bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Intercroping Maize-Soybean on Grain Quality Traits in Kenya
Authors: Jean Pierre Habineza M. , Kinama Josiah M. , Olubayo Florence M. , Wanderi Susan W. , Muthomi James W. , Nzuve Felister M. 
Published: January 2018

An experiment was conducted in Kenya to determine the effect of intercropping maize-soybean on soybean grain quality traits. A randomized complete block design replicated three times with seven treatments was used. Data were collected and analysed for soybean protein content, oil content and dry matter while grain size was done for maize and soybean. Data were subjected to ANOVA and means separated using LSD0.05. The results showed that TGX1990-5F variety recorded high protein content (p ≤ 0.05) in sole crop compared to intercropping with 42.96% and 38.4% respectively while SB19 obtained 36.57% and 40.41% of protein between sites for the first season. A bout the second season, TGX1990-5F gave 40.84% of protein compared to 31.98% for GAZELLE in intercrop at both sites. GAZELLE showed higher oil content followed by TGX1990-5F and SB19 was the last in both seasons. TGX1990-5F showed higher dry matter followed by GAZELLE and SB19 was the last in intercrop. In addition, GAZELLE a local variety showed greater size than SB19 in both rainy seasons. Intercropping affected slightly the protein content, oil content and gain size than sole crop but it did not affect the dry matter in both seasons.Thus, TGX1990-5F can be recommended to small-scale farmers for intercropping with maize because it produced higher value of protein and small-scale farmers could use it to fight mal nutrition. GAZELLE variety can be also recommended for oil production. Maize grain size was not affected by intercropping system.
De implementatie van de vierde en vijfde anti-witwasrichtlijn
Authors: van Poelgeest J.M. 
Published: January 2018

De implementatie van de vierde en vijfde anti-witwasrichtlijn
De vierde anti-witwasrichtlijn is in werking getreden en diende uiterlijk 26 juni 2017 te zijn geïmplementeerd. In verband met de implementatie van de richtlijn wijzigt onder meer de Wet ter voorkoming van witwassen en financieren van terrorisme (Wwft). In dit artikel worden de belangrijkste wijzigingen besproken als gevolg van de Implementatiewet registratie uiteindelijk belanghebbenden en de Implementatiewet vierde anti-witwasrichtlijn. De implementatie heeft een aanzienlijke impact op het beleid van alle instellingen die onder de Wwft vallen. Zo zullen de instellingen hun beleid moeten aanpassen en gebruik moeten gaan maken van het register met uiteindelijk belanghebbenden. De risicogebaseerde benadering komt nog meer naar voren in het cliëntenonderzoek dat door de instellingen moet worden verricht.
Influence of occupational dysfunction on the psychological problem in healthcare workers: A study using structural equation modeling
Authors: Teraoka Mutsumi , Kyougoku Makoto 
Published: January 2018

Purpose: This study identified the effect of occupational dysfunction on psychological factors of stress response, burnout syndrome, and depression in healthcare workers.
Method: Three cross sectional studies were conducted to assess the following relations: 1) occupational dysfunction on stress response (n = 468), 2) occupational dysfunction on burnout syndrome (n = 1142), and 3) occupational dysfunction on depression (n = 687). Personal characteristics were collected through a questionnaire (such as age, gender, and job category, opportunities for refreshment, time spent on leisure activities, and work relationships) as well as the Classification and Assessment of Occupational Dysfunction (CAOD). Furthermore, study 1 included the Stress Response Scale-18 (SRS-18), study 2 used the Japanese Burnout Scale (JBS), and study 3 employed the Center for Epidemiological Studies Depression Scale (CES-D). The Kolmogorov–Smirnov test, confirmatory factor analysis (CFA), exploratory factor analysis (EFA), and path analysis of structural equation modeling (SEM) analysis were used in all of the studies. EFA and CFA were used to measure structural validity of four assessments; CAOD, SRS-18, JBS, and CES-D. For examination of a potential covariate, we assessed the correlation of the total score of CAOD and personal factors in all studies. Moreover, direct and indirect effects of occupational dysfunction on stress response (Study 1), burnout syndrome (Study 2), and depression (Study 3) were also analyzed.
Results: CAOD had 16 items and 5 factors. SRS-18 had 18 items and 3 factors, JBS had 17 items and 3 factors, CES-D had 20 items and 4 factors. All studies found that there were significant correlations between the CAOD total score and the personal factor that included opportunities for refreshment, time spent on leisure activities, and work relationships (p<0.01). The causal sequence model results suggest that the classification of occupational dysfunction had positive causal effects on the stress response (RMSEA = 0.058, CFI = 0.951, and TLI = 0.947), burnout syndrome (RMSEA = 0.074, CFI = 0.922, and TLI = 0.915), and depression (RMSEA=0.059, CFI=0.926, TLI=0.920). Moreover, the positive effect of external covariates include opportunities for refreshment, time spent on leisure activities, and work relationships on occupational dysfunction.
Conclusion: The classification of occupational dysfunction indicated a possibility of increase in the stress response, burnout syndrome, and depression in healthcare workers. Furthermore, occupational dysfunction affected personal factors including opportunities for refreshment, time spent on leisure activities, and work relationships. Therefore, it is necessary to adopt occupational therapy strategies to prevent this problem.
Accessing biological data with semantic web technologies
Authors: Willighagen Egon 
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.
Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.
Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene.
Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
Accessing biological data in R with semantic web technologies
Authors: Willighagen Egon 
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.
Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.
Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services.
Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
Predictive analytics using a novel simulation application: Validation of an effective decision support tool for Emergency Department flow
Authors: Hurwitz Joshua E , Lopiano Kenneth K , Bohrmann Thomas F , Swan Wendy , Falgiani Michael , Tyndall J Adrian 
Published: January 2018

Objectives: To develop a scalable software application that can predict the effects of operational decisions in a variety of emergency care environments. Validate the ability of the application's core simulation model to recreate and predict site-specific patient flow at both a large academic center and a freestanding ED. Evaluate the utility of the application for use by ED managers to inform operational decisions.
Methods: The application was developed through a public-private partnership between University of Florida Health and Roundtable Analytics, Inc., supported by a National Science Foundation Small Business Technology Transfer (STTR) grant. The core simulation model was parameterized using site-specific data and Monte Carlo studies were performed to validate its ability to predict the effects of management interventions at two EDs. At one ED, the medical director conducted simulation studies to evaluate the sustainability of the current operational strategy and predict the effects of specific interventions. After implementation, the fidelity of the model's predictions was evaluated.
Results: The application was successfully built and deployed at two qualitatively distinct EDs. When equipped with site-specific parameters, the model accurately recreated the each ED's throughput and faithfully predicted the effects of specific management interventions. One ED model also identified a point when increasing arrivals dictate that the current operational strategy will become less effective than an alternative strategy. As actual arrivals approached this point, decision-makers used the application to simulate a variety different interventions and incorporated this information in their decision to implement a new strategy. The observed outcomes resulting from this intervention fell within the range of predictions from the model. An online demonstration of this application is available at http://solutions.roundtableanalytics.com/Emergency-Department-Simulation/
Conclusion: This application overcomes technical barriers to entry that have kept simulation modeling out of the hands of key decision-makers. Using this technology, ED managers with no programming experience were able to conduct simulation studies customized to their ED. Moreover, the incorporation of these results by decision-makers had a direct positive impact on ED operations. The effective use of simulation modeling promises to replace inefficient trial-and-error approaches and become a useful and accessible tool for healthcare managers challenged to make operational decisions in environments of increasingly scarce resources.
Adeno-associated virus Type 2 Rep proteins mediate integration of lentiviral vectors
Authors: McAlister Victor J , Craig Anthony T , Owens Roland A 
Published: January 2018

Aims: Adeno-associated virus type 2 (AAV2) is a naturally defective human parvovirus that is being developed as a gene therapy vector. In dividing cells, AAV2 DNA persists by integration into the host chromosomes. AAV2 is unique among mammalian viruses in its ability to integrate preferentially into a particular locus within human chromosome 19, designated AAVS1(also known as Mbs 85). The AAV2 Rep68 and Rep78 proteins mediate this integration. Recent data suggest that Rep68 and Rep78 can mediate integration of non-AAV2 DNA with free ends. To test this hypothesis, we targeted insertion of different lentiviral vectors to AAVS1.
Methods: Cells were co-infected with wild-type AAV2, and integrase-proficient or integrase-deficient lentivirus vectors. A highly specific PCR-based assay was used to detect lentivirus integration at AAVS1. Similar experiments were performed using lentiviral vectors containing the AAV2 rep gene.
Results: All lentiviral vectors tested integrated at AAVS1, if the rep gene was present either within the lentiviral vector or supplied in trans. All that was required for integration at AAVS1 was the amino acid sequence shared between Rep68 and Rep78. The results were similar with integrase-proficient or integrase-deficient lentiviral vectors.
Conclusions: The inclusion of the rep gene with lentiviral vectors may produce more predictable integration patterns.
SKIMMR: Facilitating knowledge discovery in life sciences by machine-aided skim reading
Authors: Novacek Vit , Burns Gully APC 
Published: January 2018

Background: Unlike full reading, 'skim-reading' involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles in life sciences.
Methods: To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used top construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed.
Results: We provide a web-based prototype (called `SKIMMR') that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson's Disease. Last but not least, we describe a methodology for automated experimental evaluation of SKIMMR instances. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. The results of experiments performed on three different instances of SKIMMR show that the presented method for machine-aided skim reading outperforms state of the art tools like PubMed regarding focused browsing and informativeness of the browsing context.
Conclusions: In preliminary trials, users find new, interesting and non-trivial facts with SKIMMR. Our evaluation showed a high potential of the presented work for facilitating knowledge discovery in life sciences.
Genetic profiling of the isoprenoid and sterol biosynthesis pathways of Trypanosoma cruzi
Authors: Cosentino Raul O , Diosque Patricio , Agüero Fernán 
Published: January 2018

Background. Sterols such as cholesterol, are important components of cellular membranes. But unlike mammalian cells, the main sterols found in the membranes of trypanosomes and fungi are ergosterol, and other 24-methyl sterols, which are required for growth and viability. In spite of this strict requirement, this group of organisms have evolved different strategies to produce and/or obtain sterols. Trypanosoma cruzi is the causative agent of Chagas Disease. In this parasite, one of the few validated targets for chemotherapeutic intervention is the sterol biosynthesis pathway. In this work we present a study of the genetic diversity observed in genes of the isoprenoid and sterol biosynthesis pathways in T. cruzi, and a comparative analysis of the diversity found in other trypanosomatids.
Methodology/Principal Findings. Using a number of bioinformatic strategies, we first completed a number of holes in the pathway by identifying the sequences of genes that were missing and/or were truncated in the draft T. cruzi genome. Based on this analysis we identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO) and propose that the orthologs of ERG25 have been lost in trypanosomes (but not in leishmanias). Next, starting from a set of 16 T. cruzi strains representative of six major evolutionary lineages, we have amplified and sequenced ~ 24Kbp from 18 genes of the pathway, and identified a total of 975 SNPs or fixed differences, of which 28% represent nonsynonymous changes. We observed different patterns of accumulation of nucleotide changes for different genes of the pathway, from genes with a density of substitutions ranging from those close to the average (~2.5/100 bp) to some showing a high number of changes (11.4/100 bp, for a putative lathosterol oxidase gene). The majority of genes are under apparent purifying selection. However, two genes (TcPMK, TcSMO-like) have a ratio of nonsynonymous to synonymous changes that is close to neutrality. None of the nonsynonymous changes identified affect a catalytic or a ligand binding site residue. However, after mapping these changes on top of available structural data, we identified a number of changes that are in the close vicinity (7 Angstrom) of key residues, and that could therefore be functionally important. A comparative analysis of the corresponding T. brucei and Leishmania genes, obtained from available complete genomes highlights a high degree of conservation of the pathway, but with differences in the genes that are under apparent purifying selection in each case.
Conclusions/Significance. We have identified a number of genes of the sterol biosynthesis pathway that were missing from the T. cruzi genome assembly. Also, we have identified unequal apparent selection acting on these genes, which may provide essential information for the future of drug development studies focused on this pathway.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica , Silver Pamela A 
Published: January 2018

Bacterial from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical.
Here we show that B. subtilis, an organism which typically does not respond to media compression, can be induced to do so with two simple and synergistically perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells.
These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a genetically tractable chassis for engineering compression sensitive organisms in the future. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica , Silver Pamela A 
Published: January 2018

Bacterial from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical.
Here we show that B. subtilis, an organism which typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells.
These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a genetically tractable chassis for engineering compression sensitive organisms in the future. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.