bluuebunny/crossref_metadata_2025_split huggingface dataset:
NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction
Authors: Kushwaha Sandeep K. , Chauhan Pallavi , Hedlund Katarina , Ahrén Dag 
Published: December 2015

Abstract
Summary: The nucleotide binding site leucine-rich repeats (NBSLRRs) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time-consuming task. Therefore, we have developed a support vector machine-based high-throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from three dicot and two monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays.
Availability and implementation: The NBSPred pipeline is available at http://soilecology.biol.lu.se/nbs/.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: sandeep.kushwaha@biol.lu.se
Human Immune Response Varies by the Degree of Relative Cryptococcal Antigen Shedding
Authors: Boulware David R. , von Hohenberg Maximilian , Rolfes Melissa A. , Bahr Nathan C. , Rhein Joshua , Akampurira Andrew , Williams Darlisha A. , Taseera Kabanda , Schutz Charlotte , McDonald Tami , Muzoora Conrad , Meintjes Graeme , Meya David B. , Nielsen Kirsten , Huppler Hullsiek Katherine ,   For the Cryptococcal Optimal ART Timing (COAT) Trial Team, Musubire Abdu K. , Nabeta Henry W. , Thienemann Friedrich , Rajasingham Radha , Scriven James E. , Mwesigy James , Wagubi Robert , Kajumbula Henry , Ndyetukira Jane Francis , Ahimbisibwe Cynthia , Kugonza Florence , Ndyatunga Liberica , Noeme Busingye , Memela Brian , Sigila Yolisa , Sadiq Alisat , Magwayi Monica , Kwizera Richard , Ninsiima Emily , Najjuka Grace , Strain Anna , Wiesner Darin , Nanteza Catherine , Mushagara Rhina , Hassanally Leya , Namawejje Mariam , Ssennono Mark , Kiragga Agnes , Butler Elissa K. , Bahr Nathan C. 
Published: December 2015

AbstractBackground.  Cerebrospinal fluid (CSF) cryptococcal glucuronoxylomannan antigen (CrAg) titers generally correlate with quantitative fungal culture burden; however, correlation is not precise. Some patients have higher CrAg titers with lower fungal burdens and vice versa. We hypothesized that the relative discordancy between CrAg titer and quantitative culture burden reflects the relative degree of CrAg shedding by Cryptococcus neoformans and is associated with human immune responses.Methods.  One hundred ninety human immunodeficiency virus-infected individuals with cryptococcal meningitis were enrolled in Uganda and South Africa. We compared initial CSF CrAg titers relative to their CSF quantitative cultures to determine low (n = 58), intermediate (n = 68), or high (n = 64) CrAg shedders. We compared cytokines measured by Luminex multiplex assay on cryopreserved CSF and 10-week mortality across shedding groups using linear and logistic regression and distribution of genotypes by multilocus sequence typing.Results.  The relative degree of CrAg shedding was positively associated with increasing CSF levels of the following: interleukin (IL)-6, IL-7, IL-8, and tumor necrosis factor-α (each P &lt; 0.01), which are all secreted by antigen-presenting cells and negatively associated with vascular endothelial growth factor (P = .01). In addition, IL-5, IL-13, granulocyte colony-stimulating factor, and macrophage chemotactic protein were decreased in low-CrAg shedders compared with intermediate shedders (each P ≤ .01). Type 1 T-helper cells (Th1) cytokine responses and 10-week mortality did not differ between the shedding groups. Cryptococcal genotypes were equally distributed across shedding groups.Conclusions.  Discordancy between CrAg shedding and expected shedding based on quantitative fungal burden is associated with detectable immunologic differences in CSF, primarily among secreted cytokines and chemokines produced by antigen-presenting cells and Th2.
Study on the Effects of Individualized Learning Therapy on Cognitive Function and Behavioral and Psychological Symptoms of Dementia in the Institutionalized Older Adults
Authors: Chen Hsiao-Mei , Tsai Li-Jane , Chao Shu-Yuan , Clark Mary Jo 
Published: December 2015

ABSTRACT

Background:
The increasing number of elderly people affected by dementia in Taiwan has made dementia care a crucial issue of concern. This issue is particularly important in terms of the proper management of behavioral symptoms and improvement of the cognitive functions of those affected by this disease.

Purpose:
This study examined the effects of individualized learning therapy on cognition and neuropsychiatric symptoms among elderly people with dementia.

Methods:
A quasi-experimental, pretest–posttest research design was adopted. We recruited elderly people with dementia at the only two institutions for elderly patients with dementia in Central Taiwan. These institutions were assigned randomly as the experimental or control group, with totals of 23 and 21 participants, respectively. The participants in the experimental group received individualized learning therapy for 30 minutes twice weekly for 3 months. The comparison group received usual care only. The cognitive function and neuropsychiatric symptoms of all participants were measured using the Mini-Mental Status Examination (MMSE) before the start of and immediately after the 12-week intervention and the Chinese version of the Neuropsychiatric Inventory (CNPI), which was administered once per week during the intervention. Independent t tests (or Mann–Whitney U tests), chi-square tests (or Fisher’s exact tests), paired t test, and generalized estimating equations were used for data analysis.

Results:
Participants in the experimental group had significantly higher MMSE scores (p < .01) and lower CNPI scores (p < .01) than their comparison group peers after the intervention. Furthermore, the neuropsychiatric symptoms in the experimental group such as hallucinations, bizarre behavior, depression, apathetic expression, irritability, and sleep disorder had significantly improved by the seventh week.

Conclusions/Implications for Practice:
Individualized learning therapy may be an effective approach to improve cognitive function and reduce neuropsychiatric symptoms among older people with dementia. Therefore, future clinical application is warranted.
New crystal form of human ubiquitin in the presence of magnesium
Authors: Camara-Artigas Ana , Plaza-Garrido Marina , Martinez-Rodriguez Sergio , Bacarizo Julio 
Published: December 2015

Ubiquitin is a small globular protein that has a considerable number of lysine residues on its surface. This results in a high surface entropy that precludes the formation of crystal-packing interactions. To date, only a few structures of the native form of ubiquitin have been solved, and most of the crystals that led to these structures were obtained in the presence of different divalent metal cations. In this work, a new crystallographic structure of human ubiquitin solved from crystals grown in the presence of magnesium is presented. The crystals belonged to a triclinic space group, with unit-cell parametersa= 29.96,b = 30.18,c= 41.41 Å, α = 88.52, β = 79.12, γ = 67.37°. The crystal lattice is composed of stacked layers of human ubiquitin molecules with a large hydrophobic interface and a smaller polar interface in which the magnesium ion lies at the junction between adjacent layers in the crystal. The metal ion appears in a hexa-aquo coordination, which is key to facilitating the crystallization of the protein.
The financial impact of a withdrawn ISO 9001 certificate
Authors: Cândido Carlos J.F. , Coelho Luís M.S. , Peixinho Rúben M.T. 
Published: December 2015

Purpose– The purpose of this paper is to assess to what extent the loss of the ISO 9001 certification affects the decertified firms’ financial performance.Design/methodology/approach– Using standard event study methods, this paper matches a sample of 143 Portuguese companies that lost their ISO 9001 certification with similar non-event counterpart firms (according to return-on-assets (ROA) and size) and compares the performance of these two groups of firms using financial data collected from the AMADEUS database.Findings– Results show no statistical significant differences in the financial performance (as measured by ROA, return-on-sales (ROS) and sales growth) between companies that lost their ISO 9001 certification and their matched firms. Although the literature suggests that certification improves firms’ performance and that the benefits of certification may last over long periods of time, this paper’s results suggest that, after decertification, companies do not exhibit over or underperformance in their operationsvis-à-viscomparable firms that do not undergo the same event.Originality/value– As far as the authors are aware, this is the first study assessing the impact of ISO 9001 certificate withdrawal on the decertified firms’ financial performance.
The once and future editorial
Authors: Bawden David 
Published: December 2015

Purpose
– The purpose of this paper is to discuss the changing nature of abstracts in scholarly journals, with particular reference to Journal of Documentation.

Design/methodology/approach
– Selective literature review.

Findings
– The nature of the editorial is changing towards a more stand-alone and substantive article.

Originality/value
– The first discussion of the nature of the editorial in a scholarly information science journal.
Infrastructure and the experience of documents
Authors: Carter Daniel 
Published: December 2015

Purpose– The purpose of this paper is to contribute to understandings of how documents are experienced by looking to work in reception studies for methodological examples. Based on a review of research from literary studies, communication studies and museum studies, it identifies existing approaches and challenges. Specifically, it draws attention to problems cited in relation to small-scale user studies and suggests an alternative approach that focusses on how infrastructures influence experience.Design/methodology/approach– This paper presents data collected from over a year of ethnographic work at a cultural archive and exhibition space and analyses the implications of infrastructural features such as institutional organization, database structures and the organization of physical space for making available certain modes of reception.Findings– This research suggests that infrastructure provides a useful perspective on how experiences of documents are influenced by larger systems.Research limitations/implications– This research was conducted to explore the implications of an alternative research methodology. Based on the ethnographic study presented, it suggests that this approach produces results that warrant further work. However, as it is intended only to be a test case, its scope is limited, and future research following the approach discussed here should more fully engage with specific findings in relation to the experience of documents.Originality/value– This paper presents an alternative approach to studying the experience of documents that responds to limitations in previous work. The research presented suggests that infrastructures can reveal ways that the experience is shared across contexts, shifting discussions from individuals and objects to technical systems, institutions and social structures.
The Twenty‐First‐Century Quest for Feminism and the Global Urban
Authors: Peake Linda 
Published: December 2015

AbstractThe purpose of this essay is to initiate a conversation about the production and analysis of knowledge on women and the urban. Starting with a brief overview of how women have been addressed in the field of urban studies, I turn to their treatment in works by critical urban scholars, revealing how women fall away from urban theories. The dismissal of women from theory construction and the impact on women's lives of the imbrication of the gendered subject into neoliberal discourses about the city adds urgency to a feminist intervention. A feminist analytic requires the promotion of a new kind of global urban studies that takes seriously women's struggles, strategies and everyday desires.
A double‐blind randomised controlled trial on the effect of dehydroepiandrosterone on ovarian reserve markers, ovarian response and number of oocytes in anticipated normal ovarian responders
Authors: Yeung TWY , Chai J , Li RHW , Lee VCY , Ho PC , Ng EHY 
Published: December 2015

ObjectiveTo assess the effect of dehydroepiandrosterone (DHEA) on antral follicle count (AFC), ovarian response to a standard low dose of gonadotrophin stimulation and number of oocytes in anticipated normal responders undergoing in vitro fertilisation (IVF).DesignRandomised, double‐blind, placebo‐controlled study.SettingTertiary reproductive unit.PopulationSeventy‐two subfertile women with AFC of 5–15 scheduled for IVF.MethodsEligible women were randomised into the DHEA group (n = 36), who received DHEA (GNC®, 25 mg three times a day), or the placebo group (n = 36), who received placebo, starting from 12 weeks before the scheduled IVF treatment according to a computer‐generated randomisation list. Monthly assessment of AFC, serum anti‐Mullerian hormone (AMH) and follicle‐stimulating hormone (FSH) levels, ovarian response to a standard dose of gonadotrophin stimulation at week 8 and the number of oocytes obtained were compared.Main outcome measuresThe primary outcome was AFC after 12 weeks of DHEA or placebo.ResultsDHEA for 12 weeks prior to IVF treatment in anticipated normal responders leads to significantly higher serum and follicular DHEA‐S and testosterone relative to placebo. However, no significant differences in AFC, AMH and FSH, ovarian response to standard‐dose ovarian stimulation and IVF cycle outcomes can be detected.ConclusionNo significant differences in AFC, ovarian response to a standard low dose of gonadotrophin stimulation and number of oocytes obtained were detected in anticipated normal responders receiving 12 weeks of DHEA prior to IVF treatment relative to placebo.Tweetable abstractNo difference in ovarian response markers in normal responders receiving 12 weeks of DHEA.
Using occupancy modelling to compare environmental DNA to traditional field methods for regional‐scale monitoring of an endangered aquatic species
Authors: Schmelzle Molly C. , Kinziger Andrew P. 
Published: December 2015

AbstractEnvironmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered and invasive species in comparison with traditional field approaches. Herein, eDNA approaches and traditional seining methods were applied at 29 research locations to compare method‐specific estimates of detection and occupancy probabilities for endangered tidewater goby (Eucyclogobius newberryi). At each location, multiple paired seine hauls and water samples for eDNA analysis were taken, ranging from two to 23 samples per site, depending upon habitat size. Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance. Compared to traditional field sampling, eDNA provided improved occupancy parameter estimates and can be applied to increase management efficiency across a broad spatial range and within a diversity of habitats.
Barbados Spirits Inc.
Authors: Kalesnikoff Douglas K. S. 
Published: December 2015

AbstractThis case focuses on the audit of a subsidiary in Barbados of a Multi‐National Entity (“MNE”), a distiller in Toronto. The MNE is a large and important international client to the accounting firm. The firm provides both tax advisory and audit services to the MNE. The MNE, following advice of the accounting firm, has utilized an offshore related party to structure transactions that avoid taxes in Barbados. These related party transactions are a detriment to the interests of critical users of the financial statements, namely the minority shareholders and the tax authorities of Barbados. The auditor is now faced with evaluating the adequacy of the related party note disclosure and the completeness of the income tax provision. Independence issues of a self‐interest threat (importance of the client) and self‐review threat (evaluating the adequacy of the income tax provision based on tax advice provided by the firm) are explored.
Trichodysplasia spinulosa: a polyomavirus infection specifically targeting follicular keratinocytes in immunocompromised patients
Authors: Rouanet J. , Aubin F. , Gaboriaud P. , Berthon P. , Feltkamp M.C. , Bessenay L. , Touzé A. , Nicol J.T.J. , Franck F. , D'Incan M. 
Published: December 2015

SummaryTrichodysplasia spinulosa (TS) is a rare skin disease, caused by a specific polyomavirus, occurring in immunocompromised patients. The pathophysiological mechanisms of TS are not yet fully understood. By using polymerase chain reaction and skin biopsy immunostaining we report evidence, in a paediatric case, of follicular keratinocytes being the primary target of trichodysplasia spinulosa-associated polyomavirus.
The development of worry throughout childhood: Avon Longitudinal Study of Parents and Children data
Authors: Caes Line , Fisher Emma , Clinch Jacqui , Tobias Jonathan H. , Eccleston Christopher 
Published: December 2015

ObjectivesAnxiety is a normal part of childhood and adolescence; however, longitudinal research investigating the development of worrisome thoughts throughout childhood is lacking. This study investigated mothers’ perspectives on their child's normal development of worry as the cognitive component of anxiety and its impact on child functioning in a longitudinal population‐based cohort.MethodsThe data for this study were extracted from the Avon Longitudinal Study of Parents and Children. Mothers (N = 2,227) reported on their child's worry content, frequency, control, emotional disruption, and interference when their child was 7, 10, and 13 years old using the parent component of the Development and Well‐being Assessment. At age 10 and 13, pubertal status was assessed using children's self‐report of pubic hair developmental progress.ResultsMothers reported a peak of worrisome thoughts at 10. Emotional disruption was highest at 10, and the highest level of interference in daily life was observed at 13, especially for girls. Advanced pubertal status and worry frequency were positively associated for boys at 10 and girls at 13. Advanced puberty at 10 was also associated with overall higher worry frequency and emotional disruption.ConclusionsFindings are discussed within a developmental framework outlining the normal development of worrisome thoughts, associated distress, and interference throughout early adolescence. Increased knowledge of normative worry could be informative to further our understanding of adolescence as a vulnerable period for the development of mental health problems, such as generalized anxiety disorder.
Statement of contribution

What is already known on this subject?

Worrying is a normal part of childhood, making distinguishing between normal and pathological worrying challenging.

Worry content remains consistent between age 4 and 7, but only for boys.

The complexity and elaboration of worrisome thoughts increase from 8 years onwards.

What does this study add?

Worry frequency peaks at 10 and a low ability to control those worries can be observed at this age.

The highest level of interference in performing daily activities due to worries is observed at age 13.

Child sex and pubertal status play a role in understanding how normal worry patterns develop from age 10 onwards.
Frontal Electroencephalogram Asymmetry and Temperament Across Infancy and Early Childhood: An Exploration of Stability and Bidirectional Relations
Authors: Howarth Grace Z. , Fettig Nicole B. , Curby Timothy W. , Bell Martha Ann 
Published: December 2015

The stability of frontal electroencephalogram (EEG) asymmetry, temperamental activity level and fear, as well as bidirectional relations between asymmetry and temperament across the first 4 years of life, were examined in a sample of 183 children. Children participated in annual laboratory visits through 48 months, providing EEG and maternal report of temperament. EEG asymmetry showed moderate stability between 10 and 24 months. Analyses revealed that more left asymmetry predicted later activity level across the first 3 years. Conversely, asymmetry did not predict fear. Rather, fear at 36 months predicted more right asymmetry at 48 months. Results highlight the need for additional longitudinal research of infants and children to increase understanding of bidirectional relations between EEG and temperament in typically developing populations.
Plasma-induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment-naive paediatric inflammatory bowel disease
Authors: Gurram B , Salzman N H , Kaldunski M L , Jia S , Li B U K , Stephens M , Sood M R , Hessner M J 
Published: December 2015

Summary
The inflammatory state associated with Crohn's disease (CD) and ulcerative colitis (UC) remains incompletely defined. To understand more clearly the extracellular milieu associated with inflammatory bowel disease (IBD), we employed a bioassay whereby plasma of treatment naive paediatric IBD patients (n = 22 CD, n = 15 UC) and unrelated healthy controls (uHC, n = 10) were used to induce transcriptional responses in a healthy leucocyte population. After culture, gene expression was measured comprehensively with microarrays and analysed. Relative to uHC, plasma of CD and UC patients induced distinct responses consisting, respectively, of 985 and 895 regulated transcripts [|log2 ratio| ≥ 0·5 (1·4-fold); false discovery rates (FDR) ≤ 0·01]. The CD:uHC and UC:uHC signatures shared a non-random, commonly regulated, intersection of 656 transcripts (χ2 = P &lt; 0·001) and were highly correlative [Pearson's correlation coefficient = 0·96, 95% confidence interval (CI) = 0.96, 0.97]. Despite sharing common genetic susceptibility loci, the IBD signature correlated negatively with that driven by plasma of type 1 diabetes (T1D) patients (Pearson's correlation coefficient = –0·51). Ontological analyses revealed the presence of an immunoregulatory plasma milieu in IBD, as transcripts for cytokines/chemokines, receptors and signalling molecules consistent with immune activation were under-expressed relative to uHC and T1D plasma. Multiplex enzyme-linked immunosorbent assay (ELISA) and receptor blockade studies confirmed transforming growth factor (TGF)-β and interleukin (IL)-10 as contributors to the IBD signature. Analysis of CD patient signatures detected a subset of transcripts associated with responsiveness to 6-mercaptopurine treatment. Through plasma-induced signature analysis, we have defined a unique, partially TGF-β/IL-10-dependent immunoregulatory signature associated with IBD that may prove useful in predicting therapeutic responsiveness.