bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm formation on agricultural waste pretreated with cold low-pressure nitrogen plasma and corona plasma discharges
Authors: Farber Ravit , Dabush-Busheri Inbal , Chaniel Gilad , Rozenfeld Shmuel , Bormashenko Edward , Multanen Victor , Cahan Rivka 
Published: April 2018

AbstractAgricultural waste (AW) was pretreated with cold low-pressure nitrogen plasma (LPD) and corona atmospheric plasma discharges (CAPD), in an attempt to increase the bacterial attachment and biofilm formation. Biofilm formation was examined in the presence of exogenously addedP. putidaandB. cereusas well as in a sterile medium where only the indigenous bacteria which grow naturally on the wood surface could form biofilm. The exposure of AW to (LPD) led to a 3.5-fold increase in biofilm formation of the exogenously addP. putidaF1 in MMT (minimal medium supplied with toluene) and a 1.6-fold increase in MMG (minimal medium supplied with glucose) compared to the untreated AW. The increase in biofilm formation was also observed with the exogenously addedB. cereusor with indigenous bacteria that grow naturally on the AW. The effect of the CAPD on biofilm formation was weak. SEM analysis of the LPD-treated AW showed an increase in surface roughness, which we assume is one of the reasons for the enhancement of the biofilm formation. The apparent contact angle of a sessile drop on the surface of LPD-treated AW as well as on the bacterial layer showed their hydrophilic nature. In conclusion, the increase in biofilm formation of the exogenously addedP. putidaorB. cereuswas due to the LPD treatment.ImportanceTo the best of our knowledge, this is the first study to describe the effect of wood plasma treatment on biofilm formation. This technology can be further implemented for bioremediation of contaminated soils.
Single-Cell Amplicon Sequencing Reveals Community Structures and Transmission Trends of Protist-Associated Bacteria in a Termite Host
Authors: Stephens Michael E. , Gage Daniel J. 
Published: April 2018

AbstractThe hindgut protists of wood-feeding termites are usually colonized by prokaryotic symbionts. Many of the hurdles that have prevented a better understanding of these symbionts arise from variation among protist and termite host species and the inability to maintain prominent community members in culture. These issues have made it difficult to study the fidelity, acquisition, and differences in colonization of protists by bacterial symbionts. In this study, we use high throughput amplicon sequencing of the V4 region of 16S rRNA genes to determine the composition of bacterial communities associated with single protist cells of six protist species, from the genera Pyrsonympha, Dinenympha, and Trichonympha that are present in the hindgut of the termite Reticulitermes flavipes. By analyzing amplicon sequence variants (ASVs), the diversity and distribution of protist-associated bacteria was compared within and across these six different protist species. ASV analysis showed that, in general, each protist genus associated with a distinct community of bacterial symbionts which were conserved across different termite colonies. However, some ASVs corresponding to ectosymbionts (Spirochaetes) were shared between different Dinenympha species and to a lesser extent with Pyrsonympha and Trichonympha hosts. This suggested that certain bacterial symbionts may be cosmopolitan to some degree and perhaps acquired by horizontal transmission. Using a fluorescence-based cell assay, we could observe the horizontal acquisition of surface-bound bacteria. This acquisition was shown to be time-dependent, involve active processes, and was non-random with respect to binding locations on some protists.
Molecular determinants of enterotoxigenicEscherichia coliheat-stable toxin secretion and delivery
Authors: Zhu Yuehui , Luo Qingwei , Davis Sierra M. , Westra Chase , Vickers Tim J. , Fleckenstein James M. 
Published: April 2018

AbstractEnterotoxigenicEscherichia coli(ETEC), a heterogeneous diarrheal pathovar defined by production of heat-labile (LT) and/or heat-stable (ST) toxins, remain major causes of mortality among children in developing regions, and cause substantial morbidity in individuals living in or traveling to endemic areas. Studies demonstrating a major burden of ST-producing ETEC have focused interest on ST toxoids for ETEC vaccines. We therefore examined fundamental aspects of ETEC ST biology using ETEC H10407, which carriesestHandestPgenes encoding ST-H and ST-P, respectively, in addition toeltABgenes responsible for LT. In this background, we found that deletion ofestHsignificantly diminished cGMP activation in target epithelia, while deletion ofestPhad a surprisingly modest impact, and a dualestH/estPmutant was not appreciably different than theestHmutant. Nevertheless, either ST-H or ST-P recombinant peptides stimulated cGMP production. We also found that the TolC efflux protein was essential for both toxin secretion and delivery, providing a potential avenue for efflux inhibitors in treatment of acute diarrheal illness. In addition, we demonstrated that the EtpA adhesin is required for optimal delivery of ST and that antibodies against either the adhesin or ST-H significantly impaired toxin delivery and cGMP activation in target T84 cells. Finally, we used FLAG epitope fusions to demonstrate that the ST-H pro-peptide sequence is secreted by the bacteria, potentially providing additional targets for antibody neutralization. These studies collectively extend our understanding of ETEC pathogenesis and potentially inform additional avenues to mitigate disease by these common diarrheal pathogens.
ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
Authors: Andersen Kasper S. , Kirkegaard Rasmus H. , Karst Søren M. , Albertsen Mads 
Published: April 2018

AbstractSummaryMicrobial community analysis using 16S rRNA gene amplicon sequencing is the backbone of many microbial ecology studies. Several approaches and pipelines exist for processing the raw data generated through DNA sequencing and convert the data into OTU-tables. Here we present ampvis2, an R package designed for analysis of microbial community data in OTU-table format with focus on simplicity, reproducibility, and sample metadata integration, with a minimal set of intuitive commands. Unique features include flexible heatmaps and simplified ordination. By generating plots using the ggplot2 package, ampvis2 produces publication-ready figures that can be easily customised. Furthermore, ampvis2 includes features for interactive visualisation, which can be convenient for larger, more complex data.Availabilityampvis2 is implemented in the R statistical language and is released under the GNU A-GPL license. Documentation website and source code is maintained at:https://github.com/MadsAlbertsen/ampvis2ContactMads Albertsen (ma@bio.aau.dk)
FBXL19 recruits CDK-Mediator to the CpG islands of developmental genes to prime them for activation during lineage commitment
Authors: Dimitrova Emilia , Kondo Takashi , Feldmann Angelika , Nakayama Manabu , Koseki Yoko , Konietzny Rebecca , Kessler Benedikt M , Koseki Haruhiko , Klose Robert J 
Published: April 2018

AbstractCpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.
Brain scans from 21297 individuals reveal the genetic architecture of hippocampal subfield volumes
Authors: Meer Dennis van der , Rokicki Jaroslav , Kaufmann Tobias , Córdova-Palomera Aldo , Moberget Torgeir , Alnæs Dag , Bettella Francesco , Frei Oleksandr , Doan Nhat Trung , Agartz Ingrid , Bertolino Alessandro , Bralten Janita , Brandt Christine L. , Buitelaar Jan K. , Djurovic Srdjan , Donkelaar Marjolein van , Dørum Erlend S. , Espeseth Thomas , Faraone Stephen V. , Fernández Guillén , D.Phil. Simon E. Fisher , Franke Barbara , Haatveit Beathe , Hartman Catharina A. , Hoekstra Pieter J. , Håberg Asta K. , Jönsson Erik G. , Kolskår Knut K. ,   Cand. Psychol., Hellard Stephanie Le , Lund Martina J. , Lundervold Astri J. , Lundervold Arvid , Melle Ingrid , Sánchez Jennifer Monereo , Norbom Linn C. , Nordvik Jan E. , Nyberg Lars , Oosterlaan Jaap , Papalino Marco , Papassotiropoulos Andreas , Pergola Giulio , de Quervain Dominique J.F. , Richard Geneviève , Sanders Anne-Marthe , Selvaggi Pierluigi , Shumskaya Elena , Steen Vidar M. , Tønnesen Siren , Cand.Psychol. Kristine M. Ulrichsen , Zwiers Marcel P. , Lars Ole A. Andreassen , Westlye Lars T. 
Published: April 2018

ABSTRACTThe hippocampus is a heterogeneous structure, comprising histologically distinguishable subfields. These subfields are differentially involved in memory consolidation, spatial navigation and pattern separation, complex functions often impaired in individuals with brain disorders characterized by reduced hippocampal volume, including Alzheimer’s disease (AD) and schizophrenia. Given the structural and functional heterogeneity of the hippocampal formation, we sought to characterize the subfields’ genetic architecture. T1-weighted brain scans (n=21297, 16 cohorts) were processed with the hippocampal subfields algorithm in FreeSurfer v6.0. We ran a genome-wide association analysis on each subfield, covarying for total hippocampal volume. We further calculated the single nucleotide polymorphism (SNP)-based heritability of twelve subfields, as well as their genetic correlation with each other, with other structural brain features, and with AD and schizophrenia. All outcome measures were corrected for age, sex, and intracranial volume. We found 15 unique genome-wide significant loci across six subfields, of which eight had not been previously linked to the hippocampus. Top SNPs were mapped to genes associated with neuronal differentiation, locomotor behaviour, schizophrenia and AD. The volumes of all the subfields were estimated to be heritable (h2 from .14 to .27, all p< 1×10-16) and clustered together based on their genetic correlations compared to other structural brain features. There was also evidence of genetic overlap of subicular subfield volumes with schizophrenia. We conclude that hippocampal subfields have partly distinct genetic determinants associated with specific biological processes and traits. Taking into account this specificity may increase our understanding of hippocampal neurobiology and associated pathologies.
Acute effects of drugs onC.elegansmovement reveal complex responses and plasticity
Authors: Spensley Mark , Del Borrello Samantha , Pajkic Djina , Fraser Andrew G 
Published: April 2018

AbstractMany drugs act very rapidly — they can turn on or off their targets within minutes in a whole animal. What are the acute effects of drug treatment and how does an animal respond to these? We developed a simple assay to measure the acute effects of drugs onC.elegansmovement and examined the effects of a range of compounds including neuroactive drugs, toxins, environmental stresses and novel compounds on worm movement over a time period of 3 hours. We find that many treatments show complex acute responses — a phase of rapid paralysis is followed by one or more recovery phases. The recoveries are not the result of some generic stress response but are specific to the drug e.g. recovery from paralysis due to a neuroactive drug requires neurotransmitter pathways whereas recovery from a metabolic inhibitor requires metabolic changes. Finally, we also find that acute responses can vary greatly across development and that there is extensive and complex natural variation in acute responses. In summary, acute responses are sensitive probes of the ability of biological networks to respond to drug treatment and these responses can reveal the action of unexplored pathways.Author SummaryDrugs are powerful tools that let us switch on or off key pathways in whole animals and watch the effects. Here we set up a simple assay to measure how drugs affect the movement of the simple nematodeC.elegans— crucially, we look how those responses change over time. We find that worms have complex responses to many different drugs — they go through clear phases of paralysis and recovery. The recovery from the initial effect of any drug is not due to a generic stress response but is specific to the way each drug acts. We find for example that worms can recover from paralysis driven by one neurotransmitter pathway by activating a different neurotransmitter pathway or from paralysis caused by loss of one metabolic pathway by turning on a second one. These complex responses show how the basic genetic networks that are needed for normal behaviour and function can rewire and respond to the effect of many drugs. Importantly, the responses can vary in many ways — different aged worms or different individuals can have different responses and capturing how drug responses change over time is critical to dissect this complexity.
Confidence Analysis of DEER Data and its Structural Interpretation with Ensemble-Biased Metadynamics
Authors: Hustedt Eric J. , Marinelli Fabrizio , Stein Richard A. , Faraldo-Gómez José D. , Mchaourab Hassane S. 
Published: April 2018

ABSTRACTGiven its ability to measure multicomponent distance distributions between electron-spin probes, Double Electron-Electron Resonance spectroscopy (DEER) has become a leading technique to assess the structural dynamics of biomolecules. However, methodologies to evaluate the statistical error of these distributions are not standard, often hampering a rigorous interpretation of the experimental results. Distance distributions are often determined from the experimental DEER data through a mathematical method known as Tikhonov regularization, but this approach makes rigorous error estimates difficult. Here, we build upon an alternative model-based approach in which the distance probability distribution is represented as a sum of Gaussian components and use propagation of errors to calculate an associated confidence band. Our approach considers all sources of uncertainty, including the experimental noise, the uncertainty in the fitted background signal, and the limited time-span of the data collection. The resulting confidence band reveals the most and least reliable features of the probability distribution, thereby informing the structural interpretation of DEER experiments. To facilitate this interpretation, we also generalize the molecular-simulation method known as Ensemble-Biased Metadynamics. This method, originally designed to generate maximum-entropy structural ensembles consistent with one or more probability distributions, now also accounts for the uncertainty in those target distributions, exactly as dictated by their confidence bands. After careful benchmarks, we demonstrate the proposed techniques using DEER results from spin-labeled T4 lysozyme.
Exploring challenges to ICT utilisation in construction site management
Authors: Ozumba Aghaegbuna Obinna U. , Shakantu Winston 
Published: April 2018

Purpose
The purpose of this paper is to explore the nature and occurrence, and peculiarities and dynamics, if any, of perceived challenges to the adoption of information and communication technologies (ICT) in construction site management; using South Africa as context for empirical study.

Design/methodology/approach
Literature on the constraints to technology transfer and ICT adoption in construction is used as basis for the study. A national survey of registered persons in South Africa was used to collect qualitative data. A robust multi-stepped analytical approach was used to derive results.

Findings
Findings suggest appreciable similarity between literature and primary data, in types of individual challenges and their categories. Lack of technology and management support, and knowledge and information related issues, are relatively more prevalent in site management. There is a fair level of commonality in perception of technical barriers among the various categories of respondents who are active in site management. However, project managers seem to be more sensitive to some inhibiting factors, more than other respondent groups.

Research limitations/implications
Inherent limitations of survey strategy were experienced, but highly qualitative data were collected at a national level. The study highlights the range of barriers to ICT in site management, and compounding effects of technology-, knowledge- and management-related constraints.

Practical implications
The possibility of knowledge-based factors remotely manifesting in other categories was highlighted. There is need to consider all challenges in planning for ICT in projects, and prioritise technology-, knowledge- and management-related challenges. A classification for exploring challenges to ICT in the site management process is also proposed.

Social implications
Appreciable paucity remains in research focused on ICT in the site management process, as opposed to the popular operations/application focus of IT/ICT studies. Furthermore, there is still scarcity of ICT research in Africa, with regard to the built environment and specifically site management.

Originality/value
This study contributes to research in ICT innovation adoption in the construction industry, by developing a better understanding of the dynamics of perceived challenges to ICT adoption in the site management process; according to types and classifications of challenges, and roles and age groups of stakeholders. The study further sets a baseline for future studies in this area by proposing a frame of categorisation that is focused on site management.
Using geostatistical techniques to map adaptive capacities of resource-poor communities to climate change
Authors: Chari Martin Munashe , Hamandawana Hamisai , Zhou Leocadia 
Published: April 2018

Purpose
This paper aims to present a case study-based approach to identify resource-poor communities with limited abilities to cope with the adverse effects of climate change. The study area is the Nkonkobe Local Municipality, in the Eastern Cape which is one of South Africa’s provinces ranked as being extremely vulnerable to the adverse effects of climate change because of high incidences of poverty and limited access to public services such as water and education. Although adaptive capacity and vulnerability assessments help to guide policy formulation and implementation by identifying communities with low coping capacities, policy implementers often find it difficult to fully exploit the utility of these assessments because of difficulties in identifying vulnerable communities. The paper attempts to bridge this gap by providing a user-friendly, replicable, practically implementable and adaptable methodology that can be used to cost-effectively and timeously identify vulnerable communities with low coping capacities.

Design/methodology/approach
A geostatistical approach was used to assess and evaluate adaptive capacities of resource-poor communities in the Nkonkobe Local Municipality. The geospatial component of this approach consisted of a multi-step Geographical Information Systems (GIS) based technique that was improvised to map adaptive capacities of different communities. The statistical component used demographic indicators comprising literacy levels, income levels, population age profiles and access to water to run automated summation and ranking of indicator scores in ArcGIS 10.2 to produce maps that show spatial locations of communities with varying levels of adaptive capacities on a scale ranging from low, medium to high.

Findings
The analysis identified 14 villages with low adaptive capacities from a total of 180 villages in the Nkonkobe Local Municipality. This finding is important because it suggests that our methodology can be effectively used to objectively identify communities that are vulnerable to climate change.

Social implications
The paper presents a tool that could be used for targeting assistance to climate change vulnerable communities. The methodology proposed is of general applicability in guiding public policy interventions aimed at reaching, protecting and uplifting socio-economically disadvantaged populations in both rural and urban settings.

Originality/value
The approach’s ability to identify vulnerable communities is useful because it aids the identification of resource-poor communities that deserve priority consideration when planning adaptation action plans to deliver support and assistance to those least capable of effectively coping with the adverse effects of climate change induced vulnerabilities.
Competences management for improving performance in health organizations
Authors: Fanelli Simone , Lanza Gianluca , Zangrandi Antonello 
Published: April 2018

PurposeThe purpose of this paper is to describe the design and construction of a privilege mapping system (clinical and organizational competences) of the medical staff of the Niguarda Hospital in Milan, Italy. The second aim is to measure and assess the impact of implementing an evaluation process of clinical competences at the same hospital.Design/methodology/approachThe paper retraces the development and implementation of the evaluation of the privilege system, highlighting the subjects involved, the phases and outputs. Moreover, a questionnaire was distributed to 50 heads of unit involved in the planning, building and implementation of competences mapping. Five areas were investigated: competences evaluation for professional development; the impact on work organization and professional roles; professional collaboration; its impact according to context (hospital or unit) and time scale (short or long term); and ability to evaluate clinical outcome.FindingsResults reveal success factors for the development and implementation of a privilege mapping system. Furthermore, the survey revealed that clinical leaders are aware of the importance of competences evaluation. In particular, they consider it as a management tool useful for professional development, for identifying excellence and planning operational activities.Originality/valueLiterature and practical evidence recognize the need to assess the clinical and organizational competences in order to assign tasks and responsibilities. However, there are no studies that describe the construction of systems of evaluation of privileges, as it has never been investigated as professionals perceive these tools.