bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing
Authors: Doyle Stephen R. , Sankaranarayan Geetha , Allen Fiona , Berger Duncan , Jimenez Castro Pablo D. , Collins James Bryant , Crellen Thomas , Duque-Correa María A. , Ellis Peter , Jaleta Tegegn G. , Laing Roz , Maitland Kirsty , McCarthy Catherine , Moundai Tchonfienet , Softley Ben , Thiele Elizabeth , Ouakou Philippe Tchindebet , Tushabe John Vianney , Webster Joanne P. , Weiss Adam J. , Lok James , Devaney Eileen , Kaplan Ray M. , Cotton James A. , Berriman Matthew , Holroyd Nancy 
Published: April 2019

AbstractWhole genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative, however, these samples are typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole genome sequencing of individual immature helminth samples. These approaches do not use whole genome amplification, a common but costly approach to increase the yield of low input samples. We first tested individual parasites from two species spotted onto FTA cards - egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni - before further testing on an additional six species - Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Dracunculus medinensis, Strongyloides stercoralis, and Trichuris muris - with an optimal protocol. Whole genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation between species, and within species but between life stages, described. These results demonstrate the feasibility of whole genome sequencing of individual parasites, and highlight a new avenue towards generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.
MNC-RED A Chemically-Defined Method to Produce Enucleated Red Blood Cells from Adult Peripheral Blood Mononuclear Cells
Authors: Zhang Shouping , Olivier Emmanuel N , Yan Zi , Suzuka Sandra , Roberts Karl , Wang Kai , Bouhassira Eric E 
Published: April 2019

AbstractMany methods have been developed to produce red blood cellsin vitrobut translational applications have been hampered by the high cost of production. We have developed R6, a chemically-defined, albumin-free, low-transferrin culture medium, and MNC-RED, a protocol to differentiate peripheral blood mononuclear cells into enucleated erythroid cells that does not require any albumin or any animal components. Erythropoiesis requires large amounts of iron for hemoglobin synthesis. In all existing protocols, these large iron needs are met by increasing the concentration of holo-transferrin. This is necessary because transferrin recycling does not take place in existing erythroid culture conditions. In the R6 medium, iron is provided to the differentiating erythroblasts by small amounts of recombinant transferrin supplemented with FeIII-EDTA, an iron chelator that allows transferrin recycling to take place in cell culture. As a result of the absence of albumin and the use of low amounts of transferrin, the production of cultured red blood cells using the MNC-RED protocol is much less expensive than with existing protocols. The MNC-RED protocol should therefore help make the many translational applications of cultured RBCs economically more feasible.HighlightsWe have developed R6, a chemically-defined, albumin-free low-transferrin culture medium, and MNC-RED, a protocol to differentiate peripheral blood mononuclear cells into enucleated erythroid ER6 is suitable for red blood cell culture despite the low transferrin amounts because of the presence of FeIII-EDTA, an iron chelator that allows transferrin recycling to take place in cell culture.The MNC-RED protocol should help make the many translational applications of cultured RBCs more economically feasible.
Syntenizer 3000: Synteny-based analysis of orthologous gene groups
Authors: Moslemi Camous , Skovbjerg Cathrine Kiel , Moeskjær Sara , Andersen Stig Uggerhøj 
Published: April 2019

AbstractMotivationThe amorphous nature of genes combined with the prevalence of duplication events makes establishing correct genetic phylogenies challenging.Since homologous gene groups are traditionally formed on basis of sequence similarity, both orthologs and paralogs are often placed in the same gene group by existing tools. Certain tools such as PoFF take syntenic relationship of genes into consideration when forming gene groups. However, a method to form gene groups consisting of only true syntelogs has not yet been developed.In order to obtain orthologous gene groups consisting of the most likely syntelogs we need a method to filter out paralogs. If one strain has two or more copies of the same gene in a gene group we want to keep only the true syntelog in the group, and remove the paralogous copies by distinguishing between the two using synteny analysis.ResultsWe present a novel algorithm for measuring the degree of synteny shared between two genes and successfully disambiguate gene groups. This synteny measure is the basis for a number of other useful functions such as gene neighbourhood visualisation to inspect suspect gene groups, strain visualisation for assessing assembly quality and finding genomic areas of interest, and chromosome/plasmid classification of contigs in partially classified datasets.AvailabilityThe latest version of Syntenizer 3000 can be downloaded from the GitHub repository at https://github.com/kamiboy/Syntenizer3000/Consult the manual.pdf file in the repository for instructions on how to build and use the tool, as well as a in depth explanation of the algorithms utilised.
Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks
Authors: Miskovic Ljubisa , Tokic Milenko , Savoglidis Georgios , Hatzimanikatis Vassily 
Published: April 2019

ABSTRACTAnalysis of the dynamic and steady-state properties of biochemical networks hinge on information about the parameters of enzyme kinetics. The lack of experimental data characterizing enzyme activities and kinetics along with the associated uncertainties impede the development of kinetic models, and researchers commonly use Monte Carlo sampling to explore the parameter space. However, the sampling of parameter spaces is a computationally expensive task for larger biochemical networks. To address this issue, we exploit the fact that reaction rates of biochemical reactions and network responses can be expressed as a function of displacements from thermodynamic equilibrium of elementary reaction steps and concentrations of free enzymes and their intermediary complexes. For a set of kinetic mechanisms ubiquitously found in biochemistry, we express kinetic responses of enzymes to changes in network metabolite concentrations through these quantities both analytically and schematically. The tailor-made sampling of these quantities allows for characterizing the missing kinetic parameters and accelerating the efforts towards building genome-scale kinetic metabolic models.
Multi-Template Matching: a versatile tool for object-localization in microscopy images
Authors: Thomas Laurent S. V. , Gehrig Jochen 
Published: April 2019

AbstractWe implemented multiple template matching as both a Fiji plugin and a KNIME workflow, providing an easy-to-use method for the automatic localization of objects of interest in images. We demonstrate its application for the localization of entire or partial biological objects. The Fiji plugin can be installed by activating the Multi-Template-Matching and IJ-OpenCV update sites. The KNIME workflow can be downloaded from nodepit space or the associated GitHub repository. Python source codes and documentations are available on the following GitHub repositories: LauLauThom/MultiTemplateMatching and LauLauThom/MultipleTemplateMatching-KNIME.
EphB1 in Endothelial Cells Regulates Caveolae Formation and Endocytosis
Authors: Tiruppathi Chinnaswamy , Regmi Sushil C. , Wang Dong-Mei , Mo Gary C.H. , Toth Peter T. , Vogel Stephen M. , Stan Radu V. , Henkemeyer Mark , Minshall Richard D. , Malik Asrar B. 
Published: April 2019

AbstractCaveolae, the cave-like structures abundant in endothelial cells (ECs), are important in regulating key functions such as caveolae-mediated endocytosis and generation of nitric oxide. Here we show that deletion of the receptor tyrosine kinase EphB1 (EphB1−/−) in mice markedly reduced the caveolae number in ECs of heart and lung vessels and prevented caveolae-mediated endocytosis. EphB1 expressed in adult ECs was shown to bind the caveolin-1 (Cav-1) scaffold domain (CSD) via the CSD binding motif (CSDBM) on EphB1. We demonstrated that activation of EphB1 by the native ligand Ephrin B1 uncoupled EphB1 from Cav-1, and licensedSrc-dependent Y-14 Cav-1 phosphorylation. Deletion of CSDBM on EphB1 prevented EphB1/Cav-1 interaction and the activation ofSrcandSrcmediated Y-14 Cav-1 phosphorylation. These studies identify the central role of endothelium expressed EphB1 in regulating caveolae biogenesis and caveolae-mediated endocytosis.
Validation of a CRISPR/cas9-based technology platform for examining specific immune gene functions in an experimental murine model of IBD
Authors: Wang Rui , Graham Sean , Sun Ning , McCarthy Donna , Peng Ruoqi , Erickson Jamie , Zhu Xiaochun , Wurbel Marc , Dunstan Robert , Chung Namjin , Fiebiger Edda , Ghayur Tariq , Gu Jijie 
Published: April 2019

AbstractInflammatory bowel diseases (IBD) are complex, multifactorial disorders characterized by chronic relapsing intestinal inflammation. Association studies have identified hundreds of genes that are linked to IBD and potentially regulate its pathology. The further dissection of the genetic network underlining IBD pathogenesis and pathophysiology is hindered by the limited capacity to investigate the role of each GWAS association through functional studies, including the generation of knockout animal models for each of the associated genes. The CRISPR/Cas9 system represents a cutting edge technology which has the potential to transform the field of IBD research by facilitating the introduction of genetic alterations in an efficient and effective manner. Using the CD40-mediated-colitis model, our results demonstrate the validity of a CRISPR/Cas9-based platform as a tool for the validation of target genes or interference strategies in experimental IBD. The utilization of this discovery strategy will allow for the timelyin vivovalidation of therapeutic targets as the rapidly emerge from current genetic and genomics efforts with human disease tissue. As such, the CRISPR/Cas9-based platform can significantly shorten the time span between target identification and generation of proof of principle experiments for drug discovery.
Deprivation of dietary fiber enhances susceptibility of mice to cryptosporidiosis
Authors: Oliveira Bruno César Miranda , Bresciani Katia Denise Saraiva , Widmer Giovanni 
Published: April 2019

ABSTRACTBased on our initial observations showing that mice consuming a probiotic product develop more severe cryptosporidiosis, we investigated the impact of other dietary interventions on the intracellular proliferation ofCryptosporidium parvumandC. tyzzeriin the mouse. Mice were orally infected with oocysts and parasite multiplication measured by quantifying fecal oocyst output. High-throughput sequencing of 16S ribosomal RNA amplicons was used to correlate oocyst output with diet and with the composition of the intestinal microbiota. On average, mice fed a diet without fiber (cellulose, pectin and inulin) developed more severe infections. As expected, a diet without fibers also significantly altered the fecal microbiota. Consistent with these observations, mice fed a prebiotic product sold for human consumption excreted significantly fewer oocysts. The fecal microbiota of mice consuming no plant polysaccharides was characterized by a lower relative abundance of Bacteroidetes bacteria. Since bacterial metabolites play an important role in the physiology of intestinal enterocytes, we hypothesize based on these observations that the impact of diet on parasite proliferation is mediated primarily by the metabolic activity of the anaerobic microbiota, specifically by the effect of certain metabolites on the host. This model is consistent with the metabolic dependence of intracellular stages of the parasite on the host cell. These observations underscore the potential of dietary interventions to alleviate the impact of cryptosporidiosis, particularly in infants at risk of recurrent enteric infections.AUTHOR SUMMARYThe infection withCryptosporidiumparasite, a condition known as cryptosporidiosis, is a common cause of infant diarrhea in developing countries. We have previously shown that mice infected withC. parvum, one of the main cause of human cryptosporidiosis, develop a more severe infection if given probiotics. To investigate the mechanism of this effect, we fed mice prebiotics and diet lacking plant fiber. We found that fermentable fiber, whether administered as a prebiotic supplement or is part of the diet, has a protective effect against cryptosporidiosis in mice. We also observed a significant association between the severity of infection and the composition of the gut microbiota. A significant inverse correlation was found between severity of cryptosporidiosis and the ratio between the abundance of bacteria belonging to the phylum Bacteroidetes and the abundance of Firmicute bacteria. This ratio is frequently viewed as a marker of a healthy microbiota. These results raise the possibility that dietary interventions could be used to alleviate the impact of cryptosporidiosis.
Characterizing transmissive diamond gratings as beam splitters for the hard X-ray single-shot spectrometer of the European XFEL
Authors: Kujala Naresh , Makita Mikako , Liu Jia , Zozulya Alexey , Sprung Michael , David Christian , Grünert Jan 
Published: April 2019

The European X-ray Free Electron Laser (EuXFEL) offers intense, coherent femtosecond pulses, resulting in characteristic peak brilliance values a billion times higher than that of conventional synchrotron facilities. Such pulses result in extreme peak radiation levels of the order of terawatts cm−2 for any optical component in the beam and can exceed the ablation threshold of many materials. Diamond is considered the optimal material for such applications due to its high thermal conductivity (2052 W mK−1 at 300 K) and low absorption for hard X-rays. Grating structures were fabricated on free-standing CVD diamond of 10 µm thickness with 500 µm silicon substrate support. The grating structures were produced by electron-beam lithography at the Laboratory for Micro- and Nanotechnology, Paul Scherrer Institut, Switzerland. The grating lines were etched to a depth of 1.2 µm, resulting in an aspect ratio of 16. The characterization measurements with X-rays were performed on transmissive diamond gratings of 150 nm pitch at the P10 beamline of PETRA III, DESY. In this paper, the gratings are briefly described, and a measured diffraction efficiency of 0.75% at 6 keV in the first-order diffraction is shown; the variation of the diffraction efficiency across the grating surface is presented.
Investigative decision-making: interviews with detectives
Authors: Spanoudaki Elpiniki , Ioannou Maria , Synnott John , Tzani-Pepelasi Calli , Pylarinou Ntaniella Roumpini 
Published: April 2019

PurposeThe purpose of this paper is to explore investigative decision-making processes in the context of major crimes as experienced by the law enforcement agents.Design/methodology/approachEpisodic interviews were conducted with six agents from medium-sized police forces in the UK. Following the framework of naturalistic inquiry, qualitative content analysis took place with the assistance of Atlas.ti software. To ensure the validity of findings, the within method triangulation was preferred, by additionally analysing the interview transcripts with Alceste.FindingsFindings from this study revealed a variety of internal factors at play, shaping the decision-making course into an act of balancing various desired goals. Detectives appear to assess a situation based on their experiences confirming that the naturalistic decision-making model may assist in understanding investigative decision-making.Research limitations/implicationsDue to the busy schedule of law enforcement agents the number of participants was limited and availability difficult; therefore, this study can be thought of as a pilot study that will inspire researchers to use the same method for in-depth understanding of investigative decision-making.Practical implicationsResults captured the ill-defined goals in the police environment and provided ways of decreasing their impact on investigative decision-making thus should help detectives to understand their decision-making limitations and strengths.Social implicationsThis project will enhance the psychological understanding of investigative decision-making.Originality/valueThis project assists in understanding the psychological aspect of investigative decision-making during police duty and provides the opportunity to law enforcement agents to re-evaluate situations in order to improve the investigative decision-making process; while adds to existing literature.
Determinants of Marathoners’ event expenditures: an in-depth exploration of past experience
Authors: Park Kwangsoo , Park Jeong-Yeol , Back Robin M. 
Published: April 2019

Purpose
The purpose of this paper is to explore the determinants of Marathon event spending by estimated expenditure models.

Design/methodology/approach
This study analyzes the impact of socio-demographic and travel-context factors on aggregated and disaggregated expenditures by event visitors who participated in the Fargo Marathon in Fargo, North Dakota.

Findings
The results indicate that event satisfaction does not have an influence on any types of expenditure. As the planning time increases, however, there is a positive effect on total expenditure. First-time visitors are shown to spend more money, especially on food and beverage, lodging and total expenditure. Conversely, the number of past experiences of the event had a negative influence on these expenditure types.

Originality/value
In addition to travel-related factors and socio-demographic variables, researchers had not examined the influence of repeat visits on travelers’ spending. The originality of this study lies in revealing that repeat visits decrease spending in specific categories, especially in the case of a Marathon event.
Progress on technology use in tourism
Authors: Cai Wenjie , Richter Shahper , McKenna Brad 
Published: April 2019

Purpose
With the rapid development and implementation of cutting-edge information technologies in tourism and hospitality, it is necessary to update the progress of technology use in the past 18 years and set up research agenda for future research. By adopting information systems (IS) as a reference discipline, this paper aims to create a literature review of technology and tourism papers around the theme of use.

Design/methodology/approach
Following the systematic literature review process of Aguinis et al. (2018), 314 papers were downloaded to determine how they applied the concept of technology use.

Findings
Three themes about technology use emerged: types of processing, organisational use and users. Among various types of technology processing, interactive and online are largely addressed in the tourism and hospitality literature. The organisational use theme explores how the competitive and strategic use of technology provides management support for organisations. There was a large amount of research focussed on direct users, such as individual characteristics, user attitudes and user behaviour. The theories of technology acceptance model and unified theory of acceptance and use of technology have been widely applied in these studies.

Originality/value
This paper provides a review of key issues which has been discussed in tourism research in relation to technology use. By applying the scheme developed in the IS discipline, this study provides new insights into the development of technology in tourism. In addition, it also gives us the opportunity to suggest a research agenda by identifying research gaps and future research collaboration opportunities between these two fields.
Sustainable manufacturing evaluation model focusing leather industries in India
Authors: Dwivedi Ashish , Agrawal Dindayal , Madaan Jitender 
Published: April 2019

Purpose
Sustainability is an integrating concept and demands strategic attention in developing countries like India. Due to strict environmental regulations and ongoing government sustainable policies such as “Namami Gange,” leather industries are extensively facing challenges to conform themselves toward these sustainable policies. The major challenge faced by leather industries is the exponentially increasing cost of adaptation to sustainable product and process. Under these operational constraints, survival of Indian leather industries has become a major challenge. In this context, this paper aims to identify and evaluate sustainable manufacturing policies. The key performance indicators (KPIs) based on triple bottom line of sustainability can assist leather industries that are about to initiate adopting sustainable practices.

Design/methodology/approach
This paper demonstrates the role of KPIs for evaluating sustainable manufacturing policies for leather industries in India. Initially, an in-depth literature review analysis has been carried out to identify indicators for evaluation of sustainable manufacturing policies. In this work, an integrated methodology has been developed to refine the priority map of the aforementioned KPIs based on consensus building among experts using Kappa analysis. Total interpretive structural modeling (TISM) has been used to demonstrate relationships which explain the significance of the KPIs. Further, Matriced Impact Croises Multiplication Applique analysis has been carried out to explore the relationships amongst KPIs.

Findings
Based on above analysis, identified interactive relationships among the KPIs will assist managers and decision-makers to incorporate effective sustainable policies in leather industries.

Practical implications
It is expected that these identified interactive interrelationships between KPIs will certainly facilitate the leather industry to achieve higher sustainable performance and competitiveness.

Originality/value
This study carries out an in-depth literature review analysis of sustainable manufacturing policies in leather industry. The author proposes an integrated methodology using kappa analysis, consensus building and TISM for evaluation of sustainable policies based on the literature review analysis and expert opinion.