bluuebunny/crossref_metadata_2025_split huggingface dataset:
AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes
Authors: Zhang Yuqi , Sanner Michel F 
Published: May 2019

Abstract

Motivation
Protein–peptide interactions mediate a wide variety of cellular and biological functions. Methods for predicting these interactions have garnered a lot of interest over the past few years, as witnessed by the rapidly growing number of peptide-based therapeutic molecules currently in clinical trials. The size and flexibility of peptides has shown to be challenging for existing automated docking software programs.

Results
Here we present AutoDock CrankPep or ADCP in short, a novel approach to dock flexible peptides into rigid receptors. ADCP folds a peptide in the potential field created by the protein to predict the protein–peptide complex. We show that it outperforms leading peptide docking methods on two protein–peptide datasets commonly used for benchmarking docking methods: LEADS-PEP and peptiDB, comprised of peptides with up to 15 amino acids in length. Beyond these datasets, ADCP reliably docked a set of protein–peptide complexes containing peptides ranging in lengths from 16 to 20 amino acids. The robust performance of ADCP on these longer peptides enables accurate modeling of peptide-mediated protein–protein interactions and interactions with disordered proteins.

Availability and implementation
ADCP is distributed under the LGPL 2.0 open source license and is available at http://adcp.scripps.edu. The source code is available at https://github.com/ccsb-scripps/ADCP.

Supplementary information
Supplementary data are available at Bioinformatics online.
WDSPdb: an updated resource for WD40 proteins
Authors: Ma Jing , An Ke , Zhou Jing-Bo , Wu Nuo-Si , Wang Yang , Ye Zhi-Qiang , Wu Yun-Dong 
Published: May 2019

Abstract

Summary
The WD40-repeat proteins are a large family of scaffold molecules that assemble complexes in various cellular processes. Obtaining their structures is the key to understanding their interaction details. We present WDSPdb 2.0, a significantly updated resource providing accurately predicted secondary and tertiary structures and featured sites annotations. Based on an optimized pipeline, WDSPdb 2.0 contains about 600 thousand entries, an increase of 10-fold, and integrates more than 37 000 variants from sources of ClinVar, Cosmic, 1000 Genomes, ExAC, IntOGen, cBioPortal and IntAct. In addition, the web site is largely improved for visualization, exploring and data downloading.

Availability and implementation
http://www.wdspdb.com/wdsp/ or http://wu.scbb.pkusz.edu.cn/wdsp/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Limited intrinsic postzygotic reproductive isolation despite chromosomal rearrangements between closely related sympatric species of small ermine moths (Lepidoptera: Yponomeutidae)
Authors: Hora Katerina H , Marec František , Roessingh Peter , Menken Steph B J 
Published: May 2019

AbstractIn evolutionarily young species and sympatric host races of phytophagous insects, postzygotic incompatibility is often not yet fully developed, but reduced fitness of hybrids is thought to facilitate further divergence. However, empirical evidence supporting this hypothesis is limited. To assess the role of reduced hybrid fitness, we studied meiosis and fertility in hybrids of two closely related small ermine moths, Yponomeuta padella and Yponomeuta cagnagella, and determined the extent of intrinsic postzygotic reproductive isolation. We found extensive rearrangements between the karyotypes of the two species and irregularities in meiotic chromosome pairing in their hybrids. The fertility of reciprocal F1 and, surprisingly, also of backcrosses with both parental species was not significantly decreased compared with intraspecific offspring. The results indicate that intrinsic postzygotic reproductive isolation between these closely related species is limited. We conclude that the observed chromosomal rearrangements are probably not the result of an accumulation of postzygotic incompatibilities preventing hybridization. Alternative explanations, such as adaptation to new host plants, are discussed.
Bone histology of two pareiasaurs from Russia (Deltavjatia rossica and Scutosaurus karpinskii) with implications for pareiasaurian palaeobiology
Authors: Boitsova Elizaveta A , Skutschas Pavel P , Sennikov Andrey G , Golubev Valeriy K , Masuytin Vladimir V , Masuytina Olga A 
Published: May 2019

Abstract
Pareiasaurs were one of the main clades of large herbivorous tetrapods in Middle–Late Permian continental ecosystems. Despite abundant pareiasaur material, many aspects of their biology remain poorly known. This paper provides a description of ontogenetic changes in long-bone and rib microanatomy/histology of two Upper Permian pareiasaurs from Russia, Deltavjatia rossica and Scutosaurus karpinskii. Analysis of a growth series of bones of Deltavjatia and Scutosaurus revealed rapid and cyclical growth early in ontogeny (as indicated by fast-growing fibrolamellar bone with lines of arrested growth). This was followed by a change in the growth pattern (as indicated by an outer avascular layer of lamellar bone in the cortex) and a decrease in the growth rate after 50% of maximum body size was reached in Deltavjatia and 75% in Scutosaurus (larger body sizes in Scutosaurus were attained through an extended initial period of fast skeletal growth). The study confirms that the bones of all pareiasaurs are histologically and microanatomically uniform [spongious (porous) microstructure and a very thin compact cortex] and indicate a similar growth strategy (a short initial period of rapid and cyclical growth followed by a long period of slow growth). The microanatomical characteristics of pareiasaurs do not provide a clear indication of their lifestyle.
Early imaging predictors of long-term outcomes in relapse-onset multiple sclerosis
Authors: Brownlee Wallace J , Altmann Dan R , Prados Ferran , Miszkiel Katherine A , Eshaghi Arman , Gandini Wheeler-Kingshott Claudia A M , Barkhof Frederik , Ciccarelli Olga 
Published: May 2019

AbstractThe clinical course of relapse-onset multiple sclerosis is highly variable. Demographic factors, clinical features and global brain T2 lesion load have limited value in counselling individual patients. We investigated early MRI predictors of key long-term outcomes including secondary progressive multiple sclerosis, physical disability and cognitive performance, 15 years after a clinically isolated syndrome. A cohort of patients with clinically isolated syndrome (n = 178) was prospectively recruited within 3 months of clinical disease onset and studied with MRI scans of the brain and spinal cord at study entry (baseline) and after 1 and 3 years. MRI measures at each time point included: supratentorial, infratentorial, spinal cord and gadolinium-enhancing lesion number, brain and spinal cord volumetric measures. The patients were followed-up clinically after ∼15 years to determine disease course, and disability was assessed using the Expanded Disability Status Scale, Paced Auditory Serial Addition Test and Symbol Digit Modalities Test. Multivariable logistic regression and multivariable linear regression models identified independent MRI predictors of secondary progressive multiple sclerosis and Expanded Disability Status Scale, Paced Auditory Serial Addition Test and Symbol Digit Modalities Test, respectively. After 15 years, 166 (93%) patients were assessed clinically: 119 (72%) had multiple sclerosis [94 (57%) relapsing-remitting, 25 (15%) secondary progressive], 45 (27%) remained clinically isolated syndrome and two (1%) developed other disorders. Physical disability was overall low in the multiple sclerosis patients (median Expanded Disability Status Scale 2, range 0–10); 71% were untreated. Baseline gadolinium-enhancing (odds ratio 3.16, P < 0.01) and spinal cord lesions (odds ratio 4.71, P < 0.01) were independently associated with secondary progressive multiple sclerosis at 15 years. When considering 1- and 3-year MRI variables, baseline gadolinium-enhancing lesions remained significant and new spinal cord lesions over time were associated with secondary progressive multiple sclerosis. Baseline gadolinium-enhancing (β = 1.32, P < 0.01) and spinal cord lesions (β = 1.53, P < 0.01) showed a consistent association with Expanded Disability Status Scale at 15 years. Baseline gadolinium-enhancing lesions was also associated with performance on the Paced Auditory Serial Addition Test (β = − 0.79, P < 0.01) and Symbol Digit Modalities Test (β = −0.70, P = 0.02) at 15 years. Our findings suggest that early focal inflammatory disease activity and spinal cord lesions are predictors of very long-term disease outcomes in relapse-onset multiple sclerosis. Established MRI measures, available in routine clinical practice, may be useful in counselling patients with early multiple sclerosis about long-term prognosis, and personalizing treatment plans.
Language Without Speech: Segregating Distinct Circuits in the Human Brain
Authors: Finkl Theresa , Hahne Anja , Friederici Angela D , Gerber Johannes , Mürbe Dirk , Anwander Alfred 
Published: May 2019

Abstract
Language is a fundamental part of human cognition. The question of whether language is processed independently of speech, however, is still heavily discussed. The absence of speech in deaf signers offers the opportunity to disentangle language from speech in the human brain. Using probabilistic tractography, we compared brain structural connectivity of adult deaf signers who had learned sign language early in life to that of matched hearing controls. Quantitative comparison of the connectivity profiles revealed that the core language tracts did not differ between signers and controls, confirming that language is independent of speech. In contrast, pathways involved in the production and perception of speech displayed lower connectivity in deaf signers compared to hearing controls. These differences were located in tracts towards the left pre-supplementary motor area and the thalamus when seeding in Broca’s area, and in ipsilateral parietal areas and the precuneus with seeds in left posterior temporal regions. Furthermore, the interhemispheric connectivity between the auditory cortices was lower in the deaf than in the hearing group, underlining the importance of the transcallosal connection for early auditory processes. The present results provide evidence for a functional segregation of the neural pathways for language and speech.
Integrating physiological data with the conservation and management of fishes: a meta-analytical review using the threatened green sturgeon (Acipenser medirostris)
Authors: Rodgers Essie M , Poletto Jamilynn B , Gomez Isaza Daniel F , Van Eenennaam Joel P , Connon Richard E , Todgham Anne E , Seesholtz Alicia , Heublein Joe C , Cech Joseph J , Kelly John T , Fangue Nann A 
Published: May 2019

Abstract
Reversing global declines in the abundance and diversity of fishes is dependent on science-based conservation solutions. A wealth of data exist on the ecophysiological constraints of many fishes, but much of this information is underutilized in recovery plans due to a lack of synthesis. Here, we used the imperiled green sturgeon (Acipenser medirostris) as an example of how a quantitative synthesis of physiological data can inform conservation plans, identify knowledge gaps and direct future research actions. We reviewed and extracted metadata from peer-reviewed papers on green sturgeon. A total of 105 publications were identified, spanning multiple disciplines, with the primary focus being conservation physiology (23.8%). A meta-analytical approach was chosen to summarize the mean effects of prominent stressors (elevated temperatures, salinity, low food availability and contaminants) on several physiological traits (growth, thermal tolerance, swimming performance and heat shock protein expression). All examined stressors significantly impaired green sturgeon growth, and additional stressor-specific costs were documented. These findings were then used to suggest several management actions, such as mitigating salt intrusion in nursery habitats and maintaining water temperatures within optimal ranges during peak spawning periods. Key data gaps were also identified; research efforts have been biased towards juvenile (38.1%) and adult (35.2%) life-history stages, and less data are available for early life-history stages (embryonic, 11.4%; yolk-sac larvae, 12.4%; and post yolk-sac larvae, 16.2%). Similarly, most data were collected from single-stressor studies (91.4%) and there is an urgent need to understand interactions among stressors as anthropogenic change is multi-variate and dynamic. Collectively, these findings provide an example of how meta-analytic reviews are a powerful tool to inform management actions, with the end goal of maximizing conservation gains from research efforts.
The intestinal microbiota and cardiovascular disease
Authors: Katsimichas Themistoklis , Antonopoulos Alexios S , Katsimichas Alexandros , Ohtani Tomohito , Sakata Yasushi , Tousoulis Dimitris 
Published: May 2019

AbstractThe intestinal microbiota of human hosts is the community of microorganisms living in the small and, mainly, the large intestine of humans. This microbial ecosystem has co-evolved with humans across the millennia, has come to play an important interactive role in human physiology and has been aptly called our forgotten organ. Significant properties of the microbiota benefiting its host include energy harvest from food sources indigestible by humans, protection from pathogen colonization, and vitamin synthesis. Mounting evidence has linked changes in the composition or metabolic profiles of the microbiota with human disease, including disorders of the cardiovascular spectrum. Although cause and effect mechanisms are as yet essentially unproven in the relevant literature, the established associations point to the importance of the microbiota in the pathophysiology of cardiovascular disease (CVD). In this review, we first summarize key information on the gut microbial communities and the elaborate tools developed to analyse their structure and metabolic functions. Ecological terms are explained and analytical techniques are simplified, to enhance the understanding of published studies. Statistical methods used in microbial analysis are also described in simple terms. We then present published literature on the association of the compositional and functional changes of the microbiota with CVD, including heart failure, hypertension, and atherosclerosis. Each section of the review deals with the underlying pathophysiology of the relevant associations, connecting the observational and mechanistic aspects. Finally, we discuss the challenges that remain to be met before this field of research can generate knowledge which can impact everyday clinical practice.
Apixaban enhances endogenous fibrinolysis in patients with atrial fibrillation
Authors: Spinthakis Nikolaos , Gue Ying , Farag Mohamed , Srinivasan Manivannan , Wellsted David , Arachchillage Deepa R J , Lip Gregory Y H , Gorog Diana A 
Published: May 2019

Abstract

Aims
Approximately 20% of ischaemic stroke patients exhibit spontaneous arterial recanalization, attributable to endogenous fibrinolysis, which strongly relates to improved functional outcome. The impact of oral anticoagulants on endogenous fibrinolysis is unknown. Our aim was to test the hypothesis that apixaban enhances endogenous fibrinolysis in non-valvular atrial fibrillation (NVAF).

Methods and results
In a prospective cross-sectional analysis, we compared endogenous fibrinolysis in NVAF patients (n = 180) taking aspirin, warfarin, or apixaban. In a prospective longitudinal study, patients were tested before and after apixaban (n = 80). Endogenous fibrinolysis was assessed using the Global Thrombosis Test (GTT) and thromboelastography (TEG). Endogenous fibrinolysis [measured by GTT lysis time (LT)] was shorter on apixaban compared with warfarin or aspirin [median 1850 (IQR 1591–2300) vs. 2758 (2014–3502) vs. 2135 (1752–2463) s, P < 0.0001]. Among TEG indices, a small but significant difference in clot lysis time (CLT) was observed [apixaban 60.0 (45.0–61.0) vs. warfarin 61.0 (57.0–62.0) vs. aspirin 61.0 (59.0–61.0) min, P = 0.036]. Apixaban improved endogenous fibrinolysis measured using the GTT [LT pre-treatment 2204 (1779–2738) vs. on-treatment 1882 (1607–2374) s, P = 0.0003], but not by using TEG. Change in LT (ΔLT) with apixaban correlated with baseline LT (r = 0.77, P < 0.0001). There was weak correlation between ΔLT and ΔCLT in response to apixaban (r = 0.28, P = 0.02) and between on-apixaban LT and CLT (r = 0.25, P = 0.022).

Conclusion
Apixaban enhances endogenous fibrinolysis, with maximal effect in those with impaired fibrinolysis pre-treatment. Apixaban-treated patients exhibit more favourable fibrinolysis profiles than those taking warfarin or aspirin. Whether apixaban may confer additional thrombotic risk reduction in NVAF patients with impaired fibrinolysis, compared to warfarin, merits further study.
Bio-surfactin stabilised silver nanoparticles exert inhibitory effect over New-Delhi metallo-beta-lactamases (NDMs) and the cells harbouring NDMs
Authors: Kumar N Ganesh , Kumar Gaurav , Mallick Sathi , Ghosh Sudip Kumar , Pramanick Panchanan , Ghosh Anindya S 
Published: May 2019

Abstract
Silver nanoparticles (AgNPs) are used as an antimicrobial agent since the ages. However, it is unknown whether AgNPs exert inhibitory effects over the bacterial cells carrying metallo-beta-lactamases (MBLs). Here, using bio-surfactin stabilised AgNPs having a size range from 5 to 25 nm we established its antimicrobial effects against NDMs harbouring cells. Antimicrobial effectiveness of AgNPs is assessed on the E. coli cells carrying New Delhi MBL (NDM) genes, which shows that the cells expressing NDM becomes susceptible to AgNPs and when combined with various groups of beta-lactam a synergistic increase in sensitivity is observed. Purified NDMs are also inhibited by AgNPs as revealed by the hydrolysis of nitrocefin (a chromogenic cephalosporin), though the expression NDM genes remain unchanged. Further, the results obtained from biochemical analysis attribute that the Ag+ ions possibly bind to sulfhydryl (SH) group of cystine in NDMs to inactivate these enzymes. Nonetheless, these AgNPs has the ability to exert antimicrobial activity without affecting the host cell viability when used at a moderate concentration. Overall, we conclude that bio-surfactin-stabilised AgNP is a good candidate to serve as an inhibitor of NDMs, either individually or in combination with beta-lactams.
Antibiotic resistance breakers: current approaches and future directions
Authors: Laws Mark , Shaaban Ali , Rahman Khondaker Miraz 
Published: May 2019

ABSTRACTInfections of antibiotic-resistant pathogens pose an ever-increasing threat to mankind. The investigation of novel approaches for tackling the antimicrobial resistance crisis must be part of any global response to this problem if an untimely reversion to the pre-penicillin era of medicine is to be avoided. One such promising avenue of research involves so-called antibiotic resistance breakers (ARBs), capable of re-sensitising resistant bacteria to antibiotics. Although some ARBs have previously been employed in the clinical setting, such as the β-lactam inhibitors, we posit that the broader field of ARB research can yet yield a greater diversity of more effective therapeutic agents than have been previously achieved. This review introduces the area of ARB research, summarises the current state of ARB development with emphasis on the various major classes of ARBs currently being investigated and their modes of action, and offers a perspective on the future direction of the field.
ARBoR: an identity and security solution for clinical reporting
Authors: Venner Eric , Murugan Mullai , Hale Walker , Jones Jordan M , Lu Shan , Yi Victoria , Gibbs Richard A 
Published: May 2019

Abstract

Motivation
Clinical genome sequencing laboratories return reports containing clinical testing results, signed by a board-certified clinical geneticist, to the ordering physician. This report is often a PDF, but can also be a paper copy or a structured data file. The reports are frequently modified and reissued due to changes in variant interpretation or clinical attributes.

Materials and Methods
To precisely track report authenticity, we developed ARBoR (Authenticated Resources in a Hashed Block Registry), an application for tracking the authenticity and lineage of versioned clinical reports even when they are distributed as PDF or paper copies. ARBoR tracks clinical reports as cryptographically signed hash blocks in an electronic ledger file, which is then exactly replicated to many clients.

Results
ARBoR was implemented for clinical reporting in the Human Genome Sequencing Center Clinical Laboratory, initially as part of the National Institute of Health's Electronic Medical Record and Genomics (eMERGE) project.

Conclusions
To date, we have issued 15 205 versioned clinical reports tracked by ARBoR. This system has provided us with a simple and tamper-proof mechanism for tracking clinical reports with a complicated update history.
Molecular Survey of Babesia microti (Aconoidasida: Piroplasmida) in Wild Rodents in Turkey
Authors: Usluca Selma , Celebi Bekir , Karasartova Djursun , Gureser A Semra , Matur Ferhat , Oktem M Ali , Sozen Mustafa , Karatas Ahmet , Babur Cahit , Mumcuoglu Kosta Y , Taylan Ozkan Aysegul 
Published: May 2019

AbstractBabesia microti (Aconoidasida: Piroplasmida) (Franca, 1910) is an important tick-borne zoonotic parasite with rodents serving as reservoir hosts. In the present study, 536 rodents were captured from Burdur, Bartin, Giresun, and Yozgat provinces of Turkey between the years 2010 and 2012, and blood samples were examined for the presence of Babesia spp. using conventional PCR which targeted the 18S rRNA gene. The sequence analysis of PCR amplicons was tested for B. microti as well as for Hepatozoon spp., and Sarcocystis spp. Overall, 5.8% of the rodents were positive for B. microti: 41% in Myodes glareolus, 7.7% in Chionomys roberti, and 2% in Apodemus spp., whereas no Babesia DNA was detected in Mus macedonicus and Microtus spp. Six rodents were positive for Hepatozoon spp. and one rodent was positive for Sarcocystis spp. Overall, 14.9 and 4.5% of rodents captured from Bartin and Giresun provinces, respectively, were PCR positive for B. microti, whereas none of rodents captured in Burdur and Yozgat were positive for Babesia spp. The sequence data of B. microti from rodents revealed that all sequences belonged to the zoonotic genotype. Sequences of B. microti obtained from rodents of the Bartin province were genotypically closer to European isolates, whereas those obtained from rodents of the Giresun province were closer to Russian and Mongolian isolates.
Total Shoulder Arthroplasty
Authors: Sobey Christopher , Byrne David 
Published: May 2019

Abstract
This chapter describes patients undergoing total shoulder arthroplasty (TSA), who often present an array of challenging considerations regarding anesthetic management and perioperative pain control. Unlike in other types of shoulder surgery, patients undergoing TSA often have more significant comorbidities such as advanced age and morbid obesity that can affect outcomes in the perioperative period. Preoperative screening should be performed to allow adequate planning for the day of surgery and to ensure adequate postoperative monitoring. Because the procedure is an open surgical approach, it can be very stimulating, and extra consideration for perioperative analgesia should be taken. Careful consideration of multimodal (balanced) analgesic modalities to account for potential respiratory compromise, and incorporation of regional anesthetic modalities can contribute to successful delivery of anesthesia and safe recovery thereafter.