bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community
Authors: Uritskiy Gherman , Tisza Michael J. , Gelsinger Diego R , Munn Adam , Taylor James , DiRuggiero Jocelyne 
Published: November 2019

SummaryMicrobial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behavior. This aspect of microbiome function has not been well characterized in natural high-salt environments. To address this knowledge gap, and to build a general framework of relating the genomic and transcriptomic components in a microbiome, we performed a meta-omic survey of extremophile communities inhabiting halite (salt) nodules in the Atacama Desert. We found that the major phyla of this halophilic community have very different levels of total transcriptional activity and that different metabolic pathways were activated in their transcriptomes. We report that a novelDolichomastixalga – the only eukaryote found in this system – was by far the most active community member. It produced the vast majority of the community’s photosynthetic transcripts despite being outnumbered by members of theCyanobacteria. The divergence in the transcriptional landscapes of these segregated communities, compared to the relatively stable metagenomic functional potential, suggests that microbiomes in each salt nodule undergo unique transcriptional adjustments to adapt to local conditions. We also report the characterization of several previously unknown halophilic viruses, many of which exhibit transcriptional activity indicative of host infection.Originality-Significance StatementWhile the metagenomics of hypersaline environments have already led to many discoveries, the transcriptional adaptations and functions of halophilic microbial communities in natural environments remains understudied. We perform the first robust meta-omic investigation of a hypersaline desert ecosystem, linking the genomic and transcriptional elements of the community. Our analysis unexpectedly revealed that Eukaryotes may be the main primary producers in this extreme environment, despite halophilic Archaea and Bacteria dominating the biomass. We also expand on the existing known diversity of halophilic viruses and demonstrate abundance (copies per million reads) and metatranscriptomic activity (transcripts per million reads); putative hosts are shown on the right.
RASflow: An RNA-Seq Analysis Workflow with Snakemake
Authors: Zhang Xiaokang , Jonassen Inge 
Published: November 2019

AbstractBackgroundWith the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq data has to be processed through a number of steps resulting in a quantification of expression of each gene / transcript in each of the analyzed samples. A number of workflows are available to help researchers perform these steps on their own data, or on public data to take advantage of novel software or reference data in data re-analysis. However, many of the existing workflows are limited to specific types of studies. We therefore aimed to develop a maximally general workflow, applicable to a wide range of data and analysis approaches and at the same time support research on both model and non-model organisms. Furthermore, we aimed to make the workflow usable also for users with limited programming skills.ResultsUtilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis pipeline: RNA-Seq Analysis Snakemake Workflow (RASflow). Utilizing Snakemake and Conda alleviates challenges with library dependencies and version conflicts and also supports reproducibility. To be applicable for a wide variety of applications, RASflow supports mapping of reads to both genomic and transcriptomic assemblies. RASflow has a broad range of potential users: it can be applied by researchers interested in any organism and since it requires no programming skills, it can be used by researchers with different backgrounds. RASflow is an open source tool and source code as well as documentation, tutorials and example data sets can be found on GitHub: https://github.com/zhxiaokang/RASflowConclusionsRASflow is a simple and reliable RNA-Seq analysis workflow which is a full pack of RNA-Seq analysis.
Practical parameter identifiability for spatiotemporal models of cell invasion
Authors: Simpson Matthew J , Baker Ruth E , Vittadello Sean T , Maclaren Oliver J 
Published: November 2019

AbstractWe examine the practical identifiability of parameters in a spatiotemporal reaction-diffusion model of a scratch assay. Experimental data involves fluorescent cell cycle labels, providing spatial information about cell position and temporal information about the cell cycle phase. Cell cycle labelling is incorporated into the reaction–diffusion model by treating the total population as two interacting subpopulations. Practical identifiability is examined using a Bayesian Markov chain Monte Carlo (MCMC) framework, confirming that the parameters are identifiable when we assume the diffusivities of the subpopulations are identical, but that the parameters are practically non-identifiable when we allow the diffusivities to be distinct. We also assess practical identifiability using a profile likelihood approach, providing similar results to MCMC with the advantage of being an order of magnitude faster to compute. Therefore, we suggest that the profile likelihood ought to be adopted as a screening tool to assess practical identifiability before MCMC computations are performed.
Real-time tracking reveals the catalytic process of Rad51-driven DNA strand exchange
Authors: Ito Kentaro , Murayama Yasuto , Kurokawa Yumiko , Kanamaru Shuji , Kokabu Yuichi , Maki Takahisa , Argunhan Bilge , Tsubouchi Hideo , Ikeguchi Mitsunori , Takahashi Masayuki , Iwasaki Hiroshi 
Published: November 2019

AbstractDuring homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for second donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA family recombinases.
Mechanism of the secretion of the lanthipeptide nisin
Authors: Lagedroste Marcel , Reiners Jens , Smits Sander H.J. , Schmitt Lutz 
Published: November 2019

AbstractLanthipeptides are ribosomally synthesized and post-translationally modified peptides containing dehydrated amino acids and (methyl-)lanthionine rings. One of the best-studied example is nisin, which is synthesized as a precursor peptide comprising of an N-terminal leader peptide and a C-terminal core peptide. Amongst others, the leader peptide is crucial for enzyme recognition and acts as a secretion signal for the ABC transporter NisT which secrets nisin in a proposed channeling mechanism. Here, we present anin vivosecretion analysis of this process in the presence and absence of the maturation machinery composed of the dehydratase NisB and the cyclase NisC. The data clearly demonstrated that the function of NisC, but the mere presence of NisB modulated the apparent secretion rates. Additional in vitro studies of detergent-solubilized NisT revealed how the activity of this ABC transporter is again influenced by the enzymes of the maturation machinery, but not the substrate.
eyes absentin the cockroach panoistic ovaries regulates proliferation and differentiation through ecdysone signalling
Authors: Ramos S. , Chelemen F. , Pagone V. , Elshaer N. , Irles P. , Piulachs M.D. 
Published: November 2019

AbstractEyes absent (Eya), is a protein structurally conserved from hydrozoans to humans, for which two basic roles have been reported: it can act as a transcription cofactor and as a protein tyrosine phosphatase. Eya was discovered in the flyDrosophila melanogasterin relation to its function in eye development, and the same function was later reported in other insects. Eya is also involved in insect oogenesis, although studies in this sense are limited toD. melanogaster, which has meroistic ovaries, and whereeyamutations abolish gonad formation.In the present work we studied the function ofeyain the panoistic ovary of the cockroachBlattella germanica. We show thateyais essential for correct development of panoistic ovaries. InB. germanica, eyaacts at different level and in a distinct way in the germarium and the vitellarium. In the germarium,eyacontributes to maintain the correct number of somatic and germinal cells by regulating the expression of steroidogenic genes in the ovary. In the vitellarium,eyafacilitates follicle cells proliferation and contributes to regulate the cell program, in the context of basal ovarian follicle maturation. Thus,eya-depleted females ofB. germanicaarrest the growth and maturation of basal ovarian follicles and become sterile.
Serviceability analysis of a cable-supported footbridge subjected to human-induced loads
Authors: Li Zhen , Li Dejian , Lu Yao , Cheng Kepei , Wu Qianqiu 
Published: November 2019

Purpose
The purpose of this paper is to obtain the response time history curves of vertical and lateral acceleration in the span of the main beam under different loads through the finite element time-history analysis method, so as to realize the Serviceability Analysis of a Cable-Supported Footbridge Subjected to Human-Induced Loads, taking the long-span cable-supported footbridge over Dongtan River as an example.

Design/methodology/approach
The finite element method is used for analysis of the footbridge.

Findings
It is found that under the condition of low-density pedestrians walking freely, the response of human vertical vibration acceleration and the load conditions of pedestrian overpasses cannot meet the requirements of normal use. Therefore, the vertical acceleration of the footbridge should be designed to reduce vibration. Under these two loading conditions, the lateral acceleration response meets the requirements of normal use.

Originality/value
On the basis of summarizing the research at home and abroad, the analysis of human-induced vibration is mainly considered from two aspects: frequency regulation and dynamic response control. The walking load models mainly include Fourier series model, self-excitation model, impulse model, stochastic model and more; the crowd load models are divided into groups: low-density crowd walking freely, high-density crowd flowing and more. Therefore, it is very important to calculate the structural vibration response in the design of long-span cable-supported footbridges under pedestrian excitation to meet comfort requirements.
A polyhydroxyalkanoate‐based encapsulating strategy for ‘bioplasticizing’ microorganisms
Authors: González Erika , Herencias Cristina , Prieto M. Auxiliadora 
Published: November 2019

SummaryOver the past few decades, considerable interest has been shown in developing nano‐ and microcarriers with biocompatible and biodegradable materials for medical and biotechnological applications. Microencapsulation is a technology capable of enhancing the survival rate of bacteria, providing stability in harsh environments. In the present paper, we developed a technology to encapsulate microorganisms within polyhydroxyalkanoate (PHA)‐based microcapsules (MPs), employing a modified double emulsion solvent evaporation technique, with Pseudomonas putida KT2440 as a biotechnological model strain. The resulting MPs display a spherical morphology and an average particle size of 10 μm. The stability of the MPs was monitored under different conditions of storage and stress. The MPs remained stable for at least 24 days stored at 4°C in a water suspension. They exhibited greater tolerance to stress conditions; encapsulated cells remained viable for 2 h in alkaline solution and after 24 h of H2O2 exposure at 10 and 20 mM. Results suggested the potential of MPs as a microcontainer of bacterial cells, even for biotechnological applications requiring high alkaline conditions and oxidative stress. We validated the potential applicability of the PHA‐based microencapsulation method in other microorganisms by encapsulating the predatory bacterium Bdellovibrio bacteriovorus.
Diamondoids are not forever: microbial biotransformation of diamondoid carboxylic acids
Authors: Folwell Benjamin D. , McGenity Terry J. , Whitby Corinne 
Published: November 2019

SummaryOil sands process‐affected waters (OSPW) contain persistent, toxic naphthenic acids (NAs), including the abundant yet little‐studied diamondoid carboxylic acids. Therefore, we investigated the aerobic microbial biotransformation of two of the most abundant, chronically toxic and environmentally relevant diamondoid carboxylic acids: adamantane‐1‐carboxylic acid (A1CA) and 3‐ethyl adamantane carboxylic acid (3EA). We inoculated into minimal salts media with diamondoid carboxylic acids as sole carbon and energy source two samples: (i) a surface water sample (designated TPW) collected from a test pit from the Mildred Lake Settling Basin and (ii) a water sample (designated 2 m) collected at a water depth of 2 m from a tailings pond. By day 33, in TPW enrichments, 71% of A1CA and 50% of 3EA was transformed, with 50% reduction in EC20 toxicity. Similar results were found for 2 m enrichments. Biotransformation of A1CA and 3EA resulted in the production of two metabolites, tentatively identified as 2‐hydroxyadamantane‐1‐carboxylic acid and 3‐ethyladamantane‐2‐ol respectively. Accumulation of both metabolites was less than the loss of the parent compound, indicating that they would have continued to be transformed beyond 33 days and not accumulate as dead‐end metabolites. There were shifts in bacterial community composition during biotransformation, with Pseudomonas species, especially P. stutzeri, dominating enrichments irrespective of the diamondoid carboxylic acid. In conclusion, we demonstrated the microbial biotransformation of two diamondoid carboxylic acids, which has potential application for their removal and detoxification from vast OSPW that are a major environmental threat.
An approach to gut microbiota profile in children with autism spectrum disorder
Authors: Andreo‐Martínez Pedro , García‐Martínez Nuria , Sánchez‐Samper Elvira Pilar , Martínez‐González Agustín Ernesto 
Published: November 2019

SummaryIn recent years, there has been an increase in studies on the implications of gut microbiota (GM) on the behaviour of children with autism spectrum disorders (ASD) due to a dysbiosis in GM that can trigger onset, development or progression of ASD through the microbiota–gut–brain axis. The aim of this study is to carry out a systematic review of articles from the last 6 years that analyse GM in children with ASD compared to GM in control groups. Children with ASD showed a higher abundance of Roseburia and Candida genera, and lower abundance of Dialister, Bilophila, Veillonella, Streptococcus, Coprococcus and Prevotella genera. Those differences can be attributed to factors such as different nationalities, nature of control groups, place where the sample was taken, gastrointestinal (GI) problems or bacterial detection methods. It is still too early to define a specific GM profile of children with ASD, and future studies should focus on homogenizing the characteristics of samples and control groups. Furthermore, new multicentre studies should also focus on the impact of GM on GI physiology, neurophysiology and behaviour of children with ASD, and on performing psychometric analyses of the correlation between the severity of ASD behavioural symptoms and GM profiles.
Cue‐induced effects on decision‐making distinguish subjects with gambling disorder from healthy controls
Authors: Genauck Alexander , Andrejevic Milan , Brehm Katharina , Matthis Caroline , Heinz Andreas , Weinreich André , Kathmann Norbert , Romanczuk‐Seiferth Nina 
Published: November 2019

AbstractWhile an increased impact of cues on decision‐making has been associated with substance dependence, it is yet unclear whether this is also a phenotype of non‐substance‐related addictive disorders, such as gambling disorder (GD). To better understand the basic mechanisms of impaired decision‐making in addiction, we investigated whether cue‐induced changes in decision‐making could distinguish GD from healthy control (HC) subjects. We expected that cue‐induced changes in gamble acceptance and specifically in loss aversion would distinguish GD from HC subjects.Thirty GD subjects and 30 matched HC subjects completed a mixed gambles task where gambling and other emotional cues were shown in the background. We used machine learning to carve out the importance of cue dependency of decision‐making and of loss aversion for distinguishing GD from HC subjects.Cross‐validated classification yielded an area under the receiver operating curve (AUC‐ROC) of 68.9% (p = .002). Applying the classifier to an independent sample yielded an AUC‐ROC of 65.0% (p = .047). As expected, the classifier used cue‐induced changes in gamble acceptance to distinguish GD from HC. Especially, increased gambling during the presentation of gambling cues characterized GD subjects. However, cue‐induced changes in loss aversion were irrelevant for distinguishing GD from HC subjects. To our knowledge, this is the first study to investigate the classificatory power of addiction‐relevant behavioral task parameters when distinguishing GD from HC subjects. The results indicate that cue‐induced changes in decision‐making are a characteristic feature of addictive disorders, independent of a substance of abuse
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads
Authors: Vollger Mitchell R. , Logsdon Glennis A. , Audano Peter A. , Sulovari Arvis , Porubsky David , Peluso Paul , Wenger Aaron M. , Concepcion Gregory T. , Kronenberg Zev N. , Munson Katherine M. , Baker Carl , Sanders Ashley D. , Spierings Diana C.J. , Lansdorp Peter M. , Surti Urvashi , Hunkapiller Michael W. , Eichler Evan E. 
Published: November 2019

AbstractThe sequence and assembly of human genomes using long‐read sequencing technologies has revolutionized our understanding of structural variation and genome organization. We compared the accuracy, continuity, and gene annotation of genome assemblies generated from either high‐fidelity (HiFi) or continuous long‐read (CLR) datasets from the same complete hydatidiform mole human genome. We find that the HiFi sequence data assemble an additional 10% of duplicated regions and more accurately represent the structure of tandem repeats, as validated with orthogonal analyses. As a result, an additional 5 Mbp of pericentromeric sequences are recovered in the HiFi assembly, resulting in a 2.5‐fold increase in the NG50 within 1 Mbp of the centromere (HiFi 480.6 kbp, CLR 191.5 kbp). Additionally, the HiFi genome assembly was generated in significantly less time with fewer computational resources than the CLR assembly. Although the HiFi assembly has significantly improved continuity and accuracy in many complex regions of the genome, it still falls short of the assembly of centromeric DNA and the largest regions of segmental duplication using existing assemblers. Despite these shortcomings, our results suggest that HiFi may be the most effective standalone technology for de novo assembly of human genomes.
Radiologic sinus inflammation and symptoms of chronic rhinosinusitis in a population‐based sample
Authors: Hirsch Annemarie G. , Nordberg Cara , Bandeen‐Roche Karen , Tan Bruce K. , Schleimer Robert P. , Kern Robert C. , Sundaresan Agnes , Pinto Jayant M. , Kennedy Thomas L. , Greene Joseph Scott , Kuiper Jordan R. , Schwartz Brian S. 
Published: November 2019

AbstractBackgroundChronic rhinosinusitis (CRS) epidemiology has been largely studied using symptom‐based case definitions, without assessment of objective sinus findings.ObjectiveTo describe radiologic sinus opacification and the prevalence of CRS, defined by the co‐occurrence of symptoms and sinus opacification, in a general population‐based sample.MethodsWe collected questionnaires and sinus CT scans from 646 participants selected from a source population of 200 769 primary care patients. Symptom status (CRSS) was based on guideline criteria, and objective radiologic inflammation (CRSO) was based on the Lund‐Mackay (L‐M) score using multiple L‐M thresholds for positivity. Participants with symptoms and radiologic inflammation were classified as CRSS+O. We performed negative binomial regression to assess factors associated with L‐M score and logistic regression to evaluate factors associated with CRSS+O. Using weighted analysis, we calculated estimates for the source population.ResultsThe proportion of women with L‐M scores ≥ 3, 4, or 6 (CRSO) was 11.1%, 9.9%, and 5.7%, respectively, and 16.1%, 14.6%, and 8.7% among men. The respective proportion with CRSS+O was 1.7%, 1.6%, and 0.45% among women and 8.8%, 7.5%, and 3.6% among men. Men had higher odds of CRSS+O compared to women. A greater proportion of men (vs women) had any opacification in the frontal, anterior ethmoid, and sphenoid sinuses.ConclusionIn a general population‐based sample in Pennsylvania, sinus opacification was more common among men than in women and opacification occurred in different locations by sex. Male sex, migraine headache, and prior sinus surgery were associated with higher odds of CRSS+O.