bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multivariate AND-gate substrate probes as enhanced contrast agents for fluorescence-guided surgery
Authors: Widen John C. , Tholen Martina , Yim Joshua J. , Antaris Alexander , Casey Kerriann M. , Rogalla Stephan , Klaassen Alwin , Sorger Jonathan , Bogyo Matthew 
Published: July 2019

AbstractThe greatest challenges for surgical management of cancer are precisely locating lesions and clearly defining the margins between tumors and normal tissues. This is confounded by the characteristics of the tissue where the tumor is located as well as its propensity to form irregular boundaries with healthy tissues. To address these issues, molecularly targeted optical contrast agents have been developed to define margins in real-time during surgery1,2. However, selectivity of a contrast agent is often limited by expression of a target enzyme or receptor in both tumor and healthy tissues. Here we introduce a concept of multivariate ‘AND-gate’ optical imaging probes that require sequential processing by multiple tumor-specific enzymes to produce a fluorescent signal. This results in dramatically improved specificity as well as overall enhanced sensitivity. This general approach has the potential to be broadly applied to selectively target complex patterns of enzyme activities in diverse disease tissues for detection, treatment and therapy response monitoring.
High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications
Authors: Stojković Vanja , Myasnikov Alexander G. , Young Iris D. , Frost Adam , Fraser James S. , Fujimori Danica Galonić 
Published: July 2019

ABSTRACTPost-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here we present a cryo-electron microscopy (cryo-EM) structure of Escherichia coli (E. coli) 50S subunit at an average resolution of 2.2Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for identification of post-transcriptional rRNA modifications using a cryo-EM map. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow
Authors: Crits-Christoph Alexander , Olm Matthew , Diamond Spencer , Bouma-Gregson Keith , Banfield Jillian 
Published: July 2019

AbstractSoil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species and how population structures are affected by dispersal, recombination, and selection. Genomic inferences about population structure can be made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in the population. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in specialized metabolite biosynthesis and extracellular transport were characterized by elevated genetic diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high site-specific differentiation of alleles, fewer recombinant events, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape local soil bacterial genetic variation.
Conservation of gene architecture and domains amidst sequence divergence in thehsrωlncRNA gene across theDrosophilagenus: Anin silicoanalysis
Authors: Sahu Ranjan Kumar , Mutt Eshita , Lakhotia Subhash Chandra 
Published: July 2019

AbstractThe developmentally active and cell-stress responsivehsrω locus inDrosophila melanogastercarries two exons, oneomegaintron, one short translatable open reading frame ORFω, long stretch of unique tandem repeats and an overlappingmir-4951near its 3’ end. It produces multiple lncRNAs using two transcription start and four termination sites. Earlier studies revealed functional conservation in severalDrosophilaspecies but with little sequence conservation, in three experimentally examined species, of ORFω, tandem repeat and other regions but ultra-conservation of 16nt at 5’ and 60nt at 3’ splice-junctions of theomegaintron. Present bioinformatic study, using the splice-junction landmarks inDrosophila melanogaster hsrω, identified orthologues in publicly available 34Drosophilaspecies genomes. Each orthologue carries the short ORFω, ultra-conserved splice junctions ofomegaintron, repeat region, conserved 3’-end locatedmir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in repeat sequences. Intriguingly, only the intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested inChironomusandCeratitisspecies. Amidst the high sequence divergence, the conserved organization of exons, ORFω andomegaintron in this gene’s proximal part and tandem repeats in distal part across theDrosophilagenus is remarkable and possibly reflects functional importance of higher order structure ofhsrω lncRNAs and the small Omega peptide.
Zika virus infection in Collaborative Cross mice
Authors: Mattocks Melissa D. , Plante Kenneth S. , Fritch Ethan J. , Baric Ralph S. , Ferris Martin T. , Heise Mark T. , Lazear Helen M. 
Published: July 2019

AbstractThe 2015-2016 emergence of Zika virus (ZIKV) in the Americas, and recognition that ZIKV infection during pregnancy can result in birth defects, revealed a need for small animal models to study ZIKV pathogenic mechanisms and evaluate candidate vaccines and antivirals. Mice would be an attractive system for such studies, but ZIKV replicates poorly in laboratory mice because it fails to antagonize murine STAT2 and STING. To address this, most ZIKV pathogenesis studies have used mice with impaired interferon signaling (e.g. Ifnar1−/− or treatment with IFNAR1-blocking antibodies). However, using mice with severe defects in innate antiviral signaling confounds studies of viral pathogenic mechanisms. Collaborative Cross (CC) mice have proven to be a valuable system for developing new mouse pathogenesis models for viral infections that are not well modeled in conventional laboratory mouse lines. To test whether CC mice could provide an immune-competent model for ZIKV pathogenesis, we infected CC lines with ZIKV and assessed weight loss, viremia, and production of neutralizing antibodies. We tested 21 CC lines (CC001, CC002, CC003, CC004, CC005, CC006, CC011, CC012, CC013, CC019, CC024, CC028, CC040, CC041, CC042, CC046, CC051, CC059, CC061, CC068, and CC072, 13 of which have non-functional alleles of the flavivirus restriction factor Oas1b) and 3 ZIKV strains (MR766, H/PF/2013, and a mouse-adapted variant of Dakar 41525). ZIKV infection did not induce weight loss compared to mock-infected controls and accordingly only low levels of viral RNA were detected in serum. Only a subset of mice developed neutralizing antibodies to ZIKV, likely due to overall low levels of infection and viremia. Our results are consistent with other studies demonstrating poor ZIKV infection in interferon-intact mice and suggest that the tested CC lines do not include polymorphic host genes that greatly increase susceptibility to ZIKV infection.
Local extinction of a montane, endemic grassland bird driven by landscape change across its global distribution
Authors: Lele Abhimanyu , Arasumani M. , Vishnudas C. K. , Jathanna Devcharan , Robin V. V. 
Published: July 2019

AbstractContextTropical montane habitats support high biodiversity, and are hotspots of endemism, with grasslands being integral components of many such landscapes. The montane grasslands of the Western Ghats have seen extensive land-use change over anthropogenic timescales. The factors influencing the ability of grassland-dependent species to persist in habitats experiencing loss and fragmentation, particularly in montane grasslands, are poorly known.ObjectivesWe studied the relationship between the Nilgiri pipit Anthus nilghiriensis, a threatened endemic bird that typifies these montane grasslands, and its habitat, across most of its global distribution. We examined what habitat features make remnants viable habitat, which is necessary for effective management.MethodsWe conducted 663 surveys in 170 sites and used both single-season occupancy modelling and N-mixture modelling to account for processes influencing detection, presence, and abundance.ResultsElevation had a positive influence on species presence, patch size had a moderate positive influence and patch isolation a moderate negative influence. Species abundance was positively influenced by elevation and characteristics related to habitat structure, and negatively influenced by the presence of invasive woody vegetation.ConclusionsThe strong effect of elevation on the highly range-restricted Nilgiri pipit makes it vulnerable to, and an indicator of, climate change. This highly range-restricted species is locally extinct at several locations and persists at low densities in remnants of recent fragmentation, suggesting an extinction debt. Our findings indicate a need to control and reverse the spread of exotic woody invasives to preserve the grasslands themselves and the specialist species dependent upon them.
A comprehensive dataset of TLX1 positive ALL-SIL lymphoblasts and primary T-cell acute lymphoblastic leukemias
Authors: Verboom Karen , Van Loocke Wouter , Clappier Emmanuelle , Soulier Jean , Vandesompele Jo , Speleman Frank , Durinck Kaat 
Published: July 2019

AbstractMost currently available transcriptome data of T-cell acute lymphoblastic leukemia (T-ALL) are based on polyA[+] RNA sequencing methods thus lacking non-polyadenylated transcripts. Here, we present the data of polyA[+] and total RNA sequencing in the context of in vitro TLX1 knockdown in ALL-SIL cells and a primary T-ALL cohort. We extended this dataset with ATAC sequencing and H3K4me1 and H3K4me3 ChIP sequencing data to map putative gene regulatory regions. In this data descriptor, we present a detailed report of how the data were generated and which bioinformatics analyses were performed. Through several technical validations, we showed that our sequencing data are of high quality and that our in vitro TLX1 knockdown was successful. We also validated the quality of the ATAC and ChIP sequencing data and showed that ATAC and H3K4me3 ChIP peaks are enriched at transcription start sites. We believe that this comprehensive set of sequencing data can be reused by others to further unravel the complex biology of T-ALL in general and TLX1 in particular.
The effect of competency-based education in obstetric emergencies on midwifery students in clinical skill lab, based on Kirkpatrick evaluation model: A randomized controlled trial
Authors: Hakimi Masumah , Kheirkhah Masoomeh , Abolghasemi Jamileh , Hakimi Razia , farshad Fatemeh 
Published: July 2019

AbstractBackgroundObstetric emergency is one of the most important causes of maternal and neonatal mortality, and competency-based education is one of the efficient approaches to cover this. Objective structured clinical examination is one of the valid methods in measuring students’ competency and performance. Kirkpatrick evaluation model is a great method to assess a training impact.ObjectivesThis study was designed to determine the effect of competency-based education on midwifery students based on Kirkpatrick evaluation model.DesignRandomized controlled trialSettingNursing and Midwifery School in Islamic Republic of Iran (Iran University of Medical Sciences)Participantseighty students in third to fifth term of associate and bachelor’s degree in midwifery (intervention group=40, control group=40)MethodsUsing stratified random sampling, research team trained learners of intervention group in 4 sessions, 5 hours/day in a month in emergency obstetric cares. Both groups had been receiving the routine schedule of the faculty. Knowledge, skills, and self-confidence were assessed three times, before, immediately and 6 weeks after training by researcher made questionnaire, Objective Structured Clinical Examination (OSCE) and self-reported questionnaire respectively. Data were analyzed with descriptive, inferential statistics.ResultsThe level of knowledge, skills, and self-confidence increased significantly in the intervention group, in immediate and 6 weeks after intervention (P<0.001). In intervention group, Mean ± S.D of all variables were 5.05±2.074, 143.30±12.146 and 11.65±2.045, which increased to 10.17±1.318, 527.70±19.995 and 18.97±1.980 and remained at the same levels 6 weeks later, 9.37±2.215, 521.80±19.784 and 19.00±2.631; in the control group, this trend was not significant (P=0.380, P=0.455 and P=0.191).ConclusionCompetency-based education can be used in midwifery education and in-service training. We need to use new educational approaches such as competency-based to have a valuable impact on knowledge skills and self-confidence. This may affect health indexes indirectly.
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
Authors: Sharma Vasudha , Majumdar Sharmistha 
Published: July 2019

AbstractBackgroundChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task.ResultsThis study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction.ConclusionBy studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.
Modelling variation in bushmeat harvesting among seven African ecosystems using the Madingley Model: yield, survival and ecosystem impacts
Authors: Barychka Tatsiana , Mace Georgina M. , Purves Drew W. 
Published: July 2019

AbstractIn principle, both the maximum sustainable yields of bushmeat, and the ecosystem impacts of extracting those yields, are likely to vary among ecosystems due to differences in the structure and function of ecosystems, but the data necessary to estimate this variation is lacking. Here, we compare seven different ecosystems on a North-South latitudinal gradient in Central Africa in terms of their trophic structure and capacity to support yields from bushmeat harvesting, using the Madingley General Ecosystem Model. The only factor that varies across simulations of these ecosystems is the climate which drives differences in vegetation structure and function, leading in turn to differences in the structure of the ecological community that emerge from the model. In a series of experiments (n=30), we simulate constant proportional harvesting of small and medium-sized warm-bloodied heterotrophs (1-23kg) over 30 years, recording expected bushmeat yields, and impacts on ecosystem structure, including trophic structure. Predictions for animal densities and trophic structures in the pristine (no harvesting) case varied among the ecosystems, with implications for bushmeat harvesting. For example, wooded savannah ecosystems stood out as having the greatest pristine densities in the target groups (11000-12000 animals per kilometre squared), greatest yields (100% higher than the tropical forest and 1000% higher than the desert ecosystem), and were the most resilient to harvesting. By contrast, small and medium-sized endothermic heterotrophs contributed only a small proportion of heterotrophs in the desert ecosystem, and thus the potential for bushmeat harvesting here was low. In all ecosystems, harvesting at the rate that maximised yield (55-65% population per year, except for the southern desert ecosystem) had strong impacts, causing drastic reductions in target functional groups, coupled with increases in smaller- and larger-bodied animals. Forest and desert ecosystems were particularly sensitive. Overall, the results suggest that, even for similar functional groups, bushmeat harvesting policies will need to vary substantially among ecosystems – and show that general ecosystem models could be a useful tool in helping to guide these policies.
Promoter-specific dynamics of TATA-binding protein association with the human genome
Authors: Hasegawa Yuko , Lieb Jason D. , Struhl Kevin 
Published: July 2019

ABSTRACTTranscription factor binding to target sites in vivo is a dynamic process that involves cycles of association and dissociation, with individual proteins differing in their binding dynamics. The dynamics at individual sites on a genomic scale has been investigated in yeast cells, but comparable experiments have not been done in multicellular eukaryotes. Here, we describe a tamoxifen-inducible, time-course ChIP-seq approach to measure transcription factor binding dynamics at target sites throughout the human genome. As observed in yeast cells, the TATA-binding protein (TBP) typically displays rapid turnover at RNA polymerase (Pol) II-transcribed promoters, slow turnover at Pol III promoters, and very slow turnover at the Pol I promoter. Interestingly, turnover rates vary widely among Pol II promoters in a manner that does not correlate with the level of TBP occupancy. Human Pol II promoters with slow TBP dissociation preferentially contain a TATA consensus motif, support high transcriptional activity of downstream genes, and are linked with specific activators and chromatin remodelers. These properties of human promoters with slow TBP turnover differ from those of yeast promoters with slow turnover. These observations suggest that TBP binding dynamics differentially affect promoter function and gene expression, possibly at the level of transcriptional reinitiation/bursting.
BIM-linked data integration for asset management
Authors: Farghaly Karim , Abanda F.H. , Vidalakis Christos , Wood Graham 
Published: July 2019

Purpose
The purpose of this paper is to investigate the transfer of information from the building information modelling (BIM) models to either conventional or advanced asset management platforms using Linked Data. To achieve this aim, a process for generating Linked Data in the asset management context and its integration with BIM data is presented.

Design/methodology/approach
The research design employs a participatory action research (PAR) approach. The PAR approach utilized two qualitative data collection methods, namely; focus group and interviews to identify and evaluate the required standards for the mapping of different domains. Also prototyping which is an approach of Software Development Methodology is utilized to develop the ontologies and Linked Data.

Findings
The proposed process offers a comprehensive description of the required standards and classifications in construction domain, related vocabularies and object-oriented links to ensure the effective data integration between different domains. Also the proposed process demonstrates the different stages, tools, best practices and guidelines to develop Linked Data, armed with a comprehensive use case Linked Data generation about building assets that consume energy.

Originality/value
The Linked Data generation and publications in the domain of AECO is still in its infancy and it also needs methodological guidelines to support its evolution towards maturity in its processes and applications. This research concentrates on the Linked Data applications with BIM to link across domains where few studies have been conducted.
Effect of leadership and communication practices on the safety climate and behaviour of construction workgroups
Authors: Lingard Helen , Zhang Rita Peihua , Oswald David 
Published: July 2019

PurposeThe leadership style and communication practices of supervisors in the Australian construction industry were measured. The purpose of this paper is to investigate the effect of leadership style and communication practices of Australian construction supervisors on workgroup health and safety (H&S) climate and behaviour.Design/methodology/approachA questionnaire was administered to members of 20 workgroups engaged in rail construction work on the Level Crossing Removal Project and the Melbourne Metro Tunnel Project in Victoria, Australia. The survey measured components of supervisors’ transformational and transactional leadership, communication practices, the group H&S climate and workers’ self-reported H&S compliance and participation.FindingsSupervisors’ transformational and transactional leadership, as well as communication practices, were all positively and significantly correlated with group H&S climate and workers’ self-reported H&S behaviours. The transformational leadership component of providing an appropriate model was the strongest predictor of H&S participation, while H&S compliance was predicted by the transactional leadership component of providing contingent reward, as well as supervisors’ communication practices. H&S climate fully mediated the relationship between supervisory leadership and workers’ self-reported H&S behaviour.Originality/valueThe research demonstrates that both transformational and transactional supervisory leadership are important in the construction context. Effective communication between supervisors and workers is also important for H&S. The findings suggest that supervisory leadership development programmes may be an effective way to improve H&S performance in predominantly subcontracted construction workgroups.