bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Procoagulant Response of Cytomegalovirus Infected Endothelial Cells
Authors: van Dam-Mieras M C E , Muller A D , van Hinsbergh V W M , Mullers W J H A , Bomans P H H , Bruggeman C A 
Published: July 2018

SummaryThe report describes the effect of an in vitro infection of human umbilical vein endothelial cells with human Cytomegalovirus (CMV). The parameters studied are cellular procoagulant activity, secretion of plasminogen activator inhibitor (PAI-1) and urokinase-type plasminogen activator (u-PA), activation and internalization of factor X and Merocyanine 540 staining.The infection does not result in an increase in PAI-1 and u-PA secretion, but it brings about a procoagulant response, which is relatively rapid compared to the tissue factor mediated response induced by inflammatory mediators. The time course and the coagulation factor dependency suggest a facilitated interaction of coagulation factors on the surface of infected cells. Chromogenic activity measurements after the addition of purified factor X and electron microscopic examination of the cells after addition of colloidal gold-factor X conjugates both point to an internalization of factor X and/or Xa after interaction with the endothelial cell surface. Merocyanine 540 staining suggests that CMV infection leads to membrane pertubations.
Genetic Variation in the Syntaxin-Binding Protein STXBP5 in Type 1 von Willebrand Disease Patients
Authors: Lind-Halldén Christina , Manderstedt Eric , Carlberg Daniel , Lethagen Stefan , Halldén Christer 
Published: July 2018

Abstractvon Willebrand factor (VWF) levels in healthy individuals and in patients with type 1 von Willebrand disease (VWD) are influenced by genetic variation in several genes, for example, VWF, ABO and STXBP5. Here, we comprehensively screen for STXBP5 variants and investigate their association with type 1 VWD in Swedish patients and controls. The coding region of the STXBP5 gene was re-sequenced in 107 type 1 VWD patients and the detected variants were genotyped in the type 1 VWD population and a Swedish control population (464 individuals). The functional effects of missense alleles were predicted in silico and the pattern of genetic variation in STXBP5 was analysed. Re-sequencing of 107 type 1 VWD patients identified three missense and three synonymous variants in the coding sequence of STXBP5. The low-frequency missense variants rs144099092 (0.005) and rs148830578 (0.029) were predicted to be damaging, but were not accumulated in patients. No other rare candidate mutations were detected. STXBP5 showed a high level of linkage disequilibrium and a low overall nucleotide diversity of π = 3.2 × 10−4 indicating intolerance to variants affecting protein function. Three previously type 1 VWD-associated single nucleotide polymorphisms were located on one haplotype that showed an increased frequency in patients versus controls. No differences in messenger ribonucleic acid abundance among haplotypes could be found using Genotype-Tissue Expression project data. In conclusion, a haplotype containing the STXBP5 Asn436Ser (rs1039084) mutation is associated with type 1 VWD and no rare STXBP5 mutations contribute to type 1 VWD in the Swedish population.
Urinuntersuchung – Schritt für Schritt
Authors: Kimmel Martin , Biegger Dagmar , Alscher Mark 
Published: July 2018

AbstractThe examination of the urine is the oldest and a very basic technique for every nephrologist. It helps to detect, diagnose and classify diseases of the kidneys and the urinary tract. Proteinuria is an important sign of kidney disease and an own factor in the pathophysiology of renal progression. Acanthocytes in the urine (> 5 %) have a high specifity (98 – 100 %) for diagnosing a glomerular hematuria.
Real Kummer quartics and their Heisenberg invariance
Authors: Krasnov V. A. 
Published: July 2018

Abstract
We consider two classifications of real Kummer quartics. They use the Heisenberg invariance of Kummer quartics. The first divides the whole variety of real Kummer quartics into four classes according to the Heisenberg-invariance type and then subdivides each class into subclasses to obtain a deformation classification. This subdivision into subclasses is performed by means of the topological classification of the real parts of real Kummer quartics. The second classification deals with the set of real Kummer quartics with a fixed Heisenberg group. Such a set consists of a continuous part and a discrete part. We describe the deformation classes of the continuous part and describe its discrete part.
Diffusion samples as a high-throughput screening method for alloy development
Authors: Ratschbacher Karin , Klotz Ulrich E. , Eisenbart Miriam 
Published: July 2018

Diffusion couples of copper alloys are presented as screening tool for high-throughput alloy development. It allows estimating the precipitation hardening potential in multicomponent alloys of a vast number of compositions within one sample. The components were diffusion welded and annealed to form compositional gradients which were characterised through a grid of energy dispersive X-ray spectroscopy measurements. After splitting the different sample parts underwent different tempering treatments. Thereafter micro hardness grids matching the spectroscopy data were recorded and displayed in contour plots as a function of alloy composition that instantly show composition areas with hardening potential. A critical assessment of the reliability of the method is provided and checked for cu-Al/mn-Sn-ti systems against literature data. This paper is part of a Thematic Issue on Copper and its Alloys.
Identification and characterization of a rhamnosyltransferase involved in rutin biosynthesis in Fagopyrum esculentum (common buckwheat)
Authors: Koja Eiki , Ohata Soichiro , Maruyama Yoshinori , Suzuki Hideyuki , Shimosaka Makoto , Taguchi Goro 
Published: July 2018

ABSTRACT
Rutin, a 3-rutinosyl quercetin, is a representative flavonoid distributed in many plant species, and is highlighted for its therapeutic potential. In this study, we purified uridine diphosphate-rhamnose: quercetin 3-O-glucoside 6″-O-rhamnosyltransferase and isolated the corresponding cDNA (FeF3G6″RhaT) from seedlings of common buckwheat (Fagopyrum esculentum). The recombinant FeF3G6″RhaT enzyme expressed in Escherichia coli exhibited 6″-O-rhamnosylation activity against flavonol 3-O-glucoside and flavonol 3-O-galactoside as substrates, but showed only faint activity against flavonoid 7-O-glucosides. Tobacco cells expressing FeF3G6″RhaT converted the administered quercetin into rutin, suggesting that FeF3G6″RhaT can function as a rhamnosyltransferase in planta. Quantitative PCR analysis on several organs of common buckwheat revealed that accumulation of FeF3G6″RhaT began during the early developmental stages of rutin-accumulating organs, such as flowers, leaves, and cotyledons. These results suggest that FeF3G6″RhaT is involved in rutin biosynthesis in common buckwheat.
Serum Potassium and Cardiovascular Events in Heart Failure With Preserved Left Ventricular Ejection Fraction Patients
Authors: Nishihara Taiki , Tokitsu Takanori , Sueta Daisuke , Takae Masafumi , Oike Fumi , Fujisue Koichiro , Usuku Hiroki , Takashio Seiji , Hanatani Shinsuke , Kanazawa Hisanori , Arima Yuichiro , Sakamoto Kenji , Izumiya Yasuhiro , Yamabe Hiroshige , Kaikita Koichi , Yamamoto Eiichiro , Tsujita Kenichi 
Published: July 2018

Abstract

BACKGROUND
Although serum potassium (sK) levels are closely associated with the prognosis of chronic heart failure patients, the clinical significance of sK levels in cardiovascular outcomes of heart failure with preserved ejection fraction (HFpEF) patients is not fully understood.

METHODS
This study was a retrospective, single-center, observational study. We enrolled 506 consecutive HFpEF patients admitted to Kumamoto University Hospital and divided them into four groups according to the quartiles of the sK levels at discharge (Q1: sK &lt; 4.1 mEq/l, Q2: 4.1 ≤ sK &lt; 4.4 mEq/l, Q3: 4.4 ≤ sK &lt; 4.7 mEq/l, and Q4: sK ≥ 4.7 mEq/l).

RESULTS
No significant differences were observed in the use of all drugs (loop diuretics, mineralocorticoid receptor antagonists, renin-angiotensin-aldosterone system inhibitors, calcium channel blockers, β-blockers, and statins) among the four groups. Hemoglobin, the estimated glomerular filtration rate, and pulse wave velocity levels were lower, and the serum sodium levels were higher in the Q4 group compared with those in the Q2 group. Kaplan–Meier analysis revealed significantly higher probabilities of both cardiovascular and HF-related events in the Q1, Q3, and Q4 groups than those in the Q2 group. Multivariate Cox proportional hazard analysis revealed that the Q1, Q3, and Q4 groups had significantly and independently higher probabilities of cardiovascular events compared with those in the Q2 group, indicating a J-shaped association between sK levels and cardiovascular events.

CONCLUSIONS
sK levels at discharge could provide important prognostic information in regard to HFpEF. Further evaluation in a larger number of patients might be needed.

Clinical Trials Registration
UMIN-CTR (http://www.umin.ac.jp/ctr/).

Identifier
UMIN000029600.

Public Access Information
Opt-out materials are available at the website: http://www.kumadai-junnai.com/home/wp-content/uploads/houkatsu.pdf.
iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data
Authors: Patel Mitulkumar V 
Published: July 2018

Abstract

Summary
Interactive platform for single-cell RNA-sequencing (iS-CellR) is a web-based Shiny application that is designed to provide user-friendly, comprehensive analysis of single-cell RNA sequencing data. iS-CellR has the capability to run on any modern web browser and provides an accessible graphical user interface that enables the user to perform complex single-cell RNA-sequencing analysis without requiring programming skills.

Availability and implementation
iS-CellR is open source and available through GitHub at https://github.com/immcore/iS-CellR. iS-CellR is implemented in Docker and can be launched on any operating system with Docker installed.

Supplementary information
Supplementary data are available at Bioinformatics online.
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications
Authors: Damerell David R , Strain-Damerell Claire , Garsot Sefa , Joyce Stephen P , Barrett Paul , Marsden Brian D 
Published: July 2018

Abstract

Summary
SATurn is a modular, open-source, bioinformatics platform designed to specifically address the problems of maintenance and longevity commonly associated with the development of simple tools funded by academic research grants. Applications developed in SATurn can be deployed as web-based tools, standalone applications or hybrid tools which have the benefits of both. Within the Structural Genomics Consortium we have utilized SATurn to create a bioinformatics portal which routinely supports a diverse group of scientists including those interested in structural biology, cloning, glycobiology and chemical biology.

Availability and implementation
https://github.com/ddamerell53/SATurn

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results
Authors: Frainay Clément , Aros Sandrine , Chazalviel Maxime , Garcia Thomas , Vinson Florence , Weiss Nicolas , Colsch Benoit , Sedel Frédéric , Thabut Dominique , Junot Christophe , Jourdan Fabien 
Published: July 2018

Abstract

Motivation
Metabolomics has shown great potential to improve the understanding of complex diseases, potentially leading to therapeutic target identification. However, no single analytical method allows monitoring all metabolites in a sample, resulting in incomplete metabolic fingerprints. This incompleteness constitutes a stumbling block to interpretation, raising the need for methods that can enrich those fingerprints. We propose MetaboRank, a new solution inspired by social network recommendation systems for the identification of metabolites potentially related to a metabolic fingerprint.

Results
MetaboRank method had been used to enrich metabolomics data obtained on cerebrospinal fluid samples from patients suffering from hepatic encephalopathy (HE). MetaboRank successfully recommended metabolites not present in the original fingerprint. The quality of recommendations was evaluated by using literature automatic search, in order to check that recommended metabolites could be related to the disease. Complementary mass spectrometry experiments and raw data analysis were performed to confirm these suggestions. In particular, MetaboRank recommended the overlooked α-ketoglutaramate as a metabolite which should be added to the metabolic fingerprint of HE, thus suggesting that metabolic fingerprints enhancement can provide new insight on complex diseases.

Availability and implementation
Method is implemented in the MetExplore server and is available at www.metexplore.fr. A tutorial is available at https://metexplore.toulouse.inra.fr/com/tutorials/MetaboRank/2017-MetaboRank.pdf.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Bayesian approach to Mendelian randomization with multiple pleiotropic variants
Authors: Berzuini Carlo , Guo Hui , Burgess Stephen , Bernardinelli Luisa 
Published: July 2018

SummaryWe propose a Bayesian approach to Mendelian randomization (MR), where instruments are allowed to exert pleiotropic (i.e. not mediated by the exposure) effects on the outcome. By having these effects represented in the model by unknown parameters, and by imposing a shrinkage prior distribution that assumes an unspecified subset of the effects to be zero, we obtain a proper posterior distribution for the causal effect of interest. This posterior can be sampled via Markov chain Monte Carlo methods of inference to obtain point and interval estimates. The model priors require a minimal input from the user. We explore the performance of our method by means of a simulation experiment. Our results show that the method is reasonably robust to the presence of directional pleiotropy and moderate correlation between the instruments. One section of the article elaborates the model to deal with two exposures, and illustrates the possibility of using MR to estimate direct and indirect effects in this situation. A main objective of the article is to create a basis for developments in MR that exploit the potential offered by a Bayesian approach to the problem, in relation with the possibility of incorporating external information in the prior, handling multiple sources of uncertainty, and flexibly elaborating the basic model.
The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation
Authors: Hood Wendy R , Austad Steven N , Bize Pierre , Jimenez Ana Gabriela , Montooth Kristi L , Schulte Patricia M , Scott Graham R , Sokolova Inna , Treberg Jason R , Salin Karine 
Published: July 2018

Abstract
Animals display tremendous variation in their rates of growth, reproductive output, and longevity. While the physiological and molecular mechanisms that underlie this variation remain poorly understood, the performance of the mitochondrion has emerged as a key player. Mitochondria not only impact the performance of eukaryotes via their capacity to produce ATP, but they also play a role in producing heat and reactive oxygen species and function as a major signaling hub for the cell. The papers included in this special issue emerged from a symposium titled “Inside the Black Box: The Mitochondrial Basis of Life-history Variation and Animal Performance.” Based on studies of diverse animal taxa, three distinct themes emerged from these papers. (1) When linking mitochondrial function to components of fitness, it is crucial that mitochondrial assays are performed in conditions as close as the intracellular conditions experienced by the mitochondria in vivo. (2) Functional plasticity allows mitochondria to retain their performance, as well as that of their host, over a range of exogenous conditions, and selection on mitochondrial and nuclear-derived proteins can optimize the match between the environment and the bioenergetic capacity of the mitochondrion. Finally, (3) studies of wild and wild-derived animals suggest that mitochondria play a central role in animal performance and life history strategy. Taken as a whole, we hope that these papers will foster discussion and inspire new hypotheses and innovations that will further our understanding of the mitochondrial processes that underlie variation in life history traits and animal performance.
Challenges to Arbitrators, Counsel, and Experts
Authors: Commission Jeffery , Moloo Rahim 
Published: July 2018

Abstract
This chapter discusses challenges to arbitrators in International Centre for Settlement of Investment Disputes (ICSID) and ICSID Additional-Facility arbitrations, challenges to arbitrators in UNCITRAL arbitrations, and challenges to counsel and experts in ICSID and UNCITRAL arbitrations. Disqualification proposals have become a routine procedural mechanism used by both claimants and respondents in ICSID and UNCITRAL investment arbitrations. During the period 1982–2017, parties filed 121 disqualification proposals in ICSID proceedings. These included not only original arbitration proceedings, but also post-award proceedings, such as rectification, interpretation and annulment proceedings. In addition to arbitrators, disqualification proposals now target counsel, party-appointed experts, and tribunal-appointed experts. The chapter examines the relevant articles and rules that apply when challenges are against ICSID arbitrators, the timeliness of challenge application, the potential waiver of the right to seek disqualification, and arbitrator resignations in response to disqualification proposals. It also considers the procedure for adjudicating challenges to arbitrators in UNCITRAL arbitrations.
Non-Disputing Party Participation and Transparency
Authors: Commission Jeffery , Moloo Rahim 
Published: July 2018

Abstract
This chapter examines the issue of transparency in treaty-based investment arbitration by focusing on the participation of third parties or non-disputing parties in disputes. More specifically, it considers the procedural issues that transparency mechanisms in bilateral-investment treaties and free-trade agreements, as well as in recently revised arbitral rules, create for arbitral tribunals and those appearing before them. After discussing non-disputing party practice in investment arbitrations, the chapter explains the practice of non-disputing state parties in UNCITRAL and International Centre for Settlement of Investment Disputes (ICSID) arbitrations. It also analyses transparency mechanisms beyond the participation of non-disputing parties in investment arbitrations from the written procedure through to the oral procedure, culminating in a tribunal's decisions and award.
Other Procedures
Authors: Commission Jeffery , Moloo Rahim 
Published: July 2018

Abstract
This chapter examines other procedures in investment arbitration proceedings, with particular emphasis on how International Centre for Settlement of Investment Disputes (ICSID) and UNCITRAL tribunals have addressed them in practice. ICSID has schematically set out what it describes as ‘the steps in the process’ in an ICSID arbitration using a flow chart. However, this flow chart is not able to anticipate with much certainty the potential impact of certain other procedures. The chapter first explains the determination of the legal place or seat of arbitration in non-ICSID Convention arbitrations before discussing the practice of early dismissal mechanisms, specifically, ICSID Rule 41(5) objections for manifest lack of legal merit. It then considers the question of site visits conducted by tribunals in ICSID and UNCITRAL arbitrations, the practice of tribunal-appointed experts, and requests for reconsideration. It also outlines the features of multi-party arbitration, including the procedures and issues associated with mass claims.
Statements or Submissions on Costs
Authors: Commission Jeffery , Moloo Rahim 
Published: July 2018

Abstract
This chapter considers the duration and costs of investment arbitrations as well as the procedural mechanics of cost submissions or statements of costs. It first examines the timing, format, and content of cost submissions and statements of costs before discussing the relevant arbitral rules that govern such submissions in International Centre for Settlement of Investment Disputes (ICSID) Convention and ICSID Additional-Facility arbitration proceedings, along with the average amount of such costs. It then explains the UNCITRAL Arbitration Rules on costs submissions, taking into account the average amount of those costs, and the duration of arbitration proceedings. It also analyses how arbitral tribunals have allocated costs in ICSID and UNCITRAL proceedings and highlights the factors deemed relevant by tribunals in those decisions.
Introduction
Authors: Haldemann Frank , Unger Thomas 
Published: July 2018

Abstract
This book provides a systematic in-depth study of the Principles, which were conceived and designed ‘as a guideline to assist States in developing effective measures for combating impunity’. The document contains 38 Principles, analyzed in the present book in the context of a host of complex theoretical and practical issues currently discussed in the arena of human rights and beyond. This introduction orients readers towards the basic issues, situating the Principles in their wider historical and political context and elucidating their conceptual and normative nature. It also clarifies the role, limitations and opportunities of the Principles in addressing current challenges, especially with respect to ‘transitional’ societies emerging from prolonged periods of armed conflict or oppression.
The Inalienable Right to the Truth
Authors: Groome Dermot 
Published: July 2018

Abstract
Principle 2 is concerned with the inalienable right to truth, a right that arises from the right to know and obliges governments to establish mechanisms to facilitate the revelation of the truth about serious violations of human rights. The right to truth has been explicitly incorporated into several international instruments and, in 2010, became expressly guaranteed in the International Convention for the Protection of All Persons from Enforced Disappearance (ICPPED). In practice, the right to truth is realized through laws enabling requests for state-held information; archives; truth commissions; national and international courts; and human rights commissions. After providing a contextual and historical overview of Principle 2, this chapter describes its normative (legal/ethical) foundation, focusing on how its interpretation is influenced by international law and how it relates to notions of transitional justice. It also analyzes the applications of the Principle in practice.
The Victims’ Right to Know
Authors: Groome Dermot 
Published: July 2018

Abstract
Principle 4 deals with the victims’ right to know, which is most often exercised in conjunction with Principle 2, the right to truth. This principle not only guarantees families to know the ultimate fate of relatives but also requires a full and fair exposition of what happened, including the existence of human rights violations. The right to know was first articulated in Article 32 of Additional Protocol I to the Geneva Conventions and has evolved as a principle of customary international humanitarian law. Principle 4 recognizes the basic human need for families to know the fate of missing loved ones and is best understood as a right extending humanitarian protection to families of the missing. This chapter first provides a contextual and historical background on Principle 4 before discussing its theoretical framework and the ways in which the right to know is exercised in practice.