bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens
Authors: Gatt Yair E , Margalit Hanah 
Published: October 2020

AbstractWithin-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation
Authors: Meisig Johannes , Dreser Nadine , Kapitza Marion , Henry Margit , Rotshteyn Tamara , Rahnenführer Jörg , Hengstler Jan G , Sachinidis Agapios , Waldmann Tanja , Leist Marcel , Blüthgen Nils 
Published: October 2020

Abstract
Thousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are few, especially for processes affected simultaneously by two orthogonal influencing variables. We approached this problem for neuroepithelial development of human pluripotent stem cells (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual genes in these states), and time-resolved transcriptome data, a comprehensive model of spontaneous and perturbed gene expression dynamics was developed. The model made reliable predictions (average correlation of 0.85 between predicted and subsequently tested expression values). Even regulations predicted to be non-monotonic were successfully validated by PCR in new sets of experiments. Transient patterns of gene regulation were identified from model predictions. They pointed towards activation of Wnt signaling as a candidate pathway leading to a redirection of differentiation away from neuroepithelial cells towards neural crest. Intervention experiments, using a Wnt/beta-catenin antagonist, led to a phenotypic rescue of this disturbed differentiation. Thus, our broadly applicable model allows the analysis of transcriptome changes in complex time/perturbation matrices.
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies
Authors: Yue Zongliang , Zhang Eric , Xu Clark , Khurana Sunny , Batra Nishant , Dang Son Do Hai , Cimino James J , Chen Jake Y 
Published: October 2020

Abstract
PAGER-CoV (http://discovery.informatics.uab.edu/PAGER-CoV/) is a new web-based database that can help biomedical researchers interpret coronavirus-related functional genomic study results in the context of curated knowledge of host viral infection, inflammatory response, organ damage, and tissue repair. The new database consists of 11 835 PAGs (Pathways, Annotated gene-lists, or Gene signatures) from 33 public data sources. Through the web user interface, users can search by a query gene or a query term and retrieve significantly matched PAGs with all the curated information. Users can navigate from a PAG of interest to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships, totaling 19 996 993. Users can also retrieve enriched PAGs from an input list of COVID-19 functional study result genes, customize the search data sources, and export all results for subsequent offline data analysis. In a case study, we performed a gene set enrichment analysis (GSEA) of a COVID-19 RNA-seq data set from the Gene Expression Omnibus database. Compared with the results using the standard PAGER database, PAGER-CoV allows for more sensitive matching of known immune-related gene signatures. We expect PAGER-CoV to be invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients.
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
Authors: Moretti Sébastien , Tran Van Du T , Mehl Florence , Ibberson Mark , Pagni Marco 
Published: October 2020

Abstract
MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).
Radiological assessment schedule for high-grade glioma patients during the surveillance period using parametric modeling
Authors: Ji So Young , Lee Jongjin , Lee Joo Ho , Lee Soon-Tae , Won Jae Kyung , Kim Jin Wook , Kim Yong Hwy , Kim Tae Min , Choi Seung Hong , Park Sung-Hye , Kim Yongdai , Park Chul-Kee 
Published: October 2020

Abstract

Background
An optimal radiological surveillance plan is crucial for high-grade glioma (HGG) patients, which is determined arbitrarily in daily clinical practice. We propose the radiological assessment schedule using a parametric model of standardized progression-free survival (PFS) curves.

Methods
A total of 277 HGG patients (178 glioblastoma [GBM] and 99 anaplastic astrocytoma [AA]) from a single institute who completed the standard treatment protocol were enrolled in this cohort study and retrospectively analyzed. The patients were stratified into each layered risk group by genetic signatures and residual mass or through recursive partitioning analysis. PFS curves were estimated using the piecewise exponential survival model. The criterion of a 10% progression rate among the remaining patients at each observation period was used to determine the optimal radiological assessment time point.

Results
The optimal follow-up intervals for MRI evaluations of isocitrate dehydrogenase (IDH) wild-type GBM was every 7.4 weeks until 120 weeks after the end of standard treatment, followed by a 22-week inflection period and every 27.6 weeks thereafter. For the IDH mutated GBM, scans every 13.2 weeks until 151 weeks are recommended. The optimal follow-up intervals were every 22.8 weeks for IDH wild-type AA, and 41.2 weeks for IDH mutated AA until 241 weeks. Tailored radiological assessment schedules were suggested for each layered risk group of the GBM and the AA patients.

Conclusions
The optimal schedule of radiological assessments for each layered risk group of patients with HGG could be determined from the parametric model of PFS.
Smart Growth
Authors: Knaap Gerrit-Jan , Lewis Rebecca , Chakraborty Arnab , June-Friesen Katy 
Published: October 2020

In market economies such as the United States and most western nations, land-use and development patterns are influenced by government regulations and investments in infrastructure but determined largely by market forces. Under these conditions, post–World War II development patterns—when the automobile became the dominant form of transportation—became highly dispersed, haphazard, and dominated by low-density development. Scholars and planners have pejoratively characterized this as urban sprawl, to which they attribute adverse social and environmental consequences, such as high rates of farm and forest land consumption, excessive driving and resultant air pollution, costly public infrastructure, and social segmentation. For many years, efforts to combat sprawl were called “growth control” or “growth management” and primarily focused on slowing the rate of urban growth. But in the 1990s in the United States, a new term and set of ideas entered the lexicon of planners, developers, and policy makers: smart growth. Proponents of smart growth aimed to change the focus from stopping or slowing growth to assuring that growth was “smarter” in location, intensity, and form. Although the precise meaning of the term remains ambiguous, the Smart Growth Network—a national alliance of more than thirty private sector, public sector, and nongovernmental organizations—continues to advance the following ten principles: (1) mix land uses; (2) taking advantage of compact building design; (3) creating a wide range of housing opportunities and choices; (4) creating walkable neighborhoods; (5) fostering distinctive, attractive communities with a strong sense of place; (6) preserving open space, farmland, natural beauty, and critical environmental areas; (7) strengthening and directing development toward existing communities; (8) providing a variety of transportation choices; (9) making development decisions predictable, fair, and cost-effective; and (10) encouraging community and stakeholder collaboration in development decisions. Over the past twenty years, scholars have undertaken considerable research to confirm or dispute the virtues of these principles and to understand how best to implement them. Recently, smart growth advocates have begun to address more contemporary challenges, such as climate change, social equity, public health, and more. Smart growth’s underlying principles are now also represented in the popular terminologies of “sustainable development” and “urban resilience” and in broader efforts such as the United Nations 2015 Sustainable Development Goals. This article, however limited in scope to the original set of smart growth principles, traces the history of the concept and presents research that explores the validity of the principles, the challenges of implementation, and the extent of success.
Doctors’ attitudes to patient occupation information in four hospital specialties
Authors: Bayliss C , Champion A , Nwokedi E , Thanikasalam R 
Published: October 2020

Abstract

Background
Although we do not know how often doctors enquire about their patients’ work, evidence suggests that occupation is often not recorded in clinical notes. There is a lack of research into doctors’ views on the importance of patient occupation or their educational needs in this area.

Aims
To assess doctors’ attitudes to using patient occupation information for care-planning and to determine doctors’ need for specific training in occupational health.

Methods
We undertook a cross-sectional survey of doctors in cardiology, obstetrics and gynaecology, oncology and orthopaedics. Our questionnaire explored attitudes of the doctors to asking patients about their occupational status, their training and competency to do so, and their training needs in occupational health.

Results
The response rate was 42/46 (91%). Obstetrics and gynaecology 6/9 (67%) and oncology doctors 3/6 (50%) reported enquiring about the nature of patients’ occupations’ ‘most of the time’/‘always’ and that it rarely influenced clinical decisions. This contrasted with orthopaedic doctors 12/12 (100%) and cardiology doctors 14/15 (93%). Although 19/42 (45%) participants felt it was important to ask patients their occupation, only 10/42 (24%) ‘always’ asked patients about their work. The majority of participants 29/41 (71%) reported receiving no training in occupational health, but 37/42 (88%) considered that some training would be useful.

Conclusions
Training on the importance of occupation and its’ role as a clinical outcome in care-planning, might help doctors feel more competent in discussing the impact of health on work with patients.
Elasticities of taxable income and adjustment costs: bunching evidence from New Zealand
Authors: Alinaghi Nazila , Creedy John , Gemmell Norman 
Published: October 2020

Abstract
This article obtains elasticity of taxable income (ETI) estimates using data for NZ over the period, 2001–2017, and using the connection between the ETI and excess bunching at income tax thresholds. Results are reported for the top two thresholds in the tax schedule and for various taxpayer types. Adjustments to tax changes are investigated by comparing ETIs obtained from persistent bunching at thresholds when the tax regime is unchanged, with transitory values associated with specific tax reforms. Results suggest substantial bunching around both tax kinks, with ETIs of around 0.2–0.3 across all taxpayers. Evidence suggests large responses by the self-employed, with ETIs of around 0.8–1.0. No significant differences between males and females were found. Adjustment costs and/or inattention biases associated with a shift in a tax threshold were equivalent initially to around 18% (declining to 6%) of the observed excess mass at the post-reform threshold.
Phosphatidylserine Synthase from Salicornia europaea Is Involved in Plant Salt Tolerance by Regulating Plasma Membrane Stability
Authors: Lv Sulian , Tai Fang , Guo Jie , Jiang Ping , Lin Kangqi , Wang Duoliya , Zhang Xuan , Li Yinxin 
Published: October 2020

Abstract
Salinity-induced lipid alterations have been reported in many plant species; however, how lipid biosynthesis and metabolism are regulated and how lipids work in plant salt tolerance are much less studied. Here, a constitutively much higher phosphatidylserine (PS) content in the plasma membrane (PM) was found in the euhalophyte Salicornia europaea than in Arabidopsis. A gene encoding PS synthase (PSS) was subsequently isolated from S. europaea, named SePSS, which was induced by salinity. Multiple alignments and phylogenetic analysis suggested that SePSS belongs to a base exchange-type PSS, which localises to the endoplasmic reticulum. Knockdown of SePSS in S. europaea suspension cells resulted in reduced PS content, decreased cell survival rate, and increased PM depolarization and K+ efflux under 400 or 800 mM NaCl. By contrast, the upregulation of SePSS leads to increased PS and phosphatidylethanolamine levels and enhanced salt tolerance in Arabidopsis, along with a lower accumulation of reactive oxygen species, less membrane injury, less PM depolarization and higher K+/Na+ in the transgenic lines than in wild-type (WT). These results suggest a positive correlation between PS levels and plant salt tolerance, and that SePSS participates in plant salt tolerance by regulating PS levels, hence PM potential and permeability, which help maintain ion homeostasis. Our work provides a potential strategy for improving plant growth under multiple stresses.
Health Care Provider Utilization of Prescription Monitoring Programs: A Systematic Review and Meta-Analysis
Authors: Robinson Alysia , Wilson Maria N , Hayden Jill A , Rhodes Emily , Campbell Samuel , MacDougall Peter , Asbridge Mark 
Published: October 2020

Abstract

Objective
To synthesize the literature on the proportion of health care providers who access and use prescription monitoring program data in their practice, as well as associated barriers to the use of such data.

Design
We performed a systematic review using a standard systematic review method with meta-analysis and qualitative meta-summary. We included full-published peer-reviewed reports of study data, as well as theses and dissertations.

Methods
We identified relevant quantitative and qualitative studies. We synthesized outcomes related to prescription monitoring program data use (i.e., ever used, frequency of use). We pooled the proportion of health care providers who had ever used prescription monitoring program data by using random effects models, and we used meta-summary methodology to identify prescription monitoring program use barriers.

Results
Fifty-three studies were included in our review, all from the United States. Of these, 46 reported on prescription monitoring program use and 32 reported on barriers. The pooled proportion of health care providers who had ever used prescription monitoring program data was 0.57 (95% confidence interval: 0.48–0.66). Common barriers to prescription monitoring program data use included time constraints and administrative burdens, low perceived value of prescription monitoring program data, and problems with prescription monitoring program system usability.

Conclusions
Our study found that health care providers underutilize prescription monitoring program data and that many barriers exist to prescription monitoring program data use.
Promoter engineering for microbial bio-alkane gas production
Authors: Trisrivirat Duangthip , Hughes John M X , Hoeven Robin , Faulkner Matthew , Toogood Helen , Chaiyen Pimchai , Scrutton Nigel S 
Published: October 2020

Abstract
Successful industrial biotechnological solutions to biofuels and other chemicals production rely on effective competition with existing lower-cost natural sources and synthetic chemistry approaches enabled by adopting low-cost bioreactors and processes. This is achievable by mobilizing Halomonas as a next generation industrial chassis, which can be cultivated under non-sterile conditions. To increase the cost effectiveness of an existing sustainable low carbon bio-propane production strategy, we designed and screened a constitutive promoter library based on the known strong porin promoter from Halomonas. Comparative studies were performed between Escherichia coli and Halomonas using the reporter gene red fluorescent protein (RFP). Later studies with a fatty acid photodecarboxylase-RFP fusion protein demonstrated tuneable propane production in Halomonas and E. coli, with an ∼8-fold improvement in yield over comparable isopropyl-β-D-thiogalactoside-inducible systems. This novel set of promoters is a useful addition to the synthetic biology toolbox for future engineering of Halomonas to make chemicals and fuels.
The impact of cow size on cow-calf and postweaning progeny performance in the Nebraska Sandhills
Authors: Ziegler Robert L , Musgrave Jacki A , Meyer Tanya L , Funston Rick N , Dennis Elliott J , Hanford Kathryn J , MacDonald James C , Mulliniks J Travis 
Published: October 2020

Abstract
Optimizing beef production system efficiency requires an understanding of genetic potential suitable for a given production environment. Therefore, the objective of this retrospective analysis was to determine the influence of cow body weight (BW) adjusted to a common body condition score (BCS) of 5 at weaning-influenced cow-calf performance and postweaning steer and heifer progeny performance. Data were collected at the Gudmundsen Sandhills Laboratory, Whitman, NE, on crossbred, mature cows (n = 1,607) from 2005 to 2017. Cow BCS at calving, prebreeding, and weaning were positively associated (P &lt; 0.01) with greater cow BW. Increasing cow BW was positively associated (P &lt; 0.01) with the percentage of cows that conceived during a 45-d breeding season. For every additional 100-kg increase in cow BW, calf BW increased (P &lt; 0.01) at birth by 2.70 kg and adjusted 205-d weaning BW by 14.76 kg. Calf preweaning average daily gain (ADG) increased (P &lt; 0.01) 0.06 kg/d for every additional 100-kg increase in cow BW. Heifer progeny BW increased (P &lt; 0.01) postweaning with every additional 100-kg increase in dam BW. Dam BW did not influence (P ≥ 0.11) heifer puberty status prior to breeding, overall pregnancy rates, or the percentage of heifers calving in the first 21 d of the calving season. Steer initial feedlot BW increased by 7.20 kg, reimplant BW increased by 10.47 kg, and final BW increased by 10.29 kg (P ≤ 0.01) for every additional 100-kg increase in dam BW. However, steer feedlot ADG was not influenced (P &gt; 0.67) by dam BW. Hot carcass weights of steers were increased (P = 0.01) by 6.48 kg with every additional 100-kg increase in cow BW. In a hypothetical model using the regression coefficients from this study, regardless of pricing method, cow-calf producers maximize the highest amount of profit by selecting smaller cows. Overall, larger-sized cows within this herd and production system of the current study had increased reproductive performance and offspring BW; however, total production output and economic returns would be potentially greater when utilizing smaller-sized cows.
Toxoplasma oocysts in the soil of public places worldwide: a systematic review and meta-analysis
Authors: Maleki Bahman , Ahmadi Nayebali , Olfatifar Meysam , Gorgipour Mohammad , Taghipour Ali , Abdoli Amir , Khorshidi Ali , Foroutan Masoud , Mirzapour Aliyar 
Published: October 2020

Abstract
Toxoplasmosis is a zoonotic and cosmopolitan infection. Although a few studies have evaluated the prevalence of Toxoplasma oocysts in the soil of public places, the present study was conducted to provide insights into environmental contamination levels and its potential transmission to humans on a global scale. A systematic search was conducted using bibliographic databases through 30 August 2020. A random effects model was utilized to estimate pooled prevalence with 95% confidence intervals (CIs). Subgroup analysis and meta-regressions were also performed on the geographical and environmental parameters. Finally, 22 articles, wherein 15 420 soil samples were examined, met the systematic review and meta-analysis requirements. The mean pooled prevalence of Toxoplasma oocysts was estimated at 16% (95% CI 10 to 26) in public places. The estimated prevalences in Europe, South America, Asia and North America were 23% (95% CI 4 to 65), 22% (95% CI 18 to 26), 15% (95% CI 0.06 to 33) and 8% (95% CI 0.00 to 97), respectively. An increasing trend was observed in the prevalence of Toxoplasma oocysts with increasing latitude (41–56°), decreasing longitude (0–40°) and increasing relative humidity (≥76%). Loop-mediated isothermal amplification and polymerase chain reaction methods revealed the highest and lowest prevalence rates, respectively, in the detection of Toxoplasma oocysts. Awareness of the health authorities and people about Toxoplasma prevalence in the soil of public places and its risk factors is of great importance to developing effective strategies to prevent infection.