bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community-driven data analysis training for biology
Authors: Batut Bérénice , Hiltemann Saskia , Bagnacani Andrea , Baker Dannon , Bhardwaj Vivek , Blank Clemens , Bretaudeau Anthony , Brillet-Guéguen Loraine , Čech Martin , Chilton John , Clements Dave , Doppelt-Azeroual Olivia , Erxleben Anika , Freeberg Mallory Ann , Gladman Simon , Hoogstrate Youri , Hotz Hans-Rudolf , Houwaart Torsten , Jagtap Pratik , Larivière Delphine , Corguillé Gildas Le , Manke Thomas , Mareuil Fabien , Ramírez Fidel , Ryan Devon , Sigloch Florian Christoph , Soranzo Nicola , Wolff Joachim , Videm Pavankumar , Wolfien Markus , Wubuli Aisanjiang , Yusuf Dilmurat , Network Galaxy Training , Backofen Rolf , Taylor James , Nekrutenko Anton , Grüning Björn 
Published: November 2017

AbstractThe primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.
Biomolecular Simulations under Realistic Macroscopic Salt Conditions
Authors: Ross Gregory A. , Rustenburg Ariën S. , Grinaway Patrick B. , Fass Josh , Chodera John D. 
Published: November 2017

AbstractBiomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carloosmostatthat can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduce the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an (Δµ, N, p, T) ensemble. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.
An adaptable chromosome preparation methodology for use in invertebrate research organisms
Authors: Guo Longhua , Accorsi Alice , He Shuonan , Guerrero-Hernández Carlos , Sivagnanam Shamilene , McKinney Sean , Gibson Matthew , Alvarado Alejandro Sánchez 
Published: November 2017

AbstractBackgroundThe ability to efficiently visualize and manipulate chromosomes is fundamental to understand the genetic architecture of organisms. This can be challenging for many invertebrates because conventional chromosome preparation protocols deal primarily hypotonic conditions tailored for use with vertebrates and rely extensively on cultured cells which are rarely available for invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate model species is needed.ResultsWe optimized a chromosome preparation protocol and applied it to several planarian species (Phylum: Platyhelminthes), the freshwater apple snailPomacea canaliculata(Phylum: Mollusca), and the starlet sea anemoneNematostella vectensis(Phylum: Cnidaria). We showed that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with DI water was sufficient for karyotyping. The karyotypes we obtained allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla, this protocol can be effectively coupled with downstream applications, such as chromosome fluorescentin situhybridization.ConclusionThe simple and inexpensive chromosome preparation protocol reported here can be readily adapted to new invertebrate research organisms in order to expand and accelerate the discovery of new biology in understudied branches of the tree of life.
TheVibrio choleraeType VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria
Authors: Logan Savannah L. , Thomas Jacob , Yan Jinyuan , Baker Ryan P. , Shields Drew S. , Xavier Joao B. , Hammer Brian K. , Parthasarathy Raghuveer 
Published: November 2017

AbstractHost-associated microbiota help defend against bacterial pathogens; the mechanisms that pathogens possess to overcome this defense, however, remain largely unknown. We developed a zebrafish model and used live imaging to directly study how the human pathogenVibrio choleraeinvades the intestine. The gut microbiota of fish mono-colonized by commensal strainAeromonas veroniiwas displaced byV. choleraeexpressing its Type VI Secretion System (T6SS), a syringe-like apparatus that deploys effector proteins into target cells. Surprisingly, displacement was independent of T6SS-mediated killing ofAeromonas, driven instead by T6SS-induced enhancement of zebrafish intestinal movements that led to expulsion of the resident commensal by the host. Deleting an actin crosslinking domain from the T6SS apparatus returned intestinal motility to normal and thwarted expulsion, without weakeningV. cholerae′sability to killAeromonas in vitro. Our finding that bacteria can manipulate host physiology to influence inter-microbial competition has implications for both pathogenesis and microbiome engineering.
Presence of WH2 like domain in VgrG-1 toxin of Vibrio cholerae reveals the molecular mechanism of actin cross-linking
Authors: Dutta Priyanka , Jijumon A.S. , Mazumder Mohit , Dileep Drisya , Mukhopadhyay Asish K. , Gourinath Samudrala , Maiti Sankar 
Published: November 2017

AbstractType VI secretion systems (T6SS) plays a crucial role in Vibrio cholerae mediated pathogenicity and predation. Tip of T6SS is homologous to gp27/gp5 complex or tail spike of T4 bacteriophage. VgrG-1 of V. cholerae T6SS is unusual among other VgrG because its effector domain is trans-located into the cytosol of eukaryotic cells with an additional actin cross-linking domain (ACD) at its C terminal end. ACD of VgrG-1 (VgrG-1-ACD) causes T6SS dependent host cell cytotoxicity through actin cytoskeleton disruption to prevent bacterial engulfment by macrophages. ACD mediated actin cross-linking promotes survival of the bacteria in the small intestine of humans, along with other virulence factors; establishes successful infection with the onset of diarrhoea in humans. Our studies demonstrated VgrG-1-ACD can bind to actin besides actin cross-linking activity. Computational analysis of ACD revealed the presence of WH2 domain through which it binds actin. Mutations in WH2 domain lead to loss of actin binding in vitro. VgrG-1-ACD having the mutated WH2 domain cannot cross-link actin efficiently in vitro and manifests less actin cytoskeleton disruption when transfected in HeLa cells.Summary statementActin cross-linking (ACD) domain of VgrG-1 toxin of Type VI secretion in Vibrio cholera has WASP Homology domain 2 (WH2) domain. ACD interact with actin through WH2 domain, WH2 is essential for ACD mediated cross-linking and disruption of actin cytoskeleton in the host cell.
Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of S. aureus
Authors: Hardy Katherine , Sunnucks Katie , Gil Hannah , Shabir Sahida , Trampari Eleftheria , Hawkey Peter , Webber Mark 
Published: November 2017

AbstractHospital acquired infection is a major cause of morbidity and mortality and regimes to prevent infection are crucial in infection control. These include decolonisation of at-risk patients of carriage of MRSA which is commonly achieved by protocols that include the use of chlorhexidine, or octenidine as biocidal agents. There is however no standardised single decolonisation regime agreed upon in the UK or other countries and protocols include a variety of active agents. Antibiotic resistant bacteria cause major problems in hospital medicine and concern has been raised regarding the development of biocide resistance which would cause decolonisation regimes to become unreliable. In this study, we assembled a panel of isolates of S. aureus including isolates collected before the development of chlorhexidine and octenidine through to a contemporaneous panel of isolates from a major hospital trust in the UK during a period when the decolonisation regime was altered. We observed significant increases in the MIC and MBC of chlorhexidine in isolates collected from periods of high usage of chlorhexidine. No isolates had a significantly altered MIC or MBC of octenidine apart from those collected after octenidine was introduced into the trust where isolates with four-fold decreases in susceptibility emerged. There was no suggestion of cross-resistance between the two biocidal agents. A combination of VNTR, PCR for qac genes and whole genome sequencing was used to type isolates and examine possible mechanisms of resistance. The typing data showed no expansion of a single strain was associated with decreased biocide tolerance and isolates with increased chlorhexidine MIC and MBCs were found from different clonal complexes; CC8, CC22 and CC30. Biocide susceptibility did not correlate with carriage of qac efflux pump genes – carriage of qacA and qacB was detected but, with one exception was restricted to isolates of CC8. Analysis of genome sequence data for closely related pairs of strains with differential biocide susceptibility revealed no common mutations or carriage of accessory elements that correlated with biocide tolerance. Mutations with the NorA or NorB efflux pumps, previously associated with chlorhexidine export were identified suggesting this may be an important mechanism of biocide tolerance. The clinical relevance of decreased biocide tolerance in terms of efficacy of decolonisation therapies remains to be established but we present evidence here that isolates are evolving in the face of biocide challenge in patients and that changes to decolonisation regimes are reflected in changes in susceptibility of isolates. More work is needed to assess the impact of these changes to ensure effective and robust decolonisation protocols remain in place.
Developing a domain ontology for knowledge management technologies
Authors: Hashemi Parvin , Khadivar Ameneh , Shamizanjani Mehdi 
Published: November 2017

Purpose
The purpose of this paper is to develop a new ontology for knowledge management (KM) technologies, determining the relationships between these technologies and classification of them.

Design/methodology/approach
The study applies NOY methodology – named after Natalya F. Noy who initiated this methodology. Protégé software and ontology web language are used for building the ontology. The presented ontology is evaluated with abbreviation and consistency criteria and knowledge retrieval of KM technologies by experts.

Findings
All the main concepts in the scope of KM technologies are extracted from existing literature. There are 241 words, 49 out of them are domain concepts, eight terms are about taxonomic and non-taxonomic relations, one term relates to data property and 183 terms are instances. These terms are used to develop KM technologies’ ontology based on three factors: facilitating KM processes, supporting KM strategies and the position of technology in the KM technology stage model. The presented ontology is created a common understanding in the field of KM technologies.

Research limitations/implications
Lack of specific documentary about logic behind decision making and prioritizing criteria in choosing KM technologies.

Practical implications
Uploading the presented ontology in the web environment provides a platform for knowledge sharing between experts from around the world. In addition, it helps to decide on the choice of KM technologies based on KM processes and KM strategy.

Originality/value
Among the many categories of KM technologies in literature, there is no classifying according to several criteria simultaneously. This paper contributes to filling this gap and considers KM processes, KM strategy and stages of growth for KM technologies simultaneously to choice the KM technologies and also there exists no formal ontology regarding KM technologies. This study has tried to propose a formal KM technologies’ ontology.
Comparison of virtual and physical dimensions in AM resin dental devices and fit of devices with conventionally produced base plates
Authors: Al Mortadi Noor Abdullah , Eggbeer Dominic , Lewis Jeffrey , Williams Robert 
Published: November 2017

Purpose
The purpose of this study is to develop and apply clinically relevant methods of analysing the accuracy of dental appliances fabricated using additive manufacture (AM) compared to the computer-aided design (CAD) geometry. The study also compared fit between conventionally laboratory-fabricated and AM-produced base plates.

Design/methodology/approach
The techniques were applied to two types of dental devices where AM fabrication methods could foreseeably be used as an alternative to laboratory production. “L” and cubic shapes of defined dimensions and spatial locations were positioned on the devices which were fabricated using AM. For assessing the dimensions, the “L” and cubic shapes were then measured on the physical builds ten times and compared to the CAD model. To assess the fit of AM and lab-produced devices, three upper and three lower conventionally fabricated acrylic base plates were compared to three upper and three lower plates. Silicone impression material was allowed to set between the casts and the base plates which filled any discrepancy between the two surfaces. The thickness of this silicone media was measured ten times at five different points on each base plate type and the results compared.

Findings
The results indicated that the evaluated CAD/AM technique is able to produce dental appliance components that are consistent with tolerance levels that would be expected with conventional methods of baseplate design. This research demonstrated that a fully CAD/AM methodology represents a potentially viable alternative to conventional lab-based methods for two types of dental appliances.

Originality/value
This work is original. The authors do not believe any previous papers similar to the one submitted have been published.
Long‐term clinical efficacy and safety of secukinumab for Japanese patients with psoriasis: A single‐center experience
Authors: Momose Mami , Asahina Akihiko , Umezawa Yoshinori , Nakagawa Hidemi 
Published: November 2017

AbstractSecukinumab is a fully human monoclonal antibody that can selectively neutralize interleukin‐17A, and its excellent efficacy has been demonstrated in clinical trials for psoriasis. The aim of our study is to assess long‐term efficacy and safety of secukinumab for 52 weeks in real‐world clinical practise in our facility. A total of 83 patients (71 with psoriasis vulgaris and 12 with psoriatic arthritis) were included, and 49 of them were bio‐switched patients. Psoriasis Area and Severity Index (PASI) 75 and PASI‐90 responses were 80% and 64% at week 12, 77% and 65% at week 24, and 76% and 58% at week 52, respectively. No significant differences were observed in efficacy between bio‐naive and bio‐switched patients. Arthralgia showed improvement by week 12 in all patients with psoriatic arthritis with a reduction of serum C‐reactive protein level. Treatment was discontinued in 22% (18/83), including eight patients with no improvement or exacerbation of cutaneous manifestations, one patient with new onset of arthritis and two patients with transient infection. Overall, secukinumab showed a sustained clinical response with an acceptable safety profile through week 52 in Japanese psoriatic patients.
Presenting characteristics and prevalence of polypoidal choroidal vasculopathy in Scandinavian patients with treatment‐naïve exudative age‐related macular degeneration
Authors: Lorentzen Thomas Dam , Subhi Yousif , Sørensen Torben Lykke 
Published: November 2017

AbstractPurposeTo study presenting characteristics and prevalence of polypoidal choroidal vasculopathy (PCV) in Scandinavian Caucasians with treatment‐naïve exudative age‐related macular degeneration (AMD).MethodsWe reviewed all patients referred in year 2014 and diagnosed using fundus examination, optical coherence tomography, and fluorescein and indocyanine green angiography (ICGA). Details of found PCVs and its subtypes (clinical and angiographical) were correlated to the baseline best‐corrected visual acuity (BCVA).ResultsOf 299 Caucasian patients with a tentative diagnosis of exudative AMD, 18 eyes of 17 patients (5.7%, CI 95%: 3.5–9.1%) had PCV. Patients with PCV were 75.8 (SD: 7.5) years old and 11 (65%) were females. Lesions were predominantly extramacular. Most eyes (56%) had subretinal haemorrhage, 39% had the exudative type and one (6%) eye had the quiescent type. Larger lesion area and disruption of the foveal inner‐segment/outer‐segment layer correlated with worse baseline BCVA. Polypoidal choroidal vasculopathy (PCV) type 1 was present in 50% and PCV type 2 in the other 50%. Polypoidal choroidal vasculopathy (PCV) type 1 was associated with a worse baseline BCVA and greater lesion size.ConclusionPolypoidal choroidal vasculopathy (PCV) is not a rare condition in Danes with exudative AMD and presents often extramacular and with haemorrhage. This study underscores the importance of ICGA as a part of the diagnostic repertoire in AMD and suggests its routine use in Scandinavian populations.
A systems medicine approach reveals disordered immune system and lipid metabolism in multiple sclerosis patients
Authors: Pazhouhandeh M , Sahraian M-A , Siadat S D , Fateh A , Vaziri F , Tabrizi F , Ajorloo F , Arshadi A K , Fatemi E , Piri Gavgani S , Mahboudi F , Rahimi Jamnani F 
Published: November 2017

SummaryIdentification of autoimmune processes and introduction of new autoantigens involved in the pathogenesis of multiple sclerosis (MS) can be helpful in the design of new drugs to prevent unresponsiveness and side effects in patients. To find significant changes, we evaluated the autoantibody repertoires in newly diagnosed relapsing–remitting MS patients (NDP) and those receiving disease-modifying therapy (RP). Through a random peptide phage library, a panel of NDP- and RP-specific peptides was identified, producing two protein data sets visualized using Gephi, based on protein-–protein interactions in the STRING database. The top modules of NDP and RP networks were assessed using Enrichr. Based on the findings, a set of proteins, including ATP binding cassette subfamily C member 1 (ABCC1), neurogenic locus notch homologue protein 1 (NOTCH1), hepatocyte growth factor receptor (MET), RAF proto-oncogene serine/threonine-protein kinase (RAF1) and proto-oncogene vav (VAV1) was found in NDP and was involved in over-represented terms correlated with cell-mediated immunity and cancer. In contrast, transcription factor RelB (RELB), histone acetyltransferase p300 (EP300), acetyl-CoA carboxylase 2 (ACACB), adiponectin (ADIPOQ) and phosphoenolpyruvate carboxykinase 2 mitochondrial (PCK2) had major contributions to viral infections and lipid metabolism as significant events in RP. According to these findings, further research is required to demonstrate the pathogenic roles of such proteins and autoantibodies targeting them in MS and to develop therapeutic agents which can ameliorate disease severity.
Incretin‐based therapies and risk of pancreatic cancer in patients with type 2 diabetes: A meta‐analysis of randomized controlled trials
Authors: Wang Haining , Liu Ye , Tian Qing , Yang Jin , Lu Ran , Zhan Siyan , Haukka Jari , Hong Tianpei 
Published: November 2017

AimsTo perform a meta‐analysis of randomized controlled trials (RCTs), including 6 recently published large‐scale cardiovascular outcome trials (CVOTs), to evaluate the risk of pancreatic cancer with incretin‐based therapies in patients with type 2 diabetes (T2DM).Materials and MethodsFor the period January 1, 2007 to May 1, 2017, the PubMed, Embase, Cochrane Central Register and ClininalTrials.gov databases were searched for RCTs in people with T2DM that compared incretin drugs with placebo or other antidiabetic drugs, with treatment and follow‐up durations of ≥52 weeks. Two reviewers screened the studies, extracted the data and assessed the risk of bias independently and in duplicate.ResultsA total of 33 studies (n = 79 971), including the 6 CVOTs, with 87 pancreatic cancer events were identified. Overall, the pancreatic cancer risk was not increased in patients administered incretin drugs compared with controls (Peto odds ratio [OR] 0.67, 95% confidence interval [CI] 0.44‐1.02). In the 6 CVOTs, 79 pancreatic cancer events were identified in 55 248 participants. Pooled estimates of the 6 CVOTs showed an identical tendency (Peto OR 0.65, 95% CI 0.42‐1.01). Notably, in the subgroup of participants who received treatment and follow‐up for ≥104 weeks, 84 pancreatic cancer events were identified in 59 919 participants, and a lower risk of pancreatic cancer was associated with incretin‐based therapies (Peto OR 0.62, 95% CI 0.41‐0.95).ConclusionsTreatment with incretin drugs was not associated with an increased risk of pancreatic cancer in people with T2DM. Instead, it might protect against pancreatic malignancy in patients treated for ≥104 weeks.