ConclusionsOur findings suggest that cingulate structures may be altered in SUD compared with both HC and PC.Scientific SignificanceThese results are among the first to indicate that some structural alterations may be SUD‐specific, and highlight a cautionary note about using HC in psychiatric biomarker research. (Am J Addict 2021;30:72–79)
Fixing a Swamp of Cobras: The Clash between Capital and Water in Shaping Urban Vulnerabilities
Authors: Friend Richard , Hutanuwatr Khanin 
Published: November 2020

AbstractThis paper addresses how capital can refashion landscapes and patterns of risk and vulnerability. Drawing on the emblematic case of the conversion of Thailand’s Cobra Swamp into Suvarnabhumi International Airport we argue that there is a fundamental clash between the internal logic of capital accumulation and the ecology of water that occurs in places in which land is under water for much of the year. Counterintuitively investment in public infrastructure such as airports targets locations that are exposed to flood risks. While the literature on capital fixes tends to treat “land” writ large, this paper adds a dimension that has been overlooked in the theoretical work, by highlighting the significance of the ecology of the land in which such fixes occur as a means of understanding patterns of investment, land use change and vulnerability. Our analysis draws on three separate but related concepts of capital “fixes”—spatial, technological and high/low road fixes. We argue the importance of recognising the specific ecological characteristics of land that capital “fixes”. This perspective has global significance in providing critical insight into the ways in which capital creates and accommodates the kinds of vulnerabilities and risks associated with climate change.