bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioSCOOP – Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks
Authors: Jarczak J , Lach J , Borówka P , Gałka M , Bućko M , Marciniak B , Strapagiel D 
Published: August 2019

AbstractDynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.
Enabling semantic queries across federated bioinformatics databases
Authors: Sima Ana Claudia , Mendes de Farias Tarcisio , Zbinden Erich , Anisimova Maria , Gil Manuel , Stockinger Heinz , Stockinger Kurt , Robinson-Rechavi Marc , Dessimoz Christophe 
Published: August 2019

AbstractMotivation: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.Results: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.
‘One DB to rule them all’—the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs
Authors: Politano Gianfranco , Di Carlo Stefano , Benso Alfredo 
Published: August 2019

Abstract
In the last decade, genomics data have been largely adopted to sketch, study and better understand the complex mechanisms that underlie biological processes. The amount of publicly available data sources has grown accordingly, and several types of regulatory interactions have been collected and documented in literature. Unfortunately, often these efforts do not follow any data naming/interoperability/formatting standards, resulting in high-quality but often uninteroperable heterogeneous data repositories. To efficiently take advantage of the large amount of available data and integrate these heterogeneous sources of information, we built the RING (Regulatory Interaction Graph), an integrative standardized multilevel database of biological interactions able to provide a comprehensive and unmatched high-level perspective on several phenomena that take place in the regulatory cascade and that researchers can use to easily build regulatory networks around entities of interest.
SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)
Authors: Masonbrink Rick , Maier Tom R , Seetharam Arun S , Juvale Parijat S , Baber Levi , Baum Thomas J , Severin Andrew J 
Published: August 2019

AbstractSoybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.
Outcomes and Strategies to Support a Treat-to-target Approach in Inflammatory Bowel Disease: A Systematic Review
Authors: Colombel Jean-Frédéric , D’haens Geert , Lee Wan-Ju , Petersson Joel , Panaccione Remo 
Published: August 2019

Abstract

Background and Aims
Management of Crohn’s disease and ulcerative colitis has typically relied upon treatment intensification driven by symptoms alone. However, a ‘treat-to-target’ management approach may help to address underlying inflammation, minimise disease activity at early stages of inflammatory bowel disease, limit progression, and improve long-term outcomes.

Methods
A systematic literature review was conducted to identify data relevant to a treat-to-target approach in inflammatory bowel disease, published between January 1, 2007 and May 15, 2017.

Results
Consistent with recommendations of the Selecting Therapeutic Targets in Inflammatory Bowel Disease [STRIDE] working group, studies have investigated factors influencing the achievement of both endoscopic and histological mucosal healing and patient-level outcomes in inflammatory bowel disease [IBD]. Histological healing and biomarker levels have also been shown to be modifiable outcomes. Although there is a lack of prospectively derived evidence validating mucosal healing as a treatment target, data are emerging to suggest that targeting mucosal healing or inflammation rather than symptoms may be cost-effective in some settings. The review highlighted several strategies that may support the implementation of a treat-to-target approach in IBD. The prospective randomised CALM study demonstrated how tight control [whereby treatment decisions are based on close monitoring of inflammatory biomarkers] leads to improvements in endoscopic and clinical outcomes. The review also considered the influence of coordinated care from a multidisciplinary team and patient engagement with improved adherence, as well as the role of therapeutic drug monitoring in inflammatory bowel disease management.

Conclusions
A treat-to-target strategy may impact on disease progression and improve outcomes in inflammatory bowel disease. Prospective studies including long-term data are required to ensure that the most appropriate targets and strategies are identified.
The Safety Profile of Vedolizumab in Ulcerative Colitis and Crohn’s Disease: 4 Years of Global Post-marketing Data
Authors: Cohen Russell D , Bhayat Fatima , Blake Aimee , Travis Simon 
Published: August 2019

Abstract

Background and Aims
Vedolizumab is a gut-selective antibody to α 4  β 7 integrin, approved to treat moderate-to-severe ulcerative colitis and Crohn’s disease in adults. Clinical trial data on patients meeting protocol-specified criteria may not reflect real-world clinical practice. This is a descriptive analysis of 4 years of post-marketing safety data on vedolizumab.

Methods
The Vedolizumab Global Safety Database contains all adverse event reports collated by Takeda Pharmaceutical Company Ltd since vedolizumab approval [May 20, 2014]. Adverse event reports received between approval and May 19, 2018 were identified using Medical Dictionary for Regulatory Activities version 21.0 Preferred Terms. Adverse event frequencies were calculated and categorised.

Results
In approximately 208 050 patient-years of vedolizumab exposure, 32 752 patients reported 80 218 events. In patients with Crohn’s disease or ulcerative colitis, 37 662 and 34 259 events occurred in 14 191 and 14 042 patients, respectively, and 8297 events occurred in 4519 individuals with other [off-label] or unreported indications. Overall, 5230 [14%; Crohn’s disease] and 3580 [10%; ulcerative colitis] events were serious. Most frequently reported were gastrointestinal events (Crohn’s disease, 6156 [16%]; ulcerative colitis, 5701 [17%]). Patients with Crohn’s disease or ulcerative colitis reported 251 malignancies [&lt;1%], 402 hepatobiliary events [&lt;1%], and 5876 infections (1137 serious [19%], 301 opportunistic [5%]). Patients aged ≥70 years [2326 patients] reported &lt;10% of events.

Conclusions
Adverse event patterns were consistent with clinical trials, with no new safety concerns. Most reported events were non-serious and event frequency was low, considering patient-years of exposure. Although limitations of post-marketing safety reports require acknowledgement, these real-world data support a favourable safety profile of vedolizumab.
Imaging in ESC clinical guidelines: chronic coronary syndromes
Authors: Saraste Antti , Barbato Emanuele , Capodanno Davide , Edvardsen Thor , Prescott Eva , Achenbach Stephan , Bax Jeroen J , Wijns William , Knuuti Juhani 
Published: August 2019

Abstract
The European Society of Cardiology (ESC) has recently published new guidelines on the diagnosis and management of chronic coronary syndromes (CCS). The 2019 guideline identified six common clinical scenarios of CCS defined by the different evolutionary phases of coronary artery disease (CAD), excluding the situations in which an acute coronary event, often with coronary thrombus formation, dominates the clinical presentation. This review aims at providing a summary of novel or revised concepts in the guidelines together with the recent data underlying the major changes on the use of cardiac imaging in patients with suspected or known CCS.
Based on data from contemporary cohorts of patients referred for diagnostic testing, the pre-test probabilities of CAD based on age, sex and symptoms have been adjusted substantially downward as compared with 2013 ESC guidelines. Further, the impact of various risk factors and modifiers on the pre-test probability was highlighted and a new concept of ‘Clinical likelihood of CAD’ was introduced. Recommendations regarding diagnostic tests to establish or rule-out obstructive CAD have been updated with recent data on their diagnostic performance in different patient groups and impact on patient outcome. As the initial strategy to diagnose CAD in symptomatic patients, non-invasive functional imaging for myocardial ischaemia, coronary computed tomography angiography or invasive coronary angiography combined with functional evaluation may be used, unless obstructive CAD can be excluded by clinical assessment alone. When available, imaging tests instead of the exercise electrocardiogram are recommended when following the non-invasive diagnostic strategy.
Morpho-metabolic post-surgical patterns of non-infected prosthetic heart valves by [18F]FDG PET/CTA: “normality” is a possible diagnosis
Authors: Roque Albert , Pizzi María N , Fernández-Hidalgo Nuria , Permanyer Eduard , Cuellar-Calabria Hug , Romero-Farina Guillermo , Ríos Remedios , Almirante Benito , Castell-Conesa Joan , Escobar Manuel , Ferreira-González Ignacio , Tornos Pilar , Aguadé-Bruix Santiago 
Published: August 2019

AbstractAimsTo define characteristic PET/CTA patterns of FDG uptake and anatomic changes following prosthetic heart valves (PVs) implantation over time, to help not to misdiagnose post-operative inflammation and avoid false-positive cases.Methods and resultsProspective evaluation of 37 post-operative patients without suspected infection that underwent serial cardiac PET/CTA examinations at 1, 6, and 12 months after surgery, in which metabolic features (FDG uptake distribution pattern and intensity) and anatomic changes were evaluated. Standardized uptake values (SUVs) were obtained and a new measure, the valve uptake index (VUI), (SUVmax–SUVmean)/SUVmax, was tested to homogenize SUV results.In total, 111 PET/CTA scans were performed in 37 patients (19 aortic and 18 mitral valves). FDG uptake was visually detectable in 79.3% of patients and showed a diffuse, homogeneous distribution pattern in 93%. Quantitative analysis yielded a mean maximum standardized uptake value (SUVmax) of 4.46 ± 1.50 and VUI of 0.35 ± 0.10. There were no significant differences in FDG distribution or uptake values between 1, 6, or 12 months. No abnormal anatomic changes or endocarditis lesions were detected in any patient during follow-up.ConclusionsFDG uptake, often seen in recently implanted PVs, shows a characteristic pattern of post-operative inflammation and, in the absence of associated anatomic lesions, could be considered a normal finding. These features remain stable for at least 1 year after surgery, so questioning the recommended 3-month safety period. A new measure, the VUI, can be useful for evaluating the FDG distribution pattern.
Stepwise mass screening for atrial fibrillation using N-terminal B-type natriuretic peptide: the STROKESTOP II study
Authors: Kemp Gudmundsdottir Katrin , Fredriksson Tove , Svennberg Emma , Al-Khalili Faris , Friberg Leif , Frykman Viveka , Hijazi Ziad , Rosenqvist Mårten , Engdahl Johan 
Published: August 2019

Abstract

Aims
To study the prevalence of unknown atrial fibrillation (AF) in a high-risk, 75/76-year-old, population using N-terminal B-type natriuretic peptide (NT-proBNP) and handheld electrocardiogram (ECG) recordings in a stepwise screening procedure.

Methods and results
The STROKESTOP II study is a population-based cohort study in which all 75/76-year-old in the Stockholm region (n = 28 712) were randomized 1:1 to be invited to an AF screening programme or to serve as the control group. Participants without known AF had NT-proBNP analysed and were stratified into low-risk (NT-proBNP &lt;125 ng/L) and high-risk (NT-proBNP ≥125 ng/L) groups. The high-risk group was offered extended ECG-screening, whereas the low-risk group performed only one single-lead ECG recording. In total, 6868 individuals accepted the screening invitation of which 6315 (91.9%) did not have previously known AF. New AF was detected in 2.6% [95% confidence interval (CI) 2.2–3.0] of all participants without previous AF. In the high-risk group (n = 3766/6315, 59.6%), AF was diagnosed in 4.4% (95% CI 3.7–5.1) of the participants. Out of these, 18% had AF on their index-ECG. In the low-risk group, one participant was diagnosed with AF on index-ECG. The screening procedure resulted in an increase in known prevalence from 8.1% to 10.5% among participants. Oral anticoagulant treatment was initiated in 94.5% of the participants with newly diagnosed AF.

Conclusion
N-terminal B-type natriuretic peptide-stratified systematic screening for AF identified 4.4% of the high-risk participants with new AF. Oral anticoagulant treatment initiation was well accepted in the group diagnosed with new AF.
Fantastic yeasts and where to find them: the discovery of a predominantly clonal Cryptococcus deneoformans population in Saudi Arabian soils
Authors: Samarasinghe Himeshi , Aljohani Renad , Jimenez Carlene , Xu Jianping 
Published: August 2019

ABSTRACTCryptococcus deneoformans is an opportunist yeast pathogen and causative agent of meningoencephalitis in humans. It is known to be mainly distributed in temperate climates. Most of our current understanding of this species has come from clinical isolates, leaving environmental populations largely unexplored. The Middle East remains one such underexplored area with no published study to date investigating cryptococcal diversity in soil. In this study, we identified 76 C. deneoformans isolates from a survey of 562 soil samples collected from six cities in Saudi Arabia. Multilocus sequence typing revealed the presence of two major sequence types (STs), ST160 (n = 63) and ST294 (n = 9), along with four singleton STs, three of which were novel. One novel ST, ST613, was likely a recombinant product between ST160 and ST294. Among the 76 isolates, 75 belonged to mating type (MAT)α while one isolate was MATa. Our analyses suggest that the Saudi Arabian C. deneoformans population likely reproduces both asexually and sexually in nature. Our study is the first to report the occurrence of C. deneoformans in a desert climate, representing a novel expansion to this species’ currently known ecological niche.
Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly
Authors: Dinter Thomas , Geihser Simone , Gube Matthias , Daniel Rolf , Kuzyakov Yakov 
Published: August 2019

ABSTRACTSalt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.
Spatial heterogeneity of belowground microbial communities linked to peatland microhabitats with different plant dominants
Authors: Chroňáková Alica , Bárta Jiří , Kaštovská Eva , Urbanová Zuzana , Picek Tomáš 
Published: August 2019

ABSTRACTPeatland vegetation is composed mostly of mosses, graminoids and ericoid shrubs, and these have a distinct impact on peat biogeochemistry. We studied variation in soil microbial communities related to natural peatland microhabitats dominated by Sphagnum, cotton-grass and blueberry. We hypothesized that such microhabitats will be occupied by structurally and functionally different microbial communities, which will vary further during the vegetation season due to changes in temperature and photosynthetic activity of plant dominants. This was addressed using amplicon-based sequencing of prokaryotic and fungal rDNA and qPCR with respect to methane-cycling communities. Fungal communities were highly microhabitat-specific, while prokaryotic communities were additionally directed by soil pH and total N content. Seasonal alternations in microbial community composition were less important; however, they influenced the abundance of methane-cycling communities. Cotton-grass and blueberry bacterial communities contained relatively more α-Proteobacteria but less Chloroflexi, Fibrobacteres, Firmicutes, NC10, OD1 and Spirochaetes than in Sphagnum. Methanogens, syntrophic and anaerobic bacteria (i.e. Clostridiales, Bacteroidales, Opitutae, Chloroflexi and Syntrophorhabdaceae) were suppressed in blueberry indicating greater aeration that enhanced abundance of fungi (mainly Archaeorhizomycetes) and resulted in the highest fungi-to-bacteria ratio. Thus, microhabitats dominated by different vascular plants are inhabited by unique microbial communities, contributing greatly to spatial functional diversity within peatlands.
Nematicidal metabolites from endophytic fungus Chaetomium globosum YSC5
Authors: Khan Babar , Yan Wei , Wei Shan , Wang Zhiyang , Zhao Shuangshuang , Cao Lingling , Rajput Nasir Ahmed , Ye Yonghao 
Published: August 2019

ABSTRACT
Management of nematodes is a very hectic job due to a highly diverse group of organisms. To find lead compounds for new nematicide development, five metabolites (1–5) were isolated from the culture broth of Chaetomium globosum YSC5 and tested for nematicidal activities against the second stage juveniles (J2s) of Meloidogyne javanica. The results revealed that chaetoglobosin A (1), chaetoglobosin B (2) and flavipin (3) exhibited strong adverse effects (91.6, 83.8 and 87.4%, respectively) on J2 mortality at 200 μg/mL with LC50 values of 88.4, 107.7 and 99.2 μg/mL after 72 h, respectively, while 3-methoxyepicoccone (4) and 4,5,6-trihydroxy-7-methylphthalide (5) showed moderate effects (78.0 and 75.5%, respectively) with LC50 values of 124.0 and 131.6 μg/mL, respectively. Furthermore, in pot assay compounds 1 and 2 appeared to be promising metabolites at 200 μg/mL that significantly reduced nematode reproduction and showed a positive influence on plant growth. Our findings could be helpful for development of new potential bio-based pesticides for integrated management of plant-parasitic nematode.