bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mode of Growth and Temperature Dependence on Expression of Atrazine-degrading Genes inPseudomonassp. strain ADP Biofilms
Authors: Delcau Michael A. , Henry Victoria A. , Pattee Emily R. , Peeples Tonya L. 
Published: April 2018

AbstractBacterial strainPseudomonassp. strain ADP is capable of metabolizing atrazine, a synthetic herbicide, and uses atrazine as a sole nitrogen source for growth. The microbe completely mineralizes the substrate in a catabolic pathway comprised of six enzymatic steps. All enzymes, AtzA-AtzF, encoded by corresponding genes,AtzA-AtzF, are located on a self-transmissible plasmid, pADP-1. (Souza, M. L., Wackett, L.P., and Sadowsky, M.JAppl. and Environ. Microbiol. 64(6): 2323-2326, 1998) RT-qPCR was used to differentiate gene expression in atrazine-degrading genes inPseudomonassp. strain ADP cells grown as suspended cells and as biofilms. Relative gene expression was also evaluated for biofilms grown at 25°C, 30°C, and 37°C. Complementary atrazine kinetic data was collected using GC-MS for both modes of growth and temperature variance. No significant difference in expression was observed for all atrazine-degrading genes in biofilm-mediated cells relative to planktonic cells, suggesting neither decreased or increased catabolic activity at the mRNA level. In contrasting experiments concerning biofilm growth, expression was downregulated at 37°C for genes AtzA,AtzB, andAtzCand upregulated for genesAtzD, AtzE, AtzF, signifyingPseudomonassp. strain ADP biofilms catabolic activity may change in response to substantial temperature changes. Gradual decreases in atrazine concentration were apparent in cells grown in shake flasks, while biofilm-mediated cells showed transient increases and decreases in reactor effluent. The complex extracellular matrix components, quorum sensing, and genetic transfer may account for accumulation and rapid degradation of atrazine. The data collected suggest biofilm-mediated bioremediation may give insight into catabolic activity and atrazine degradation potential.ImportanceAtrazine is the second most applied herbicide in the United States. It is applied to crops including sorghum, corn, and sugarcane to prevent the growth of broad-leaved weeds. Once used, it can permeate the soil and contaminate proximal groundwater sources, which provide drinking water for over 90-million people. The Environmental Protection Agency sets the maximum contaminant level at 3 parts per billion for atrazine in drinking water, however this is frequently exceeded in rural regions which presents a public safety concern. Atrazine is an endocrine disruptor compound and a suspected teratogen in humans and freshwater species, respectively. This research is significant in evaluating the use an atrazine-degrading strain,Pseudomonassp. strain ADP, grown in a biofilm mode of growth to increase the degradation potential compared to suspended cells. Our results concerning expression and kinetics will aid the development of biofilm reactors forex situbioremediation and understanding environmental biofilms.
Development and validation of a phenotypic high-content imaging assay for assessing the antiviral activity of small-molecule inhibitors targeting the Zika virus
Authors: Bernatchez Jean A. , Yang Zunhua , Coste Michael , Li Jerry , Beck Sungjun , Liu Yan , Clark Alex E. , Zhu Zhe , Luna Lucas A. , Sohl Christal D. , Purse Byron W. , Li Rongshi , de Siqueira-Neto Jair L. 
Published: April 2018

AbstractZika virus (ZIKV) has been linked to the development of microcephaly in newborns, as well as Guillain-Barré syndrome. There are currently no drugs available to treat infection, and accordingly there is an unmet medical need for discovery of new therapies. High-throughput drug screening efforts focusing on indirect readouts of cell viability are prone to a higher frequency of false positives in cases where the virus is viable in the cell but the cytopathic effect is reduced or delayed. Here, we describe a fast and label-free phenotypic high-content imaging assay used to detect cells affected by the viral-induced cytopathic effect (CPE) using automated imaging and analysis. Protection from CPE correlates with a decrease in viral antigen production as observed by immunofluorescence. We trained our assay using a collection of nucleoside analogues against ZIKV; the previously reported antiviral activities of 2’-C-methylribonucleosides and ribavirin against the Zika virus in Vero cells were confirmed using our developed method. Profiling of a novel library of 24 natural product derivatives using our assay revealed compound 1 as an inhibitor of ZIKV-induced cytopathic effect; activity of the compound was confirmed in human fetal neural stem cells (NSCs). The described technique can be easily leveraged as a primary screening assay for profiling large compound libraries against ZIKV, and can be expanded to other ZIKV strains and other cell lines displaying morphological changes upon ZIKV infection.
The lipid environment determines the activity of theE. coliammonium transporter, AmtB
Authors: Mirandela Gaëtan Dias , Tamburrino Giulia , Hoskisson Paul A. , Zachariae Ulrich , Javelle Arnaud 
Published: April 2018

AbstractThe movement of ammonium across biological membranes is a fundamental process in all living organisms and is mediated by the ubiquitous Amt/Mep/Rh family of transporters. Recent structural analysis and coupled mass spectrometry studies have shown that theEscherichia coliammonium transporter, AmtB, specifically binds phosphatidylglycerol (PG). Upon PG binding, several residues of AmtB undergo a small conformational change, which stabilizes the protein against unfolding. However, no studies have so far been conducted to explore if PG binding to AmtB has functional consequences. Here, we used an invitroexperimental assay with purified components together with molecular dynamics simulations to characterise the relation between PG binding and AmtB activity. Firstly, our results indicate that the function of Amt in archaebacteria and eubacteria may differ. Secondly, we show that PG is an essential cofactor for AmtB activity and that in the absence of PG AmtB cannot complete the full translocation cycle. Furthermore, our simulations reveal previously undiscovered PG binding sites on the intracellular side of the lipid bilayer between the AmtB subunits. The possible molecular mechanisms explaining the functional role of PG are discussed.
In situ structures of periplasmic flagella reveal a distinct cytoplasmic ATPase complex inBorrelia burgdorferi
Authors: Qin Zhuan , Manne Akarsh , Tu Jiagang , Yu Zhou , Lees Kathryn , Yerke Aaron , Lin Tao , Li Chunhao , Norris Steven J. , Motaleb Md A. , Liu Jun 
Published: April 2018

ABSTRACTPeriplasmic flagella are essential for the distinct morphology and motility of spirochetes. A flagella-specific Type III secretion system (fT3SS) composed of a membrane-bound export apparatus and a cytosolic ATPase complex is responsible for the assembly of the periplasmic flagella. Here, we combine cryo-electron tomography and mutagenesis approaches to characterize the fT3SS machine in the Lyme disease spirocheteBorrelia burgdorferi. We define the fT3SS machine by systematically characterizing mutants lacking key component genes. We discover that a distinct cytosolic ATPase complex is attached to the flagellar C-ring through multiple spoke-like linkers. The ATPase complex not only strengthens structural rigidity of the C-ring, but also undergoes conformational changes in concert with flagellar rotation. Our studies provide structural framework to uncover the unique mechanisms underlying assembly and rotation of the periplasmic flagella and may provide the bases for the development of novel therapeutic strategies against several pathogenic spirochetes.
The spatial and temporal dynamics of the nuclear RNAi-targeted RNA transcripts inCaenorhabditis elegans
Authors: Ni Julie Zhouli , Kalinava Natallia , Mendoza Sofia Galindo , Gu Sam Guoping 
Published: April 2018

SummarySmall RNA-guided chromatin silencing, also referred to as nuclear RNAi, plays an essential role in genome surveillance in eukaryotes and provides a unique paradigm to explore the complexity in RNA-mediated chromatin regulation and transgenerational epigenetics. A well-recognized paradox in this research area is that transcription of the target loci is necessary for the initiation and maintenance of the silencing at the same loci. How the two opposing activities (transcriptional activation and repression) are coordinated during animal development is poorly understood. To resolve this gap, we took single-molecule RNA imaging, deep-sequencing, and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two exemplary endogenous germline nuclear RNAi targets inC. elegans, Cer3 and Cer8 LTR retrotransposons. By examining the wild type and a collection of mutant strains, we found that transcription and silencing cycle of Cer3 and Cer8 is tightly coupled with the early embryogenesis and germline mitotic and meiotic cell cycles. Strikingly, Cer3 and Cer8 transcripts are exclusively localized in the nuclei of germ cells in both wild type and germline nuclear RNAi-defective mutant animals. RNA-sequencing analysis found that this nuclear enrichment feature is a general feature for the endogenous targets of the germline nuclear RNAi pathway. In addition, the germline and somatic repressions of Cer3 have different genetic requirement for the three H3K9 histone methyltransferases, MET-2, SET-25, and SET-32, in conjunction with the nuclear Argonaute protein WAGO-9/HRDE-1. These results provide a first comprehensive cellular and developmental characterization of the nuclear RNAi-targeted endogenous targets throughout animal reproductive cycle. Altogether, these results support a model in which (1) both the transcriptional activation and repression steps of the germline nuclear RNAi pathway are tightly coupled with animal development, (2) the endogenous targets exhibit a hallmark of nuclear enrichment of their transcripts, and (3) different heterochromatin enzymes play distinct roles in somatic and germline silencing of the endogenous targets.
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Authors: Zhu Anqi , Ibrahim Joseph G. , Love Michael I. 
Published: April 2018

AbstractIn RNA-seq differential expression analysis, investigators aim to detect genes with changes in expression across conditions, despite technical and biological variability. A common task is to accurately estimate the effect size. When the counts are low or highly variable, the simple effect size estimate has high variance, leading to poor ranking of genes by effect size. Here we propose apeglm, which uses a heavy-tailed Cauchy prior distribution for effect sizes, resulting in lower bias than previous shrinkage estimators, while still reducing variance. apeglm is available at http://bioconductor.org/packages/apeglm, and can be used from within the DESeq2 software.
What is the post-2015 development agenda? A look from the underlying disaster risk drivers
Authors: Sarmiento Juan Pablo 
Published: April 2018

Purpose
The purpose of this paper is to explore the current and projected impacts of the three post-2015 development agendas on the underlying disaster risk drivers (UDRD): the Sendai Framework for Disaster Risk Reduction, the Sustainable Development Goals, and the Paris COP21 Agreement.

Design/methodology/approach
The methodology is based on an ontological process, understood as an exhaustive analysis of the properties and relationships of an entity or subject of study.

Findings
The process characterized and linked the objectives proposed in the three agendas through the impact of the expected results on the underlying risk drivers. First, elements related to disaster risk within each agenda were identified. Then, in following the theory of change, a series of tools were used to identify domains of change, pathways, breakthroughs, and incremental outcomes that counteract the construction of disaster risk by acting on the underlying causes. It is essential that there be coherence, complementarity, and interdependence between the three agendas analyzed in order to transcend beyond the desired economic growth, and thus underpin true sustainable development by focusing on the UDRD.

Originality/value
Applying the theory of change constitutes a novel approach to identify the pathways or domains of change needed to integrate the three 2015 development agendas.
Fire resistance of concrete walls with light aggregate
Authors: Hertz Kristian 
Published: April 2018

Purpose
The purpose of this paper is to present the design methods for fire-exposed concrete columns and walls. In addition, it presents analyses and tests showing that the methods are applicable for designing columns and walls of lightweight aggregate concrete based on expanded clay aggregate as well as heavy normal weight concrete and that the methods fit smoothly with cold design, when the fire exposure varies towards no fire.

Design/methodology/approach
During the 1990s, some of these design methods were included in the Eurocode as “the zone method”. They are still a part of the code. The rest of the methods, which were not included, served in practice, teaching and research. The present paper derives calculation methods proving their connection with common design for load cases without fire exposure. Furthermore, the paper presents full-scale tests proving the validation of the design methods for structural members of light aggregate concrete in addition to the full-scale tests of heavy concrete members.

Findings
The design methods give correct estimates of the load-bearing capacity of eccentric loaded concrete columns. An extended version of the methods estimates load-bearing capacity for walls with fire exposure on one side with sufficient accuracy for the purpose of design.

Originality/value
The author developed the main parts of the design methods in the 1980s and 1990s and others have from time to time referred to some parts of them mainly the minor parts published in the Eurocodes. However, owing to work overload, the author has not published the derivation and verification of them before. This paper provides in particular a verification against full-scale tests of light-aggregate concrete walls not published before.
A mechanistic framework to explain the immunosuppressive effects of neurotoxic pesticides on bees
Authors: Pamminger Tobias , Botías Christina , Goulson Dave , Hughes William O. H. 
Published: April 2018

Abstract

There is growing concern that declines in some managed and wild bee pollinator populations threaten biodiversity, the functioning of vital ecological processes and sustainable food production on a global scale.

In recent years, there has been increasing evidence that sublethal exposure to the neurotoxic class of insecticides (neonicotinoids) can undermine pollinator immunocompetence and amplify the effects of diseases, which have been suspected to be one of the drivers of pollinator declines. However, exactly how neonicotinoids might inhibit pollinator immunity remains elusive.

Here, we put forward a mechanistic framework to explain the effects of neurotoxic pesticides on insect immunocompetence. We propose that there is a close ontogenetic connection between the cellular arm (haemocytes) of the insect immune and nervous systems and that this connection makes the immune system of pollinators and other insects inherently susceptible to interference by neurotoxins such as neonicotinoids at sublethal doses.

Investigation of this connection is urgently needed to confirm the validity of this framework and develop a clear, mechanistically informed understanding of the interplay between neonicotinoids and disease ecology in pollinators. This in turn may enable us to develop strategies to mitigate impacts of neurotoxins on pollinators and/or enhance their impacts on pests.

A plain language summary is available for this article.
Innovative Behaviour, Trust and Perceived Workplace Performance
Authors: Hughes Mathew , Rigtering J. P. Coen , Covin Jeffrey G. , Bouncken Ricarda B. , Kraus Sascha 
Published: April 2018

AbstractBuilding on theories of social exchange, enactment and trust, we provide a theorization of innovative work behaviour at the individual (IB) and team (IBT) levels and explain how desirable performance returns occur for individuals and teams. We further propose that horizontal (between team members) and vertical (between teams and their supervisor) team trust moderate the relationship between IBTand team performance. The results, based on surveys conducted at two points in time in a large insurance company in the Netherlands, show that employees’ IB is positively associated with perceived workplace performance at the individual and team levels and that the effects vary based on the forms of trust at play. Our findings offer important new knowledge about the consequences of entrepreneurship and innovation in the workplace and the significant role that trust plays in enabling such behaviour to promote perceived workplace performance, particularly in the vital financial services sector.
The Determinants of the Technical Efficiency of Acute Inpatient Care in Canada
Authors: Wang Li , Grignon Michel , Perry Sheril , Chen Xi‐Kuan , Ytsma Alison , Allin Sara , Gapanenko Katerina 
Published: April 2018

ObjectiveTo evaluate the technical efficiency of acute inpatient care at the pan‐Canadian level and to explore the factors associated with inefficiency—why hospitals are not on their production frontier.Data Sources/Study SettingCanadian Management Information System (MIS) database (CMDB) and Discharge Abstract Database (DAD) for the fiscal year of 2012–2013.Study DesignWe use a nonparametric approach (data envelopment analysis) applied to three peer groups (teaching, large, and medium hospitals, focusing on their acute inpatient care only). The double bootstrap procedure (Simar and Wilson 2007) is adopted in the regression.Data Collection/Extraction MethodsInformation on inpatient episodes of care (number and quality of outcomes) was extracted from the DAD. The cost of the inpatient care was extracted from the CMDB.Principal FindingsOn average, acute hospitals in Canada are operating at about 75 percent efficiency, and this could thus potentially increase their level of outcomes (quantity and quality) by addressing inefficiencies. In some cases, such as for teaching hospitals, the factors significantly correlated with efficiency scores were not related to management but to the social composition of the caseload. In contrast, for large and medium nonteaching hospitals, efficiency related more to the ability to discharge patients to postacute care facilities. The efficiency of medium hospitals is also positively related to treating more clinically noncomplex patients.ConclusionsThe main drivers of efficiency of acute inpatient care vary by hospital peer groups. Thus, the results provide different policy and managerial implications for teaching, large, and medium hospitals to achieve efficiency gains.
Review article: A scoping review of physiotherapists in the adult emergency department
Authors: Ferreira Giovanni E , Traeger Adrian C , Maher Chris G 
Published: April 2018

AbstractTo provide an overview of the literature that considers physiotherapists working in the ED in relation to their roles, training levels, patient profile, safety, effectiveness, efficiency, cost‐effectiveness and the provision of low‐value care. We performed a scoping review of the literature. Four databases (PubMed, EMBASE, CINAHL and Cochrane CENTRAL) were searched from their inception to December 2016 and we updated searches on PubMed in September 2017. Two reviewers independently screened studies for eligibility. We performed a narrative synthesis of quantitative data. We included 27 studies: five randomised controlled trials (n = 1434), 12 prospective observational studies (n = 153 767), six retrospective studies (n = 9968), two survey studies (n = 61), one case report (n = 3) and one qualitative study (n = 11). Physiotherapists primarily managed patients with low urgency musculoskeletal conditions. Physiotherapists appeared to have similar clinical effectiveness and costs compared to other health providers (four randomised controlled trials). Physiotherapists were associated with increased efficiency (eight observational studies) and reduced low‐value care (one observational study). Three observational studies reported very low adverse event rates. However, none of the studies followed participants to measure adverse events that became apparent after the ED visit, nor did they consider unsafe discharge decisions or suboptimal follow‐up care. The available evidence suggests that physiotherapists may be as effective as other health providers in managing low urgency musculoskeletal conditions in the ED. There is uncertainty about appropriate training and a lack of robust studies investigating the efficiency, safety and cost‐effectiveness of this model of care.
Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production
Authors: Duque Estrella , Daddaoua Abdelali , Cordero Baldo F. , Udaondo Zulema , Molina‐Santiago Carlos , Roca Amalia , Solano Jennifer , Molina‐Alcaide Eduarda , Segura Ana , Ramos Juan‐Luis 
Published: April 2018

SummaryThe success of second‐generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β‐xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β‐xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β‐xylosidase was at least 10‐fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.