bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refractory and heat-insulating materials based on aluminosilicate SHS compositions
Authors: Kapustin R D 
Published: June 2019

Abstract
The phase composition, structure, and physical and mechanical characteristics of refractory aluminosilicate SHS materials (AS materials) were investigated taking into account the properties of initial components and the production method. Computational methods were used to reveal macrokinetics of processes and determine the possible formation of mullite structures and corundum in aluminosilicate refractory SHS materials during the synthesis reactions. Heat losses caused by the small thickness of a coating or the walls of the material between pores were found to have a significant effect on the synthesis reaction in thin coatings and porous AS materials, as well as the on the formation of various chemical compounds.
Synthesis of Ti2AlN MAX-phase by sintering in vacuum
Authors: Kondakov A A , Studenikin I A , Linde A V , Kondakova N A , Grachev V V 
Published: June 2019

Abstract
The dependence of MAX-phase synthesis on phase composition of the initial mixture and heat treatment terms in the electric furnace was investigated. Using Ti and AlN powders with the molecular ratio 2:1 as an example, the sequence of phase composition changes with increasing exposure temperature was tracked. It was established that the maximum amount of Ti2AlN MAX-phase in the end products is obtained at 1400°C. At this temperature a single phase product (100% wt Ti2AlN) was obtained for the initial mixture Ti:Al:TiN = 1:1:1. The principal possibility of scaling for obtaining a single-phase product of Ti2AlN by vacuum sintering was experimentally shown on the example of the mixture of this composition weighing 500 g at a certain mode of thermal vacuum treatment.
Synthesis of nanopowders of titanium compounds via Flow-Levitation method and study their properties
Authors: Kuskov M L , Zhigach A N , Leipunsky I O , Afanasenkova E S , Safronova O A , Berezkina N G , Vorobjeva G A 
Published: June 2019

Abstract
Nanopowders of titanium compounds TiH2 and TiC are synthesized via Flow-Levitation method using in situ reaction of nascent titanium nanoparticles with the proper reactants. The influence of manufacturing parameters on the composition and the internal structure of the synthesized nanoparticles is examined. Study of TiH2 nanoparticles using thermal methods revealed hydrogen evolution within the narrow temperature range (390-510°C), while hydrogen evolution temperature of the commercial samples is higher than 500°C.
Synthesis and investigation of highly transparent ceramics
Authors: Osipov V V , Shitov V A , Platonov V V , Maksimov R N , Lukyashin K E 
Published: June 2019

Abstract
A short review of research works carried out in the Institute of Electrophysics UrB RAS on the development of synthesis technology for laser ceramics and the analysis of their characteristics is presented. These ceramics are widely used as active media of solid-state lasers, transparent armor, envelopes of high intensity discharge lamps, heat-resistant and mechanically strong windows etc.
Features of interaction of powder high-velocity particles with the surface layer of the target
Authors: Petrov E V 
Published: June 2019

Abstract
The interaction of a stream of high-velocity particles with the surface layer of a target was investigated. The impact of discrete particles with the sample surface was shown to lead to the formation of a coating consisting of these particles and to the changes in the physical and mechanical properties of the surface layer of the target. The obtained coatings are a composite material consisting of sintered (not melted) powder particles. The impact of high-velocity particles was shown to lead to the hardening of the surface layer of samples exposed to the stream of powder particles of tungsten, nickel and titanium nitride. The maximum increase in the microhardness of targets was observed at a depth of 2 and 4 mm from the surface treated with a stream of particles.
Mechanical activation of metallic powders in planetary ball mills: multi-scale modeling and experimental observation
Authors: Politano O , Fourmont A , Gallet S Le , Baras F , Nepapushev A A , Sedegov A S , Vadchenko S G , Rogachev A S 
Published: June 2019

Abstract
Ball motion and microstructure formation in the mixtures of Al with metals (Ti, Ni) during high-energy planetary ball milling are studied by means of high-speed video recording, scanning electron microscopy and computer modeling, including molecular dynamics simulation. Possibility of production reactive composite powders with rounded particles for using in selective laser melting techniques has been demonstrated.
Applicability of molecular dynamics method to the prediction of the melting point of refractory metals and compounds
Authors: Rogachev S A 
Published: June 2019

Abstract
Various methods for measuring the melting point using embedded atom model (EAM) and from first principles modeling are considered. The features of each of them are shown. The results of the work of these methods are compared with the experimental values on the example of systems consisting of pure metals such as Fe, Pd, Ti, Pt Zr, Mo, Ta, W. Good agreement of the estimated melting points with experimental values is shown.
Voltage Supply Assessment Using Process Capability Concepts: A Case Study
Authors: Vizuete A H , Barbosa G J , Lema E M , Albán M S , Vargas R S , Ruiz L C 
Published: June 2019

Abstract
The following case study examines a company which experienced several difficulties caused by low-quality voltage supply. Two main points were considered in the analysis, one located next to the substation transformer and a second one inside the company. Voltage parameters such as harmonics presence, voltage flickers, average voltage, and power factor were measured in this study. As a result, 62 000 samples were collected. The data obtained from point 2 (control group) revealed the necessity of introducing voltage regulators in order to improve the energy efficiency and save in energy costs at the company. Therefore, 1 500 samples were collected at point 2 (treatment group) to verify the voltage regulators’ efficiency. Comparing the control and treatment group, there was a significant improvement of 93% regarding process capability in power factor phase CN.
Effect of Water Content in Waste Cooking Oil on Biodiesel Production via Ester-transesterification in a Single Reactive Distillation
Authors: Anantapinitwatna Ajala , Ngaosuwan Kanokwan , Kiatkittipong Worapon , Wongsawaeng Doonyapong , Assabumrungrat Suttichai 
Published: June 2019

Abstract
A single-column reactive distillation is employed to convert waste cooking oil to biodiesel via simultaneous esterification and transesterification reactions. The waste cooking oil contained 10 wt% of free fatty acid (FFA) and the contaminated water (2-8 wt%) was used as feedstocks for biodiesel production. Esterification was occurred in the upper of column to reduce FFA content to less than 1 wt% and to prevent the simultaneous saponification by base catalyst. Moreover, the contaminated water and by-product water (from esterification) together was removed in-situ as the distillate product. The reactive distillation has been optimally designed to have 16 stages consisting of 5 esterification, 9 transesterification stages and each stage for reboiler and condenser. The feed locations of oil and methanol were at the top of the column and at stage 6, respectively. The optimum methanol to oil ratio was 6:1 with reflux ratio 0.1 while the reboiler duty was in the range of 100-150 kW depended on the water content. This condition successfully converts 97 wt% of waste cooking oil to biodiesel with 96.5% purity.
Impact of Oxygen Vacancy on the Photocatalytic Selective Hydrogenation of 3-Nitrostyrene via Calcination of TiO2
Authors: Chaitaworn Saknarin , Mekasuwandumrong Okorn , Praserthdam Piyasan 
Published: June 2019

Abstract
In this work, P25-TiO2 was treated by calcination in air at difference temperature (600-900°C) for 5h. Treated catalysts were tested in photocatalytic selective hydrogenation of 3-nitrostyrene (3-NS) to 3-vinylaniline (3-VA). The properties of treated catalysts were characterized by using XRD, XPS, and UV-Vis spectroscopy. 3-vinylaniline and acetone were produced from photocatalytic (λ > 300nm) selective hydrogenation reaction of 3-nitrostyrene in 2-propanol and suspension with P25-TiO2. The Ti3+ at locate with oxygen defect, which at below conduction band were acted as active site for trapped electron to conduction band. These effects leading to excess oxygen defect caused low activity due to recombination center. An optimal calcination temperature was 700°C ascribed to the enhancement of high conversion (71%) with 100% 3-VA selectivity due to optimal oxygen vacancies.
A COOL Tale: Economic Effects of the U.S. Mandatory Country of Origin Labeling Repeal
Authors: Countryman Amanda M , Bonanno Alessandro 
Published: June 2019

AbstractU.S. Congress repealed Mandatory Country of Origin Labeling (COOL) for beef and pork in December 2015 to avoid retaliatory tariffs from Canada and Mexico. We simulate and compare economic impacts from these retaliatory tariffs with scenarios where COOL was repealed using a global economic modeling framework. Retaliation would have decreased North American trade, decreased U.S. welfare, and increased welfare for Canada and Mexico. Simulated effects of the COOL repeal show modest welfare increases in the United States, Mexico, and globally, with heterogeneous welfare effects for Canada. We discuss whether recent U.S. protectionist policies may lead to similar outcomes to those simulated here.
Multicenter Evaluation of HemoTypeSC as a Point-of-Care Sickle Cell Disease Rapid Diagnostic Test for Newborns and Adults Across India
Authors: Mukherjee Malay B , Colah Roshan B , Mehta Pallavi R , Shinde Nikhil , Jain Dipty , Desai Shrey , Dave Kapilkumar , Italia Yazdi , Raicha Bhavesh , Serrao Erik 
Published: June 2019

Abstract

Objectives
Sickle cell anemia is the commonest genetic disorder in India, and the frequency of the sickle cell gene is very high in the remote tribal areas where facilities are generally limited. Therefore, a rapid and affordable point-of-care test for sickle cell disease is needed.

Methods
The diagnostic accuracy of HemoTypeSC was evaluated against automated high-performance liquid chromatography (HPLC) as the gold standard for its efficacy in a newborn screening program.

Results
A total of 1,559 individuals (980 newborns and 579 adults) from four participating centers were analyzed by both methods. HemoTypeSC correctly identified 209 of 211 total hemoglobin (Hb) SS cases, for a 99.1%/99.9% total HbSS sensitivity/specificity. Overall, HemoTypeSC exhibited sensitivity and specificity of 98.1% and 99.1% for all possible phenotypes (HbAA, HbAS, and HbSS) detected. HPLC is relatively expensive and not available in most laboratories in remote tribal areas.

Conclusions
We conclude that the rapid, point-of-care testing device HemoTypeSC test is suitable for population and newborn screening for the HbS phenotype.
ShaKer: RNA SHAPE prediction using graph kernel
Authors: Mautner Stefan , Montaseri Soheila , Miladi Milad , Raden Martin , Costa Fabrizio , Backofen Rolf 
Published: June 2019

AbstractSummarySHAPE experiments are used to probe the structure of RNA molecules. We present ShaKer to predict SHAPE data for RNA using a graph-kernel-based machine learning approach that is trained on experimental SHAPE information. While other available methods require a manually curated reference structure, ShaKer predicts reactivity data based on sequence input only and by sampling the ensemble of possible structures. Thus, ShaKer is well placed to enable experiment-driven, transcriptome-wide SHAPE data prediction to enable the study of RNA structuredness and to improve RNA structure and RNA–RNA interaction prediction. For performance evaluation, we use accuracy and accessibility comparing to experimental SHAPE data and competing methods. We can show that Shaker outperforms its competitors and is able to predict high quality SHAPE annotations even when no reference structure is provided.Availability and implementationShaKer is freely available at https://github.com/BackofenLab/ShaKer.
Modelling cancer progression using Mutual Hazard Networks
Authors: Schill Rudolf , Solbrig Stefan , Wettig Tilo , Spang Rainer 
Published: June 2019

AbstractMotivationCancer progresses by accumulating genomic events, such as mutations and copy number alterations, whose chronological order is key to understanding the disease but difficult to observe. Instead, cancer progression models use co-occurrence patterns in cross-sectional data to infer epistatic interactions between events and thereby uncover their most likely order of occurrence. State-of-the-art progression models, however, are limited by mathematical tractability and only allow events to interact in directed acyclic graphs, to promote but not inhibit subsequent events, or to be mutually exclusive in distinct groups that cannot overlap.ResultsHere we propose Mutual Hazard Networks (MHN), a new Machine Learning algorithm to infer cyclic progression models from cross-sectional data. MHN model events by their spontaneous rate of fixation and by multiplicative effects they exert on the rates of successive events. MHN compared favourably to acyclic models in cross-validated model fit on four datasets tested. In application to the glioblastoma dataset from The Cancer Genome Atlas, MHN proposed a novel interaction in line with consecutive biopsies: IDH1 mutations are early events that promote subsequent fixation of TP53 mutations.Availability and implementationImplementation and data are available at https://github.com/RudiSchill/MHN.Supplementary informationSupplementary data are available at Bioinformatics online.
A helical lock and key model of polyproline II conformation with SH3
Authors: Meirson Tomer , Bomze David , Kahlon Liron , Gil-Henn Hava , Samson Abraham O 
Published: June 2019

Abstract

Motivation
More than half of the human proteome contains the proline-rich motif, PxxP. This motif has a high propensity for adopting a left-handed polyproline II (PPII) helix and can potentially bind SH3 domains. SH3 domains are generally grouped into two classes, based on whether the PPII binds in a positive (N-to-C terminal) or negative (C-to-N terminal) orientation. Since the discovery of this structural motif, over six decades ago, a systematic understanding of its binding remains poor and the consensus amino acid sequence that binds SH3 domains is still ill defined.

Results
Here, we show that the PPII interaction with SH3 domains is governed by the helix backbone and its prolines, and their rotation angle around the PPII helical axis. Based on a geometric analysis of 131 experimentally solved SH3 domains in complex with PPIIs, we observed a rotary translation along the helical screw axis, and separated them by 120° into three categories we name α (0–120°), β (120–240°) and γ (240–360°). Furthermore, we found that PPII helices are distinguished by a shifting PxxP motif preceded by positively charged residues which act as a structural reading frame and dictates the organization of SH3 domains; however, there is no one single consensus motif for all classified PPIIs. Our results demonstrate a remarkable apparatus of a lock with a rotating and translating key with no known equivalent machinery in molecular biology. We anticipate our model to be a starting point for deciphering the PPII code, which can unlock an exponential growth in our understanding of the relationship between protein structure and function.

Availability and implementation
We have implemented the proposed methods in the R software environment and in an R package freely available at https://github.com/Grantlab/bio3d.

Supplementary information
Supplementary data are available at Bioinformatics online.
MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides
Authors: Guruceaga Elizabeth , Garin-Muga Alba , Segura Victor 
Published: June 2019

Abstract

Motivation
The principal lines of research in MS/MS based Proteomics have been directed toward the molecular characterization of the proteins including their biological functions and their implications in human diseases. Recent advances in this field have also allowed the first attempts to apply these techniques to the clinical practice. Nowadays, the main progress in Computational Proteomics is based on the integration of genomic, transcriptomic and proteomic experimental data, what is known as Proteogenomics. This methodology is being especially useful for the discovery of new clinical biomarkers, small open reading frames and microproteins, although their validation is still challenging.

Results
We detected novel peptides following a proteogenomic workflow based on the MiTranscriptome human assembly and shotgun experiments. The annotation approach generated three custom databases with the corresponding peptides of known and novel transcripts of both protein coding genes and non-coding genes. In addition, we used a peptide detectability filter to improve the computational performance of the proteomic searches, the statistical analysis and the robustness of the results. These innovative additional filters are specially relevant when noisy next generation sequencing experiments are used to generate the databases. This resource, MiTPeptideDB, was validated using 43 cell lines for which RNA-Seq experiments and shotgun experiments were available.

Availability and implementation
MiTPeptideDB is available at http://bit.ly/MiTPeptideDB.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sexual selection and male-biased size dimorphism in a lineage of lungless salamander (Ampibia: Plethodontidae)
Authors: Camp Carlos D , Soelter Tabea M , Wooten Jessica A 
Published: June 2019

AbstractEvolutionary biologists have long focused on the patterns and causes of sexual size dimorphism (SSD). While female-biased SSD is common among ectotherms, a few lineages predominately exhibit male-biased SSD. One example is the clade of desmognathans, a monophyletic group of two genera within the Plethodontinae of the lungless salamander family Plethodontidae. Members of these two genera have a unique pattern of SSD: males mature earlier and at smaller sizes than females but reach greater maximum sizes. We used comparative phylogenetic methods to test whether SSD in these salamanders is the result of sexual selection on males. Spatial evolutionary and ecological vicariance analysis indicated a significant divergence in SSD associated with the phylogenetic origin of the desmognathans. Phylogenetic least-squares regression across the two most speciose genera of the subfamily determined a significant relationship between SSD and adult sex ratio. While male desmognathans are not sexually dimorphic in head size, they have a unique head morphology that causes their heads to grow more rapidly as their body size increases as compared with the heads of other salamanders. This pattern of allometric growth combines with a powerful bite force and enlarged premaxillary teeth to create formidable weaponry that probably is more responsive to sexual selection.
Diel schedules of locomotor, reproductive and feeding activity in wild populations of African annual killifish
Authors: ŽáK Jakub , Vrtílek Milan , Reichard Martin 
Published: June 2019

AbstractDiel patterns of different activities arise from adaptations to periodic cycling of environmental parameters and may involve trade-offs between acquiring benefits and minimizing associated costs. In this study, we provide fundamental baseline data on diel activity of natural populations of Nothobranchius fishes, model organisms in laboratory studies, including links between diurnal rhythms and ageing. Initially, we quantified the diel change in activity in wild populations of three African killifish species (Nothobranchius furzeri, Nothobranchius orthonotus and Nothobranchius pienaari) and compared average activity between sexes. In all species, males were more active than females, probably as a result of their active pursuit of females. Swimming activity peaked at midday. In N. furzeri, the only species occurring at all sites, oocytes were ovulated in the early morning, and most spawning events had occurred by the early afternoon. Gut fullness and diet richness increased before spawning activity and peaked in the morning. Daytime diet was dominated by chironomid larvae, whereas notonectid bugs were the dominant prey at night, perhaps as a result of different prey detectability over the diel cycle. Finally, no loyalty to any particular pool section was detected in N. furzeri. Collectively, these data provide the first empirical description of diel activity in three wild populations of African killifish.
Procalcitonin to Distinguish Viral From Bacterial Pneumonia: A Systematic Review and Meta-analysis
Authors: Kamat Ishan S , Ramachandran Vignesh , Eswaran Harish , Guffey Danielle , Musher Daniel M 
Published: June 2019

Abstract
Because of the diverse etiologies of community-acquired pneumonia (CAP) and the limitations of current diagnostic modalities, serum procalcitonin levels have been proposed as a novel tool to guide antibiotic therapy. Outcome data from procalcitonin-guided therapy trials have shown similar mortality, but the essential question is whether the sensitivity and specificity of procalcitonin levels enable the practitioner to distinguish bacterial pneumonia, which requires antibiotic therapy, from viral pneumonia, which does not. In this meta-analysis of 12 studies in 2408 patients with CAP that included etiologic diagnoses and sufficient data to enable analysis, the sensitivity and specificity of serum procalcitonin were 0.55 (95% confidence interval [CI], .37–.71; I2 = 95.5%) and 0.76 (95% CI, .62–.86; I2 = 94.1%), respectively. Thus, a procalcitonin level is unlikely to provide reliable evidence either to mandate administration of antibiotics or to enable withholding such treatment in patients with CAP.
The assessment of coronary artery disease in patients with end-stage renal disease
Authors: Poli Federica E , Gulsin Gaurav S , McCann Gerry P , Burton James O , Graham-Brown Matthew P 
Published: June 2019

AbstractCardiovascular disease (CVD) remains the leading cause of morbidity and mortality among patients with end-stage renal disease (ESRD). Clustering of traditional atherosclerotic and non-traditional risk factors drive the excess rates of coronary and non-coronary CVD in patients with ESRD. Coronary artery disease (CAD) is a key disease process, present in ∼50% of the haemodialysis population ≥65 years of age. Patients with ESRD are more likely to be asymptomatic, posing a challenge to the correct identification of CAD, which is essential for appropriate risk stratification and management. Given the lack of randomized clinical trial evidence in this population, current practice is informed by observational data with a significant potential for bias. For this reason, the most appropriate approach to the investigation of CAD is the subject of considerable discussion, with practice patterns largely varying between different centres. Traditional imaging modalities are limited in their diagnostic accuracy and prognostic value for cardiac events and survival in patients with ESRD, demonstrated by the large number of adverse cardiac outcomes among patients with negative test results. This review focuses on the current understanding of CAD screening in the ESRD population, discussing the available evidence for the use of various imaging techniques to refine risk prediction, with an emphasis on their strengths and limitations.