bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
Authors: Francis Aleena , Ghosh Srayan , Tyagi Kriti , Prakasam V. , Rani Mamta , Singh Nagendra Pratap , Pradhan Amrita , Sundaram R. M. , Priyanka C. , Laha G. S. , Kannan C. , Prasad M. S. , Chattopadhyay Debasis , Jha Gopaljee 
Published: February 2023

Abstract
Background
Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood.

Results
We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato.

Conclusions
Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.
Healthcare workers knowledge of cholera multi-stranded interventions and its determining factors in North-East Nigeria: planning and policy implications
Authors: Elimian Kelly , King Carina , Dewa Ozius , Pembi Emmanuel , Gandi Benjamin , Yennan Sebastian , Myles Puja , Pritchard Catherine , Forsberg Birger Carl , Alfvén Tobias 
Published: February 2023

Abstract
Background
Healthcare workers’ (HCWs) knowledge of multi-stranded cholera interventions (including case management, water, sanitation, and hygiene (WASH), surveillance/laboratory methods, coordination, and vaccination) is crucial to the implementation of these interventions in healthcare facilities, especially in conflict-affected settings where cholera burden is particularly high. We aimed to assess Nigerian HCWs’ knowledge of cholera interventions and identify the associated factors.

Methods
We conducted a cross-sectional study using a structured interviewer-administered questionnaire with HCWs from 120 healthcare facilities in Adamawa and Bauchi States, North-East Nigeria. A knowledge score was created by assigning a point for each correct response. HCWs’ knowledge of cholera interventions, calculated as a score, was recoded for ease of interpretation as follows: 0–50 (low); 51–70 (moderate); ≥ 71 (high). Additionally, we defined the inadequacy of HCWs’ knowledge of cholera interventions based on a policy-relevant threshold of equal or lesser than 75 scores for an intervention. Multivariable logistic regression was used to identify the factors associated with the adequacy of knowledge score.

Results
Overall, 490 HCWs participated in the study (254 in Adamawa and 236 in Bauchi), with a mean age of 35.5 years. HCWs’ knowledge score was high for surveillance/laboratory methods, moderate for case management, WASH, and vaccination, and low for coordination. HCWs’ knowledge of coordination improved with higher cadre, working in urban- or peri-urban-based healthcare facilities, and secondary education; cholera case management and vaccination knowledge improved with post-secondary education, working in Bauchi State and urban areas, previous training in cholera case management and response to a cholera outbreak—working in peri-urban areas had a negative effect. HCWs’ knowledge of surveillance/laboratory methods improved with a higher cadre, 1-year duration in current position, secondary or post-secondary education, previous training in cholera case management and response to a cholera outbreak. However, HCWs’ current position had both positive and negative impacts on their WASH knowledge.

Conclusions
HCWs in both study locations recorded a considerable knowledge of multi-stranded cholera interventions. While HCWs’ demographic characteristics appeared irrelevant in determining their knowledge of cholera interventions, geographic location and experiences from the current position, training and involvement in cholera outbreak response played a significant role.
Study protocol for a factorial-randomized controlled trial evaluating the implementation, costs, effectiveness, and sustainment of digital therapeutics for substance use disorder in primary care (DIGITS Trial)
Authors: Glass Joseph E. , Dorsey Caitlin N. , Beatty Tara , Bobb Jennifer F. , Wong Edwin S. , Palazzo Lorella , King Deborah , Mogk Jessica , Stefanik-Guizlo Kelsey , Idu Abisola , Key Dustin , Fortney John C. , Thomas Rosemarie , McWethy Angela Garza , Caldeiro Ryan M. , Bradley Katharine A. 
Published: February 2023

Abstract
Background
Experts recommend that treatment for substance use disorder (SUD) be integrated into primary care. The Digital Therapeutics for Opioids and Other SUD (DIGITS) Trial tests strategies for implementing reSET® and reSET-O®, which are prescription digital therapeutics for SUD and opioid use disorder, respectively, that include the community reinforcement approach, contingency management, and fluency training to reinforce concept mastery. This purpose of this trial is to test whether two implementation strategies improve implementation success (Aim 1) and achieve better population-level cost effectiveness (Aim 2) over a standard implementation approach.

Methods/Design
The DIGITS Trial is a hybrid type III cluster-randomized trial. It examines outcomes of implementation strategies, rather than studying clinical outcomes of a digital therapeutic. It includes 22 primary care clinics from a healthcare system in Washington State and patients with unhealthy substance use who visit clinics during an active implementation period (up to one year). Primary care clinics implemented reSET and reSET-O using a multifaceted implementation strategy previously used by clinical leaders to roll-out smartphone apps (“standard implementation” including discrete strategies such as clinician training, electronic health record tools). Clinics were randomized as 21 sites in a 2x2 factorial design to receive up to two added implementation strategies: (1) practice facilitation, and/or (2) health coaching. Outcome data are derived from electronic health records and logs of digital therapeutic usage. Aim 1’s primary outcomes include reach of the digital therapeutics to patients and fidelity of patients’ use of the digital therapeutics to clinical recommendations. Substance use and engagement in SUD care are additional outcomes. In Aim 2, population-level cost effectiveness analysis will inform the economic benefit of the implementation strategies compared to standard implementation. Implementation is monitored using formative evaluation, and sustainment will be studied for up to one year using qualitative and quantitative research methods.

Discussion
The DIGITS Trial uses an experimental design to test whether implementation strategies increase and improve the delivery of digital therapeutics for SUDs when embedded in a large healthcare system. It will provide data on the potential benefits and cost-effectiveness of alternative implementation strategies. ClinicalTrials.gov Identifier: NCT05160233 (Submitted 12/3/2021). https://clinicaltrials.gov/ct2/show/NCT05160233
Impact of the COVID-19 pandemic on children and adolescents: determinants and association with quality of life and mental health—a cross-sectional study
Authors: Richard Viviane , Dumont Roxane , Lorthe Elsa , Loizeau Andrea , Baysson Hélène , Zaballa María-Eugenia , Pennacchio Francesco , Barbe Rémy P. , Posfay-Barbe Klara M. , Guessous Idris , Stringhini Silvia ,   SEROCoV-KIDS Study Group, Amrein Deborah , Arm-Vernez Isabelle , Azman Andrew S. , Bal Antoine , Balavoine Michael , Berthelot Julie , Bleich Patrick , Boehm Livia , Bryand Gaëlle , Bucolli Viola , Collombet Prune , Cudet Alain , Davidovic Vladimir , de Mestral Carlos , D’Ippolito Paola , Dubos Richard , Eckerle Isabella , El Merjani Nacira , Favier Marion , Francioli Natalie , Graindorge Clément , Harnal Séverine , Hurst Samia , Kaiser Laurent , Kherad Omar , Lamour Julien , Lescuyer Pierre , L’Huillier Arnaud G , Loizeau Andrea , Martinez Chantal , Mermet Stéphanie , Nehme Mayssam , Noël Natacha , Perez-Saez Javier , Perrin Anne , Pittet Didier , Portier Jane , Poulain Géraldine , Pugin Caroline , Pullen Nick , Rinaldi Frederic , Rochat Deborah , Sahyoun Cyril , Sakvarelidze Irine , Samir Khadija , Santa Ramirez Hugo Alejandro , Rizzo Jessica , Schrempft Stephanie , Semaani Claire , Testini Stéphanie , Tisserand Yvain , Urrutia Rivas Deborah , Verolet Charlotte , Villers Jennifer , Violot Guillemette , Vuilleumier Nicolas , Yerly Sabine , Zavlanou Christina 
Published: February 2023

Abstract
Background
The medium-term impact of the COVID-19 pandemic on the wellbeing of children and adolescents remains unclear. More than 2 years into the pandemic, we aimed to quantify the frequency and determinants of having been severely impacted by the COVID-19 pandemic and estimate its impact on health-related quality of life (HRQoL) and mental health.

Methods
Data was drawn from a population-based cohort of children and adolescents, recruited between December 2021 and June 2022, in Geneva, Switzerland. The Coronavirus impact scale was used to assess the multidimensional impact of the pandemic on children through parent’s report. A score higher than one standard deviation above the mean was deemed a severe impact. Parents additionally reported about their offspring HRQoL and mental health with validated scales. Determinants of having been severely impacted were assessed with logistic models, as were the associations between having experienced a severe impact and poor HRQoL or mental health.

Results
Out of 2101 participants aged 2–17, 12.7% had experienced a severe pandemic impact. Having a lasting health condition, a pandemic-related worsening of lifestyle habits or an unfavorable family environment were associated with having been severely impacted by the pandemic, while a previous anti-SARS-CoV-2 infection was not. Participants who had experienced a severe pandemic impact were more likely to present poor HRQoL (aOR = 3.1; 95% CI 2.3–4.4) and poor mental health (aOR = 3.9; 95% CI 2.5–6.2).

Conclusion
The COVID-19 pandemic may have persistent consequences on the wellbeing of children and adolescents, especially among those with health and family vulnerabilities.
Effectiveness and cost-effectiveness of a personalised self-management intervention for living with long COVID: protocol for the LISTEN randomised controlled trial
Authors: Potter Claire , Leggat Fiona , Lowe Rachel , Pallmann Philip , Riaz Muhammad , Barlow Christy , Edwards Adrian , Siriwardena Aloysius Niroshan , Sevdalis Nick , Sewell Bernadette , McRae Jackie , Fish Jessica , de Sousa de Abreu Maria Ines , Jones Fiona , Busse Monica 
Published: February 2023

Abstract
Background
Individuals living with long COVID experience multiple, interacting and fluctuating symptoms which can have a dramatic impact on daily living. The aim of the Long Covid Personalised Self-managemenT support EvaluatioN (LISTEN) trial is to evaluate effects of the LISTEN co-designed self-management support intervention for non-hospitalised people living with long COVID on participation in routine activities, social participation, emotional well-being, quality of life, fatigue, and self-efficacy. Cost-effectiveness will also be evaluated, and a detailed process evaluation carried out to understand how LISTEN is implemented.

Methods
The study is a pragmatic randomised effectiveness and cost-effectiveness trial in which a total of 558 non-hospitalised people with long COVID will be randomised to either the LISTEN intervention or usual care. Recruitment strategies have been developed with input from the LISTEN Patient and Public Involvement and Engagement (PPIE) advisory group and a social enterprise, Diversity and Ability, to ensure inclusivity. Eligible participants can self-refer into the trial via a website or be referred by long COVID services. All participants complete a range of self-reported outcome measures, online, at baseline, 6 weeks, and 3 months post randomisation (the trial primary end point). Those randomised to the LISTEN intervention are offered up to six one-to-one sessions with LISTEN-trained intervention practitioners and given a co-designed digital resource and paper-based book. A detailed process evaluation will be conducted alongside the trial to inform implementation approaches should the LISTEN intervention be found effective and cost-effective.

Discussion
The LISTEN trial is evaluating a co-designed, personalised self-management support intervention (the LISTEN intervention) for non-hospitalised people living with long COVID. The design has incorporated extensive strategies to minimise participant burden and maximise access. Whilst the duration of follow-up is limited, all participants are approached to consent for long-term follow-up (subject to additional funding being secured).

Trial registration
LISTEN ISRCTN36407216. Registered on 27/01/2022.
Autochthonous Onchocerca lupi infection of a domestic dog in Austria
Authors: Unterköfler Maria Sophia , Huck Alexandra , Silbermayr Katja , Fuehrer Hans-Peter 
Published: February 2023

AbstractOnchocerca lupi is an emerging canine ocular pathogen with zoonotic potential. In Europe, known endemic areas are the Iberian Peninsula and Greece, but the parasite has also been found in Romania, Hungary, and Germany. A 5-year-old Irish Wolfhound was presented in August 2021 with ocular discharge. A subconjunctival granulomatous nodule containing several nematode fragments was removed. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I gene confirmed the presence of O. lupi genotype 1. This is the first report of autochthonous O. lupi infection in a dog from Austria.
Graphical Abstract
Tumor stemness score to estimate epithelial-to-mesenchymal transition (EMT) and cancer stem cells (CSCs) characterization and to predict the prognosis and immunotherapy response in bladder urothelial carcinoma
Authors: Zhang Yanlong , Zhang Xin , Huang Xuefeng , Tang Xiaomeng , Zhang Menghan , Li Ziyi , Hu Xiaopeng , Zhang Min , Wang Xi , Yan Yong 
Published: February 2023

Abstract
Background
A growing number of investigations have suggested a close link between cancer stem cells (CSCs), epithelial-to-mesenchymal transition (EMT), and the tumor microenvironment (TME). However, the relationships between these physiological processes in bladder urothelial carcinoma (BLCA) remain unclear.

Methods
We first explored biomarkers of tumor stemness (TS) by single-cell sequencing analysis. Then, subtypes of bladder urothelial carcinoma (BLCA) were identified using clustering analysis based on TS biomarkers. The TS score was constructed using principal component analysis to quantify tumor stemness in BLCA. Then, meta-analysis was performed to measure the hazard ratio of the TS score in BLCA cohorts. Moreover, we evaluated the clinical value of the TS score for predicting the response to tumor immunotherapy using immunotherapy cohorts. Finally, we built an EMT cell model by treating T24 cells with TGF-β and validated the relationship between the TS score and the EMT process in tumors by real-time quantitative PCR, cell invasion assays, and RNA-seq. In total, 3846 BLCA cells, 6 cell lines, 1627 BLCA samples, and 9858 samples from 32 other types of tumors were included in our study.

Results
Three TS clusters and two TS-related gene clusters were identified with differential EMT activity status, CSC features, and TME characteristics in BLCA. Then, a TS scoring system was established with 61 TS-related genes to quantify the TS. The prognostic value of the TS score was then confirmed in multiple independent cohorts. A high TS score was associated with high EMT activity, CSC characteristics, high stromal cell content, high TP53 mutation rate, poor prognosis, and high tumor immunotherapy tolerance. The cell line experiment and RNA-seq further validated that our TS score can reflect the EMT and CSC characterization of tumor cells.

Conclusion
Overall, this research provides a better understanding of tumor invasion and metastasis mechanisms through an analysis of TS patterns with different EMT processes and CSC characteristics. The TS score provides an index for EMT and CSC research and helps clinicians develop treatment plans and predict outcomes for patients.
Book review of “Media culture in nomadic communities” by Allison Hahn
Authors: Waters-Bayer Ann 
Published: February 2023

Book detailsHahn, Allison H., Media culture in nomadic communities. Amsterdam: University of Amsterdam Press B.V.; 2021. 221 pp. ISBN: 978 94 63723022 (hardcover), e-ISBN: 978 90 4855030 2. DOI 10.5117/9789463723022.
Hippo signaling activates hedgehog signaling by Taz-driven Gli3 processing
Authors: Tang Chao , Wang Jirong , Yao Minli , Ji Xing , Shi Wei , Xu Chengyun , Zeng Ling-Hui , Wu Ximei 
Published: February 2023

AbstractThe overlapping roles of Hippo and Hedgehog signaling in biological functions and diseases prompt us to investigate their potential interactions. Activation of Hippo signaling enhances the transcriptional output of Hedgehog signaling, and the role of Hippo signaling in regulating Hedgehog signaling relies on the Hippo pathway key effector, Taz. Interestingly, Taz exhibits a gradient expression across the posterior-to-anterior of limb bud mesoderms, similar to Sonic hedgehog (Shh). Importantly, Taz drives PKA to phosphorylate Gli3, resulting in the Gli3 processing into its repressor and attenuation of Hedgehog signaling in the Shh-independent manner. Specifically, Taz deletion in mouse embryonic limb bud mesenchyme not only enhances the Hedgehog signaling but partially restores the phenotypes from Shh deletion in causing severe defects of anteroposterior patterning and digit number and identity. Together, these results uncover Taz-dependent Gli3 processing as a hitherto uncharacterized mechanism controlling Hedgehog signaling, highlighting its cross-regulation by Hippo signaling.
A smartphone-based zero-effort method for mitigating epidemic propagation
Authors: Wang Qu , Fu Meixia , Wang Jianquan , Sun Lei , Huang Rong , Li Xianda , Jiang Zhuqing 
Published: February 2023

AbstractA large number of epidemics, including COVID-19 and SARS, quickly swept the world and claimed the precious lives of large numbers of people. Due to the concealment and rapid spread of the virus, it is difficult to track down individuals with mild or asymptomatic symptoms with limited human resources. Building a low-cost and real-time epidemic early warning system to identify individuals who have been in contact with infected individuals and determine whether they need to be quarantined is an effective means to mitigate the spread of the epidemic. In this paper, we propose a smartphone-based zero-effort epidemic warning method for mitigating epidemic propagation. Firstly, we recognize epidemic-related voice activity relevant to epidemics spread by hierarchical attention mechanism and temporal convolutional network. Subsequently, we estimate the social distance between users through sensors built-in smartphone. Furthermore, we combine Wi-Fi network logs and social distance to comprehensively judge whether there is spatiotemporal contact between users and determine the duration of contact. Finally, we estimate infection risk based on epidemic-related vocal activity, social distance, and contact time. We conduct a large number of well-designed experiments in typical scenarios to fully verify the proposed method. The proposed method does not rely on any additional infrastructure and historical training data, which is conducive to integration with epidemic prevention and control systems and large-scale applications.
The landscape overview of CD47-based immunotherapy for hematological malignancies
Authors: Yang Hua , Xun Yang , You Hua 
Published: February 2023

AbstractExtensive clinical and experimental evidence suggests that macrophages play a crucial role in cancer immunotherapy. Cluster of differentiation (CD) 47, which is found on both healthy and malignant cells, regulates macrophage-mediated phagocytosis by sending a "don't eat me" signal to the signal regulatory protein alpha (SIRPα) receptor. Increasing evidence demonstrates that blocking CD47 interaction with SIRPα can enhance cancer cell clearance by macrophages. Additionally, inhibition of CD47/SIRPα interaction can increase antigen cross-presentation, leading to T-cell priming and an activated adaptive antitumor immune response. Therefore, inhibiting CD47/SIRPα axis has a significant impact on tumor immunotherapy. Studies on CD47 monoclonal antibodies are at the forefront of research, and impressive results have been obtained. Nevertheless, hematotoxicity, especially anemia, has become the most common adverse effect of the CD47 monoclonal antibody. More specific targeted drugs (i.e., bispecific antibodies, SIRPα/Fc fusion protein antibodies, and small-molecule inhibitors) have been developed to reduce hematotoxicity. Here, we review the present usage of CD47 antagonists for the treatment of lymphomas and hematologic neoplasms from the perspectives of structure, function, and clinical trials, including a comprehensive overview of the drugs in development.