bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular cloning, characterization and expression of immunoglobulin D on pathogen challenge and pathogen associated molecular patterns stimulation in freshwater carp, Catla catla
Authors: Banerjee Rajanya , Patel Bhakti , Basu Madhubanti , Lenka Saswati S. , Paicha Mahismita , Samanta Mrinal , Das Surajit 
Published: September 2017

ABSTRACTThe primordial immunoglobulin class, IgD, was the first non‐IgM isotype discovered in teleosts. The crucial roles of IgM and IgZ in imparting systemic and mucosal immunity, respectively, in various fish species have been widely established. However, the putative function of a unique IgD isotype during pathogenic invasions has not been well explored. The present study reports the existence of an IgD ortholog in freshwater carp, Catla catla, and further evaluates its differential expression profile in response to bacterial, parasitic and viral antigenic exposure and pathogen associated molecular patterns (PAMPs) stimulation. The IgD of C. catla (CcIgD) cDNA sequence was found to encode 226 amino acids and confirmed homology with heavy chain delta region of Cyprinidae family members. Phylogenetic analysis of CcIgD exhibited greatest similarity with Ctenopharyngodon idella. qRT‐PCR analysis revealed significant upregulation (P < 0.001) of IgD gene expression in kidney with respect to other tissues at 24 hr post‐Aeromonas hydrophila challenge. CcIgD gene expression in skin was enhanced following Streptococcus uberis infection and in blood following Argulus infection and inactivated rhabdoviral antigen stimulation. Further, the treatment of bacterial and viral products (PAMPs) also triggered significant (P < 0.05) increases in CcIgD mRNA expression in kidney. These findings indicate the functional importance of teleost IgD in orchestrating tissue specific neutralization of antigens on stimulation with different pathogens and PAMPs.
The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database
Authors: Maitner Brian S. , Boyle Brad , Casler Nathan , Condit Rick , Donoghue John , Durán Sandra M. , Guaderrama Daniel , Hinchliff Cody E. , Jørgensen Peter M. , Kraft Nathan J.B. , McGill Brian , Merow Cory , Morueta‐Holme Naia , Peet Robert K. , Sandel Brody , Schildhauer Mark , Smith Stephen A. , Svenning Jens‐Christian , Thiers Barbara , Violle Cyrille , Wiser Susan , Enquist Brian J. 
Published: September 2017

Abstract

There is an urgent need for large‐scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling human‐biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.

The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and co‐occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an r package that provides easy access to these data.

The bien r package allows users to access the multiple types of data in the BIEN database. Functions in this package query the BIEN database by turning user inputs into optimised PostgreSQL functions. Function names follow a convention designed to make it easy to understand what each function does. We have also developed a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the bien r package.

The development of the BIEN database represents a significant achievement in biological data integration, cleaning and standardization. Likewise, the bien r package represents an important tool for open science that makes the BIEN database freely and easily accessible to everyone.
INCLUSIVE GOVERNANCE IN SOCIAL ENTERPRISES IN THE NETHERLANDS – A CASE STUDY
Authors: COLENBRANDER Aalt , ARGYROU Aikaterini , LAMBOOY Tineke , BLOMME Robert J. 
Published: September 2017

ABSTRACTAn element that policymakers and academics often believe to be constitutive in the governance of a social enterprise is the use of inclusive and responsible decision‐making processes. This entails the involvement of various categories of stakeholders. In this paper, a case study is used to explore how a work integration social enterprise based in the Netherlands, AutiTalent BV, has organized its governance. The Netherlands has not developed legislation specifically dealing with social enterprises, in contrast to many other EU Member States (16 out of 28), and it does not require, although it allows for, the establishment of inclusive governance. By examining how (national Dutch) law affects the governance of a work‐integration‐oriented social enterprise, the authors aim to contribute to emerging theory on participatory and inclusive governance of social enterprises – as a legal concept but also as an organizational concept – shaped by (tailor‐made and/or ordinary) law. The case study reveals that the investigated work integration social enterprise has not set up formal inclusive governance, suggesting that a social enterprise may not be stimulated by legislation which allows but not requires the participation of stakeholders in decision making. At the same time, informal direct communication channels exist between the people who influence the decision‐making processes and people from various stakeholder categories.
An Efficient Hybrid Incompressible SPH Solver with Interface Handling for Boundary Conditions
Authors: Takahashi Tetsuya , Dobashi Yoshinori , Nishita Tomoyuki , Lin Ming C. 
Published: September 2017

AbstractWe propose a hybrid smoothed particle hydrodynamics solver for efficientlysimulating incompressible fluids using an interface handling method for boundary conditions in the pressure Poisson equation. We blend particle density computed with one smooth and one spiky kernel to improve the robustness against both fluid–fluid and fluid–solid collisions. To further improve the robustness and efficiency, we present a new interface handling method consisting of two components: free surface handling for Dirichlet boundary conditions and solid boundary handling for Neumann boundary conditions. Our free surface handling appropriately determines particles for Dirichlet boundary conditions using Jacobi‐based pressure prediction while our solid boundary handling introduces a new term to ensure the solvability of the linear system. We demonstrate that our method outperforms the state‐of‐the‐art particle‐based fluid solvers.
Parent‐reported indicators for detecting feeding and swallowing difficulties and undernutrition in preschool‐aged children with cerebral palsy
Authors: Benfer Katherine A , Weir Kelly A , Ware Robert S , Davies Peter S W , Arvedson Joan , Boyd Roslyn N , Bell Kristie L 
Published: September 2017

AimTo determine the most accurate parent‐reported indicators for detecting (1) feeding/swallowing difficulties and (2) undernutrition in preschool‐aged children with cerebral palsy (CP).MethodThis was a longitudinal, population‐based study, involving 179 children with CP, aged 18 to 60 months (mean 34.1mo [SD 11.9] at entry, 111 males, 68 females [Gross Motor Function Classification System level I, 84; II, 23; III, 28; IV, 18; V, 26], 423 data points). Feeding/swallowing difficulties were determined by the Dysphagia Disorders Survey and 16 signs suggestive of pharyngeal phase impairment. Undernutrition was indicated by height–weight and skinfold composite z‐scores less than −2. Primary parent‐reported indicators included mealtime duration, mealtime stress, concern about growth, and respiratory problems. Other indicators were derived from a parent feeding questionnaire, including ‘significant difficulty eating and drinking’. Data were analysed using multilevel mixed‐effects regression and diagnostic statistics.ResultsPrimary parent‐reported indicators associated with feeding/swallowing were ‘moderate–severe parent stress’ (odds ratio [OR]=3.2 [95% confidence interval {CI} 1.3–7.8]; p<0.01), ‘moderate–severe concern regarding growth’ (OR=4.5 [95% CI 1.7–11.9]; p<0.01), and ‘any respiratory condition’ (OR=1.8 [95% CI 1.4–5.8]; p<0.01). The indicator associated with undernutrition was ‘moderate–severe concern regarding growth’ (height–weight OR=13.5 [95% CI 3.0–61.3]; p<0.01; skinfold OR=19.1 [95% CI 3.7–98.9]; p<0.01). ‘Significant difficulty eating and drinking’ was most sensitive/specific for feeding outcome (sensitivity=58.6%, specificity=100.0%), and ‘parent concern regarding growth’ for undernutrition (sensitivity=77.8%, specificity=77.0%).InterpretationParent‐reported indicators are feasible for detecting feeding and swallowing difficulties and undernutrition in children with CP, but need formal validation.What this paper adds

Parent‐reported indicators can detect feeding/swallowing difficulties and undernutrition in children with cerebral palsy.

Most accurate screening questions were 0–10 scales for ‘difficulty eating’ and ‘difficulty drinking’.

Supplementation of these scales with additional indicators would improve detection.
Ecological and landscape effects on genetic distance in an assemblage of headwater fishes
Authors: Schmidt Bjorn V. , Schaefer Jacob 
Published: September 2017

AbstractEnvironmental divergence along hierarchically structured longitudinal gradients may constitute barriers to gene flow in river networks for headwater specialised species. While known, this phenomenon has not been well studied, especially with regard to degree of headwater specialisation. We examined six headwater species that differ in habitat specialisation to assess whether patterns of differentiation vary according to geographic or environmental distance. We also identified regional environmental or anthropogenically induced fragmentation effects by comparing within‐drainage patterns of genetic distance across replicate watersheds. We used a comparative modelling framework to determine whether isolation by distance or isolation by resistance of large river habitats was a better predictor of genetic distance across species. The influence of reservoir presence and regional network characteristics that may influence the hydrology and size of large river habitats were also assessed. Resistance effects from large rivers were closely related to headwater specialisation, with increased specialisation leading to increased resistance and loss of drainagewide population connectivity. These results affirm that dendritic networks naturally fragment headwater specialised species. Further isolation from anthropogenic fragmentation was detected in two of the six drainages, indicating interactions with system‐specific conditions. Landscape variables related to the hydrology of large rivers also affected genetic distance in predicted ways, supporting the importance of large rivers in genetically structuring headwater species in drainage networks.
Towards nuclear geography: Zones, bodies, and communities
Authors: Alexis‐Martin Becky , Davies Thom 
Published: September 2017

AbstractSince the discovery of radioactivity in 1895, ionising radiation has become an increasingly prominent part of modern life. Here, we explore the diverse modes of interaction that occur between bodies and nuclear technology and point towards the scope for further research on nuclear geographies. We bring together different strands of this nascent discipline and, by doing so, highlight how nuclear technology interacts across a spectrum of geographic scales, communities, and bodies. Although nuclear geographies can be sensational and exceptionalising, such as the experiences of nuclear accident survivors and the creation of “exclusion zones,” they can also be mundane, everyday and largely unrecognised, such as the production of nuclear energy and the life‐giving nature of radioactive medicine. To frame our discussion, we take three cuts at nuclear geography, highlighting the importance of zones, bodies, and communities. By discussing this gamut of spaces and societies created through ionising radiation, we open the way for more research into the cross section of benefits, challenges, and social phenomena that arise, as we coexist with nuclear technology.
Economic geographies of value revisited
Authors: Pani Erica 
Published: September 2017

AbstractAs the debate continues in economic geography regarding the theoretical, methodological, and empirical need to abstract out from the complexity of real‐world economic activity versus the need to examine the multiplicity and specificity of actually existing economies, this article revisits an object the ontology of which sits at the heart of such debates, that is, value. For a sub‐discipline that has long‐battled to be taken seriously as a social “science,” the subject of value in economic geographies has become a battle royal between those who are willing to essentialise and those who are not, with many scholars justify their opposing positions on the grounds of theoretical salience and/or methodological rigour. In this article, I position value as the exemplar of these arguments, contrasting Roger Lee's (, ) relational understanding of value to the essentialising tendencies of Marx and neoclassicism. The paper posits that far from the openness of a relational approach being theoretically “weak,” its strength in being able to deal with real‐world complexity allows economic geographers to better explore some of societies' most important questions.
Useful laboratory markers for the diagnosis of bone marrow involvement by malignant lymphoma
Authors: Nishimura K. , Ota R. , Mikajiri Y. , Takahashi K. , Sugishima S. , Eto T. 
Published: September 2017

AbstractIntroductionThis study aimed to investigate the effect of bone marrow involvement by malignant lymphoma (BMI) on laboratory data and to determine the useful laboratory markers for diagnosing BMI.MethodsWe compared laboratory data between patients with and without BMI. We performed multivariate logistic regression and receiver operating characteristic (ROC) analyses to evaluate the diagnostic values of independent predictors.ResultsIn the BMI group, platelets in peripheral blood (PLT) and megakaryocyte count in bone marrow (MgK) were significantly lower than those in the non‐BMI group (PLT, P < .0001; MgK, P = .0384). The rate of peripheral blood involvement by malignant lymphoma (PBI), red blood cell distribution width (RDW), D‐dimer (DD), soluble interleukin‐2 receptor (sIL2R), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) was significantly higher in the BMI group than in the non‐BMI group (PBI, P < .0001; RDW, P = .0190; DD, P = .0006; sIL2R, P < .0001; AST, P = .0256; LDH, P = .0002). In multivariate analysis, PBI, PLT, sIL2R, and MgK levels were independent predictors of BMI.ConclusionPBI, PLT, sIL2R, and MgK may be the useful laboratory markers for BMI diagnosis.
Quality‐of‐life evaluation in chronic wounds: comparative analysis of three disease‐specific questionnaires
Authors: Augustin Matthias , Baade Katrin , Heyer Kristina , Price Patricia E , Herberger Katharina , Wild Thomas , Engelhardt Michael , Debus Eike S 
Published: September 2017

AbstractThe study directly compared the feasibility and performance of three instruments measuring health‐related quality of life (HRQoL) in chronic ulcers: the Freiburg Life Quality Assessment for wounds (FLQA‐w), the Cardiff Wound Impact Schedule (CWIS) and the Würzburg Wound Score (WWS). The questionnaires were evaluated in a randomly assigned order in a longitudinal observational study of leg ulcer patients. Psychometric properties (internal consistency, responsiveness and construct validity) were analysed. Patient acceptance was recorded. Analysis ofn= 154 patients revealed good internal consistency (Cronbach's alpha ≥ 0·85) for all instruments. There were minor floor effects in all questionnaires (<1%) and some ceiling effects in theCWIS. Construct validity was satisfactory, for example, correlation withEuroQoL‐5Dwasr= 0·70 in theFLQA‐w,r= 0·47/0·67/0·68 in theCWISdimensions andr= 0·60 in theWWS. The proportion of missing values was higher in theCWIS, and overall patient acceptance was highest in theFLQA‐w for wounds (54% best preferences) and lowest in theWWS(14%). In conclusion, theFLQA‐w, theCWISand theWWSare reliable, sensitive and valid instruments for the assessment ofHRQoLin leg ulcers. However, they show differences in clinical feasibility and patient acceptance.
Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross
Authors: Yin Changbin , Li Huihui , Zhao Zhigang , Wang Zhiquan , Liu Shijia , Chen Liangming , Liu Xi , Tian Yunlu , Ma Juan , Xu Lidong , Zhang Dashuang , Zhu Susong , Li Danting , Wan Jianmin , Wang Jiankang 
Published: September 2017

AbstractThe size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size (e.g., length and width) when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines (RILs) and reciprocal single chromosomal segment substitution lines (SSSLs) derived from the progeny of a japonica Asominori × indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured, namely length and flag leaf, length and flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty‐three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for marker‐assisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.
Reconstructing the microstructure of polyimide–silicalite mixed‐matrix membranes and their particle connectivity using FIB‐SEM tomography
Authors: DIBLÍKOVÁ P. , VESELÝ M. , SYSEL P. , ČAPEK P. 
Published: September 2017

SummaryProperties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused‐ion beam scanning electron microscope (FIB‐SEM) tomography data, we reconstructed three mixed‐matrix membrane samples made of 6FDA‐ODA polyimide and silicalite‐1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite‐1. Second, after spatial alignment of the stacked FIB‐SEM data, the 3D image was smoothed using adaptive median and anisotropic nonlinear diffusion filters. Third, the image was segmented using the power watershed method coupled with a seeding algorithm based on geodesic reconstruction from the markers. If the resulting volume fraction did not match the target value quantified by chemical analysis of the sample, the BSE and SE signals were mixed in another ratio and the procedure was repeated until the target volume fraction was achieved. Otherwise, the segmented 3D image (replica) was accepted and its microstructure was thoroughly characterized with special attention paid to connectivity of the silicalite phase. In terms of the phase connectivity, Monte Carlo simulations based on the pure‐phase permeability values enabled us to calculate the effective permeability tensor, the main diagonal elements of which were compared with the experimental permeability. In line with the hypothesis proposed in our recent paper (Čapek, P. et al. (2014) Comput. Mater. Sci. 89, 142–156), the results confirmed that the existence of particle clusters was a key microstructural feature determining effective permeability.
Health beliefs of salt intake among patients undergoing haemodialysis
Authors: Xie Jianfei , Ding Siqing , Liu Lifang , Liu Zina , Zhang Qiuxiang , Duan Yinglong , Wang Chunyan , Zhou Jianda 
Published: September 2017

SUMMARYBackgroundHigh salt intake has been recognised as a risk factor that contributes to a poor outcome in patients with end stage kidney disease (ESKD). This study examined health beliefs about salt intake among patients undergoing haemodialysis.Materials and methodsThis was a cross‐sectional study using a convenience sample. 307 outpatients completed the health beliefs of sodium intake scale (HBSIS).ResultsIn this cohort, the score for the perceived self‐efficacy subscale (3.59 ± 0.76) was highest, while the score for perceived barriers (2.52 ± 0.67) subscale was lowest. These perceived benefits, susceptibility for the reduction, and no reduction of sodium intake subscale scores were significantly higher in female than in male patients (p < 0.05). The scores for the subscale of perceived barriers, and the seriousness for the reduction and no reduction of sodium intake were significantly higher in haemodialysis patients who had been educated above high school compared with patients with middle school education and below (p < 0.05). The scores for the subscale of perceived benefits, susceptibility, and self‐efficacy for reduction or no reduction of sodium intake were also significantly higher in haemodialysis patients with higher income compared to those with lower income (p < 0.05 to p < 0.001). The score for the subscale of perceived seriousness for no reduction of sodium intake was significantly higher in patients who had received transplants than in patients who had not received a transplant (p < 0.01).ConclusionPatients undergoing haemodialysis have a low level of health belief about salt intake.
Chinese medical students’ knowledge, attitude and practice towards human papillomavirus vaccination and their intention to recommend the vaccine
Authors: Liu Anthony , Ho Frederick K , Chan Lily KL , Ng Joanne YW , Li Sophia L , Chan Godfrey CF , Leung Ting Fan , Ip Patrick 
Published: September 2017

AimThe human papillomavirus (HPV) vaccine is effective in preventing cervical cancer, but its global uptake rate in vulnerable populations is unsatisfactory. Physician's recommendation is an important determinant for vaccine uptake, but we have limited understanding on the contributing factors of physician's recommendation. This study investigated whether the knowledge, attitudes and vaccination status of medical students would affect their intention to recommend HPV vaccination.MethodsThis is a population‐representative survey of medical schools in Hong Kong.ResultsParticipants included 1022 Chinese medical students (46.9% of all in Hong Kong; 46.3% female). Better HPV‐related knowledge and a more positive attitude towards HPV vaccination were important factors predicting vaccine uptake and intention to recommend. HPV vaccination status and intention to receive the vaccine were positively associated with intention to recommend among females.ConclusionBetter HPV‐related medical education may be a feasible way to promote the HPV vaccine in regions without universal coverage. Medical students who have not received the HPV vaccine should also be encouraged to receive the vaccine.