bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusarium verticillioides SNARE protein FvSyn1 harbors two key functional motifs that play selective roles in fungal development and virulence
Authors: Zhang Huan , Yan Huijuan , Shim Won Bo 
Published: April 2019

ABSTRACTFusarium verticillioides is one of the key fungal pathogens responsible for maize stalk rots. While stalk rot pathogens are prevalent worldwide, our understanding of stalk rot virulence mechanism in pathogenic fungi is still very limited. We previously identified F. verticillioides FvSYN1 gene, which was demonstrated to plays an important role in maize stalk rot virulence. FvSyn1 belongs to a family of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins that play critical roles in a variety of developmental processes. In this study, we further characterized the cellular features of FvSyn1 protein motifs in F. verticillioides development and virulence. We generated FvSyn1 motif-specific deletion mutants to further investigate how different motifs contribute to development and virulence. Microscopic observation showed that Δfvsyn1 mutant exhibits rough and hyper-branched hyphae when compared to the wild type progenitor. Moreover, Δfvsyn1 mutant was sensitive to cell wall stress agents resulting in vegetative growth reduction. We showed that FvSyn1::GFP protein is associated with endomembrane but this outcome did not clarify why the deletion of this protein led to stress sensitivity and aberrant hyphal development. Characterization of FvSyn1 domains indicated that both Syntaxin N-terminus (SynN) domain and SNARE C-terminus domain play distinct roles in fungal development but collectively function in virulence. We also determined that two domains in FvSyn1 is not required for fumonisin production. Interestingly, these two domains were involved in carbon nutrient utilization including pectin, starch and sorbitol. This study further characterized the role of FvSyn1 in hyphal growth, localization, cell wall stress response and virulence in F. verticillioides.Highlights► F. verticillioides SNARE protein FvSYN1 is important for vegetative growth and virulence.► FvSYN1 deletion mutant performed better under cell wall stressors.► Dissecting of two domains and investigate the roles.
Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics
Authors: Rochette Nicolas C. , Rivera-Colón Angel G. , Catchen Julian M. 
Published: April 2019

AbstractFor half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively-parallel, short-read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here we describe the first software capable of using paired-end sequencing to derive short contigs from de novo RAD data natively. Stacks version 2 employs a de Bruijn graph assembler to build contigs from paired-end reads and overlap those contigs with the corresponding single-end loci. The new architecture allows all the individuals in a meta population to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes – generating RAD loci that are 400-800bp in length. To prove its recall and precision, we test the software with simulated data and compare reference-aligned and de novo analyses of three empirical datasets. We show that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired-end de novo datasets.
Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
Authors: Huang Zheng Y. X. , Xu Chi , van Langevelde Frank , Ma Yuying , Langendoen Tom , Mundkur Taej , Si Yali , Tian Huaiyu , Kraus Robert H. S. , Gilbert Marius , Han Guan‐Zhu , Ji Xiang , Prins Herbert H. T. , de Boer Willem F. 
Published: April 2019

Abstract

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long‐distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related.

Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental‐scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity.

Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence.

Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.
Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology
Authors: Nissimov Jozef I. , Talmy David , Haramaty Liti , Fredricks Helen F. , Zelzion Ehud , Knowles Ben , Eren A. Murat , Vandzura Rebecca , Laber Christien P. , Schieler Brittany M. , Johns Christopher T. , More Kuldeep D. , Coolen Marco J. L. , Follows Michael J. , Bhattacharya Debashish , Van Mooy Benjamin A. S. , Bidle Kay D. 
Published: April 2019

SummaryCoccolithoviruses (EhVs) are large, double‐stranded DNA‐containing viruses that infect the single‐celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom‐forming, calcifying, photoautotroph, E. huxleyi–EhV interactions play a key role in oceanic carbon biogeochemistry. Virally‐encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus‐encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less‐virulent EhVs in natural EhV communities. The majority of EhV‐derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab‐, field‐ and mathematical model‐based data and simulations support ecological scenarios whereby slow‐infecting, less‐virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast‐infecting, virulent EhVs during active infection or by having access to a broader host range.
Perspectives of Central and Eastern European Countries on Research and Innovation in the New CAP
Authors: Pokrivčák Ján , Ciaian Pavel , Drabik Dušan 
Published: April 2019

SummaryThe Commission's proposals on the Common Agricultural Policy (CAP) post‐2020 made the Research‐Innovation‐Advice nexus a key priority with the aim of promoting sustainable growth in agricultural productivity and rural development. The proposal allocates €10 billion for this priority through the EU's Horizon Europe research programme, and it envisages strengthening the Agricultural Knowledge and Innovation Systems as well as knowledge exchange through the European Innovation Partnership. We argue that despite the evident productivity gaps between farms in the EU Member States from Central and Eastern Europe (EU‐CEE) and the EU‐15, greater support for research and innovation is not a priority for EU‐CEE countries because of structural differences in their agricultural sectors as well as a comparative disadvantage in research and innovation relative to more developed countries of the EU‐15. Other policy priorities for the future CAP – such as increasing the size of the CAP budget, which represents €365 billion in the post‐2020 financial period, external convergence, and capping of direct payments – relegate support for research and innovation to a secondary priority in the EU‐CEE. This position of the EU‐CEE might not only affect the final agreement on the CAP but also its actual implementation.
Another Reform of the Common Agricultural Policy: What to Expect
Authors: Petit Michel 
Published: April 2019

SummaryAnother reform of the CAP is on the agenda. This common policy, which was initiated almost 60 years ago is criticised by almost everybody. Even farmers, who are the main beneficiaries, are critical. Moreover, many NGOs that are concerned with a broad range of issues such as the environment, food safety, animal welfare, etc. argue that the CAP makes matters worse in these domains. These shortcomings and criticisms of the CAP suggest that a radical reform is in order. Yet, an analysis of the main determinants of the CAP since its inception suggests that such an outcome is very unlikely. The article focus is on a few long‐term economic and institutional forces which determine the interests of, and positions taken by, the main actors involved in the political process where they pursue their own objectives. The CAP debate today is dominated more than ever by the contradiction between the extreme pressures to cut public expenditures and the desire to protect farmers’ incomes which will be greatly affected by cuts in European payments. In this context, other societal concerns, although very vocal, will probably not be much taken into account. Similarly, equity concerns raised by the uneven distribution of payments received by farmers will probably be addressed only marginally.
Rational application of antibiotics—The influence of anaesthetists’ gender on self‐confidence and knowledge
Authors: Heim Markus , Schneider Frederick , Mutlak Haitham , Schulz Christian M. , Hachenberg Thomas , Zoller Michael , Soukup Jens , Pawlik Michael , Schön Julika , Kees Martin , Hübler Matthias , Sander Michael , Ernst Christian , Jacob Matthias , May Matthias ,   MR2 Study Group
Published: April 2019

BackgroundHigh rates of multiresistant pathogens require detailed knowledge about rational utilization of antibiotics. Many physicians consider themselves uncertain about the interpretation of microbiological diagnostics. We examined whether self‐confidence, self‐rated knowledge, and objective knowledge regarding the use of antibiotics are associated with gender.MethodsFor this survey study, in 2017, anaesthesiologists and residents of 16 anaesthetic departments in Germany were asked to complete the Multiinstitutional Reconnaissance of practice with Multiresistant bacteria (MR2) survey. It consists of 55 items evaluating self‐confidence regarding the practical use of antibiotics (n = 6), self‐rated theoretical knowledge (n = 16), and objective knowledge (n = 5). Their answers to these items in relation to their gender were analysed using Chi‐square, Kruskal‐Wallis‐H‐Tests, and unadjusted as well as adjusted logistic regression models.ResultsSix hundred eighty‐four (response rate: 53.9 %) questionnaires were returned and were available for analysis. Female doctors (35.5 %) felt less self‐confident (P < 0.001). Self‐rated knowledge differed in overall mean (P = 0.014) and the unadjusted (odds ratio [OR]: 0.55; P = 0.013) but not in the adjusted logistic regression (OR: 0.84; P = 0.525). Objective knowledge differed after pooling questions (61.2% correct answers vs 65.4%, P = 0.01) but not with respect to single items and the adjusted logistic regression (OR: 0.83, P = 0.356).ConclusionLess self‐confidence and a lower self‐rated knowledge were found in female anaesthetists; this is consistent to the gender phenomena observed by other researchers. Nevertheless, between the 2 groups objective knowledge did not differ significantly in any item.
A significant incidental finding on cone beam computed tomography: multiple myeloma
Authors: Biun J , Lok V , Koong B , Huang TC 
Published: April 2019

AbstractCone beam computed tomography is widely used in dentistry. Incidental findings are common, with many requiring intervention or monitoring. We present a rare case of previously undiagnosed, asymptomatic multiple myeloma first identified incidentally on cone beam computed tomography and panoramic radiography. This case highlights the diverse range of lesions that may appear on cone beam computed tomography and the importance of radiologic interpretation.
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses
Authors: Holl H. M. , Pflug K. M. , Yates K. M. , Hoefs‐Martin K. , Shepard C. , Cook D. G. , Lafayette C. , Brooks S. A. 
Published: April 2019

SummaryVariations in the SLC45A2 gene are responsible for the dilution phenotypes cream and pearl in domestic horses. Cream dilution is inherited in an incomplete dominant manner, diluting only red in the heterozygous state but both red and black pigments when two alleles are present. The pearl dilution is recessive and dilutes only the red and black pigment in the homozygous state or when paired with a cream allele. Horses that inherit one copy of pearl (Cprl) and one copy of the dominant cream allele (CCr) display a dilution phenotype similar to that of homozygous cream, suggesting that pearl is the result of a different variation in the same gene responsible for cream. We sequenced SLC45A2 in two ‘false double dilute’ horses that appeared phenotypically homozygous cream but tested as possessing only a single CCr allele. We also sequenced one known pearl carrier to screen for putative causal variants. The missense variant ECA21:SLC45A2:c.985G>A; p.Ala329Thr (Cprl) was present in one false double dilute and the pearl carrier and was also genotyped in an additional 126 horses for statistical evaluation. The genotype matched the expected phenotype in all horses (P‐value = 6.5 × 10−41) and is identical to a pearl variant found previously. The second false double dilute horse and one non‐dilute offspring genotyped as heterozygous for a novel missense variant ECA21:SLC45A2:c.568G>A (p.Gly190Arg), the proposed Csun variant (for the name of the horse). This variant produces a recessive dilution similar to pearl and indicates that multiple alleles of SLC45A2 result in dilution phenotypes in the domestic horse.
Rural pharmacy workforce: Influence of curriculum and clinical placement on pharmacists' choice of rural practice
Authors: Taylor Selina M. , Lindsay David , Glass Beverley D. 
Published: April 2019

AbstractObjectiveThis two‐phase study aimed to explore the influence of a university rural curriculum and clinical placements on pharmacists' choice to practise in a rural or remote area.DesignA sequential mixed‐methods approach involved the design of both a questionnaire and semistructured in‐depth interviews to collect quantitative and qualitative data.SettingRegional, rural and remote practice areas according to the Pharmacy Access/Remoteness Index of Australia classifications.ParticipantsNinety‐two pharmacists from varied areas of practice, working in rural and remote locations across Australia, participated in the study.Main outcome measuresUniversity curriculum and clinical placements during the degree and their influence on the current rural workforce.ResultsIn the survey sample, two‐thirds of the current rural pharmacy workforce's choice of practice location was significantly influenced by positive rural placement experiences. Rural practice was, however, not included in the curriculum for 50% of the rural workforce in the sample, although graduates from regional universities experienced up to 80% more exposure to rural curricula. In this sample, rural origin was also not found to be a significant determinant of rural practice, while rural lifestyle, family commitments, remuneration, career opportunities and other contractual agreements have had a greater influence than university education.ConclusionAlthough the positive influence of rural placements has been identified, there is still a way to go in terms of the development of a meaningful rural curriculum. This highlights that universities have a role to play in addressing this issue to produce graduates who are better prepared for the opportunities and challenges of rural pharmacy practice.
Semen quality is affected by HLA class I alleles together with sexually transmitted diseases
Authors: Marques P. I. , Gonçalves J. C. , Monteiro C. , Cavadas B. , Nagirnaja L. , Barros N. , Barros A. , Carvalho F. , Lopes A. M. , Seixas S. 
Published: April 2019

AbstractBackgroundThe human leukocyte antigen (HLA) locus includes several genes with key roles in antigen presentation and immune response, some of them inclusively found to be associated with non‐obstructive azoospermia. Still, HLA connections to other infertility phenotypes such as semen hyperviscosity (SHV), asthenozoospermia (AST), and oligozoospermia (OLI) have been often neglected.ObjectivesIn this work, we aimed to evaluate the association of HLA class I and II genes with SHV, AST, and OLI phenotypes while exploring a possible role in an adaptive immune response to sexually transmitted diseases (STD).Materials and methodsWhole‐exome sequencing was performed in a Portuguese cohort of 71 infertility cases and 68 controls, followed by HLA typing using a specific software—HLA*PRG:LA tool. Molecular screenings of seven STD were carried out in a subset of 72 samples (30 cases and 42 controls).ResultsStatistical tests uncovered three protective alleles: HLA‐A*11:01, associated with all forms of male infertility (p = 0.0006); HLA‐DQB1*03:02 with SHV and OLI (PSHV = 0.0303, POLI = 0.0153); and HLA‐A*29:02 with OLI (p = 0.0355), which was found to interfere in sperm number together with HPV (p = 0.0313). Five risk alleles were also identified: two linked with SHV (HLA‐B*50:01, p = 0.0278; and HLA‐C*06:02, p = 0.0461), another one with both SHV and OLI (HLA‐DQA1*05:01, PSHV = 0.0444 and POLI=0.0265), and two with OLI (HLA‐C*03:03, p = 0.0480; and HLA‐DQB1*03:01, p = 0.0499). Here, HLA‐C*03:03 carriers tend to be HPV infected.ConclusionsThe application of HLA*PRG:LA tool to the study of male infertility provided novel insights for an HLA correlation with semen quality, namely among SHV and OLI phenotypes. The discovery of an HLA‐A*29:02/HPV crosstalk, together with former reports of HLA alleles conferring resistance–susceptibility to diverse human pathogens, raises the hypothesis of a mechanistic link between male infertility, HLA polymorphism, and host response to STD.
Rapid and accurate detection of Helicobacter pylori from biopsy specimens using loop‐mediated isothermal amplification
Authors: Bakhtiari Somaye , Hasanvand Banafsheh , Pajavand Hamid , Alvandi Amirhooshang , Abiri Ramin 
Published: April 2019

Loop‐mediated isothermal amplification (LAMP) is a promising nucleic acid‐based assay for quick, accurate and cost‐effective diagnosis of many infectious agents. The purpose of this study was to assess the diagnostic value of LAMP for rapid and accurate detection of Helicobacter pylori in biopsy specimens. Patients suffering from one or several gastroduodenal disorders were enrolled in the study. Specificity, sensitivity, and the positive and negative predictive values of LAMP were compared with the gold standard result, which was the assembled result of culture, rapid urease test and polymerase chain reaction. Sensitivity, specificity, and the positive and negative predictive values of LAMP in comparison with the gold standard result were 100%, 30.76%, and 87.67% and 100% respectively [%95 CI]. As the diagnostic value of LAMP is favourable, the method is an optimum technique for diagnosis the presence of H. pylori in different clinical and environmental samples.
Cryopreservation of immature oocytes of the indigeneous Vietnamese Ban Pig
Authors: Somfai Tamas , Nguyen Van Khanh , Vu Huong Thu Thi , Nguyen Huong Le Thi , Quan Huu Xuan , Viet Linh Nguyen , Phan Son Le , Pham Lan Doan , Cuc Ngo Thi Kim , Kikuchi Kazuhiro 
Published: April 2019

AbstractWe report the cryopreservation of oocytes from Ban miniature pigs which are endemic in Vietnam. Immature cumulus‐oocyte complexes were collected from antral follicles of 7–8 mo old female cyclic Ban pigs and vitrified in micro‐drops. Oocyte morphology, lipid content, post‐warming survival, nuclear maturation, and embryo development were compared to those of oocytes from commercially slaughtered Landrace × Large white hybrid pigs. The size of oocytes in the two breeds was similar. However, significantly lower amounts of intracellular lipid were detected in Ban oocytes. There was no difference (p > 0.05) between Ban and Landrace × Large white oocytes in percentages of post‐warming survival (93.1 ± 3.4% vs. 70.7 ± 16.7%, respectively) and nuclear maturation after in vitro maturation (80.4 ± 5.1% vs. 90.0 ± 1.3% respectively). Similarly, cleavage (30.8 ± 7.8% vs. 10.3 ± 6.1%, respectively) and blastocyst development rates (9.4 ± 5.0% vs. 0.79 ± 0.79, respectively) were not different (p > 0.05) between vitrified Ban and Landrace × Large white oocytes after in vitro fertilization and embryo culture. In conclusion, high survival and maturation rates were achieved after vitrification of immature Ban oocytes and their cryo‐tolerance was similar to that of Landrace × Large white oocytes, despite the difference in lipid content. We succeeded to generate reasonable rates of blastocysts from vitrified Ban oocytes by in vitro fertilization.
Retinal vascular abnormalities in schizophrenia and bipolar disorder: A window to the brain
Authors: Appaji Abhishek , Nagendra Bhargavi , Chako Dona M. , Padmanabha Ananth , Hiremath Chaitra V. , Jacob Arpitha , Varambally Shivarama , Kesavan Muralidharan , Venkatasubramanian Ganesan , Rao Shyam V. , Webers Carroll A. B. , Berendschot Tos T. J. M. , Rao Naren P. 
Published: April 2019

AbstractObjectivesThe examination of retinal microvascular abnormalities through fundus photography is currently the best available non‐invasive technique for assessment of cerebral vascular status. Several studies in the last decade have reported higher incidences of adverse cerebrovascular events in Schizophrenia (SCZ) and bipolar disorder (BD). However, retinal microvasculature abnormalities in SCZ and BD have remained under‐explored, and no study has compared this aspect of SCZ and BD till date.MethodsRetinal Images of 100 SCZ patients, BD patients, and healthy volunteers each were acquired by trained individuals using a non‐mydriatic camera with a 40‐degree field of view. The retinal images were quantified using a valid semi‐automated method. The average of left and right eye diameters of the venules and arterioles passing through the extended zone between 0.5 and 2 disc diameters from the optic disc were calculated.ResultsThe groups differed significantly with respect to average diameters of both retinal venules (P < 0.001) and retinal arterioles (P < 0.001), after controlling for age and sex. Both SCZ and BD patients had significantly narrower arterioles and wider venules compared to HV. There were also significant differences between SCZ and BD patients; patients with BD had narrower arterioles and wider venules.ConclusionConsidering the affordability and easy accessibility of the investigative procedure, retinal microvascular examination could serve as a potential screening tool to identify individuals at risk for adverse cerebrovascular events. The findings of the current study also provide a strong rationale for further systematic examination of retinal vascular abnormalities in SCZ and BD.