bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incomplete resilience of a shallow lake to a brownification event
Authors: Kazanjian G. , Brothers S. , Köhler J. , Hilt S. 
Published: June 2019

AbstractDissolved organic carbon (DOC) concentrations in many freshwater ecosystems of the northern hemisphere have increased in recent decades due to additional terrestrial inputs. This phenomenon, known as brownification, can strongly alter the physical, chemical, and biological traits of aquatic ecosystems. Extreme rainfall can also cause sudden brownification, known as blackwater events in rivers, while longer term effects on lakes are unknown. Here, we investigated the resilience of a small, temperate, shallow lake to a strong natural flooding-induced brownification event in 2011-2012. From initial DOC and total phosphorus (TP) concentrations of ~12 and 0.04 mg L−1, respectively, the lake rapidly reached peak DOC and TP concentrations of 60 and 0.35 mg L−1, respectively. By the following year, water levels had returned close to initial values, yet two additional years of monitoring (until summer 2015) and a more recent sample in spring 2019 showed that the lake did not fully return to its pre-brownification state. Instead, DOC and TP concentrations plateaued at concentrations respectively 1.5-fold and twofold greater than pre-brownification values within less than two years and remained at these concentrations in spring 2019. During this initial recovery period the lake exhibited a decline of phytoplankton and a partial recovery of summer periphyton biomass and production, albeit a full return to pre-brownification values was not recorded in either case. DOC and TP concentrations were positively correlated to phytoplankton biomass and negatively to periphyton. As increases in phytoplankton production outpaced decreasing periphyton production, the net result of this brownification event has been an increase in whole-lake areal summertime primary production. This incomplete resilience to a flooding-induced brownification event implies consequences for several ecological and biogeochemical functions of shallow lakes that warrant further investigation and might contribute to the gradual increase of freshwater DOC concentrations in the northern hemisphere.
Rainfall and other meteorological factors as drivers of urban transmission of leptospirosis
Authors: Cunha Marcelo , Costa Federico , Ribeiro Guilherme S. , Carvalho Marília S. , Reis Renato B. , Júnior Nivison N. , Pischel Lauren , Gouveia Edilane L. , Santos Andreia C. , Queiroz Adriano , Wunder Elsio A. , Reis Mitermayer G. , Diggle Peter J , Ko Albert I. 
Published: June 2019

ABSTRACTBackgroundLeptospirosis is an important public health problem affecting vulnerable urban slum populations in developing country settings. However, the complex interaction of meteorological factors driving the temporal trends of leptospirosis remain incompletely understood.Methods and findingsFrom 1996 to 2010, we investigated the association between the weekly incidence of leptospirosis and climatic variables in the city of Salvador, Brazil by using a dynamic generalized linear model that accounted for time lags, overall trend and seasonal variation. Our model showed an increase of leptospirosis cases associated with rainfall, lower temperature and higher humidity. There was a lag of one-to-two weeks between weekly values for significant meteorological variables and leptospirosis incidence. Independent of the season, a weekly cumulative rainfall of 20 mm increased the risk of the leptospirosis by 10% compared to a week without rain. Finally, over the 14 year study period the incidence of leptospirosis decreased significantly by four fold (12.8 versus 3.6 per 100,000 people), independently of variations in climate.ConclusionsStrategies to control leptospirosis should focus on avoiding contact with contaminated sources ofLeptospiraas well as on increasing awareness in the population and health professionals within the short time window after both low-level and extreme rainfall events. Increased leptospirosis incidence was restricted to one-to-two weeks after those events suggesting that infectiousLeptospirasurvival may be limited to short time intervals.Author SummaryTo determine the role of meteorological variables, seasonal variation and temporal trends in the incidence of leptospirosis, we investigated the time series of leptospirosis incidence amongst residents of Salvador, Brazil, from 1996 to 2010. Exploratory and confirmatory statistical methods detected associations between meteorological factors and disease incidence. Results showed the importance of extreme meteorological conditions, particularly rainfall, as short-term predictors of leptospirosis incidence. In addition, we found a long-term decreasing trend of in disease incidence over the observation period.
Generation of a Retina Reporter hiPSC Line to Label Progenitor, Ganglion, and Photoreceptor Cell Types
Authors: Lam Phuong T. , Gutierrez Christian , Del Rio-Tsonis Katia , Robinson Michael L. 
Published: June 2019

ABSTRACTEarly in mammalian eye development, VSX2, BRN3b, and RCVRN expression marks neural retina progenitors (NRPs), retinal ganglion cells (RGCs), and photoreceptors (PRs), respectively. The ability to create retinal organoids from human induced pluripotent stem cells (hiPSC) holds great potential for modeling both human retinal development and retinal disease. However, no methods allowing the simultaneous, real-time monitoring of multiple specific retinal cell types during development currently exist. Here, we describe a CRISPR/Cas9 gene editing strategy to generate a triple transgenic reporter hiPSC line (PGP1) that utilizes the endogenous VSX2, BRN3b, and RCVRN promoters to specifically express fluorescent proteins (Cerulean in NRPs, eGFP in RGCs and mCherry in PRs) without disrupting the function of the endogenous alleles. Retinal organoid formation from the PGP1 line demonstrated the ability of the edited cells to undergo normal retina development while exhibiting appropriate fluorescent protein expression consistent with the onset of NRPs, RGCs, and PRs. Organoids produced from the PGP1 line expressed transcripts consistent with the development of all major retinal cell types. The PGP1 line offers a powerful new tool to study retinal development, retinal reprogramming, and therapeutic drug screening.
Optimal markers for the identification ofColletotrichumspecies
Authors: dos Santos Vieira Willie Anderson , Bezerra Priscila Alves , da Silva Anthony Carlos , Silva Veloso Josiene , Paz Saraiva Câmara Marcos , Patrick Doyle Vinson 
Published: June 2019

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.
Deep-learning-based cell composition analysis from tissue expression profiles
Authors: Menden Kevin , Marouf Mohamed , Oller Sergio , Dalmia Anupriya , Kloiber Karin , Heutink Peter , Bonn Stefan 
Published: June 2019

AbstractWe present Scaden, a deep neural network for cell deconvolution that uses gene expression information to infer the cellular composition of tissues. Scaden is trained on single cell RNA-seq data to engineer discriminative features that confer robustness to bias and noise, making complex data preprocessing and feature selection unnecessary. We demonstrate that Scaden outperforms existing deconvolution algorithms in both precision and robustness. A single trained network reliably deconvolves bulk RNA-seq and microarray, human and mouse tissue expression data and leverages the combined information of multiple data sets. Due to this stability and flexibility, we surmise that deep learning will become an algorithmic mainstay for cell deconvolution of various data types. Scaden’s comprehensive software package is easy to use on novel as well as diverse existing expression datasets available in public resources, deepening the molecular and cellular understanding of developmental and disease processes.
Spontaneous Self-assembly of Amyloid β (1-40) into Dimers
Authors: Hashemi Mohtadin , Zhang Yuliang , Lv Zhengjian , Lyubchenko Yuri L. 
Published: June 2019

AbstractThe self-assembly and fibrillation of amyloid β (Aβ) proteins is the neuropathological hallmark of Alzheimer’s disease. However, the molecular mechanism of how disordered monomers assemble into aggregates remains largely unknown. In this work, we characterize the assembly of Aβ (1-40) monomers into dimers using long-time molecular dynamics simulations. Upon interaction, the monomers undergo conformational transitions, accompanied by change of the structure, leading to the formation of a stable dimer. The dimers are primarily stabilized by interactions in the N-terminal region (residues 5-12), in the central hydrophobic region (residues 16-23), and in the C-terminal region (residues 30-40); with inter-peptide interactions focused around the N- and C- termini. The dimers do not contain long β-strands that are usually found in fibrils.
Interactive Multiresolution Visualization of Cellular Network Processes
Authors: Ortega Oscar O. , Lopez Carlos F. 
Published: June 2019

AbstractComputational models of network-driven processes have become a standard to explain cellular systems-level behavior and predict cellular responses to perturbations. Modern models can span a broad range of biochemical reactions and species that, in principle, comprise the complexity of dynamic cellular processes. Visualization plays a central role in the analysis of biochemical network processes to identify patterns that arise from model dynamics and perform model exploratory analysis. However, most existing visualization tools are limited in their capabilities to facilitate mechanism exploration of large, dynamic, and complex models. Here, we present PyViPR, a visualization tool that provides researchers static and dynamic representations of biochemical network processes within a Python-based Literate Programming environment. PyViPR embeds network visualizations on Jupyter notebooks, thus facilitating integration with Python modeling, simulation, and analysis workflows. To present the capabilities of PyViPR, we explore execution mechanisms of extrinsic apoptosis in HeLa cells. We show how community-detection algorithms can identify groups of molecular species that represent key biological regulatory functions and simplify the apoptosis network by placing those groups into interactively collapsible nodes. We then show how dynamic execution of a signal, under different kinetic parameter sets that fit the experimental data equally well, exhibit significantly different signal-execution modes in mitochondrial outer-membrane permeabilization – the point of no return in extrinsic apoptosis execution. Therefore, PyViPR aids the conceptual understanding of dynamic network processes and accelerates hypothesis generation for further testing and validation.
Genomic sequencing of the aquaticFusariumspp. QHM and BWC1 and their potential application in environmental protection
Authors: Zhu Hongfei , Zhu Long , Ding Ning 
Published: June 2019

ABSTRACTFusariumspecies are distributed widely in ecosystems of a wide pH range and play a pivotal role in the aquatic community through the degradation of xenobiotic compounds and secretion of secondary metabolites. The elucidation of their genome would therefore be highly impactful with regard to the control of environmental pollution. Therefore, in this study, two indigenous strains of aquaticFusarium, QHM and BWC1, were isolated from a coal mine pit and a subterranean river respectively, cultured under acidic conditions, and sequenced. Phylogenetic analysis of these two isolates was conducted based on the sequences of internal transcript (ITS1 and ITS4) and encoding β-microtubulin (TUB2), translation elongation factors (TEFs) and the second large sub-unit of RNA polymerase (RPB2).Fusarium, QHM could potentially represent a new species within theFusarium fujikuroispecies complex.FusariumBWC1 were found to form a clade withFusarium subglutinansNRRL 22016, and predicted to beFusarium subglutinans.Shot-gun sequencing on the Illumina Hiseq×10 Platform was used to elucidate the draft genomes of the two species. Gene annotation and functional analyses revealed that they had bio-degradation pathways for aromatic compounds; further, their main pathogenic mechanism was found to be the efflux pump. To date, the genomes of only a limited number of acidic species from theFusarium fujikuroispecies complex, especially from the aquatic species, have been sequenced. Therefore, the present findings are novel and have important potential for the future in terms of environmental control.IMPORTANCEFusarium genus has over 300 species and were distributed in a variety of ecosystem. Increasing attention has been drawn toFusariumdue to the importance in aquatic community, pathogenicity and environmental protection. The genomes of the strains in this work isolated in acidic condition, were sequenced. The analysis has indicated that the isolates were able to biodegrade xenobiotics, which makes it potentially function as environmental bio-agent for aromatic pollution control and remediation. Meanwhile, the virulence and pathogenicity were also predicted for reference of infection control. The genome information may lay foundation for the fungal identification, disease prevention resulting from these isolates and other “-omics” research. The isolates were phylogenetically classified intoFusarium fujikuroispecies complex by means of concatenated gene analysis, serving as new addition to the big complex.
Mps1 releases Mad1 from nuclear pores to ensure a robust mitotic checkpoint and accurate chromosome segregation
Authors: Osswald Mariana , Cunha-Silva Sofia , Goemann Jana , Barbosa João , Santos Luis M , Resende Pedro , Bange Tanja , Sunkel Claudio E , Conde Carlos 
Published: June 2019

ABSTRACTThe strength of the Spindle Assembly Checkpoint (SAC) depends on the amount of the Mad1-C-Mad2 heterotetramer at kinetochores but also on its binding to Megator/Tpr at nuclear pore complexes (NPCs) during interphase. However, the molecular underpinnings controlling the spatiotemporal redistribution of Mad1-C-Mad2 as cells progress into mitosis remain elusive. Here, we show that Mps1-mediated phosphorylation of Megator/Tpr abolishes its interaction with Mad1 in vitro and in Drosophila cells. Timely activation of Mps1 during prophase triggers Mad1 release from NPCs, which we find to be required for competent kinetochore recruitment of Mad1-C-Mad2 and robust checkpoint response. Importantly, preventing Mad1 binding to Megator/Tpr rescues the fidelity of chromosome segregation and aneuploidy in larval neuroblasts of Drosophila mps1-null mutants. Our findings demonstrate that the subcellular localization of Mad1 is stringently coordinated with cell cycle progression by kinetochore-extrinsic activity of Mps1. This ensures that both NPCs in interphase and kinetochores in mitosis can generate anaphase inhibitors to efficiently preserve genomic stability.
Chromatinization ofEscherichia coliwith archaeal histones
Authors: Rojec Maria , Hocher Antoine , Merkenschlager Matthias , Warnecke Tobias 
Published: June 2019

ABSTRACTNucleosomes restrict DNA accessibility throughout eukaryotic genomes, with repercussions for replication, transcription, and other DNA-templated processes. How this globally restrictive organization emerged from a presumably more open ancestral state remains poorly understood. Here, to better understand the challenges associated with establishing globally restrictive chromatin, we express histones in a naïve bacterial system that has not evolved to deal with nucleosomal structures:Escherichia coli. We find that histone proteins from the archaeonMethanothermus fervidusassemble on theE. colichromosomein vivoand protect DNA from micrococcal nuclease digestion, allowing us to map binding footprints genome-wide. We provide evidence that nucleosome occupancy along theE. coligenome tracks intrinsic sequence preferences but is disturbed by ongoing transcription and replication. Notably, we show that higher nucleosome occupancy at promoters and across gene bodies is associated with lower transcript levels, consistent with local repressive effects. Surprisingly, however, this sudden enforced chromatinization has only mild repercussions for growth, suggesting that histones can become established as ubiquitous chromatin proteins without interfering critically with key DNA-templated processes. Our results have implications for the evolvability of transcriptional ground states and highlight chromatinization by archaeal histones as a potential avenue for controlling genome accessibility in synthetic prokaryotic systems.
Hsa-mir-210 as a novel signature predicts survival in lung squamous cell carcinoma using bioinformatics analysis
Authors: Liu Yu , Chen Yu , Li Ling-Ling , Wang Shen-Nan , Xia Shu 
Published: June 2019

AbstractIn recent years, more and more studies have shown that the expression of miRNAs is closely related to the occurrence of tumors and plays an irreplaceable role in the development and metastasis of tumors. The research was focused on lung squamous cell carcinoma. The data information is downloaded from the TCGA database and analyzed for variance, which is then verified in the GEO database. Then differential expression of miRNAs was found and survival analysis was performed, through the cut – off standard(P<0.05,|logFC|≥2), we screen the 38 up-regulated miRNAs and 14 down-regulated miRNAs from the TCGA. Finally, after the verification on the GEO database, four up-regulated miRNAs (hsa-mir-205, hsa-mir-210, hsa-mir-182, hsa-mir-224) and one down-regulated miRNA (hsa-mir-451) were obtained, which provide a new direction for the diagnosis of lung squamous cell carcinoma. In the survival analysis, it was found that the expression state of hsamir-210 was significantly correlated with patient survival. The results in the univariate and multivariate Cox analysis indicated that hsa-mir-210 was an independent prognostic factor on lung squamous cell carcinoma. The functional enrichment analysis showed that hsa-mir-210 was closely related to positive and negative regulation of cell proliferation, DNA transcription, VEGF signaling pathway, MAPK signaling pathway, hif-1 signaling pathway and choline metabolic pathway. In summary, this study suggested that hsa-mir-210 could be a potential prognostic factor for lung squamous cell carcinoma.Author SummaryMicroRNAs are single-stranded small molecular RNA that participate in the regulation of various biological functions through indirect regulation of gene expression, and have been reported to play an important role in the occurrence, development, invasion and metastasis of tumors. In recent years, the research on miRNAs has become increasingly hot, and the role of miRNAs in tumor has been proved more and more. The subjects of this study were squamous cell carcinoma in lung cancer with relatively few studies on miRNAs. Through high-throughput data analysis, miRNAs with differential expression between lung squamous cell carcinoma tissues and normal tissues were found. These differentially expressed miRNAs provide a new direction for the early diagnosis of patients. Then, survival analysis was conducted to find the miRNAs significantly correlated with the total survival time of patients, and multi-factor analysis was conducted to exclude the influence of other clinical factors, and independent risk factors (miRNAs) affecting the survival of patients were determined, so as to provide new targets for the treatment and survival prediction of patients.
Roadmap layers and processes: resilient and sustainable care facilities
Authors: Pantzartzis Efthimia , Price Andrew , Edum Fotwe Francis 
Published: June 2019

Purpose
Health and social care facilities are usually complex buildings that require continuous effort to provide resilient and sustainable responses to changes in demographics, technologies, diseases and models of care. Despite resilience and sustainability concepts being frequently used by practitioners and researchers, ambiguities in their definitions often result in a lack of operational solutions to record, monitor and improve the resilience and sustainability of health and social care facilities. Although the importance and complexity of the issues are widely acknowledged, there is little strategic guidance as to how they should be achieved. The purpose of this paper is to assess the suitability of developing a roadmap for improving the resilience and sustainability of UK health and social care facilities, and to identify the layers and processes needed to construct such a roadmap.

Design/methodology/approach
A qualitative approach was adopted, starting with a literature review of different types of roadmaps and their suitability to support the desired improvement objectives. Layers and processes were thus developed using the key issues identified in three recent research streams, and the roadmap was structured.

Findings
The major findings have been captured within a three-layer, four-step process generic roadmap for improving the resilience and sustainability of health and social care facilities that can be used to monitor performance, plans future actions and implement response to change.

Practical implications
This paper targets decision makers, especially estate managers, but the proposed layers and processes can be modified for other stakeholders.

Originality/value
This paper suggests an original approach for the development of a roadmap for resilience and sustainability of health and social care facilities, and specifically of how to structure layers and processes, envisioning a more integrated development of service provision and infrastructure asset management.