bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an HPTLC method for determination of hypoglycin A in aqueous extracts of seedlings and samaras ofAcerspecies
Authors: Habyarimana J.A. , Baise E. , Douny C. , Weber M. , Boemer F. , De Tullio P. , Franck T. , Marcillaud-Pitel C. , Frederich M. , Mouithys-Mickalad A. , Richard E. , Scippo M.-L. , Votion D. , Gustin P. 
Published: June 2017

Hypoglycin A (HGA) is a toxin contained in seeds of the sycamore maple tree (Acer pseudoplatanus). Ingestion of this amino acid causes equine atypical myopathy (AM) in Europe. Another variety,A. negundo,is claimed to be present where AM cases were reported in the US. For unknown reasons, occurrence of this disease has increased. It is important to define environmental key factors that may influence toxicity of samaras fromAcerspecies. In addition, the content of HGA in seedlings needs to be determined since AM outbreaks, during autumn period when the seeds fall but also during spring when seeds are germinating. The present study aims to validate a reliable method using high performance thin layer chromatography for determination and comparison of HGA in samaras and seedlings.The working range of the method was between 20 μg HGA to 408 μg HGA per ml water, corresponding to 12 - 244 mg/kg fresh weight or 40 - 816 mg/kg dry weight, taking into account of an arbitrary average dry matter content of 30%. Instrumental limit of detection and limit of quantification were of 10 μg HGA/ml and 20 μg HGA/ml water, respectively. Instrumental precision was 4% (RSD on 20 repeated measurements) while instrumental accuracy ranged between 86% and 121% of expected value. The HGA recovery of the analytical method estimated from spiked samaras and seedlings samples ranged between 63 and 103%. The method was applied to 9 samples of samaras fromAcer pseudoplatanus, A. platanoidesandA. campestreand 5 seedlings samples fromA. pseudoplatanus.The results confirm detection of HGA in samaras fromA. pseudoplatanusand the absence of detection in samaras of other tested species. They also suggest that detected levels of HGA are highly variable. This confirmed the suitability of the method for HGA detection in samaras or seedling.
Indexcov: fast coverage quality control for whole-genome sequencing
Authors: Pedersen Brent S. , Collins Ryan L. , Talkowski Michael E. , Quinlan Aaron R. 
Published: June 2017

AbstractThe BAM1and CRAM2formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developedindexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.Indexcovis available at:https://github.com/brentp/goleftunder the MIT license.
Phytoplankton traits from long-term oceanographic time-series
Authors: Mutshinda Crispin M , Finkel Zoe V , Widdicombe Claire E , Irwin Andrew J 
Published: June 2017

AbstractTrait values are usually extracted from laboratory studies of single phytoplankton species, which presents challenges for understanding the immense diversity of phytoplankton species and the wide range of dynamic ocean environments. Here we use a Bayesian approach and a trait-based model to extract trait values for four functional types and ten diatom species from field data collected at Station L4 in the Western Channel Observatory. We find differences in maximum net growth rate, temperature optimum and sensitivity, half-saturation constants for light and nitrogen, and density-dependent loss terms across the functional types. We find evidence of very high linear loss rates, suggesting that grazing may be even more important than commonly assumed and differences in density-dependent loss rates across functional types, indicating the presence of strong niche differentiation among functional types. Low half-saturation constants for nitrogen at the functional type level may indicate widespread mixotrophy. At the species level, we find a wide range of density-dependent effects, which may be a signal of diversity in grazing susceptibility or biotic interactions. This approach may be a way to obtain more realistic and better-constrained trait-values for functional types to be used in ecosystem modeling.
Intercellular Communication via thecomX-Inducing Peptide (XIP) ofStreptococcus Mutans
Authors: Kaspar Justin , Underhill Simon A. M. , Shields Robert C. , Reyes Adrian , Rosenzweig Suzanne , Hagen Stephen J. , Burne Robert A. 
Published: June 2017

ABSTRACTGram-positive bacteria utilize exported peptides to coordinate genetic and physiological processes required for biofilm formation, stress responses and ecological competitiveness. One example is activation of natural genetic competence by ComR and thecomX-inducing peptide (XIP) inStreptococcus mutans. Although the competence pathway can be activated by addition of synthetic XIP in defined medium, the hypothesis that XIP is able to function as an intercellular signal molecule has not been rigorously tested. Co-culture model systems were developed that included a “sender” strain that overexpressed the XIP precursor (ComS) and a “responder” strain harboring a GFP reporter fusion to a ComR-activated gene (comX) promoter. The ability of the sender strain to provide a signal to activate GFP expression was monitored at the individual cell and population levels using i) planktonic culture systems, ii) cells suspended in an agarose matrix or iii) cells growing in biofilms. XIP was shown to be freely diffusible and XIP signaling between theS. mutanssender and responder strains did not require cell-to-cell contact. The presence of a sucrose-derived exopolysaccharide matrix diminished the efficiency of XIP signaling in biofilms, possibly by affecting spatial distribution of XIP senders and potential responders. Intercellular signaling was greatly impaired in a strain lacking the primary autolysin, AtlA, and was substantially greater when the sender strain underwent lysis. Collectively, these data provide evidence thatS. mutansXIP can indeed function as a peptide signal between cells and highlight the importance of studying signaling with endogenously-produced peptide(s) in populations in various environments and physiologic states.IMPORTANCEThecomX-inducing peptide (XIP) ofStreptococcus mutansis a key regulatory element in the activation of genetic competence, which allows cells to take up extracellular DNA. XIP has been found in cell culture fluids and addition of synthetic XIP to physiologically receptive cells can robustly induce competence gene expression. However, there is a lack of consensus as to whether XIP can function as an intercellular communication signal. Here, we show that XIP indeed signals between cells inS. mutans, but that cell lysis may be a critical factor, as opposed to a dedicated secretion/processing system, in allowing for release of XIP into the environment. The results have important implications in the context of the ecology, virulence and evolution of a ubiquitous human pathogen and related organisms.
A First Order Phase Transition Underlies the Formation of Sub-Diffractive Protein Aggregates in Mammalian Cells
Authors: Narayanan Arjun , Meriin Anatoli B. , Sherman Michael Y. , Cissé Ibrahim I. 
Published: June 2017

ABSTRACTFailure in protein quality control can often lead to protein aggregation, yet in neuro-degenerative diseases, by the time aggregates can be seen, the cells have advanced well into the disease pathology. Here, we develop a quantitative imaging approach to study the protein aggregation process in living mammalian cells with unprecedented spatio-temporal resolution. We find that sub-diffractive precursor aggregates may form even in untreated cells, and their size distribution is exactly as predicted for a system undergoing a first order phase transition. Practically, this implies that as soon as aggregates reach a critical size (Rc= 162 ± 4 nm untreated cells), they will spontaneously grow into large inclusions. Our data suggest that a previously uncharacterized, RuvBL1 dependent mechanism clears aggregates above the critical size. Our study unveils the existence of sub-diffractive aggregates in living cells; and the strong agreement between cellular data and a nucleation theory, based on first order phase transition, provides insight into regulatory steps in the early stages of aggregate formation in vivo.
Graphtyper: Population-scale genotyping using pangenome graphs
Authors: Eggertsson Hannes P. , Jonsson Hakon , Kristmundsdottir Snaedis , Hjartarson Eirikur , Kehr Birte , Masson Gisli , Zink Florian , Jonasdottir Aslaug , Jonasdottir Adalbjorg , Jonsdottir Ingileif , Gudbjartsson Daniel F. , Melsted Pall , Stefansson Kari , Halldorsson Bjarni V. 
Published: June 2017

AbstractA fundamental requisite for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to utilize this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in whole-genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in population-scale sequencing studies.
Intracellular BH3 profiling reveals shifts in anti-apoptotic dependency in B-cell maturation and activation
Authors: Dai Joanne , Luftig Micah A. 
Published: June 2017

AbstractApoptosis is critical to B-cell maturation, but studies of apoptotic regulation in primary human B cells is lacking. Previously, we found that infecting human B cells with Epstein-Barr virus induces two different survival strategies (Priceet al., 2017). Here, we sought to better understand the mechanisms of apoptotic regulation in normal and activated B cells. Using intracellular BH3 profiling (iBH3), we defined the Bcl2-dependency of B-cell subsets from human peripheral blood and tonsillar lymphoid tissue as well as mitogen-activated B cells. We found that naïve and memory B cells were BCL-2 dependent, while germinal center B cells were MCL-1 dependent and plasma cells were BCL-XL dependent. Proliferating B cells activated by CpG or CD40L/IL-4 became more dependent upon MCL-1 and BCL-XL. As B-cell lymphomas often rely on survival mechanisms derived from normal and activated B cells, these findings offer new insight into potential therapeutic strategies for lymphomas.
Adaptive response prediction for aerodynamic shape optimization
Authors: Leifsson Leifur , Koziel Slawomir 
Published: June 2017

Purpose
The purpose of this paper is to reduce the overall computational time of aerodynamic shape optimization that involves accurate high-fidelity simulation models.

Design/methodology/approach
The proposed approach is based on the surrogate-based optimization paradigm. In particular, multi-fidelity surrogate models are used in the optimization process in place of the computationally expensive high-fidelity model. The multi-fidelity surrogate is constructed using physics-based low-fidelity models and a proper correction. This work introduces a novel correction methodology – referred to as the adaptive response prediction (ARP). The ARP technique corrects the low-fidelity model response, represented by the airfoil pressure distribution, through suitable horizontal and vertical adjustments.

Findings
Numerical investigations show the feasibility of solving real-world problems involving optimization of transonic airfoil shapes and accurate computational fluid dynamics simulation models of such surfaces. The results show that the proposed approach outperforms traditional surrogate-based approaches.

Originality/value
The proposed aerodynamic design optimization algorithm is novel and holistic. In particular, the ARP correction technique is original. The algorithm is useful for fast design of aerodynamic surfaces using high-fidelity simulation data in moderately sized search spaces, which is challenging using conventional methods because of excessive computational costs.
Algal bloom prediction by support vector machine and relevance vector machine with genetic algorithm optimization in freshwater reservoirs
Authors: Wang Yanjie , Xie Zhengchao , Lou InChio , Ung Wai Kin , Mok Kai Meng 
Published: June 2017

Purpose
The purpose of this paper is to examine the applicability and capability of models based on a genetic algorithm and support vector machine (GA-SVM) and a genetic algorithm and relevance vector machine (GA-RVM) for the prediction of phytoplankton abundances associated with algal blooms in a Macau freshwater reservoir, and compare their performances with an artificial neural network (ANN) model.

Design/methodology/approach
The hybrid models GA-SVM and GA-RVM were developed for the optimal control of parameters for predicting (based on the current month’s variables) and forecasting (based on the previous three months’ variables) phytoplankton dynamics in a Macau freshwater reservoir, MSR, which has experienced cyanobacterial blooms in recent years. There were 15 environmental parameters, including pH, SiO2, alkalinity, bicarbonate (HCO3−), dissolved oxygen (DO), total nitrogen (TN), UV254, turbidity, conductivity, nitrate (NO3−), orthophosphate (PO43−), total phosphorus (TP), suspended solids (SS) and total organic carbon (TOC) selected from the correlation analysis, with eight years (2001-2008) of data for training, and the most recent three years (2009-2011) for testing.

Findings
For both accuracy performance and generalized performance, the ANN, GA-SVM and GA-RVM had similar predictive powers of R2 of 0.73-0.75. However, whereas ANN and GA-RVM models showed very similar forecast performances, GA-SVM models had better forecast performances of R2 (0.862), RMSE (0.266) and MAE (0.0710) with the respective parameters of 0.987, 0.161 and 0.032 optimized using GA.

Originality/value
This is the first application of GA-SVM and GA-RVM models for predicting and forecasting algal bloom in freshwater reservoirs. GA-SVM was shown to be an effective new way for monitoring algal bloom problem in water resources.
Reducing computational time of cohesionless discrete simulations based on particle clusters
Authors: Oldal Istvan , Safranyik Ferenc , Keppler Istvan 
Published: June 2017

Purpose
The purpose of this study is the reduction of computational time demand of discrete element based modeling.

Design/methodology/approach
The methodology is the systematic changing of particle size and micromechanical parameters to reduce computational time requirements.

Findings
In some cases, the computational demand of discrete simulations can be reduced to about 95 per cent.

Originality/value
Based on the results and demonstrated methodology, the enormous computational time demand of discrete element-based modeling can be reduced significantly.
A moral case for universal healthcare for runaway and homeless youth
Authors: Harpin Scott B. , Elliott April S. , Auerswald Colette L. 
Published: June 2017

PurposeRunaway and homeless youth (RHY) are among the most vulnerable youth globally. The United Nations Convention on the Rights of the Child (UNCRC) states that all children have the right to the highest level of health, and that universal healthcare rights are afforded to RHY and all children. Social determinants of health (SDH) are universal factors that frame the experiences of RHY as facilitators or barriers for accessing healthcare. The purpose of this paper is to describe practical best approaches, and policy recommendations, for improving clinical care systems to make healthcare more accessible to RHY.Design/methodology/approachThe authors describe and apply an adapted socio-ecological framework that includes SDH specific to RHY around the globe.FindingsThere are multiple and complex factors in the social ecology of RHY that determine their chances of accessing healthcare. While many intrapersonal reasons for homelessness are the same globally, systems of care vary by country and by developing/developed country status. Structurally competent care systems offer a new lens for how to best provide care to RHY to take into account SDH and the unique needs of RHY.Originality/valueThe UNCRC serves as a moral guide and frame of universal child healthcare provision for countries around the world. The authors uniquely argue for UNCRC, tailored-SDH, and care delivered in a structurally competent manner to make a moral case for both physical and mental health for all RHY.
Comparisons of tribological properties between laser and drilled dimple textured surfaces of medium carbon steel
Authors: Shi Chenchun , Yu Aibing , Wu Jianzhao , Niu Weiyang , Wang Yanlin 
Published: June 2017

Purpose
The study aims to compare tribological properties between laser dimple textured surface and drilled dimple textured surface, and to analyze the influence of dimple hardened edges and ability of trapping wear debris on wear properties of dimple textured surfaces.

Design/methodology/approach
Circular textured dimples were produced on AISI 1,045 specimen surfaces using laser surface texturing (LST) and drilled surface texturing (DST) methods. Tribological behaviors of LST, DST and non-textured specimens were studied using ball-on-disc tribo-tester. Metallographic structures, dimples and worn surface morphologies were observed using a three-dimensional digital microscope. Hardnesses of substrate and dimple edges were measured.

Findings
There was no obvious difference in wear and friction coefficients between LST and DST specimens. Hardnesses of laser dimple edges were much higher than that of drilled dimple edges and specimen substrate. The hardened materials of laser dimple edge included recast zone and heat affect zone. Laser dimple was cone-shaped and drilled dimple was cylinder-shaped. Drilled dimple had a better ability of trapping wear debris than laser dimple. Non-uniform wear phenomenon occurred on worn surfaces of LST dimple specimens.

Originality/value
The ability of textured dimples to trap wear debris is affected by single dimple volume. Hardened edges of dimples cause non-uniform wear on worn surfaces of LST specimens.
Surfaces with pores: hydrodynamic lubrication
Authors: Burstein Leonid 
Published: June 2017

Purpose
This paper aims to assess the hydrodynamic lubrication of two opposing surfaces with identical pores having a semicircular profile. The surfaces are treated with more than one pore that allows clarification of whether there exists interaction between the pores.

Design/methodology/approach
A transient, spatial, one-dimensional model of surfaces with regular pores was developed and applied in the context of fluid lubrication. MATLAB software has been used.

Findings
Calculations show that a lubricating film between two surfaces with pores provides better hydrodynamic conditions in comparison to that on one surface with pores. It was also shown that the pores of one surface act as separate objects and can take into account only the interaction between the pores of the opposite surfaces. In addition, it was found that there are optimum values of the pore radii, gap and pore cell dimensions at which the bearing capacity of the film is maximal.

Practical implications
The computer program used for the pore parameter calculations provided the optimal lubrication.

Originality/value
This is the first study of the lubricating film hydrodynamic behavior of two opposite surfaces with pores having a semicircular profile.
Bony traits and genetics drive intraspecific variation in vertebrate elemental composition
Authors: Durston Daniel J. , El‐Sabaawi Rana W. 
Published: June 2017

Abstract

Interspecific variation in elemental composition is well known and often leads to predictable differences in ecosystem interactions, but little is known about the extent, causes and importance of intraspecific variation in elemental composition. If intraspecific variation is substantial and has a genetic basis, it may underlie an important mechanism of evolutionary interplay with ecology as individuals compensate for evolutionary changes in elemental demand.

To investigate the extent and causes of intraspecific elemental variation in vertebrates, we sampled evolutionary model species Gasterosteus aculeatus (Threespine Stickleback) from 12 locations in British Columbia, Canada. Fish were phenotyped, genotyped for Eda alleles underlying lateral plate variation and assayed for elemental content (C, N, P).

We found stickleback vary widely in elemental composition (2.2%–6.5% P; 3.0–9.4: 1 N:P). Phenotypic models explained the majority of this variation using bony armour traits (pelvis length, lateral plate count), bone mineralization, body size and condition.

Subsequent genetic models found allelic variation at Eda generates a 7%–14% change in whole organism N:P. As Eda allele frequencies are commonly changed through strong natural selection in freshwater habitats, we infer that stickleback elemental composition can evolve rapidly.

Further, as genetics are known to drive variation in many of the other influential traits, we conclude that genetic variation constitutes a major source of variation in the elemental composition of Gasterosteus aculeatus. As such, we find that elemental composition has a large evolutionary potential which may underlie important evo‐eco interactions.

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