bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete, circular genome sequence of a
Bosea
sp
.
isolate from soil
Authors: Alvarez-Arevalo Maria , Sterndorff Eva Baggesgaard , Faurdal David , Mourched Anna-Sophie , Charusanti Pep , Jørgensen Tue Sparholt , Weber Tilmann 
Published: August 2023

ABSTRACT

Here, we report the complete, circular genome sequence of a potential novel species from the underexplored Alphaproteobacterial genus
Bosea. Bosea
sp. NBC_00550 was isolated from a soil sample collected in Lyngby, Denmark. We explore the biosynthetic potential of
Bosea
sp. NBC_00550 and compare it with that of other
Bosea
species.
SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing
Authors: Mehta Priyanka , Chattopadhyay Partha , Ravi Varsha , Tarai Bansidhar , Budhiraja Sandeep , Pandey Rajesh 
Published: August 2023

ABSTRACT
Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism.

IMPORTANCE
The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.
Evolution of the Victoria Pipe Ultramafic Alkaline Melt (Anabar Region, Siberian Craton): Melt Inclusion within Olivine and Groundmass Minerals
Authors: Kargin A. V. , Prokopyev I. R. , Starikova A. E. , Kamenetsky V. S. , Golubeva Yu. Yu. 
Published: August 2023

Abstract
The results of studying primary and secondary melt inclusions within olivine macrocrysts and groundmass minerals from monticellite–nepheline damtjernites of the Victoria pipe (Anabar diamondiferous province, Siberia craton) are presented. They were used to reconstruct the evolution of the ultramafic alkaline melt during the formation of the pipe. It is shown that the primary damtjernite melts were K–Na bearing carbonate–silicate in composition. Here, K and Na in the primary melt inclusions within olivine macrocrysts enter the composition of essentially silicate daughter phases. According to this, they are different in composition from similar inclusions in olivine from aillikites and kimberlites and emphasize the more alkaline character of the damtjernitic parental melts. At the subsequent stages of melt evolution during pipe formation, Na and K in the studied inclusions not only enter silicate daughter phases but can also form alkaline phosphates, carbonates, sulfates, and halides. This leads to the formation of alkaline carbonate and saline sulfate–phosphate–chloride–carbonate solutions. According to this, the evolution of the damtjernitic melt is similar to that of aillikite and carbonatite melts and can serve as a uniform mechanism of evolution of alkaline–ultramafic melts. The further reactionary interaction of the fluid phase with olivine led to the formation of monticellite and processes of degassing.
Cyanobacteria in Hypolithic Horizons of Soils in the Larsemann Hills Oasis, East Antarctica
Authors: Velichko N. V. , Rabochaya D. E. , Dolgikh A. V. , Mergelov N. S. 
Published: August 2023

Abstract
The research is devoted to the analysis of biodiversity of Antarctic cyanobacteria in hypolithic organic-accumulative horizons of soils in the Larsemann Hills oasis. Studies of fouling glasses by the methods of light and confocal microscopy, as well as by fluorescent in situ hybridization, indicate that filamentous forms predominate among cyanobacteria in the upper layers of Antarctic hypolithic microbial communities. Strains of the genera Nostoc, Halotia, Leptolyngbya, Plectolyngbya, and Phormidesmis, as well as some new and previously undescribed cyanobacteria, were isolated from corresponding soil samples to clarify their taxonomic status. As a result, a unique collection of Antarctic cyanobacteria isolated from soils was obtained for the first time. The strains were described according to the modern polyphasic taxonomy methods based on an integrated assessment of morphological and molecular-genetic features. Phylogenetic analysis of primary 16S rRNA sequences and peculiarities of secondary structures of internal transcribed spacers enabled us to identify new taxa of potentially endemic cyanobacteria among the strains studied. The high level of similarity between the 16S rRNA gene sequences of soil strains and those previously found in benthic mats of water bodies in the Larsemann Hills confirmed the ability of cyanobacteria to expand beyond different ecological niches and to adapt to contrasting environmental conditions.
Success of health cell approach in improving knowledge, attitude and practice related to COVID-19: difference-in-differences analyses of a community-based quasi-experimental trial
Authors: Das Subhasish , Rasul Md Golam , Khan Ar-Rafi , Fahim Shah Mohammad , Sanin Kazi Istiaque , Ahmed Tahmeed 
Published: August 2023

ObjectivesThere remain hesitations and miscommunication regarding appropriate public health behaviours and conceptions related to COVID-19. We tested the effectiveness of the community-based health cell approach in improving knowledge, attitude and practice (KAP) related to COVID-19.SettingHouseholds of the Bauniabadh slum area in Mirpur, Dhaka, Bangladesh.ParticipantsHousehold heads (HHs) and homemakers (HMs) of intervention (n=211) and comparison households (n=209).InterventionsBehaviour change communication delivered at the community level in a quasi-experimental manner through small-scale community meetings and home visits.Outcome variables and methodsThe outcomes of interest were before–after mean and per cent changes in KAP scores. Data were collected from HHs and HMs before and after the intervention and difference-in-differences (DID) analysis technique was applied.ResultsWe found statistically significant (p<0.05) before–after differences in the responses to the KAP questions made by the intervention groups. The DID models estimated the improvements in COVID-19-related KAP of HHs by 16.58 (95% CI: 14.05, 19.12), 20.92 (95% CI: 18.17, 23.67) and 28.45 (95% CI: 23.84, 33.07) per cent points, respectively. The DID estimates of KAP in HMs were 17.8 (95% CI: 15.09, 20.51), 22.33 (95% CI: 19.47, 25.19) and 28.06 (95% CI: 23.18, 32.93) per cent points, respectively. Overall, 20.91 (95% CI: 18.87, 22.94) and 21.81 (95% CI: 19.68, 23.94) per cent points of improvement were observed among HHs and HMs, respectively. The DID estimates of before–after mean changes in different KAP domains ranged from 2.24 to 2.68 units and the overall changes in KAP scores among HHs and HMs were 7.11 (95% CI: 6.42, 7.8) and 7.42 (95% CI: 6.69, 8.14) units.ConclusionScientifically valid information disseminated at the community level using the health cell approach could bring positive changes in KAP related to COVID-19.
Effect of single versus multiple prophylactic antibiotic doses on prosthetic joint infections following primary total hip arthroplasty in patients with osteoarthritis at public and private hospitals in Denmark: protocol for a nationwide cross-over, cluster randomised, non-inferiority trial [The Pro-Hip-Quality Trial]
Authors: Abedi Armita Armina , Varnum Claus , Pedersen Alma Becic , Gromov Kirill , Hallas Jesper , Iversen Pernille , Jakobsen Thomas , Jimenez-Solem Espen , Kidholm Kristian , Kjerulf Anne , Lange Jeppe , Odgaard Anders , Rosenvinge Flemming S , Solgaard Søren , Sperling Kim , Stegger Marc , Christensen Robin , Overgaard Søren 
Published: August 2023

IntroductionA feared complication after total hip arthroplasty (THA) is prosthetic joint infection (PJI), associated with high morbidity and mortality. Prophylactic antibiotics can reduce the risk of PJI. However, there is no consensus on the dosages and current recommendations are based on a low evidence level. The objective is to compare the effect of a single versus multiple doses of prophylactic antibiotics administered within 24 hours on PJI.Methods and analysisThe study is designed as a cross-over, cluster randomised, non-inferiority trial. All clinical centres use both antibiotic practices (1 year of each intervention). All Danish orthopaedic surgery departments will be involved: Based on quality databases, 2-year cohorts of approximately 20 000 primary THAs conducted at 39 public and private hospitals, will be included. Inclusion criteria: age ≥18 years, all indications for THA except patients operated due to acute or sequelae from proximal femoral or pelvic fractures or bone tumour or metastasis. The primary outcome is PJI within 90 days after primary THA. Secondary outcomes include (1) serious adverse events, (2) potential PJI, (3) length of hospitalisation stay, (4) cardiovascular events, (5) hospital-treated infections, (6) community-based antibiotic use, (7) opioid use and (8) use of acetaminophen and non-steroidal anti-inflammatory drugs. All outcome measures will be extracted from national databases. Analyses will be based on the intention-to-treat population. Non-inferiority will be shown if the upper limit of the two-sided 95% CI for the OR is less than 1.32 for the single dose as compared with multiple doses. The results will establish best practice on antibiotic prophylaxis dosages in the future.Ethics and disseminationThis study has been approved by Committees on Health Research Ethics for The Capital Region of Denmark (21069108) and The Danish Medicines Agency (2021091723). All results will be presented in peer-reviewed medical journals and international conferences.Trial registration numberNCT05530551.
Multicentric, observational, longitudinal study for the evaluation of nutritional management implications in newly diagnosed Italian cancer patients: the Italian Registry of Malnutrition in Oncology (IRMO)
Authors: Bosetti Cristina , Casirati Amanda , Da Prat Valentina , Masi Sara , Crotti Silvia , Ferrari Alessandra , Perrone Lorenzo , Serra Francesco , Santucci Claudia , Cereda Emanuele , Iannelli Elisabetta , De Lorenzo Francesco , Pedrazzoli Paolo , Caccialanza Riccardo 
Published: August 2023

BackgroundMalnutrition is a frequent problem in oncology and is associated with reduced response to cancer treatments, increased drug-related toxicity, higher rates of clinical complications, reduced quality of life (QoL) and worse prognosis. Guidelines on clinical nutrition in oncology emphasise the usefulness of early assessment of nutritional status for a prompt identification of malnutrition and the implementation of effective interventions, but no real-world clinical data are available on the adequate management of nutritional support in patients with cancer in Italy.Methods and analysisThis is an observational, longitudinal, multicentre registry of patients with a new diagnosis of cancer or metastatic disease, candidates for active treatment. They will be identified in at least 15 Italian oncological centres, members of the Alliance Against Cancer Working Group ‘Survivorship Care and Nutritional Support’. At least 1500 patients with cancer are expected to be enrolled each year. Detailed clinical and nutritional data will be collected by oncologists and clinical nutritionists during the visits foreseen in the clinical practice, through an ad hoc developed digital platform (e-Nutracare). The effects of malnutrition and nutritional support—at diagnosis and during follow-up—on overall survival and progression-free survival, as well as on patients’ symptoms and QoL, will be investigated.Ethics and disseminationThe study protocol was approved by the Ethics Committee of the Fondazione IRCCS Policlinico San Matteo, Pavia, Italy and from the Ethics Committees of all other participating centres. An informed consent will be obtained from each patient enrolled in the study. Study findings will be disseminated through peer-reviewed journals, conferences and patients with cancer or professional associations. The registry will allow a better monitoring of the nutritional status of patients with cancer, promoting adequate and sustainable nutritional support, with the ultimate goal of improving the care and prognosis of these patients.
For health or for profit? Understanding how private financing and for-profit delivery operate within Canadian healthcare (4H|4P): protocol for a multimethod knowledge mobilisation research project
Authors: Hedden Lindsay , Spencer Sarah , Allin Sara , Contandriopoulos Damien , Gavin Frank , Grudniewicz Agnes , Lavergne M Ruth , Leaver Chad , Lexchin Joel , McKay Madeleine , Mathews Maria , McCracken Rita K , McGrail Kimberlyn , Palmer Karen S , Poitras Marie-Eve , Rudoler David , Spithoff Sheryl , Vanstone Meredith 
Published: August 2023

IntroductionPrivatisation through the expansion of private payment and investor-owned corporate healthcare delivery in Canada raises potential conflicts with equity principles on which Medicare (Canadian public health insurance) is founded. Some cases of privatisation are widely recognised, while others are evolving and more hidden, and their extent differs across provinces and territories likely due in part to variability in policies governing private payment (out-of-pocket payments and private insurance) and delivery.Methods and analysisThis pan-Canadian knowledge mobilisation project will collect, classify, analyse and interpret data about investor-owned privatisation of healthcare financing and delivery systems in Canada. Learnings from the project will be used to develop, test and refine a new conceptual framework that will describe public-private interfaces operating within Canada’s healthcare system. In Phase I, we will conduct an environmental scan to: (1) document core policies that underpin public-private interfaces; and (2) describe new or emerging forms of investor-owned privatisation (‘cases’). We will analyse data from the scan and use inductive content analysis with a pragmatic approach. In Phase II, we will convene a virtual policy workshop with subject matter experts to refine the findings from the environmental scan and, using an adapted James Lind Alliance Delphi process, prioritise health system sectors and/or services in need of in-depth research on the impacts of private financing and investor-owned delivery.Ethics and disseminationWe have obtained approval from the research ethics boards at Simon Fraser University, University of British Columbia and University of Victoria through Research Ethics British Columbia (H23-00612). Participants will provide written informed consent. In addition to traditional academic publications, study results will be summarised in a policy report and a series of targeted policy briefs distributed to workshop participants and decision/policymaking organisations across Canada. The prioritised list of cases will form the basis for future research projects that will investigate the impacts of investor-owned privatisation.
C1q+tumor-associated macrophages contribute to immunosuppression through fatty acid metabolic reprogramming in malignant pleural effusion
Authors: Zhang Siyu , Peng Wenbei , Wang Haolei , Xiang Xuan , Ye Linlin , Wei Xiaoshan , Wang Zihao , Xue Qianqian , Chen Long , Su Yuan , Zhou Qiong 
Published: August 2023

BackgroundAlthough immune checkpoint blockade (ICB) therapy has shown remarkable benefits in cancers, a subset of patients with cancer exhibits unresponsiveness or develop acquired resistance due to the existence of abundant immunosuppressive cells. Tumor-associated macrophages (TAMs), as the dominant immunosuppressive population, impede the antitumor immune response; however, the underlying mechanisms have not been fully elucidated yet.MethodsSingle-cell RNA sequencing analysis was performed to portray macrophage landscape and revealed the underlying mechanism of component 1q (C1q)+TAMs. Malignant pleural effusion (MPE) of human and mouse was used to explore the phenotypes and functions of C1q+TAMs.ResultsC1q+TAMs highly expressed multiple inhibitory molecules and their high infiltration was significantly correlated with poor prognosis. C1q+TAMs promote MPE immunosuppression through impairing the antitumor effects of CD8+T cells. Mechanistically, C1q+TAMs enhance fatty acid binding protein 5 (FABP5)-mediated fatty acid metabolism, which activate transcription factor peroxisome proliferator-activated receptor-gamma, increasing the gene expression of inhibitory molecules. A high-fat diet increases the expression of inhibitory molecules in C1q+TAMs and the immunosuppression of MPE microenvironment, whereas a low-fat diet ameliorates these effects. Moreover, FABP5 inhibition represses the expression of inhibitory molecules in TAMs and tumor progression, while enhancing the efficacy of ICB therapy in MPE and lung cancer.ConclusionsC1q+TAMs impede antitumor effects of CD8+T cells promoting MPE immunosuppression. Targeting C1q+TAMs effectively alleviates the immunosuppression and enhances the efficacy of ICB therapy. C1q+TAMs subset has great potential to be a therapeutic target for cancer immunotherapy.
State of current management of the heightened risk for atherosclerotic cardiovascular events in an established cohort of patients with lupus erythematosus
Authors: Zhao Megan , Feng Rui , Werth Victoria P , Williams Kevin Jon 
Published: August 2023

ObjectivePatients with lupus erythematosus (LE) are at heightened risk for clinical events, chiefly heart attacks and strokes, from atherosclerotic cardiovascular disease (ASCVD). We recently proposed new guidelines to assess and manage ASCVD event risk specifically in LE. Here, we examined current cardiovascular management in light of these new recommendations.MethodsWe studied our entire UPenn Longitudinal Lupus Cohort of patients with cutaneous LE, without (CLE-only) or with (CLE+SLE) concurrent systemic LE, for whom we had full access to medical records (n=370, LE-ASCVD Study Cohort).ResultsOf our LE-ASCVD Study Cohort, 336 out of 370 (90.8%) had a designated primary-care physician. By the new guidelines, the most recent low-density lipoprotein (LDL) levels were above-goal for 249 out of 370 (67.3%). Two-hundred sixty-six (71.9%) had hypertension, which was undertreated or untreated in 198 out of 266 (74.4%). Of current smokers, 51 out of 63 (81.0%) had no documented smoking cessation counselling or referrals. Diabetes and triglyceridaemia were generally well managed. Of the cohort, 278 qualified for two widely used online estimators of ASCVD event risk in primary prevention: the ACC-ASCVD Risk Estimator Plus and QRisk3. We also stratified these 278 patients into our recently defined categories of ASCVD event risk in LE. These three methods for estimating ASCVD event risk showed clinically meaningful discordance for 169 out of 278 (60.8%). The documented rate of ASCVD events in the first 10 years after enrolment was 13.5% (95% CI 8.9%, 17.9%), similar between CLE-only and CLE+SLE, indicating an at-risk population despite the preponderance of women and an average age at enrolment of only 47 years.ConclusionPatients with CLE-only or CLE+SLE are undertreated compared with the new guidelines and, accordingly, they experience a significant burden of ASCVD events. Moreover, it is unclear how to accurately assess their future ASCVD event risk, except that it is substantial. Efforts are underway to improve ASCVD event risk estimation and guideline implementation in patients with lupus.
Existential distress in family caregivers: scoping review of meaning-making interventions
Authors: McAndrew Natalie S , Gray Tamryn F , Wallace Lyndsey , Calkins Kelly , Guttormson Jill , Harding Eric S , Applebaum Allison J 
Published: August 2023

ObjectivesFamily and friend caregivers often feel overwhelmed by and ill-prepared for their responsibilities. Many feel helpless living with uncertainty about the outcome of the patient’s illness, which leads to existential distress. Supportive care interventions that address existential distress by promoting meaning and purpose buffer the negative effects of caregiver burden and promote resilience and growth. The purpose of this scoping review is to describe the depth and breadth of available interventions targeting caregiver existential distress.MethodsWe followed the Joanna Briggs Institute’s scoping review methods and applied the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension checklist. SCOPUS, Ovid MEDLINE and PsycINFO databases were searched for interventions that targeted existential distress by promoting meaning-making, spiritual well-being, post-traumatic growth and/or benefit finding for caregivers of seriously ill adult patients.ResultsWe screened 1377 titles/abstracts and 42 full-text articles. Thirty-one articles (28 unique studies) met inclusion criteria. Most interventions were designed for caregivers supporting patients with cancer (n=14) or patients receiving palliative care (n=9). Promising interventions included Meaning-Centered Psychotherapy for Cancer Caregivers, Meaning-Based Intervention for Patients and their Partners, Legacy Intervention for Family Enactment, Family Participatory Dignity Therapy and Existential Behavioural Therapy. More than half of the studies (n=20, 64%) were in the feasibility/acceptability/pilot stage of intervention testing.ConclusionLarge randomised controlled trials with more diverse samples of caregivers are needed. Future research should explore the impact of delivering meaning-making interventions to caregivers throughout the illness trajectory. Developing strategies for scaling up and conducting cost analyses will narrow the research and practice gap for meaning-making interventions.