bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neue Antidiabetika und kardiovaskuläre Outcome-Studien
Authors: Seufert Jochen , Laubner Katharina 
Published: September 2017

AbstractType 2 diabetes mellitus (T2DM) represents a major risk factor for the development of cardiovascular events, and cardiovascular mortality determines overall mortality in these patients. So far, glucose lowering per se has demonstrated a small effect in reduction of cardiovascular risk in T2DM patients. Due to regulatory purposes, since 2008 all novel antidiabetic medications, such as DPP4 inhibitors, GLP-1 receptor agonists and SGLT2 inhibitors are investigated in dedicated cardiovascular outcome trials to demonstrate cardiovascular safety (non-inferiority trials). While the currently completed cardiovascular outcome trials for the DPP4 inhibitors sitagliptin, saxagliptin and alogliptin consistently demonstrated a neutral effect on cardiovascular risk, those trials for the GLP-1 receptor agonists revealed differential outcomes. Lixisenatide effects were neutral on cardiovascular outcomes while Liraglutide and Semaglutide demonstrated a reduction in cardiovascular risk. Most impressively was cardiovascular mortality, overall mortality and hospitalisation for heart failure reduced by the SGLT2 inhibitor empagliflozin in its dedicated outcome trial. These results strongly imply that certain novel antihyperglycaemic agents bear the potential to strongly reduce cardiovascular risk in patients with T2DM beyond their glucose lowering potency. The potential to reduce cardiovascular risk in patients with T2DM will selectively determine the clinical application of antidiabetic medications in the future.
“It fixates”: indie quiets and the new Gothics
Authors: Hawkins Joan 
Published: September 2017

AbstractThe article attempts to make several interventions. Following Jamie Sexton’s work on Independent Horror, it revisits the vexed status of horror within American Independent Cinema. Not only is indie horror frequently omitted from discussion of American Independent Cinema, but low budget, direct-to-DVD and video-on-demand indie horror titles are frequently omitted from academic discussions of horror. This has the effect of skewing our understanding of the genre. From there the article moves to consider a specific subgenre of indie horror that has been gaining in popularity: the Quiet Horror film—a category that contains the sub-genre of indie-Gothic films. Lastly, the paper moves on to a close reading of a specific low budget indie Gothic title, Absentia.
MicroRNA-34ainduces transdifferentiation of glioma stem cells into vascular endothelial cells by targeting Notch pathway
Authors: Jin Zaishun , Zhan Tao , Tao Jing , Xu Biao , Zheng Huizhe , Cheng Yongxia , Yan Bin , Wang Hongwei , Lu Guoqiang , Lin Ying , Guo Sufen 
Published: September 2017

AbstractThe function of microRNA-34a (miR-34a) in transdifferentiation of glioma stem cells (GSCs) into vascular endothelial cells (VECs) was explored by focusing on Notch ligand Delta-like 1 (Dll1). MiR-34a mimics was transfected into CD133 + glioma cell U251. The angiogenesis feature of miR-34a transfected U251 cells was investigated and the expressions of CD31, CD34, Vwf, Notch 1, and Dll1 were quantified. Length of branching vessel-like structures in the miR-34a transfected U251 cells was significantly higher than control cells. The VEC feature of miR-34a overexpressed U251 cells was further confirmed by the expressions of CD31, CD34, and vWF. Transfection of miR-34a decreased the expression of Notch 1 and Dll1. Furthermore, the miR-34a overexpression-enhanced tube formation of GSCs was suppressed when the decreased expression of Dll1 was restored. The current study highlighted the potential of miR-34a as an inducer in GSCs’ transdifferentiation into VECs by targeting Dll1.
Acute cardiorespiratory, perceptual and enjoyment responses to high‐intensity interval exercise in adolescents
Authors: Malik Adam A. , Williams Craig A. , Bond Bert , Weston Kathryn L. , Barker Alan R. 
Published: September 2017

AbstractThis study aimed to examine adolescents’ acute cardiorespiratory and perceptual responses during high‐intensity interval exercise (HIIE) and enjoyment responses following HIIE and work‐matched continuous moderate intensity exercise (CMIE). Fifty‐four 12‐ to 15‐year olds (27 boys) completed 8 × 1‐min cycling at 90% peak power with 75‐s recovery (HIIE) and at 90% of the gas exchange threshold (CMIE). Absolute oxygen uptake (), percentage of maximal (%), heart rate (HR), percentage of maximal HR (%HRmax) and ratings of perceived exertion (RPE) were collected during HIIE. Enjoyment was measured using the physical activity enjoyment scale (PACES) following HIIE and CMIE. Boys elicited higher absolute during HIIE work (p < .01, effect size (ES) > 1.22) and recovery (p < .02, ES > 0.51) intervals but lower % during HIIE recovery intervals compared to girls (p < .01, ES > 0.67). No sex differences in HR and %HRmax were evident during HIIE and 48 participants attained ≥90% HRmax. Boys produced higher RPE at intervals 6 (p = .004, ES = 1.00) and 8 (p = .003, ES = 1.00) during HIIE. PACES was higher after HIIE compared with CMIE (p = .003, ES = 0.58). Items from PACES “I got something out of it”, “It's very exciting” and “It gives me a strong feeling of success” were higher after HIIE (all p < .01, ES > 0.32). The items “I feel bored” and “It's not at all interesting” were higher after CMIE (all p < .01, ES > 0.46). HIIE elicits a maximal cardiorespiratory response in most adolescents. Greater enjoyment after HIIE was due to elevated feelings of reward, excitement and success and may serve as a strategy to promote health in youth.
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments
Authors: Guzenko Dmytro , Strelkov Sergei V 
Published: September 2017

AbstractMotivationAccurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ∼300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases.ResultsHere we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes.Availability and implementationThe source code is freely available at https://github.com/biocryst/IF; a web server to run the program is at http://pharm.kuleuven.be/Biocrystallography/cc.Supplementary informationSupplementary data are available at Bioinformatics online.
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
Authors: Menegidio Fabiano B , Jabes Daniela L , Costa de Oliveira Regina , Nunes Luiz R 
Published: September 2017

Abstract

Summary
This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects.

Availability and implementation
Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license.
LightDock: a new multi-scale approach to protein–protein docking
Authors: Jiménez-García Brian , Roel-Touris Jorge , Romero-Durana Miguel , Vidal Miquel , Jiménez-González Daniel , Fernández-Recio Juan 
Published: September 2017

Abstract

Motivation
Computational prediction of protein–protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity complexes or transient interactions. A major challenge is how to efficiently sample the structural and energetic landscape of the association at different resolution levels, given that each scoring function is often highly coupled to a specific type of search method. Thus, new methodologies capable of accommodating multi-scale conformational flexibility and scoring are strongly needed.

Results
We describe here a new multi-scale protein–protein docking methodology, LightDock, capable of accommodating conformational flexibility and a variety of scoring functions at different resolution levels. Implicit use of normal modes during the search and atomic/coarse-grained combined scoring functions yielded improved predictive results with respect to state-of-the-art rigid-body docking, especially in flexible cases.

Availability and implementation
The source code of the software and installation instructions are available for download at https://life.bsc.es/pid/lightdock/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Overview: Risk Factors and Historic Levels of Pressure From Insect Pests of Seedling Corn, Cotton, Soybean, and Wheat in the United States
Authors: Papiernik Sharon K , Sappington Thomas W , Luttrell Randall G , Hesler Louis S , Allen K Clint 
Published: September 2017

Abstract
The use of neonicotinoid insecticides in the United States has grown by about a factor of four since the mid-2000s. Seed treatments account for a significant fraction of overall insecticide application to crops, and a large proportion of major U.S. crops are now planted using seed treated with neonicotinoids. Neonicotinoid insecticidal seed treatments are primarily intended to protect crops against sporadic or minor early-season pests. A better understanding of factors that influence the risk of economic infestations and extent of crop damage by sporadic pests is needed to target neonicotinoid insecticidal seed treatments use based on expected pest pressure. In a series of papers, we review the distribution, ecology, and historical management of seed and seedling pests targeted by neonicotinoid seed treatments in U.S. corn (Zea mays), soybean (Glycine max), wheat (Triticum aestivum), and cotton (Gossypium hirsutum L.). This information is key to region-specific management practices that reduce the risks and increase the benefits of neonicotinoid seed treatments.
AGN jet feedback on a moving mesh: cocoon inflation, gas flows and turbulence
Authors: Bourne Martin A. , Sijacki Debora 
Published: September 2017

AbstractIn many observed galaxy clusters, jets launched by the accretion process on to supermassive black holes, inflate large-scale cavities filled with energetic, relativistic plasma. This process is thought to be responsible for regulating cooling losses, thus moderating the inflow of gas on to the central galaxy, quenching further star formation and maintaining the galaxy in a red and dead state. In this paper, we implement a new jet feedback scheme into the moving mesh-code arepo, contrast different jet injection techniques and demonstrate the validity of our implementation by comparing against simple analytical models. We find that jets can significantly affect the intracluster medium (ICM), offset the overcooling through a number of heating mechanisms, as well as drive turbulence, albeit within the jet lobes only. Jet-driven turbulence is, however, a largely ineffective heating source and is unlikely to dominate the ICM heating budget even if the jet lobes efficiently fill the cooling region, as it contains at most only a few per cent of the total injected energy. We instead show that the ICM gas motions, generated by orbiting substructures, while inefficient at heating the ICM, drive large-scale turbulence and when combined with jet feedback, result in line-of-sight velocities and velocity dispersions consistent with the Hitomi observations of the Perseus cluster.
Methadone and the QTc Interval: Paucity of Clinically Significant Factors in a Retrospective Cohort
Authors: Bart Gavin , Wyman Zachary , Wang Qi , Hodges James S. , Karim Rehan , Bart Bradley A. 
Published: September 2017

Objective:
Methadone is associated with prolongation of the electrocardiographic QTc interval. QTc prolongation may be linked to cardiac dysrhythmia and sudden cardiac death. The rate of these events is unknown in methadone-maintained patients.

Methods:
This retrospective cohort study of 749 patients with opioid use disorder receiving methadone maintenance therapy through a single safety-net hospital, queried the electronic health record for electrocardiogram results, demographics, methadone dose, and diagnostic codes consistent with cardiac conduction disorder (International Classification of Disease, Ninth Revision [ICD-9] 426) and cardiac dysrhythmia (ICD-9 427). Factors associated with QTc interval were explored; Cox proportional-hazards regression models were used to analyze time to an event that may predispose to sudden cardiac death.

Results:
One hundred thirty-four patients had an electrocardiogram while on methadone, 404 while off methadone, and 211 both while on and off methadone. Mean QTc interval while on methadone (436 ms, SD 36) was significantly greater than while off methadone (423 ms, SD 33). Age and methadone dose were weakly associated with increased QTc interval (P < 0.01 and P < 0.0005, respectively, adjusted R
2 = 0.05). There were 44 ICD-9 426 and 427 events over 7064 patient-years (6.3 events/1000 patient-yrs). Having a QTc greater than sex-specific cut-off values was significantly associated with time to event (hazard ratio 3.32, 95% confidence interval 1.25–8.81), but being on methadone was not.

Conclusions:
Methadone is associated with QTc prolongation in a nonclinically significant dose-related manner. Cardiac events were rare and the sudden cardiac death rate was below that of the general population. Current recommendations for cardiac risk assessment in methadone-maintained patients should be reconsidered.
Stop and go: hematopoietic cell transplantation in the era of chimeric antigen receptor T cells and checkpoint inhibitors
Authors: Ghosh Arnab , Politikos Ioannis , Perales Miguel-Angel 
Published: September 2017

Purpose of review
For several decades, hematopoietic cell transplantation (HCT) has been considered the standard curative therapy for many patients with hematological malignancies. In addition to the cytotoxic effects of the chemotherapy and radiation used in the conditioning regimen, the benefits of HCT are derived from a reset of the immune system and harnessing the ability of donor T cells to eliminate malignant cells. With the dawn of the era of immunotherapies in the form of checkpoint inhibitors and chimeric antigen receptor (CAR) T cells, the role of HCT has evolved.

Recent findings
Immunotherapy with checkpoint inhibitors is increasingly being used for relapsed Hodgkin and non-Hodgkin lymphoma after autologous HCT. Checkpoint inhibitors are also being tested after allogeneic HCT with observable benefits in treating hematological malignancies, but with a potential risk of increased graft versus host disease and transplant-related mortality. Immunotherapy with Cluster of differentiation 19 CAR T cells are powerful options with aggressive B-cell malignancies both for therapy and as induction leading to allogeneic HCT.

Summary
Although immunotherapies with checkpoint inhibition and CAR T cells are increasingly being used to treat hematological malignancies, HCT remains a standard of care for most of the diseases with the best chance of cure. Combination of these therapies with HCT has the potential to more effectively treat hematological malignancies.
Changes in Corneal Density After Accelerated Corneal Collagen Cross-linking With Different Irradiation Intensities and Energy Exposures: 1-Year Follow-up
Authors: Akkaya Turhan Semra , Toker Ebru 
Published: September 2017

Purpose:
To determine and compare the changes in corneal density after 2 different protocols of accelerated corneal collagen cross-linking (A-CXL) in patients with progressive keratoconus.

Methods:
Two groups of eyes received A-CXL treatment; 20 eyes received A-CXL using continuous UVA light exposure at 9 mW/cm2 for 10 minutes with a total energy dose of 5.4 J/cm2, and 24 eyes received A-CXL using continuous UVA light exposure at 30 mW/cm2 for 4 minutes with a total energy dose of 7.2 J/cm2. Corneal density was measured with Scheimpflug tomography at 1, 3, 6, and 12 months of follow-up.

Results:
Densitometry peaked at 1 month (mean: 16.34 ± 3.80, P = 0.006, 9-mW/cm2 A-CXL; mean: 20.90 ± 2.81, P < 0.0001, 30-mw/cm2 A-CXL) in both groups, and it decreased over time in 30-mW/cm2 A-CXL. However, in 9-mW/cm2 A-CXL, increased corneal densitometry plateaued until 6 months postoperatively and started to decrease thereafter. Densitometry completely returned to baseline after 12 months in both groups. The mean change in density at 1- and 3-month follow-up was higher in the 30-mW A-CXL group than in the 9-mW A-CXL group (P = 0.003, P = 0.044; respectively).

Conclusions:
High-energy exposure tends to induce more haze in the early posttreatment period, but it is reversible.
Tear Osmolarity and Correlation With Ocular Surface Parameters in Patients With Dry Eye
Authors: Mathews Priya M. , Karakus Sezen , Agrawal Devika , Hindman Holly B. , Ramulu Pradeep Y. , Akpek Esen K. 
Published: September 2017

Purpose:
To analyze the distribution of tear film osmolarity in patients with dry eye and its association with other ocular surface parameters.

Methods:
Tear osmolarity and other quantitative dry eye parameters were obtained from patients with 1) clinically significant dry eye (significant symptoms and ocular surface staining, n = 131), 2) symptoms-only dry eye (significant symptoms but no significant ocular surface staining, n = 52), and 3) controls (no significant symptoms or staining, n = 42).

Results:
Tear osmolarity varied significantly across groups (P = 0.01), with patients with clinically significant dry eye having the highest tear osmolarity (312.0 ± 16.9 mOsm/L), control patients having the lowest tear osmolarity (305.6 ± 9.7 mOsm/L), and patients with symptoms-only dry eye falling in between (307.4 ± 5.6 mOsm/L). Patients with clinically significant dry eye also tended to have a greater intereye difference in osmolarity (12.0 ± 13.4) than did the individuals with symptoms-only dry eye (9.1 ± 12.4) and controls (9.0 ± 7.4) (P = 0.06). In multivariable regression models, higher tear osmolarity was associated with higher Ocular Surface Disease Index, discomfort subscore (P = 0.02), and higher corneal and conjunctival staining scores (P < 0.01 for both). Worse eye tear osmolarity was not correlated with the corresponding tear film breakup time or Schirmer test (P > 0.05 for both).

Conclusions:
Individuals with symptomatic dry eye that is not yet clinically significant seem to have higher and more variable osmolarity measurements than controls, potentially indicating that changes in osmolarity precede clinical findings.
An Aesthetic Orbicularis Oculi Myectomy Technique for Blepharospasm: Use of Topical 5-Fluorouracil and Fibrin Sealant
Authors: Stewart Krista J. , Joseph Shannon S. , Douglas Raymond S. 
Published: September 2017

Purpose:
To describe a modified technique of orbicularis oculi myectomy for refractory blepharospasm. This technique includes removal of orbicularis muscle, reformation of the eyelid crease and pretarsal platform using fibrin sealant (Tisseel), and topical 5-fluorouracil to reduce scar formation and improve aesthetic outcome.

Methods:
Retrospective chart review of 7 patients who underwent bilateral orbicularis oculi myectomy with our technique from 2013 to 2016. Outcome measures were postoperative botulinum toxin dose, frequency, duration between treatments, the amount of lagophthalmos, severity of dry eye, and patient satisfaction with aesthetic and functional outcome.

Results:
Patients who underwent the aesthetic myectomy technique had significantly decreased botulinum toxin use with relief of symptoms postoperatively. Only 1 of 7 patients experienced mild dry eye symptoms postoperatively, managed with artificial tears. All patients were satisfied with the aesthetic and functional outcome.

Conclusions:
The aesthetic myectomy technique provides effective treatment for blepharospasm with good functional and aesthetic outcome.
Osteogenesis imperfecta: diagnosis and treatment
Authors: Palomo Telma , Vilaça Tatiane , Lazaretti-Castro Marise 
Published: September 2017

Purpose of review
Here we summarize the diagnosis of osteogenesis imperfecta, discuss newly discovered genes involved in osteogenesis imperfecta, and review the management of this disease in children and adults.

Recent findings
Mutations in the two genes coding for collagen type I, COL1A1 and COL1A2, are the most common cause of osteogenesis imperfecta. In the past 10 years, defects in at least 17 other genes have been identified as responsible for osteogenesis imperfecta phenotypes, with either dominant or recessive transmission. Intravenous bisphosphonate infusions are the most widely used medical treatment. This has a marked effect on vertebra in growing children and can lead to vertebral reshaping after compression fractures. However, bisphosphonates are less effective for preventing long-bone fractures. At the moment, new therapies are under investigation.

Summary
Despite advances in the diagnosis and treatment of osteogenesis imperfecta, more research is needed. Bisphosphonate treatment decreases long-bone fracture rates, but such fractures are still frequent. New antiresorptive and anabolic agents are being investigated but efficacy and safety of these drugs, especially in children, need to be better established before they can be used in clinical practice.