bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global assembly of microbial communities
Authors: Wang Jianing , Pan Zhuo , Yu Jianshui , Zhang Zheng , Li Yue-zhong 
Published: May 2023

ABSTRACT
Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies.

IMPORTANCE
With the development of sequencing technologies, the research topic of microbial ecology has evolved from the analysis of community composition to community assembly, including the relative contribution of deterministic and stochastic processes for the formation and maintenance of community diversity. Many studies have reported the microbial assembly mechanisms in various habitats, but the assembly regularities of global microbial communities remain unknown. In this study, we analyzed the EMP data set using a combined pipeline to explore the assembly mechanisms of global microbial communities, microbial sources to construct communities, core microbes in different environment types, and community-internal factors influencing assembly. The results provide a panoramic picture and rules of global and environment-typical microbial community assemblies, which enhances our understandings of the mechanisms globally controlling community diversity and species coexistence.
Mapping the available evidence on the impact of ingested live microbes on health: a scoping review protocol
Authors: Mukherjee Arghya , Iyer Ajay , Gómez-Sala Beatriz , O’Connor Eibhlis , Kenny John G , Cotter Paul D 
Published: May 2023

IntroductionIt has been hypothesised that the regular consumption of safe, live microbes confers health-promoting attributes, including the prevention of disease. To address this hypothesis, we propose a scoping review approach that will systematically assess the large corpus of relevant literature that is now available on this research topic. This article outlines a protocol for a scoping review of published studies on interventions with live microbes in non-patient populations across eight health categories. The scoping review aims to catalogue types of interventions, measured outcomes, dosages, effectiveness, as well as current research gaps.Methods and analysisThe scoping review will follow the six-staged protocol as proposed by Arksey and O’Malley and will include the following stages: defining the research questions (stage 1); defining the eligibility criteria and finalising search strategy (stage 2); selection of studies based on the eligibility criteria (stage 3); development of a data extraction framework and charting of data (stage 4); aggregation of results and summarisation of findings (stage 5); and the optional consultation with stakeholders (stage 6), which will not be performed.Ethics and disseminationSince the scoping review synthesises information from existing literature, no separate ethical approval is required. The findings of the scoping review will be communicated for publication to an open-access, peer-reviewed scientific journal, presented at relevant conferences, and disseminated at future workshops with all relevant data and documents being available online through the Open Science Framework (https://osf.io/kvhe7).
Experiences of patients and their relatives of postoperative radiological surveillance and surveillance intensity following primary resection of a soft tissue sarcoma and its impact on their quality of life: a systematic review protocol
Authors: Maes Danielle , McMullan Christel , Ford Samuel J , Wilson Roger , Oppong Raymond , Aiyegbusi Olalekan Lee 
Published: May 2023

IntroductionPostoperative radiological surveillance following primary resection of a soft tissue sarcoma (sarcoma of the retroperitoneum, abdomen, pelvis, trunk or extremities) is standard of care in all international high-volume sarcoma centres in the world. The intensity of postoperative surveillance imaging is highly varied and knowledge of the impact of surveillance and surveillance intensity on patients’ quality of life is limited. The aim of this systematic review is to summarise the experiences of patients and their relatives/caregivers of postoperative radiological surveillance following resection of a primary soft tissue sarcoma and its impact on their quality of life.Methods and analysisWe will systematically search MEDLINE, EMBASE, PsycINFO, CINAHL Plus and Epistemonikos. Hand searching of reference lists of included studies will be conducted. Further searches will be performed via Google Scholar, to reveal further studies within unpublished ‘grey’ literature. Two reviewers will independently screen the titles and abstracts following the eligibility criteria. After retrieval of the full text of the selected studies, the methodological quality will be appraised using the Joanna Briggs Institute Critical Appraisal Checklist for Qualitative Research and the Center for Evidence-Based Management checklist for Critical Appraisal of a Cross-Sectional Study. Data on the study population, relevant themes and conclusions will be extracted from the selected papers, and a narrative synthesis will be conducted.Ethics and disseminationThe systematic review does not require ethics approval. The findings of the proposed work will be published in a peer-reviewed journal and disseminated widely to patients, clinicians and allied health professionals through the Sarcoma UK website, the Sarcoma Patient Advocacy Global Network and the Trans-Atlantic Australasian Retroperitoneal Sarcoma Working Group. In addition, the outcomes of this research will be presented at national and international conferences.PROSPERO registration numberCRD42022375118.
Cohort profile: a longitudinal study of HIV infection in the central nervous system with focus on cerebrospinal fluid – the Gothenburg HIV CSF Study Cohort
Authors: Hagberg Lars , Gisslén Magnus 
Published: May 2023

PurposeIn order to enable long-term follow-up of the natural course of HIV infection in the central nervous system, a longitudinal cohort study with repeated cerebrospinal fluid (CSF) analyses at intervals over time was initiated in 1985. When antiretrovirals against HIV were introduced in the late 1980s, short-term and long-term effects of various antiretroviral treatment (ART) regimens were added to the study.ParticipantsAll adult people living with HIV (PLWH) who were diagnosed at or referred to the Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden were asked to participate in the Gothenburg HIV CSF Study Cohort. PLWH with neurological symptoms or other clinical symptoms of HIV, as well as those with no symptoms of HIV infection, were included. Most participants were asymptomatic, which distinguishes this cohort from most other international HIV CSF studies. In addition, HIV-negative controls were recruited. These included people on HIV pre-exposure prophylaxis who served as lifestyle-matched controls to HIV-infected men who have sex with men. Since lumbar puncture (LP) is an invasive procedure, some PLHW only consented to participate in one examination. Furthermore, at the beginning of the study, several participants were lost to follow-up having died from AIDS. Of 662 PLWH where an initial LP was done, 415 agreed to continue with follow-up. Among the 415, 56 only gave permission to be followed with LP for less than 1 year, mainly to analyse the short-term effect of ART. The remaining 359 PLWH were followed up with repeated LP for periods ranging from >1 to 30 years. This group was defined as the ‘longitudinal cohort’. So far, on 7 April 2022, 2650 LP and samplings of paired CSF/blood had been performed, providing a unique biobank.Findings to dateA general finding during the 37-year study period was that HIV infection in the central nervous system, as mirrored by CSF findings, appears early in the infectious course of the disease and progresses slowly in the vast majority of untreated PLWH. Combination ART has been highly effective in reducing CSF viral counts, inflammation and markers of neural damage. Minor CSF signs of long-term sequels or residual inflammatory activity and CSF escape (viral CSF blips) have been observed during follow-up. The future course of these changes and their clinical impact require further studies.Future plansPLWH today have a life expectancy close to that of non-infected people. Therefore, our cohort provides a unique opportunity to study the long-term effects of HIV infection in the central nervous system and the impact of ART and is an ongoing study.
ADAMS project: a genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis based in the UK
Authors: Jacobs Benjamin M , Schalk Luisa , Dunne Angie , Scalfari Antonio , Nandoskar Ashwini , Gran Bruno , Mein Charles A , Sellers Charlotte , Spilker Cord , Rog David , Visentin Elisa , Bezzina Elizabeth Lindsey , Uzochukwu Emeka , Tallantyre Emma , Wozniak Eva , Sacre Eve , Hassan-Smith Ghaniah , Ford Helen L , Harris Jade , Bradley Joan , Breedon Joshua , Brooke Judith , Kreft Karim L , Tuite Dalton Katherine , George Katila , Papachatzaki Maria , O'Malley Martin , Peter Michelle , Mattoscio Miriam , Rhule Neisha , Evangelou Nikos , Vinod Nimisha , Quinn Outi , Shamji Ramya , Kaimal Rashmi , Boulton Rebecca , Tanveer Riffat , Middleton Rod , Murray Roxanne , Bellfield Ruth , Hoque Sadid , Patel Shakeelah , Raj Sonia , Gumus Stephanie , Mitchell Stephanie , Sawcer Stephen , Arun Tarunya , Pogreban Tatiana , Brown Terri-Louise , Begum Thamanna , Antoine Veronica , Rashid Waqar , Noyce Alastair J , Silber Eli , Morris Huw , Giovannoni Gavin , Dobson Ruth 
Published: May 2023

PurposeGenetic studies of multiple sclerosis (MS) susceptibility and severity have focused on populations of European ancestry. Studying MS genetics in other ancestral groups is necessary to determine the generalisability of these findings. The genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis (ADAMS) project aims to gather genetic and phenotypic data on a large cohort of ancestrally-diverse individuals with MS living in the UK.ParticipantsAdults with self-reported MS from diverse ancestral backgrounds. Recruitment is via clinical sites, online (https://app.mantal.co.uk/adams) or the UK MS Register. We are collecting demographic and phenotypic data using a baseline questionnaire and subsequent healthcare record linkage. We are collecting DNA from participants using saliva kits (Oragene-600) and genotyping using the Illumina Global Screening Array V.3.Findings to dateAs of 3 January 2023, we have recruited 682 participants (n=446 online, n=55 via sites, n=181 via the UK MS Register). Of this initial cohort, 71.2% of participants are female, with a median age of 44.9 years at recruitment. Over 60% of the cohort are non-white British, with 23.5% identifying as Asian or Asian British, 16.2% as Black, African, Caribbean or Black British and 20.9% identifying as having mixed or other backgrounds. The median age at first symptom is 28 years, and median age at diagnosis is 32 years. 76.8% have relapsing–remitting MS, and 13.5% have secondary progressive MS.Future plansRecruitment will continue over the next 10 years. Genotyping and genetic data quality control are ongoing. Within the next 3 years, we aim to perform initial genetic analyses of susceptibility and severity with a view to replicating the findings from European-ancestry studies. In the long term, genetic data will be combined with other datasets to further cross-ancestry genetic discoveries.
Epidemiological characteristics of pulmonary tuberculosis among students in Guizhou, China: a retrospective study from 2010 to 2020
Authors: Zhou Jian , Ma Xiaoxue , Lu Ting-Jia , Zhuang Yan , Li Jin-Lan , Chen Huijuan 
Published: May 2023

ObjectiveWe described epidemiological characteristics of pulmonary tuberculosis (PTB) among students and evaluated susceptible populations and areas in Guizhou province and also to provide scientific suggestions for prevention and control.SettingGuizhou, China.DesignThis is a retrospective epidemiological study on PTB in students.MethodsData are from the China Information System for Disease Control and Prevention. We collected all PTB cases among the student population from 2010 to 2020 in Guizhou. Incidence, composition ratio and hotspot analysis were used to describe epidemiological and some clinical characteristics.ResultsA total of 37 147 new student PTB cases were registered among the population aged 5–30 years during 2010–2020. The proportions of men and women were 53.71% and 46.29%, respectively. Cases aged 15–19 years dominated (63.91%), and the proportion of ethnic groups was increasing during the period. Generally, the raw annual incidence of PTB among the population was increasing from 32.585 per 100 000 persons in 2010 to 48.872 per 100 000 persons in 2020 (c2trend=1283.230, p<0.001). March and April were the peak months of a year, and cases were clearly grouped in Bijie city. New cases were mainly identified via physical examination, and cases from active screening were still low (0.76%). Additionally, secondary PTB accounted for 93.68%, positive rate of pathogen was only 23.06%, and the recovery rate was 94.60%.ConclusionsThe population aged 15–19 years is the vulnerable population, and Bijie city is the susceptible area. BCG vaccination and promotion for active screening should be the priority of futural PTB prevention and control. Tuberculosis laboratory capacity should be improved.
Evaluating an audit and feedback intervention for reducing overuse of pathology test requesting by Australian general practitioners: protocol for a factorial cluster randomised controlled trial
Authors: O'Connor Denise A , Glasziou Paul , Schram Dina , Gorelik Alexandra , Elwick Amelia , McCaffery Kirsten , Thomas Rae , Buchbinder Rachelle 
Published: May 2023

IntroductionConsistent evidence shows pathology services are overused worldwide and that about one-third of testing is unnecessary. Audit and feedback (AF) is effective for improving care but few trials evaluating AF to reduce pathology test requesting in primary care have been conducted. The aim of this trial is to estimate the effectiveness of AF for reducing requests for commonly overused pathology test combinations by high-requesting Australian general practitioners (GPs) compared with no intervention control. A secondary aim is to evaluate which forms of AF are most effective.Methods and analysisThis is a factorial cluster randomised trial conducted in Australian general practice. It uses routinely collected Medicare Benefits Schedule data to identify the study population, apply eligibility criteria, generate the interventions and analyse outcomes. On 12 May 2022, all eligible GPs were simultaneously randomised to either no intervention control or to one of eight intervention groups. GPs allocated to an intervention group received individualised AF on their rate of requesting of pathology test combinations compared with their GP peers. Three separate elements of the AF intervention will be evaluated when outcome data become available on 11 August 2023: (1) invitation to participate in continuing professional development-accredited education on appropriate pathology requesting, (2) provision of cost information on pathology test combinations and (3) format of feedback. The primary outcome is the overall rate of requesting of any of the displayed combinations of pathology tests of GPs over 6 months following intervention delivery. With 3371 clusters, assuming no interaction and similar effects for each intervention, we anticipate over 95% power to detect a difference of 4.4 requests in the mean rate of pathology test combination requests between the control and intervention groups.Ethics and disseminationEthics approval was received from the Bond University Human Research Ethics Committee (#JH03507; approved 30 November 2021). The results of this study will be published in a peer-reviewed journal and presented at conferences. Reporting will adhere to Consolidated Standards of Reporting Trials.Trial registration numberACTRN12622000566730.
Voice of persons with a life-limiting illness in conversation with healthcare professionals: systematic review and meta-synthesis
Authors: Sikhosana Nqobile , Whitehead Dean , Moxham Lorna , Karacsony Sara , Namasivayam Pathmavathy , Fernandez Ritin 
Published: May 2023

BackgroundHealthcare organisations are transforming the way care is delivered to people with a life-limiting illness with an increased focus on recognising the voice of the persons experiencing the illness and putting them in the centre of decision-making. However, the clinical practice remains largely based on the views of healthcare professionals and families or carers of the person with the illness.ObjectivesTo synthesise the best available evidence on the experience of persons living with a life-limiting illness about expressing their voice during communication with healthcare professionals.DesignSystematic review and meta-synthesis.Data sourcesCINAHL, Embase, Medline, PsycINFO, ProQuest Dissertations and Theses.Review methodsA structured search was conducted to identify qualitative studies that reported on the experience of persons living with a life-limiting illness. The methodological quality of included studies was assessed using the Joanna Briggs Institute (JBI) critical appraisal checklists. The review was undertaken using the JBI and PRISMA guidelines.ResultsThe expression of the voice of persons living with a life-limiting illness is influenced by: (1) the uncertain future surrounding illness trajectory and prognosis; (2) what is known from experience, media, family and friends; (3) emotional and psychological factors and (4) control and personal autonomy.ConclusionsIn the early stages of a life-limiting illness, the voice of those experiencing the disease is not always audible. Instead, this voice is potentially present but silent and carried and promoted within healthcare professionals’ values of accountability, professionalism, respect, altruism, equality, integrity and morality.
Status report of the n_TOF facility after the 2nd CERN long shutdown period
Authors: Patronis N. , Mengoni A. , Goula S. , Aberle O. , Alcayne V. , Altieri S. , Amaducci S. , Andrzejewski J. , Babiano-Suarez V. , Bacak M. , Balibrea Correa J. , Beltrami C. , Bennett S. , Bernardes A. P. , Berthoumieux E. , Beyer R. , Boromiza M. , Bosnar D. , Caamaño M. , Calviño F. , Calviani M. , Cano-Ott D. , Casanovas A. , Castelluccio D. M. , Cerutti F. , Cescutti G. , Chasapoglou S. , Chiaveri E. , Colombetti P. , Colonna N. , Console Camprini P. , Cortés G. , Cortés-Giraldo M. A. , Cosentino L. , Cristallo S. , Dellmann S. , Di Castro M. , Di Maria S. , Diakaki M. , Dietz M. , Domingo-Pardo C. , Dressler R. , Dupont E. , Durán I. , Eleme Z. , Fargier S. , Fernández B. , Fernández-Domínguez B. , Finocchiaro P. , Fiore S. , García-Infantes F. , Gawlik-Ramiega A. , Gervino G. , Gilardoni S. , González-Romero E. , Guerrero C. , Gunsing F. , Gustavino C. , Heyse J. , Hillman W. , Jenkins D. G. , Jericha E. , Junghans A. , Kadi Y. , Kaperoni K. , Kaur G. , Kimura A. , Knapová I. , Kokkoris M. , Krtička M. , Kyritsis N. , Ladarescu I. , Lederer-Woods C. , Lerendegui-Marco J. , Lerner G. , Manna A. , Martínez T. , Masi A. , Massimi C. , Mastinu P. , Mastromarco M. , Maugeri E. A. , Mazzone A. , Mendoza E. , Michalopoulou V. , Milazzo P. M. , Mucciola R. , Murtas F. , Musacchio-Gonzalez E. , Musumarra A. , Negret A. , Pérez de Rada A. , Pérez-Maroto P. , Pavón-Rodríguez J. A. , Pellegriti M. G. , Perkowski J. , Petrone C. , Pirovano E. , Plaza del Olmo J. , Pomp S. , Porras I. , Praena J. , Quesada J. M. , Reifarth R. , Rochman D. , Romanets Y. , Rubbia C. , Sánchez-Caballero A. , Sabaté-Gilarte M. , Schillebeeckx P. , Schumann D. , Sekhar A. , Smith A. G. , Sosnin N. V. , Stamati M. E. , Sturniolo A. , Tagliente G. , Tarifeño-Saldivia A. , Tarrío D. , Torres-Sánchez P. , Vagena E. , Valenta S. , Variale V. , Vaz P. , Vecchio G. , Vescovi D. , Vlachoudis V. , Vlastou R. , Wallner A. , Woods P. J. , Zarrella R. , Zugec P. 
Published: May 2023

AbstractDuring the second long shutdown period of the CERN accelerator complex (LS2, 2019-2021), several upgrade activities took place at the n_TOF facility. The most important have been the replacement of the spallation target with a next generation nitrogen-cooled lead target. Additionally, a new experimental area, at a very short distance from the target assembly (the NEAR Station) was established. In this paper, the core commissioning actions of the new installations are described. The improvement in the n_TOF infrastructure was accompanied by several detector development projects. All these upgrade actions are discussed, focusing mostly on the future perspectives of the n_TOF facility. Furthermore, some indicative current and future measurements are briefly reported.
Metformin Reprograms Tryptophan Metabolism to Stimulate CD8+ T-cell Function in Colorectal Cancer
Authors: Huang Xiaowen , Sun Tiantian , Wang Jilin , Hong Xialu , Chen Huimin , Yan Tingting , Zhou Chengbei , Sun Danfeng , Yang Chen , Yu TaChung , Su Wenyu , Du Wan , Xiong Hua 
Published: May 2023

Abstract

Colorectal carcinogenesis coincides with immune cell dysfunction. Metformin has been reported to play a role in stimulating antitumor immunity, suggesting it could be used to overcome immunosuppression in colorectal cancer. Herein, using single-cell RNA sequencing (scRNA-seq), we showed that metformin remodels the immune landscape of colorectal cancer. In particular, metformin treatment expanded the proportion of CD8+ T cells and potentiated their function. Analysis of the metabolic activities of cells in the colorectal cancer tumor microenvironment (TME) at a single-cell resolution demonstrated that metformin reprogrammed tryptophan metabolism, which was reduced in colorectal cancer cells and increased in CD8+ T cells. Untreated colorectal cancer cells outcompeted CD8+ T cells for tryptophan, leading to impaired CD8+ T-cell function. Metformin in turn reduced tryptophan uptake by colorectal cancer cells, thereby restoring tryptophan availability for CD8+ T cells and increasing their cytotoxicity. Metformin inhibited tryptophan uptake in colorectal cancer cells by downregulating MYC, which led to a reduction in the tryptophan transporter SLC7A5. This work highlights metformin as an essential regulator of T-cell antitumor immunity by reprogramming tryptophan metabolism, suggesting it could be a potential immunotherapeutic strategy for treating colorectal cancer.

Significance:
Analysis of the impact of metformin on the colorectal cancer immunometabolic landscape at a single-cell resolution shows that metformin alters cancer cell tryptophan metabolism to stimulate CD8+ T-cell antitumor activity.