bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post COVID-19 Condition in South Africa: 3-month follow-up after hospitalisation with SARS-CoV-2
Authors: Dryden Murray , Mudara Caroline , Vika Caroline , Blumberg Lucille , Mayet Natalie , Cohen Cheryl , Tempia Stefano , Parker Arifa , Nel Jeremy , Perumal Rubeshan , Groome Michelle J. , Conradie Francesca , Ndjeka Norbert , Sigfrid Louise , Merson Laura , Jassat Waasila 
Published: March 2022

AbstractBackgroundPost COVID-19 Condition (PCC) as defined by WHO refers to a wide range of new, returning, or ongoing health problems experienced by COVID-19 survivors, and represents a rapidly emerging public health priority. We aimed to establish how this developing condition has impacted patients in South Africa and which population groups are at risk.MethodsIn this prospective cohort study, participants ≥18 years who had been hospitalised with laboratory-confirmed SARS-CoV-2 infection during the second and third wave between December 2020 and August 2021 underwent telephonic follow-up assessment up at one-month and three-months after hospital discharge. Participants were assessed using a standardised questionnaire for the evaluation of symptoms, functional status, health-related quality of life and occupational status. Multivariable logistic regression models were used to determine factors associated with PCC.FindingsIn total, 1,873 of 2,413 (78%) enrolled hospitalised COVID-19 participants were followed up at three-months after hospital discharge. Participants had a median age of 52 years (IQR 41-62) and 960 (51.3%) were women. At three-months follow-up, 1,249 (66.7%) participants reported one or more persistent COVID-related symptom(s), compared to 1,978/2,413 (82.1%) at one-month post-hospital discharge. The most common symptoms reported were fatigue (50.3%), shortness of breath (23.4%), confusion or lack of concentration (17.5%), headaches (13.8%) and problems seeing/blurred vision (10.1%). On multivariable analysis, factors associated with new or persistent symptoms following acute COVID-19 were age ≥65 years [adjusted odds ratio (aOR) 1.62; 95%confidence interval (CI) 1.00-2.61]; female sex (aOR 2.00; 95% CI 1.51-2.65); mixed ethnicity (aOR 2.15; 95% CI 1.26-3.66) compared to black ethnicity; requiring supplemental oxygen during admission (aOR 1.44; 95% CI 1.06-1.97); ICU admission (aOR 1.87; 95% CI 1.36-2.57); pre-existing obesity (aOR 1.44; 95% CI 1.09-1.91); and the presence of ≥4 acute symptoms (aOR 1.94; 95% CI 1.19-3.15) compared to no symptoms at onset.InterpretationThe majority of COVID-19 survivors in this cohort of previously hospitalised participants reported persistent symptoms at three-months from hospital discharge, as well as a significant impact of PCC on their functional and occupational status. The large burden of PCC symptoms identified in this study emphasises the need for a national health strategy. This should include the development of clinical guidelines and training of health care workers, in identifying, assessing and caring for patients affected by PCC, establishment of multidisciplinary national health services, and provision of information and support to people who suffer from PCC.
A multi-phenotype analysis reveals 19 novel susceptibility loci for basal cell carcinoma and 15 for squamous cell carcinoma
Authors: Seviiri Mathias , Law Matthew H. , Ong Jue-Sheng , Gharahkhani Puya , Fontanillas Pierre ,   23andMe Research Team, Olsen Catherine M. , Whiteman David C. , MacGregor Stuart 
Published: March 2022

ABSTRACTBasal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the most common forms of skin cancer. There is genetic overlap between skin cancers, pigmentation traits, and autoimmune diseases. We use linkage disequilibrium score regression to identify 20 traits (melanoma, pigmentation traits, autoimmune diseases, and blood biochemistry biomarkers) with a high genetic correlation (rg > 10%, P < 0.05) with BCC (20,791 cases and 286,893 controls in the UK Biobank) and SCC (7,402 cases and 286,892 controls in the UK Biobank), and use a multi-trait genetic analysis to identify 78 and 69 independent genome-wide significant (P < 5 × 10-8) susceptibility loci for BCC and SCC respectively; 19 BCC and 15 SCC loci are both novel and replicated (P < 0.05) in a large independent cohort; 23andMe, Inc (BCC: 251,963 cases and 2,271,667 controls, and SCC: 134,700 cases and 2,394,699 controls. Novel loci are implicated in BCC/SCC development and progression (e.g. CDKL1), pigmentation (e.g. DSTYK), cardiometabolic pathways (e.g. FADS2), and immune-regulatory pathways including; innate immunity against coronaviruses (e.g. IFIH1), and HIV-1 viral load modulation and disease progression (e.g. CCR5). We also report a powerful and optimised BCC polygenic risk score that enables effective risk stratification for keratinocyte cancer in a large prospective Canadian Longitudinal Study of Aging (794 cases and 18139 controls); e.g. percentage of participants reclassified; MTAGPRS = 36.57%, 95% CI = 35.89-37.26% versus UKBPRS= 33.23%, 95% CI=32.56-33.91%).
Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion
Authors: Deborde Sylvie , Gusain Laxmi , Powers Ann , Marcadis Andrea , Yu Yasong , Chen Chun- Hao , Frants Anna , Kao Elizabeth , Tang Laura , Vakiani Efsevia , Calo Annalisa , Omelchenko Tatiana , Jessen Kristian R. , Reva Boris , Wong Richard J. 
Published: March 2022

ABSTRACTNerves are a component of the tumor microenvironment contributing to cancer progression, but the role of cells from nerves in facilitating cancer invasion remains poorly understood. Here we show that Schwann cells (SCs) activated by cancer cells collectively function as Tumor Activated Schwann cell Tracks (TASTs) that promote cancer cell migration and invasion. Non-myelinating SCs form TASTs and have cell gene expression signatures that correlate with diminished survival in patients with pancreatic ductal adenocarcinoma. In TASTs, dynamic SCs form tracks that serve as cancer pathways and apply forces on cancer cells to enhance cancer motility. These SCs are activated by c-Jun, analogous to their reprogramming during nerve repair. This study reveals a mechanism of cancer cell invasion that co-opts a wound repair process and exploits the ability of SCs to collectively organize into tracks. These findings establish a novel paradigm of how cancer cells spread and reveal therapeutic opportunities.SIGNIFICANCEHow the tumor microenvironment participates in pancreatic cancer progression is not fully understood. Here, we show that Schwann cells are activated by cancer cells and collectively organize into tracks that dynamically enable cancer invasion in a c-Jun dependent manner.
Dynamic changes of gut microbiota associated with blood glucose levels in sows from pregnancy through lactation
Authors: Wang Mingjun , Li Jiaju , Chen Bo , Li Haitao , Ren Jun 
Published: March 2022

AbstractGut microbiota plays important roles in metabolism and physiological homeostasis throughout the lifespan of mammals, including in pregnancy. To evaluate the effects of practically adopted restricted feeding during gestation on blood glucose level and fecal microbiota composition, 31 sows were used to identify the shifts in bacterial assemblages by 16S rRNA sequencing in their early pregnancy, late pregnancy and late lactation stages. We find that the blood glucose was elevated significantly (p < 0.001) in sows offered abundant feed in the late lactation as compared with those of the same cohort in the pregnancy stages when on limited feed. Five bacterial genera were differentially abundant among three stages, and the abundances of Streptococcus (padj < 0.001) and unclassified_f_Lachnospiraceae (padj < 0.001) were increased, whereas the abundances of Lactobacillus (padj = 0.035) and Escherichia-Shigella (padj< 0.001) were decreased in the latter two stages. The genus Prevotellaceae_NK3B31_group (padj = 0.026) displayed higher abundance in the late lactation stage. A significant correlation in the Pearson’s analysis indicates that three out of these five differentially abundant genera were related to blood glucose change. Our data show that restricted-fed gestating sows have aberrant blood glucose level and may affect the intestinal microbiota.
Nucleotide augmentation for machine learning-guided protein engineering
Authors: Minot Mason , Reddy Sai T. 
Published: March 2022

AbstractMachine learning-guided protein engineering is a rapidly advancing field. Despite major experimental and computational advances however, collecting protein genotype (sequence) and phenotype (function) data remains time and resource intensive. As a result, the quality and quantity of training data is often a limiting factor in developing machine learning models. Data augmentation techniques have been successfully applied to the fields of computer vision and natural language processing, however, there is a lack of such augmentation techniques for biological sequence data. Towards this end we develop nucleotide augmentation (NTA), which leverages natural nucleotide codon degeneracy to augment protein sequence data in a biologically meaningful way. As a proof of concept for protein engineering, we apply NTA to train machine learning models with benchmark data sets of protein genotype and phenotype, revealing performance gains on par and surpassing benchmarks models, even when only using a fraction of the training data. NTA also enables substantial improvements for classification tasks under heavy class imbalance.Availability and implementationThe code to use NTA and to reproduce the analyses in this study is publicly available at https://github.com/minotm/NTA
Superoxide Dismutase 1 translocates to the nucleus in spinal cord mixed cells from newborn rats
Authors: Santos Nathália V. , Machado Camila M. L. , Cerchiaro Giselle 
Published: March 2022

AbstractSuperoxide dismutase 1 (SOD1) catalyzes the superoxide conversion to oxygen and hydrogen peroxide in general. SOD1 can translocate to the cell nucleus in response to oxidative stress in yeast and human fibroblasts. Here, we report the translocation of sod1 to the cell nucleus in primary co-cultures of neurons and astrocytes derived from newborn rats explants even in the absence of oxidative stress stimuli. The successful tissue explants from rats allowed simplistic and clean modeling of Amyotrophic lateral sclerosis (ALS)-simile tissue microenvironment. This mixed-cells-population was responsive to H2O2 (100 μM) oxidative stress with a progressive dying process up to 6 h after stimuli. However, no differences in SOD1 nucleus translocation were observed in rat amyotrophic lateral sclerosis (ALS)-simile tissue microenvironment up to 6 hours under oxidative stress. These results altogether point to a robust cellular collaboration between neurons and astrocytes so that the tissue can equilibrate this SOD1 translocation during the oxidative stress response and in the early animal development.
Distinct phospho-variants of STAT3 regulate naïve pluripotency and developmental pacein vivo
Authors: Azami Takuya , Kraunsoe Sophie , Martello Graziano , Pei Yihan , Boroviak Thorsten , Nichols Jennifer 
Published: March 2022

AbstractSTAT3 has been studied extensively in the context of self-renewal of naïve pluripotent mouse embryonic stem cells. We uncovered acute roles for STAT3 and its target, TFCP2L1, in maintenance of epiblast and primitive endoderm duringin vivodiapause. On an outbred genetic background, we observed consistent developmental retardation from implantation until embryonic day 11.5, beginning with significant reduction of epiblast cells at implantation inStat3null embryos. Remarkably, mutants closely resemble non-affected embryos from the previous day at all postimplantation stages examined. We attribute this phenotype to loss of the active serine phosphorylated form of STAT3 required for neural differentiation and implicated in growth defects in mice and humans. Bulk RNA-sequencing analysis of isolated epiblasts revealed compromised lipid metabolism inStat3null embryos by embryonic day 6.5. Furthermore, we demonstrate that gastruloids generated fromStat3null ESCs failed to extend the posterior axis or maintain BRACHYURY expression and were underrepresented in this region when mixed with wild type cells in chimaeric gastruloids. Our study implicates a role for STAT3 in temporal control of embryonic progression and metabolic mechanisms.
Rescue by gene swamping as a gene drive deployment strategy
Authors: Harris Keith D. , Greenbaum Gili 
Published: March 2022

AbstractGene drives are genetic constructs that can spread deleterious alleles with potential application to population suppression of harmful species. Given that a gene drive can potentially spill over to other populations or even other species, control measures and fail-safes strategies must be considered. Gene drives are designed to generate a rapid demographic decline, while at the same time generating a dynamic change in the population’s genetics. Since these evolutionary and demographic processes are linked and are expected to occur at a similar time-scale during gene drive spread, feedback between these processes may significantly affect the outcome of deployment. To study this feedback and to understand how it affects gene drive spillovers, we developed a gene drive model that combines evolutionary and demographic dynamics in a two-population setting. The model demonstrates how feedback between evolutionary and demographic dynamics can generate additional outcomes to those generated by the evolutionary dynamics alone. We identify an outcome of particular interest, where the short-term suppression of the target population is followed by gene swamping and loss of the gene drive. This outcome could be useful for designing gene drive deployments that temporarily suppress the population, but ultimately do not remain in the population. Using our model, we demonstrate the robustness of this outcome to spillover and to the evolution of resistance, and suggest that it could be used as a fail-safe strategy for gene drive deployment.
Comparative Genomic Analysis of Salmonella enterica serovar Typhimurium from Passerines Reveals Two Lineages Circulating in Europe, New Zealand, and the United States
Authors: Fu Yezhi , M’ikanatha Nkuchia M. , Dudley Edward G. 
Published: March 2022

ABSTRACTSalmonella enterica serovar Typhimurium from passerines have caused wild bird mortality and human salmonellosis outbreaks in Europe, Oceania, and North America. Here, we performed comparative genomic analysis to explore the emergence, genetic relationship, and evolution of geographically dispersed passerine isolates. We found that passerine isolates from Europe and the United States clustered to form two lineages (EU and US passerine lineages), which were distinct from major S. Typhimurium lineages circulating in other diverse hosts (e.g., humans, cattle, pigs, chicken, other avian hosts such as pigeons and ducks). Further, passerine isolates from New Zealand clustered to form a sublineage (NZ passerine lineage) of the US passerine lineage. We inferred that the passerine isolates mutated at a rate of 3.2 × 10-7 substitutions/site/year, and the US, EU, and NZ passerine lineages emerged in ca. 1952, 1970, and 1996, respectively. Isolates from the three lineages presented genetic similarity such as lack of antimicrobial resistance genes and accumulation of same virulence pseudogenes. In addition, genetic diversity due to microevolution existed in the three passerine lineages. Specifically, pseudogenization in type 1 fimbrial gene fimC (deletion of G at position 87) was only detected in the US and NZ passerine isolates, while a single-base deletion in type 3 secretion system effector genes (i.e., gogB, sseJ, and sseK2) solely concurred in the EU passerine isolates. These findings provide insights into evolution, host adaptation, and epidemiology of S. Typhimurium in passerines.IMPORTANCEPasserine-associated S. Typhimurium have been linked to human salmonellosis outbreaks in recent years. Here we investigated the phylogenetic relationship of globally distributed passerine isolates and profiled their genomic similarity and diversity. Our study reveals two passerine-associated S. Typhimurium lineages circulating in Europe, Oceania, and North America. Isolates from the two lineages presented phylogenetic and genetic signatures that were distinct from isolates of other hosts. The findings shed light on host adaptation of S. Typhimurium in passerines and are important for source attribution of S. Typhimurium to avian hosts. Further, we found S. Typhimurium definitive phage type (DT) 160 from passerines that caused decade-long human salmonellosis outbreaks in New Zealand and Australia formed a sublineage of the US passerine lineage, suggesting that DT160 may have originated from passerines outside Oceania. Our study demonstrates the importance of whole-genome sequencing and genomic analysis of historical microbial collections to modern day epidemiologic surveillance.
Application of decision support tool in design-build projects: a quasi-experiment with novice decision makers
Authors: Lee Zheng Ping , Rahman Rahimi A. , Doh Shu Ing 
Published: March 2022

PurposeDesign-Build (DB) is known as the alternative for Design-Bid-Build in the Malaysian construction industry. For DB projects, it is critical to adopt effective decision support tool to ensure the execution of a systematic decision-making technique. This study aimed to examine the impact of a decision support tool for novice decision makers to reject or adopt DB for their construction projects.Design/methodology/approachLiterature review and qualitative input from experts identified several key-selection factors pertaining to critical success factors and design-build drivers. This resulted in the development of Decision Support Tool for Design-Build (DST-DB). A quasi-experiment, which involved 382 novice decision makers in the construction industry, was conducted to test the DST-DB quantitatively. The participants were required to compare two construction projects using DST-DB and traditional decision-making methods. Multivariate analysis was performed to analyse all collected data.FindingsThe quasi-experiment data suggests that DST-DB enables significantly higher usability, likelihood, precision, confidence and satisfaction rate when compared to the traditional decision-making process. The pre- and post-surveys indicated that the DST-DB is effective in improving decision-making performance through selection factors of client-briefing, maximised resources and sharing expertise. The participants also agreed that DST-DB is easy to use and helps them to gain better understanding of the decision-making process for construction projects.Originality/valueThis research contributes to the existing body of knowledge through the impact of DST on the decisions of novices. The novice decision makers found that DST-DB is practically adaptable and comparatively effective for decision-making process than traditional decision-making methods. This contributes to the practical application of construction companies to provide DST-DB training to the fresh graduate employees to enhance their competencies in the decision-making process.
Hybrid nanoliquid flow through a microchannel with particle shape factor, slip and convective regime
Authors: Sindhu S. , B.J. Gireesha , Sowmya G. , Makinde Oluwole Daniel 
Published: March 2022

Purpose
This study aims to portray the systematic study of hybrid nanofluid with particle shape effect on significant heat transfer enhancement. The steady flow of hybrid nanoliquid in a microchannel with the aid of porous medium has been considered. The dispersion of copper and Al2O3 in water is taken as hybrid mixture. The impact of thermal radiation, slip length and convective conditions on flow and thermal features are examined numerically.

Design/methodology/approach
The modelled equations are made dimensionless by means of nondimensional entities. The solutions are computed numerically by the implementation of Runge–Kutta-based shooting technique. The results depict that the shape of hybrid mixtures plays a significant role in convective heat transfer. Relevant results on flow velocity, temperature, Nusselt number and friction factor for various physical constraints have been perused. The obtained outcomes are displayed graphically.

Findings
The acquired results depict that Nusselt number augments with Eckert number and solid volume fraction of hybrid nanoparticles, which has a vibrant role in enriching the heat transfer coefficient. Also, it is emphasized that the Nusselt number is larger for blade-shaped nanoparticle compared to other shapes.

Originality/value
The analysis of individual effect of thermal radiation, Joule heating, viscous dissipation and magnetic field on the flow of Cu and Al2O3 hybrid nanofluid through microchannel has vivacious role in augmenting heat transmission. Along with this, the impact of porous medium, shape factor, slip and convective peripheral conditions are also emphasized.
Online branding strategies of family SME wineries: a Hungarian-German comparative study
Authors: Paunovic Ivan , Obermayer Nóra , Kovari Edit 
Published: March 2022

PurposeBoth Hungary and Germany belong to the old-world wine-producing countries and have long winemaking traditions. This paper aims at exploring and comparing online branding strategies of family SME (small and medium sized enterprises) wineries at Lake Balaton (Hungary) and Lake Constance (Germany), as two wine regions with similar geographic characteristics.Design/methodology/approachThis paper, based on a total sample of 37 family wineries, 15 at Lake Balaton and 22 at Lake Constance, investigates the differences in brand identity on the website, brand image in social media and online communication channels deployed in both wine regions. The study applies a qualitative methodology using MaxQDA software for conducting content analysis of texts in websites and social media. Descriptive statistics and t-test were conducted to compare the usage of different communication channels and determine statistical significance.FindingsAt Lake Balaton, the vineyard, the winery and the family, while at Lake Constance, the lake itself and the grape are highlighted regarding family winery brand identity. The customer-based brand image of Hungarian family wineries emphasizes wine, food and service, with the predominant use of Facebook. In the German family wineries, the focus of brand identity is on wine, friendliness and taste and includes more extensive usage of websites.Originality/valueThe paper deploys a novel methodology, both in terms of tools used as well as geographic focus to uncover online branding patterns of family wineries, thereby providing implications for wine and tourism industries at lake regions. It compares the share of selected most-used words in the overall text in websites and in social media, and presents the key findings from this innovative approach.