bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genome analysis unravels pathogenicity of Xanthomonas albilineans causing sugarcane leaf scald disease
Authors: Li MeiLin , Bao YiXue , Li YiSha , Akbar Sehrish , Wu GuangYue , Du JinXia , Wen Ronghui , Chen Baoshan , Zhang MuQing 
Published: September 2022

AbstractBackgroundXanthomonasis a genus of gram-negative bacterium containing more than 35 species. Among these pathogenic species,Xanthomonas albilineans(Xal) is of global interest, responsible for leaf scald disease in sugarcane. Another notableXanthomonasspecies isXanthomonas sachari(Xsa), a sugarcane-associated agent of chlorotic streak disease.ResultThe virulence of 24Xanthomonasstrains was evaluated by disease index (DI) and Area Under Disease Progress Curve (AUDPC) in the susceptible inoculated plants (GT 46) and clustered into three groups of five highly potent, seven mild virulent, and twelve weak virulent strains. The highly potent strain (X. albilineans,XalJG43) and its weak virulent related strain (X. sacchari,XsaDD13) were sequenced, assembled, and annotated in the circular genomes. The genomic size of JG43 was smaller than that of DD13. Both strains (JG43 and DD13) lacked a Type III secretory system (T3SS) and T6SS. However, JG43 possessed Salmonella pathogenicity island-1 (SPI-1). More pathogen-host interaction (PHI) genes and virulent factors in 17 genomic islands (GIs) were detected in JG43, among which six were related to pathogenicity. Albicidin and a two-component system associated with virulence were also detected in JG43. Furthermore, 23Xanthomonasstrains were sequenced and classified into three categories based on Single Nucleotide Polymorphism (SNP) mutation loci and pathogenicity, using JG43 as a reference genome. Transitions were dominant SNP mutations, while structural variation (SV) is frequent intrachromosomal rearrangement (ITX). Two essential genes (rpfC/rpfG) of the two-component system and another gene related to SNP were mutated to understand their virulence effect. The mutation ofrpfGresulted in a decrease in pathogenicity.ConclusionThese findings revealed virulence of 24Xanthomonasstrains and variations by 23Xanthomonasstrains. We sequenced, assembled, and annotated the circular genomes ofXalJG43 andXsaDD13, identifying diversity detected by pathogenic factors and systems. Furthermore, complete genomic sequences and sequenced data will provide a theoretical basis for identifying pathogenic factors responsible for sugarcane leaf scald disease.
Gentamicin promoted the production of CD4+CD25+ Tregs via the STAT5 signaling pathway in mice sepsis
Authors: Li Jinfeng , Xu Fengdan , Li Song , Xie Mingyu , Li Ning 
Published: September 2022

Abstract
Background
Increasing studies have reported that gentamicin (GNT) plays an essential role in sepsis; however, its underlying mechanism is still unclear. In this study, we investigated the mechanism of GNT in sepsis.

Results
We observed that GNT enhanced survival and alleviated inflammatory injuries of the lungs, liver, kidneys, and intestines in mice with sepsis. Furthermore, regulatory T cells (Tregs) showed enhanced inhibitory function, and pro-inflammatory cytokines IL-1β, TNF-α, and IL-2 and anti-inflammatory cytokine IL-10 showed decreased and increased peritoneal fluid levels, respectively, after treatment with GNT. GNT showed enhanced phosphorylation of signal transducer and activator of transcription 5 (p-STAT5) in Tregs in vivo and in vitro. The STAT5 inhibitor restrained the increased functional changes of Tregs and reduced inflammatory responses induced by GNT in vitro. Moreover, the STAT5 inhibitor reversed GNT-mediated impacts on survival and inflammation, and the percentage, apoptosis, and phenotypic and functional changes of Tregs in neonatal sepsis.

Conclusions
Our study revealed that GNT regulates the function of Tregs via the STAT5 signaling pathway, alleviating inflammatory injuries, and provides novel evidence in the treatment of neonatal sepsis.
Availability of and factors related to interventional procedures for refractory pain in patients with cancer: a nationwide survey
Authors: Uehara Yuko , Matsumoto Yoshihisa , Kosugi Toshifumi , Sone Miyuki , Nakamura Naoki , Mizushima Akio , Miyashita Mitsunori , Morita Tatsuya , Yamaguchi Takuhiro , Satomi Eriko 
Published: September 2022

Abstract
Background
Cancer pain may be refractory to standard pharmacological treatment. Interventional procedures are important for quality of analgesia. The aim of the present study was to clarify the availability of four interventional procedures (celiac plexus neurolysis/splanchnic nerve neurolysis, phenol saddle block, epidural analgesia, and intrathecal analgesia), the number of procedures performed by specialists, and their associated factors. In addition, we aimed to establish how familiar home hospice physicians and oncologists are with the different interventional procedures available to manage cancer pain.

Methods
A cross-sectional survey using a self-administered questionnaire was conducted. Subjects were certified pain specialists, interventional radiologists, home hospice physicians, and clinical oncologists.

Results
The numbers of valid responses/mails were 545/1,112 for pain specialists, 554/1,087 for interventional radiology specialists, 144/308 for home hospice physicians, and 412/800 for oncologists. Among pain specialists, depending on intervention, 40.9-75.2% indicated that they perform each procedure by themselves, and 47.5-79.8% had not performed any of the procedures in the past 3 years. Pain specialists had performed the four procedures 4,591 times in the past 3 years. Among interventional radiology specialists, 18.1% indicated that they conduct celiac plexus neurolysis/splanchnic nerve neurolysis by themselves. Interventional radiology specialists had performed celiac plexus neurolysis/splanchnic nerve neurolysis 202 times in the past 3 years. Multivariate analysis revealed that the number of patients seen for cancer pain and the perceived difficulty in gaining experience correlated with the implementation of procedures among pain specialists. Among home hospice physicians and oncologists, depending on intervention, 3.5-27.1% responded that they were unfamiliar with each procedure.

Conclusions
Although pain specialists responded that the implementation of each intervention was possible, the actual number of the interventions used was limited. As interventional procedures are well known, it is important to take measures to ensure that pain specialists and interventional radiology physicians are sufficiently utilized to manage refractory cancer pain.
A pyroptosis-associated signature plays a role in prognosis prediction in clear cell renal cell carcinoma
Authors: Li Zhiyuan , Xia Zhinan , Yu Yipeng , Cai Licheng , Jian Wengang , Wang Tengda , Xue Wei , Wang Xingyuan , Wang Bowen , Zhang Peng , Yao Wenhao , Zhang Cheng , Wang Chunyang 
Published: September 2022

Abstract
Background
Approximately 90% of renal malignancies are RCCs (renal cell carcinomas), and the primary subtype in histology is ccRCC (clear cell RCC). In recent years, pyroptosis has been considered a kind of inflammation-related programmed cell death that participates in the invasion, metastasis, and proliferation of tumour cells, thereby influencing tumour prognosis. Nonetheless, the expression level of pyroptosis-associated genes in RCCs and their relationship with prognosis remain obscure.

Results
In our research, 44 regulators of pyroptosis that were differentially expressed between normal kidney and ccRCC tissues were identified. ccRCC cases were categorized into 2 subgroups according to prognostic-related DEGs (differentially expressed genes), and there was a significant difference in OS (overall survival) between them. The prognostic value of pyroptosis-associated genes was assessed as a signature based on a cohort from TCGA (The Cancer Genome Atlas). Following Cox regression with DEGs and LASSO (least absolute shrinkage and selection operator), a 6-gene signature was established, and all ccRCC cases in the cohort from TCGA were categorized into an LR (low-risk) or HR (high-risk) group (P < 0.001). In combination with clinical features, risk scores were considered a predictive factor of OS in ccRCC. KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses suggest increased immunity and enrichment of genes related to immunity in the HR group.

Conclusions
Our findings indicate that genes related to pyroptosis have an important role in tumour immunity and may be used to predict the prognosis of ccRCC.
Mitochondrial oxidative stress in the tumor microenvironment and cancer immunoescape: foe or friend?
Authors: Kuo Cheng-Liang , Ponneri Babuharisankar Ananth , Lin Ying-Chen , Lien Hui-Wen , Lo Yu Kang , Chou Han-Yu , Tangeda Vidhya , Cheng Li-Chun , Cheng An Ning , Lee Alan Yueh-Luen 
Published: September 2022

AbstractThe major concept of "oxidative stress" is an excess elevated level of reactive oxygen species (ROS) which are generated from vigorous metabolism and consumption of oxygen. The precise harmonization of oxidative stresses between mitochondria and other organelles in the cell is absolutely vital to cell survival. Under oxidative stress, ROS produced from mitochondria and are the major mediator for tumorigenesis in different aspects, such as proliferation, migration/invasion, angiogenesis, inflammation, and immunoescape to allow cancer cells to adapt to the rigorous environment. Accordingly, the dynamic balance of oxidative stresses not only orchestrate complex cell signaling events in cancer cells but also affect other components in the tumor microenvironment (TME). Immune cells, such as M2 macrophages, dendritic cells, and T cells are the major components of the immunosuppressive TME from the ROS-induced inflammation. Based on this notion, numerous strategies to mitigate oxidative stresses in tumors have been tested for cancer prevention or therapies; however, these manipulations are devised from different sources and mechanisms without established effectiveness. Herein, we integrate current progress regarding the impact of mitochondrial ROS in the TME, not only in cancer cells but also in immune cells, and discuss the combination of emerging ROS-modulating strategies with immunotherapies to achieve antitumor effects.
Repellent activity against Anopheles gambiae of the leaves of nesting trees in the Sebitoli chimpanzee community of Kibale National Park, Uganda
Authors: Lacroux Camille , Pouydebat Emmanuelle , Rossignol Marie , Durand Sophie , Aleeje Alfred , Asalu Edward , Chandre Fabrice , Krief Sabrina 
Published: September 2022

AbstractBackgroundEvery evening, chimpanzees (Pan troglodytes) build a sleeping platform so called “nest” by intertwining branches of tree. Most of chimpanzees’ communities studied have a preference for tree species in which they nest. As female mosquitoes are feeding on the blood of their host at nighttime, chimpanzees may prevent being disturbed and bitten by mosquitoes by selecting tree species having properties to repel them.MethodsTo test the hypothesis that chimpanzees choose tree species for their aromatic properties, data related to 1,081 nesting trees built between 2017 and 2019 in the Sebitoli community of Kibale National Park (Uganda) were analysed. The 10 most used trees were compared to the 10 most common trees in the habitat that were not preferred for nesting. Leaves from the 20 trees species were collected and hydro-distillated to obtain essential oils and one of the by-products for behavioural bioassays against females of the African mosquito,Anopheles gambiae.ResultsSebitoli chimpanzees showed tree preferences: 10 species correspond to more than 80% of the nesting trees. Out of the essential oil obtained from the 10 nesting trees, 7 extracts for at least one concentration tested showed spatial repellency, 7 were irritant by contact and none were toxic. In the other hand, for the abundant trees in their habitat not used by chimpanzees, only 3 were repellent and 5 irritants.Discussion and conclusionThis study contributes to evidence that chimpanzees, to avoid annoying mosquitoes, may select their nesting trees according to their repellent properties (linked to chemical parameters), a potential inspiration for human health.
Employing the equity lens to understand multisectoral partnerships: lessons learned from a mixed-method study in Canada
Authors: Gupta Suvadra Datta , Pisolkar Vaidehi , Alhassan Jacob Albin Korem , Judge Allap , Engler-Stringer Rachel , Gauvin Lise , Muhajarine Nazeem 
Published: September 2022

Abstract
Background
Multisectoral approaches to health are collaborations between stakeholders across multiple sectors, usually formed to address issues that affect health but go beyond the purview of one particular sector. The significance of multisectoral partnerships to attain health equity has been widely acknowledged. However, the extent which equity can be attained depends upon the perceptions of various stakeholders. We examine how multisectoral partnerships promoting healthy eating and active living conceptualized and employed an equity lens in their work.

Method
This study is part of a larger pan-Canadian mixed-method research and knowledge sharing program entitled MUSE (Multisectoral Urban Systems for health and Equity in Canadian cities). Data collected from both quantitative and qualitative sources for two sites of the MUSE project-Saskatoon and Toronto were analyzed. In the qualitative part, 30 semi-structured key informant interviews were conducted with key stakeholders from six different multisectoral partnerships based in Saskatoon and Toronto. Data were analyzed in an inductive way. In the quantitative part, a survey with 37 representatives of stakeholder organizations was carried out. Simple descriptive statistics (means and percentages) were used to observe the distribution of data and to complement the qualitative analysis.

Results
Equity was not a central component in program design although participants addressing equity, did so by discussing accessibility. How much consideration was given to equity varied as a function of the type of partnership. Most participants emphasized geographical accessibility but a few mentioned financial accessibility. Collaborative leadership style facilitated a participatory decision-making process, and thereby upholding equity in the partnership decision-making process. Communication, networking, and negotiation skills were found to be core competencies of a leader that contributed in upholding equity in partnership dynamics. The study also showed some challenges to embed equity in partnership works, such as the lack of comprehensive understanding of population health and its equity tenet.

Conclusions
Findings indicate that multisectoral partnerships aimed at promoting healthy eating and physical activity experience several challenges to attain equity within the partnership as well as in the partnership-based works aimed at reducing health equity in populations. Factors identified can support decision makers commit to and work to attaining equity within their partnerships as well as in the partnership-based work in the community and beyond.
Long noncoding RNA TUG1 induces angiogenesis of endothelial progenitor cells and dissolution of deep vein thrombosis
Authors: Feng Yaping , Lei Bo , Zhang Huan , Niu Luyuan , Li Xiangtao , Luo Xiaoyun , Zhang Fuxian 
Published: September 2022

Abstract
Objective
Long non-coding RNA (lncRNA) essentially controls many physiological and pathological processes of deep vein thrombosis (DVT). Based on that, lncRNA taurine upregulated gene 1 (TUG1)-involved angiogenesis of endothelial progenitor cells (EPCs) and dissolution of DVT was explored.

Methods
In the in-vitro experiments, EPCs were engineered with mimic, inhibitor, siRNA, and plasmid, after which tube formation, proliferation, migration, and apoptosis were checked. In the in-vivo experiments, a DVT mouse model was established. Before the DVT operation, the mice were injected with agomir, antagomir, siRNA, and plasmid. Subsequently, thrombosis and damage to the femoral vein were pathologically evaluated. TUG1, miR-92a-3p, and 3-Hydroxy-3-methylglutaryl coenzyme A reductase (Hmgcr) expression in the femoral vein was tested. The relationship between TUG1, miR-92a-3p, and Hmgcr was validated.

Results
DVT mice showed suppressed TUG1 and Hmgcr expression, and elevated miR-92a-3p expression. In EPCs, TUG1 overexpression or miR-92a-3p inhibition promoted cellular angiogenesis, whereas Hmgcr silencing blocked cellular angiogenesis. In DVT mice, elevated TUG1 or inhibited miR-92a-3p suppressed thrombosis and damage to the femoral vein whilst Hmgcr knockdown acted oppositely. In both cellular and animal models, TUG1 overexpression-induced effects could be mitigated by miR-92a-3p up-regulation. Mechanically, TUG1 interacted with miR-92a-3p to regulate Hmgcr expression.

Conclusion
Evidently, TUG1 promotes the angiogenesis of EPCs and dissolution of DVT via the interplay with miR-92a-3p and Hmgcr.
Can clinician champions reduce potentially inappropriate medications in people living with dementia? Study protocol for a cluster randomized trial
Authors: Parchman Michael L. , Perloff Jennifer , Ritter Grant 
Published: September 2022

Abstract
Background
For people living with dementia (PLWD) the overuse of potentially inappropriate medications (PIMs) remains a persistent problem. De-prescribing trials in the elderly have mixed results. Clinician champions may be uniquely suited to lead efforts to address this challenge. Here we describe the study protocol for a 24-month embedded pragmatic cluster-randomized clinical trial within two accountable care organizations (ACOs) of such a clinician champion intervention. The specific aims are to (1) assess the effectiveness of a clinician champion on de-implementing PIMs in PLWD, (2) determine if the intervention is associated with a reduction in emergency department (ED) visits and hospitalizations attributed to a fall, and (3) examine five implementation outcomes: appropriateness, feasibility, fidelity, penetration, and equity.

Methods/design
Two ACOs agreed to participate: United States Medical Management (USMM) and Oschner Health System. The unit of randomization will be the primary care clinic. A clinician champion will be recruited from each of the intervention clinics to participate in a 6-month training program and then work with clinicians and staff in their clinic for 12 months to reduce the use of PIMs in their PLWD population. For aims 1 and 2, Medicare claims data will be used to assess outcomes. The outcome for aim #1 will be medication possession rates per quarter, for the three therapeutic classes of PIMs among patients with dementia in intervention clinics versus control clinics. For aim #2, we will assess the incidence of falls using a previously validated algorithm. For both aims 1 and 2, we will construct hierarchical models with time period observations nested within patient using generalized estimating equations (GEE) with robust standard errors. The key variable of interest will be the treatment indicator assigned based on practice. For aim #3, we will conduct qualitative thematic analysis of documentation by the clinician champions in their project workbooks to evaluate the five implementation outcomes.

Discussion
This embedded pragmatic trial will add to our existing knowledge regarding the effectiveness of a clinician champion strategy to de-prescribe potentially inappropriate medication among patients with dementia as well as its appropriateness, feasibility, fidelity, penetration, and equity.

Trial registration
Clinicaltrials.govNCT05359679, Registered May 4, 2022
The SCRIPT trial: study protocol for a randomised controlled trial of a polygenic risk score to tailor colorectal cancer screening in primary care
Authors: Saya Sibel , Boyd Lucy , Chondros Patty , McNamara Mairead , King Michelle , Milton Shakira , Lourenco Richard De Abreu , Clark Malcolm , Fishman George , Marker Julie , Ostroff Cheri , Allman Richard , Walter Fiona M. , Buchanan Daniel , Winship Ingrid , McIntosh Jennifer , Macrae Finlay , Jenkins Mark , Emery Jon 
Published: September 2022

Abstract
Background
Polygenic risk scores (PRSs) can predict the risk of colorectal cancer (CRC) and target screening more precisely than current guidelines using age and family history alone. Primary care, as a far-reaching point of healthcare and routine provider of cancer screening and risk information, may be an ideal location for their widespread implementation.

Methods
This trial aims to determine whether the SCRIPT intervention results in more risk-appropriate CRC screening after 12 months in individuals attending general practice, compared with standard cancer risk reduction information. The SCRIPT intervention consists of a CRC PRS, tailored risk-specific screening recommendations and a risk report for participants and their GP, delivered in general practice. Patients aged between 45 and 70 inclusive, attending their GP, will be approached for participation. For those over 50, only those overdue for CRC screening will be eligible to participate. Two hundred and seventy-four participants will be randomised to the intervention or control arms, stratified by general practice, using a computer-generated allocation sequence. The primary outcome is risk-appropriate CRC screening after 12 months. For those in the intervention arm, risk-appropriate screening is defined using PRS-derived risk; for those in the control arm, it is defined using family history and national screening guidelines. Timing, type and results of the previous screening are considered in both arms. Objective health service data will capture screening behaviour. Secondary outcomes include cancer-specific worry, risk perception, predictors of CRC screening behaviour, screening intentions and health service use at 1, 6 and 12 months post-intervention delivery.

Discussion
This trial aims to determine whether a PRS-derived personalised CRC risk estimate delivered in primary care increases risk-appropriate CRC screening. A future population risk-stratified CRC screening programme could incorporate risk assessment within primary care while encouraging adherence to targeted screening recommendations.

Trial registration
Australian and New Zealand Clinical Trial Registry ACTRN12621000092897p. Registered on 1 February 2021.