bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes Associated With Blastomycosis in Solid Organ and Hematopoietic Cell Transplant Recipients
Authors: Nair Vaisak O. , Johnson Bradley , Vergidis Paschalis , Ranganath Nischal 
Published: December 2024

ABSTRACTIntroductionWith reports of expanding epidemiology of blastomycosis across the United States, the purpose of this study was to evaluate the incidence and outcomes associated with blastomycosis in solid organ transplant (SOT) and hematopoietic cell transplant (HCT) recipients.MethodsWe conducted a retrospective case series of adult SOT and HCT recipients at a tertiary care medical center between January 1, 2005 and September 30, 2023. Cases were defined as culture‐proven blastomycosis. We performed descriptive statistical analysis to evaluate diagnosis, management, and outcomes (mortality) of blastomycosis in SOT.ResultsThe cumulative incidence of blastomycosis was 0.11% with a median time to infection following transplant of 743 days. Of the 19 cases, the majority of patients were SOT recipients (90%). Supratherapeutic immunosuppression within 30 days of diagnosis was observed in 42% of cases with documented drug monitoring. Urine antigen testing was highly sensitive (100%). Fourteen (73.7%) patients received induction therapy with liposomal amphotericin B followed by azole therapy for a minimum of 12 months. Despite appropriate treatment, 1‐year mortality was high at 26.3%, with attributable mortality of 21.1%.ConclusionsWhile rates of blastomycosis remain low among SOT and HCT recipients, infection is associated with poor posttransplant outcomes. Antigen testing can aid in timely assessment of disease severity and initiation of appropriate therapy. Among survivors, no relapses were observed while on lifelong secondary suppression. Future studies should aim to better define risk factors associated with developing blastomycosis and establish effective strategies for prevention.
Persistence of human Aichi virus infectivity from raw surface water to drinking water
Authors: Sdiri-Loulizi Khira , Khachou Amira , Lemaire Stephanie , Bour Jean-Baptiste , Ayouni Siwar , Kaplon Jérôme , Sakly Nabil , Aouni Mahjoub , Belliot Gael , de Rougemont Alexis 
Published: December 2024

ABSTRACT

Human Aichi virus 1 (AiV-1) is a water- and food-borne infection-associated picornavirus that causes gastroenteritis in humans. Recent studies on environmental waters showed a high frequency and abundance of AiV-1, suggesting that it might be an appropriate indicator of fecal contamination. We screened 450 surface and drinking water samples from a Tunisian drinking water treatment plant (DWTP) and the Sidi Salem dam for AiV-1 by real time reverse transcriptase PCR (RT-qPCR). The persistence of infectious particles was evaluated using an integrated cell culture approach coupled with quantitative molecular detection (ICC-RT-qPCR). In all, 85 (18.9%) water samples were positive for AiV-1 with viral loads ranging from 0.47 to 11.62 log
10
cp/L and a median of 4.97 log
10
cp/L, including 30/100 raw, 18/50 decanted, 14/50 flocculated, 9/100 treated, 1/50 tap, and 13/100 surface water samples. Of these, 15 (17.6%) samples contained infectious AiV-1 genotype A particles, including five raw, four decanted, one surface, three flocculated, and two treated water samples. Our data suggest that the persistence of infectious AiV-1 particles in environmental waters might represent a potential threat to public health. This study also indicates that the ICC-RT-qPCR is a practical tool for monitoring human waterborne viral risk in aquatic environments.

IMPORTANCE
Human Aichi virus 1 (AiV-1) is a water- and food-borne infection-associated picornavirus that causes gastroenteritis in humans. Its high frequency and abundance in environmental waters would suggest that it might be an appropriate indicator of fecal contamination. The analysis of surface and drinking water samples from a Tunisian drinking water treatment plant (DWTP) and the Sidi Salem dam using an integrated cell culture approach coupled with a quantitative molecular detection (ICC-RT-qPCR) confirmed the persistence of infectious AiV-1 particles in samples at all stages of the treatment process, except in tap water. This suggests that the persistence of AiV-1 infectivity in environmental waters might represent a potential threat to public health. This study also indicates that the ICC-RT-qPCR is a practical tool for monitoring human waterborne viral risk in aquatic environments.
Assessing environmental gradients in relation to dark CO
2
fixation in estuarine wetland microbiomes
Authors: Grüterich Luise , Woodhouse Jason Nicholas , Mueller Peter , Tiemann Amos , Ruscheweyh Hans-Joachim , Sunagawa Shinichi , Grossart Hans-Peter , Streit Wolfgang R. 
Published: December 2024

ABSTRACT

The rising atmospheric concentration of CO
2
is a major concern to society due to its global warming potential. In soils, CO
2
-fixing microorganisms are preventing some of the CO
2
from entering the atmosphere. Yet, the controls of dark CO
2
fixation are rarely studied
in situ
. Here, we examined the gene and transcript abundance of key genes involved in microbial CO
2
fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO
2
fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood–Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood–Ljungdahl pathway was favored by reducing, O
2
-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO
2
fixation was mainly linked to a few bacterial phyla, namely,
Desulfobacterota
,
Methylomirabilota
,
Nitrospirota
,
Chloroflexota
, and
Pseudomonadota
.

IMPORTANCE

The increasing concentration of atmospheric CO
2
has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO
2
fixation by soil microbes (a.k.a. dark CO
2
fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO
2
-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO
2
fixation and its potential role in the global climate system.
Influenza B virus infection alters the regenerative potential of murine alveolar type 2 pneumocytes
Authors: Nakano Satoko , Hamele Cait E. , Tata Aleksandra , Tata Purushothama Rao , Heaton Nicholas S. 
Published: December 2024

ABSTRACT

Respiratory epithelial cells can survive direct infection by influenza viruses, and the long-term consequences of that infection have been characterized in a subset of proximal airway cell types. The impact on the cells that survive viral infection in the distal lung epithelia, however, is much less well-characterized. Utilizing a Cre-expressing influenza B virus (IBV) and a lox-stop-lox tdTomato reporter mouse model, we identified that alveolar type 2 (AT2) pneumocytes, a progenitor cell type in the distal lung, can survive viral infection. We show that survival of infection is associated with transcriptional dysregulation compared to bystander AT2 pneumocytes from the same lung. Furthermore,
ex vivo
experiments revealed a significant reduction in proliferation rates in survivor AT2 pneumocytes compared to matched, non-directly infected bystander cells. Our findings not only enhance our understanding of the AT2 pneumocyte response to IBV infection but could also have broader implications for the mechanisms of respiratory epithelial repair post-viral infection.

IMPORTANCE
Alveolar type 2 (AT2) pneumocytes are a cell type critical for repair of the distal lung after an injury, such as a viral infection. After epithelial damage, AT2 pneumocytes proliferate for both self-renewal and differentiation into type I pneumocytes to repopulate the epithelium. Theoretically, some of the long-term lung sequelae associated with viral infections could be the result of inappropriate AT2 behavior. Here, the authors report that during an influenza B virus infection, some of the actively infected AT2 pneumocytes can ultimately eliminate all traces of the viral RNA and persist in the host long term. As a consequence of having been infected, however, the cells display an altered transcriptional profile and decreased proliferative capacity. These data together suggest a mechanism for how an acute viral infection can have long-term impacts on the pulmonary system.
Decomposition of the pangenome matrix reveals a structure in gene distribution in the
Escherichia coli
species
Authors: Chauhan Siddharth M. , Ardalani Omid , Hyun Jason C. , Monk Jonathan M. , Phaneuf Patrick V. , Palsson Bernhard O. 
Published: December 2024

ABSTRACT

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of
Escherichia coli
for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of
E. coli
plus
Shigella
: A, B1, B2, C, D, E, F, G, and
Shigella
. The analysis resulted in a detailed structure of the genetic basis of the phylogroups’ differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

IMPORTANCE

The comprehensive analysis of the pangenome of
Escherichia coli
presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete
E. coli
genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.
Deciphering the biosynthetic landscape of biofilms in glacier-fed streams
Authors: Geers Aileen Ute , Michoud Grégoire , Busi Susheel Bhanu , Peter Hannes , Kohler Tyler J. , Ezzat Leïla ,   The Vanishing Glaciers Field Team, Battin Tom J. , Styllas Michael , Schön Martina , Tolosano Matteo , Staercke Vincent de , Peter Hannes , Kohler Tyler , Battin Tom J. 
Published: December 2024

ABSTRACT

Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the
Vanishing Glaciers
project from the world’s major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll
a
and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.

IMPORTANCE

Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll
a
. In the face of climate change, our study offers new insights into a vanishing ecosystem.
Prediction of functional remission in patients with schizophrenia after antipsychotic discontinuation (FURSAD): protocol for a real-world case-control study
Authors: Lu Chang , Dong Yuke , Zhai Zhaolin , Gao Tianhao , Luo Mengyi , Feng Tienan , Ma Xiangyi , Chang Di , Chen Jing , Xue Jingxin , Zhao Yuqing , Li Xuan , Shao Chunhong , Liu Dengtang 
Published: December 2024

IntroductionAlthough maintenance treatment is recommended for the prevention of relapse, in real-world settings, a subset of patients discontinue antipsychotics while having a good prognosis. The prediction of functional remission in patients with schizophrenia after antipsychotic discontinuation (FURSAD) study aims to obtain real-world knowledge regarding the characteristics of schizophrenia (SCZ) patients who achieve functional remission after antipsychotic discontinuation for 1 year or more. This study also aims to establish a prediction model to identify patients likely to benefit from antipsychotic discontinuation.Methods and analysisThe FURSAD study employs a real-world case-control design. Researchers will first screen patients with a diagnosis of SCZ (ICD-10) from the Shanghai Mental Health Center discharged patient pool to identify 480 participants who have been off-antipsychotic for at least 1 year. They will be assigned to the functional remission group or the functional non-remission group according to their social functioning assessment scores, including the self-assessment questionnaire WHO Quality of Life abbreviated version (WHOQoL-BREF) and the peer-assessment scale Functional Remission of General Schizophrenia (FROGS) Scale. Sociodemographic, symptom and treatment information of participants during their hospitalisation and after discharge will be extracted from the Hospital Information System and collected via interviews, respectively, to find independent variables for good prognosis after antipsychotic discontinuation. A nomogram will visualise the prediction model results to help psychiatrists make decisions.Ethics and disseminationFull ethical approval for the study (study design, data acquisition license and informed consent) was granted by the ethics committee at Shanghai Mental Health Center, Shanghai, China (approval letter number: 2022–59). The findings of the FURSAD study will be published in peer-reviewed journals or disseminated in conference presentations.Trial registration numberNCT05667961.
Assessing the impact of different donor milk treatments on infant health and growth: a systematic review protocol
Authors: Klotz Daniel , Bzikowska-Jura Agnieszka , Giribaldi Marzia , Cassidy Tanya , Cavallarin Laura , Gandino Serena , Karcz Karolina , Peila Chiara , Smith Carolyn , Walczak Bartłomiej , Wesolowska Aleksandra 
Published: December 2024

IntroductionDonor human milk (DHM) is the first alternative if mother’s own milk is unavailable or contraindicated. Much DHM research has focused on its nutritional, immunological and biochemical composition in response to various maternal variables, standard human milk banking procedures and storage protocols. The current systematic review protocol, however, aims to systematically gather and analyse existing data pertaining to the impact of these aforementioned factors on the clinical, health-related and developmental outcomes observed in infants fed with DHM.Methods and analysisWe will apply a predefined search strategy including Cochrane Central Register of Controlled Trials, Global Index Medicus, CINAHL on Ebscohost, Medline, Embase, Emcare, Pubmed, Global Health on OVID, Google Scholar, clinicaltrials.gov, the WHO International Trials Registry and Platform and the European Union/European Economic Area Clinical Trials Register. No setting, patient population, date or language restrictions will be applied. The search strategy will consist of search words on the key concepts of ‘donated human milk’ and ‘effect on infants’. Published or unpublished primary research studies are eligible for inclusion if there is an abstract available in English. Conference proceedings, animal studies and publications with no original data will be excluded.Authors of unpublished or partially published studies will be contacted and eligible data added if provided. Risk of bias will be evaluated according to CASP using appropriate tools depending on study type (RoB 2, ROBINS-I, Newcastle Ottawa Scale). Data will be synthesised in a quantitative format describing significant results as well as presenting the results of the quality assessment of studies.Ethics and disseminationThis systematic review does not require ethical approval, as we will not collect primary data. The review will be published in a peer-reviewed journal and disseminated electronically and in print.PROSPERO registration numberCRD42024522015.
Monitoring low-value care in medical patients from Swiss university hospitals using a Findable, Accessible, Interoperable, Reusable (FAIR) national data stream and patient and public involvement: LUCID study protocol
Authors: Guffi Tommaso , Ehrsam Julien , Débieux Marie , Rossel Jean-Benoît , Crevier Marie-Josée , Reny Jean-Luc , Stirnemann Jerome , Meier Christoph A , Aujesky Drahomir , Bassetti Stefano , Aubert Carole Elodie , Méan Marie 
Published: December 2024

IntroductionHealthcare practices providing minimal or no benefit to recipients have been estimated to represent 20% of healthcare costs. However, defining, measuring and monitoring low-value care (LVC) and its downstream consequences remain a major challenge. The purpose of the National Data Stream (LUCID NDS) is to identify and monitor LVC in medical inpatients using routinely collected hospital data.Methods and analysisThis protocol describes a multistep approach to the identification and surveillance of LVC: (1) creating an NDS based on Findable, Accessible, Interoperable, Reusable (FAIR) principles using routinely collected hospital data from medical inpatients who signed a general consent for data reuse from 2014 onwards; (2) selecting recommendations applicable to medical inpatients using data from LUCID NDS to develop a comprehensive and robust set of LVC indicators; (3) establishing expert consensus on the most relevant and actionable recommendations to prevent LVC; (4) applying the Strength of Recommendation Taxonomy methodology to assess the level of evidence of recommendations; (5) involving patients and the public at various stages of LUCID NDS; and (6) designing monitoring rules within the LUCID NDS and validating quality measures.Ethics and disseminationThe ethics committees of all five participating university hospitals (Basel, Bern, Geneva, Lausanne and Zurich) approved LUCID NDS as a national registry on quality of care. We will disseminate our findings in peer-reviewed journals, at professional conferences, and through short reports sent to participating entities and stakeholders; moreover, lay summaries are provided for patients and the broader public on our webpage (www.LUCID-nds.ch).
Treatment for peripheral nerve injury: a protocol for a systematic review and Bayesian network meta-analysis
Authors: Yang Yongke , Gu Wenlong , Xu Shuting , Wang Shuai , Shi Huiyan , Zhang Lili , Meng Xiang-gang , Hong Feng , Du Yuzheng 
Published: December 2024

IntroductionAvailable therapies for peripheral nerve injury (PNI) include surgical and non-surgical treatments. Surgical treatment includes neurorrhaphy, grafting (allografts and autografts) and tissue-engineered grafting (artificial nerve guide conduits), while non-surgical treatment methods include electrical stimulation, magnetic stimulation, laser phototherapy and administration of nerve growth factors. However, the treatments currently available to best manage the different PNI manifestations remain undetermined. This systematic review and network meta-analysis (NMA) aims to address this and determine the best treatment or combination of treatments for PNI.Methods and analysisA comprehensive search of MEDLINE (via PubMed), Embase, Cochrane Library, Web of Science, Chinese Biomedical Database, China National Knowledge Infrastructure, VIP Database, Wanfang Database, WHO International Clinical Trials Registry Platform, ClinicalTrials.gov and the Chinese Clinical Trial Register will be completed using the following keywords: peripheral nerve injury, therapies and related entry terms. Studies will be included based on specific eligibility criteria, and the reference lists of the included studies will be manually searched. Relevant data will be extracted from the included studies using a specially designed data extraction sheet. The risk of bias in the included studies will be assessed, and the overall strength of the evidence will be summarised. A random-effects model was used for all pairwise meta-analyses (95% CI). Bayesian NMA is used to explore the relative benefits of various treatments. The review will be reported using the Preferred Reporting Items for Systematic Reviews incorporating NMA statement.Ethics and disseminationAs the protocol for this systematic review and Bayesian NMA is based on studies with published results and does not involve patient interventions, no ethical review is required. The results will be published in a peer-reviewed journal.PROSPERO registration numberCRD42023475135.