bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity
Authors: Marini Simone , Nazzicari Nelson , Biscarini Filippo , Wang Guang-Zhong 
Published: January 2017

Abstract

Motivation
Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations.

Results
We developed Dscam1 Web Server to quickly predict Dscam1 self- and hetero- binding affinity for batches of Dscam1 isomers. The server can help the study of Dscam1 affinity and help researchers navigate through the tens of millions of possible isomer combinations to isolate the strong-binding ones.

Availability and Implementation
Dscam1 Web Server is freely available at: http://bioinformatics.tecnoparco.org/Dscam1-webserver. Web server code is available at https://gitlab.com/ne1s0n/Dscam1-binding.

Supplementary information
Supplementary data are available at Bioinformatics online.
FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions
Authors: Iwayama Koji , Aisaka Yuri , Kutsuna Natsumaro , Nagano Atsushi J 
Published: January 2017

Abstract

Motivation
Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application.

Results
We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions.

Availability and Implementation
Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/).

Supplementary information
Supplementary data are available at Bioinformatics online
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
Authors: Haraldsdóttir Hulda S , Cousins Ben , Thiele Ines , Fleming Ronan M.T , Vempala Santosh 
Published: January 2017

Abstract

Summary
In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. We apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks.

Availability and Implementation
https://github.com/opencobra/cobratoolbox.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins
Authors: Tian Wei , Lin Meishan , Naveed Hammad , Liang Jie 
Published: January 2017

Abstract

Motivation
Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure–function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs.

Results
We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein.

Availability and Implementation
An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe.

Supplementary information
Supplementary data are available at Bioinformatics online.
Assessment of phagocytic activity in live macrophages-tumor cells co-cultures by Confocal and Nomarski Microscopy
Authors: Martinez-Marin Dalia , Jarvis Courtney , Nelius Thomas , Filleur Stéphanie 
Published: January 2017

AbstractMacrophages have been recognized as the main inflammatory component of the tumor microenvironment. Although often considered as beneficial for tumor growth and disease progression, tumor-associated macrophages have also been shown to be detrimental to the tumor depending on the tumor microenvironment. Therefore, understanding the molecular interactions between macrophages and tumor cells in relation to macrophages functional activities such as phagocytosis is critical for a better comprehension of their tumor-modulating action. Still, the characterization of these molecular mechanisms in vivo remains complicated due to the extraordinary complexity of the tumor microenvironment and the broad range of tumor-associated macrophage functions. Thus, there is an increasing demand for in vitro methodologies to study the role of cell–cell interactions in the tumor microenvironment. In the present study, we have developed live co-cultures of macrophages and human prostate tumor cells to assess the phagocytic activity of macrophages using a combination of Confocal and Nomarski Microscopy. Using this model, we have emphasized that this is a sensitive, measurable, and highly reproducible functional assay. We have also highlighted that this assay can be applied to multiple cancer cell types and used as a selection tool for a variety of different types of phagocytosis agonists. Finally, combining with other studies such as gain/loss of function or signaling studies remains possible. A better understanding of the interactions between tumor cells and macrophages may lead to the identification of new therapeutic targets against cancer.
Performance of hospitals according to the ESC ACCA quality indicators and 30-day mortality for acute myocardial infarction: national cohort study using the United Kingdom Myocardial Ischaemia National Audit Project (MINAP) register
Authors: Bebb Owen , Hall Marlous , Fox Keith A. A. , Dondo Tatendashe B. , Timmis Adam , Bueno Hector , Schiele François , Gale Chris P. 
Published: January 2017

Aims
To investigate the application of the European Society of Cardiology Acute Cardiovascular Care Association quality indicators (QI) for acute myocardial infarction for the study of hospital performance and 30-day mortality.

Methods and results
National cohort study (n = 118,075 patients, n = 211 hospitals, MINAP registry), 2012-13. Overall, 16 of the 20 QIs could be calculated. Eleven QIs had a significant inverse association with GRACE risk adjusted 30-day mortality (all P &lt; 0.005). The association with the greatest magnitude was high attainment of the composite opportunity-based QI (80-100%) vs. zero attainment (odds ratio 0.04, 95% confidence interval 0.04-0.05, P &lt; 0.001), increasing attainment from low (0.42, 0.37- 0.49, P &lt; 0.001) to intermediate (0.15, 0.13-0.16, P &lt; 0.001) was significantly associated with a reduced risk of 30-day mortality. A 1% increase in attainment of this QI was associated with a 3% reduction in 30-day mortality (0.97, 0.97-0.97, P &lt; 0.001). The QI with the widest hospital variation was ′fondaparinux received among NSTEMI′ (interquartile range 84.7%) and least variation ′centre organisation′ (0.0%), with seven QIs depicting minimal variation (&lt;11%). GRACE risk score adjusted 30-day mortality varied by hospital (median 6.7%, interquartile range 5.4-7.9%).

Conclusions
Eleven QIs were significantly inversely associated with 30-day mortality. Increasing patient attainment of the composite quality indicator was the most powerful predictor; a 1% increase in attainment represented a 3% decrease in 30-day standardised mortality. The ESC QIs for acute myocardial infarction are applicable in a large health system and have the potential to improve care and reduce unwarranted variation in death from acute myocardial infarction.
Sex hormones affect outcome in arrhythmogenic right ventricular cardiomyopathy/dysplasia: from a stem cell derived cardiomyocyte-based model to clinical biomarkers of disease outcome
Authors: Akdis Deniz , Saguner Ardan M. , Shah Khooshbu , Wei Chuanyu , Medeiros-Domingo Argelia , von Eckardstein Arnold , Lüscher Thomas F. , Brunckhorst Corinna , Chen H.S. Vincent , Duru Firat 
Published: January 2017

Aims
Arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) is characterized by fibrofatty infiltration of the myocardium and ventricular arrhythmias that may lead to sudden cardiac death. It has been observed that male patients develop the disease earlier and present with more severe phenotypes as compared to females. Thus, we hypothesized that serum levels of sex hormones may contribute to major arrhythmic cardiovascular events (MACE) in patients with ARVC/D.

Methods and results
The serum levels of five sex hormones, sex hormone-binding globulin, high sensitivity troponin T, pro-brain natriuretic peptide, cholesterol, triglycerides, insulin, and glucose were measured in 54 ARVC/D patients (72% male). Twenty-six patients (48%) experienced MACE. Total and free testosterone levels were significantly increased in males with MACE as compared to males with a favourable outcome, whereas estradiol was significantly lower in females with MACE as compared to females with a favourable outcome. Increased testosterone levels remained independently associated with MACE in males after adjusting for age, body mass index, Task Force criteria, ventricular function, and desmosomal mutation status. Furthermore, an induced pluripotent stem cell-derived ARVC/D cardiomyocyte model was used to investigate the effects of sex hormones. In this model, testosterone worsened and estradiol improved ARVC/D-related pathologies such as cardiomyocyte apoptosis and lipogenesis, strongly supporting our clinical findings.

Conclusions
Elevated serum testosterone levels in males and decreased estradiol levels in females are independently associated with MACE in ARVC/D, and directly influence disease pathology. Therefore, determining the levels of sex hormones may be useful for risk stratification and may open a new window for preventive interventions.
Determinants and clinical outcome of uptitration of ACE-inhibitors and beta-blockers in patients with heart failure: a prospective European study
Authors: Ouwerkerk W. , Voors A.A. , Anker S.D. , Cleland J.G. , Dickstein K. , Filippatos G. , van der Harst P. , Hillege H.L. , Lang C.C. , ter Maaten J.M. , Ng L.L. , Ponikowski P. , Samani N.J , van Veldhuisen D.J. , Zannad F. , Metra M. , Zwinderman A.H. 
Published: January 2017

Abstract

Introduction
Despite clear guidelines recommendations, most patients with heart failure and reduced ejection–fraction (HFrEF) do not attain guideline-recommended target doses. We aimed to investigate characteristics and for treatment-indication-bias corrected clinical outcome of patients with HFrEF that did not reach recommended treatment doses of ACE-inhibitors/Angiotensin receptor blockers (ARBs) and/or beta-blockers.

Methods and results
BIOSTAT-CHF was specifically designed to study uptitration of ACE-inhibitors/ARBs and/or beta-blockers in 2516 heart failure patients from 69 centres in 11 European countries who were selected if they were suboptimally treated while initiation or uptitration was anticipated and encouraged. Patients who died during the uptitration period (n = 151) and patients with a LVEF &gt; 40% (n = 242) were excluded. Median follow up was 21 months. We studied 2100 HFrEF patients (76% male; mean age 68 ±12), of which 22% achieved the recommended treatment dose for ACE-inhibitor/ARB and 12% of beta-blocker. There were marked differences between European countries. Reaching &lt;50% of the recommended ACE-inhibitor/ARB and beta-blocker dose was associated with an increased risk of death and/or heart failure hospitalization. Patients reaching 50–99% of the recommended ACE-inhibitor/ARB and/or beta-blocker dose had comparable risk of death and/or heart failure hospitalization to those reaching ≥100%. Patients not reaching recommended dose because of symptoms, side effects and non-cardiac organ dysfunction had the highest mortality rate (for ACE-inhibitor/ARB: HR 1.72; 95% CI 1.43–2.01; for beta-blocker: HR 1.70; 95% CI 1.36–2.05).

Conclusion
Patients with HFrEF who were treated with less than 50% of recommended dose of ACE-inhibitors/ARBs and beta-blockers seemed to have a greater risk of death and/or heart failure hospitalization compared with patients reaching ≥100%.
Renal sodium avidity in heart failure: from pathophysiology to treatment strategies
Authors: Mullens Wilfried , Verbrugge Frederik Hendrik , Nijst Petra , Tang Wai Hong Wilson 
Published: January 2017

Abstract
Increased neurohumoral stimulation resulting in excessive sodium avidity and extracellular volume overload are hallmark features of decompensated heart failure. Especially in case of concomitant renal dysfunction, the kidneys often fail to elicit effective natriuresis. While assessment of renal function is generally performed by measuring serum creatinine–a surrogate for glomerular filtration-, this only represents part of the nephron’s function. Alterations in tubular sodium handling are at least equally important in the development of volume overload and congestion. Venous congestion and neurohumoral activation in advanced HF further promote renal sodium and water retention. Interestingly, early on, before clinical signs of heart failure are evident, intrinsic renal derangements already impair natriuresis. This clinical review discusses the importance of heart failure (HF) induced changes in different nephron segments. A better understanding of cardiorenal interactions which ultimately result in sodium avidity in HF might help to treat and prevent congestion in chronic and acute HF.
Duration of device-detected subclinical atrial fibrillation and occurrence of stroke in ASSERT
Authors: Van Gelder Isabelle C. , Healey Jeff S. , Crijns Harry J.G.M. , Wang Jia , Hohnloser Stefan H. , Gold Michael R. , Capucci Alessandro , Lau Chu-Pak , Morillo Carlos A. , Hobbelt Anne H. , Rienstra Michiel , Connolly Stuart J. 
Published: January 2017

Background
ASSERT demonstrated that subclinical atrial fibrillation (SCAF) is common in pacemaker patients without prior AF and is associated with increased risk of ischemic stroke or systemic embolism. SCAF episodes vary in duration and little is known about the incidence of different durations of SCAF, or their prognosis.

Methods and results
ASSERT followed 2580 patients receiving a pacemaker or ICD, aged &gt;65 years with hypertension, without prior AF. The effect of SCAF duration on subsequent risk of ischemic stroke or embolism was evaluated with time-dependent covariate Cox models. Patients in whom the longest SCAF was ≤6 min were excluded from the analysis (n=125). Among 2455 patients during mean follow-up of 2.5 years, the longest single episode of SCAF lasted &gt;6 min to 6 h in 462 patients (18.8%), &gt;6–24 h in 169 (6.9%), and &gt;24 h in 262 (10.7%). SCAF duration &gt;24 h was associated with a significant increased risk of subsequent stroke or systemic embolism (adjusted hazard ratio [HR] 3.24, 95% confidence interval [CI] 1.51–6.95, P=0.003). The risk of ischemic stroke or systemic embolism in patients with SCAF between 6 min and 24 h was not significantly different from patients without SCAF.

Conclusions
SCAF &gt;24 h is associated with an increased risk of ischemic stroke or systemic embolism.
Une mémoire critique de la Fronde: formes et fonctions du pastiche dans les Mémoires apocryphes de Courtilz de Sandras
Authors: Tribout Bruno 
Published: January 2017

Résumé

Si la mémoire de la Fronde (1648
–
53) n’a pas fait l’objet d’une étude systématique, la critique s’est néanmoins beaucoup intéressée à la représentation de la guerre civile dans les Mémoires authentiques, écrits pour la plupart dans les premières décennies du règne de Louis XIV. Cet article se propose au contraire d’en étudier la représentation dans le genre des Mémoires apocryphes en vogue dans la seconde moitié du règne, en se penchant sur deux œuvres de Courtilz de Sandras (1644
–
1712): les
Mémoires de Mr. L. C. D. R.
(1687) et les
Mémoires de Mr. d’Artagnan
(1700). Ceux-ci permettent d’analyser la réception et la réécriture d’un premier ensemble de textes suscités par la Fronde. En abordant ces pseudo-Mémoires sous l’angle de l’imitation et du pastiche, on verra qu’ils font revivre une riche bibliothèque satirique où figurent, à côté des Mémoires authentiques, nombre de mazarinades et de romans historiques. La charge idéologique de cet intertexte conduira alors à s’interroger sur les fonctions du pastiche chez Courtilz de Sandras: on étudiera comment la réécriture pastichante de discours hétérogènes sur la Fronde sert moins ici une optique idéologique qu’une mise à distance ludique de l’histoire, promouvant des modes d’analyse critique du passé.
Les Projets du hérisson oreillard: l’écriture anti-référentielle d’Éric Chevillard
Authors: Piguet Raphaël 
Published: January 2017

Résumé

Cet article analyse l’écriture d’Éric Chevillard, considérée comme problématique par la critique contemporaine, sous un angle économique. Il montre que son œuvre entière, conçue comme dépense somptuaire de signifiants, refusant toute logique référentielle et s’inscrivant de fait dans une certaine tradition (Georges Bataille notamment), connaît un bouleversement significatif lorsque l’auteur se trouve confronté au réel (voyage au Mali) et veut en rendre compte avec
Oreille rouge
(2005). Contraint de faire du référentiel, Chevillard opte pour une stratégie qui lui permet de surmonter l’obstacle (mise en abyme par l’interpolation du personnage d’Oreille rouge, figure d’auteur partant en Afrique pour en tirer un poème), mais qui dévoile aussi les rouages de son œuvre: écrire pour publier, c’est
projeter
le vécu dans l’économique. Cette effraction du réel dans le système clos de son écriture affecte la production subséquente de l’auteur:
Démolir Nisard
(2006) s’attaque à un personnage double, écrivain-voyageur et critique littéraire, et cette lutte se prolonge dans
L’Auteur et moi
(2012): la problématique de la littérature référentielle rejoint celle du travail critique. Dans les deux cas, il s’agit toujours d’accumuler un capital référentiel à faire fructifier, et c’est précisément le propre de l’écriture de Chevillard que d’échapper à ce mode de production.
Towards automating underwater measurement of fish length: a comparison of semi-automatic and manual stereo–video measurements
Authors: Shafait Faisal , Harvey Euan S. , Shortis Mark R. , Mian Ajmal , Ravanbakhsh Mehdi , Seager James W. , Culverhouse Philip F. , Cline Danelle E. , Edgington Duane R. 
Published: January 2017

Abstract
Underwater stereo–video systems are widely used for counting and measuring fish in aquaculture, fisheries, and conservation management. Length measurements are generated from stereo–video recordings by a software operator using a mouse to locate the head and tail of a fish in synchronized pairs of images. This data can be used to compare spatial and temporal changes in the mean length and biomass or frequency distributions of populations of fishes. Since the early 1990s stereo–video has also been used for measuring the lengths of fish in aquaculture for quota and farm management. However, the costs of the equipment, software, the time, and salary costs involved in post processing imagery manually and the subsequent delays in the availability of length information inhibit the adoption of this technology.
We present a semi-automatic method for capturing stereo–video measurements to estimate the lengths of fish. We compare the time taken to make measurements of the same fish measured manually from stereo–video imagery to that measured semi-automatically. Using imagery recorded during transfers of Southern Bluefin Tuna (SBT) from tow cages to grow out cages, we demonstrate that the semi-automatic algorithm developed can obtain fork length measurements with an error of less than 1% of the true length and with at least a sixfold reduction in operator time in comparison to manual measurements. Of the 22 138 SBT recorded we were able to measure 52.6% (11 647) manually and 11.8% (2614) semi-automatically. For seven of the eight cage transfers recorde,d there were no statistical differences in the mean length, weight, or length frequency between manual and semi-automatic measurements. When the data were pooled across the eight cage transfers, there was no statistical difference in mean length or weight between the stereo–video-based manual and semi-automated measurements. Hence, the presented semi-automatic system can be deployed to significantly reduce the cost involved in adoption of stereo–video technology.