bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailam paramyxovirus C protein inhibits viral replication
Authors: Zhou Lu , Kang Haixian , Xu Shuya , Chen Jinbi , Wang Xianyang , Long Haishang , Li Geng , Xu Pei , He Biao 
Published: January 2024

ABSTRACT

Jeilongviruses are emerging single-stranded negative-sense RNA viruses in the Paramyxoviridae family. Tailam paramyxovirus (TlmPV) is a
Jeilongvirus
that was identified in 2011. Very little is known about the mechanisms that regulate viral replication in these newly emerging viruses. Among the non-structural viral proteins of TlmPV, the C protein is predicted to be translated from an open reading frame within the phosphoprotein gene through alternative translation initiation. Though the regulatory roles of C proteins in virus replication of other paramyxoviruses have been reported before, the function of the TlmPV C protein and the relevant molecular mechanisms have not been reported. Here, we show that the C protein is expressed in TlmPV-infected cells and negatively modulates viral RNA replication. The TlmPV C protein interacts with the P protein, negatively impacting the interaction between N and P, resulting in inhibition of viral RNA replication. Deletion mutagenesis studies indicate that the 50 amino-terminal amino acid residues of the C protein are dispensable for its inhibition of virus RNA replication and interaction with the P protein.

IMPORTANCE

Tailam paramyxovirus (TlmPV) is a newly identified paramyxovirus belonging to the
Jeilongvirus
genus, of which little is known. In this work, we confirmed the expression of the C protein in TlmPV-infected cells, assessed its function, and defined a potential mechanism of action. This is the first time that the existence of a
Jeilongvirus
C protein has been confirmed and its role in viral replication has been reported.
Calcineurin-dependent contributions to fitness in the opportunistic pathogen
Candida glabrata
Authors: Pavesic Matthew W. , Gale Andrew N. , Nickels Timothy J. , Harrington Abigail A. , Bussey Maya , Cunningham Kyle W. 
Published: January 2024

ABSTRACT

The protein phosphatase calcineurin is vital for the virulence of the opportunistic fungal pathogen
Candida glabrata
. The host-induced stresses that activate calcineurin signaling are unknown, as are the targets of calcineurin relevant to virulence. To potentially shed light on these processes, millions of transposon insertion mutants throughout the genome of
C. glabrata
were profiled
en masse
for fitness defects in the presence of FK506, a specific inhibitor of calcineurin. Eighty-seven specific gene deficiencies depended on calcineurin signaling for full viability
in vitro
both in wild-type and
pdr1∆
null strains lacking pleiotropic drug resistance. Three genes involved in cell wall biosynthesis (
FKS1
,
DCW1
,
FLC1
) possess co-essential paralogs whose expression depended on calcineurin and Crz1 in response to micafungin, a clinical antifungal that interferes with cell wall biogenesis. Interestingly, 80% of the FK506-sensitive mutants were deficient in different aspects of vesicular trafficking, such as endocytosis, exocytosis, sorting, and biogenesis of secretory proteins in the endoplasmic reticulum (ER). In response to the experimental antifungal manogepix that blocks GPI-anchor biosynthesis in the ER, calcineurin signaling increased and strongly prevented cell death independent of Crz1, one of its major targets. Comparisons between manogepix, micafungin, and the ER-stressing tunicamycin reveal a correlation between the degree of calcineurin signaling and the degree of cell survival. These findings suggest that calcineurin plays major roles in mitigating stresses of vesicular trafficking. Such stresses may arise during host infection and in response to antifungal therapies.

IMPORTANCE

Calcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen
Candida glabrata
using a genome-wide analysis
in vitro
. The findings could lead to antifungal developments that also avoid immunosuppression.
Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient
Authors: Hartman Wyatt H. , Bueno de Mesquita Clifton P. , Theroux Susanna M. , Morgan-Lang Connor , Baldocchi Dennis D. , Tringe Susannah G. 
Published: January 2024

ABSTRACT

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH
4
). While sulfate loading from seawater intrusion may reduce CH
4
production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH
4
fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH
4
fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH
4
fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH
4
fluxes observed in oligohaline sediments.

IMPORTANCE
Low-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.
Genome-based assessment of antimicrobial resistance reveals the lineage specificity of resistance and resistance gene profiles in
Riemerella anatipestifer
from China
Authors: Yang Zhishuang , Wang Mingshu , Jia Renyong , Chen Shun , Liu Mafeng , Zhao Xinxin , Yang Qiao , Wu Ying , Zhang Shaqiu , Huang Juan , Ou Xumin , Mao Sai , Gao Qun , Sun Di , Tian Bin , He Yu , Wu Zhen , Zhu Dekang , Cheng Anchun 
Published: January 2024

ABSTRACT

Riemerella anatipestifer
(
R. anatipestifer
) is an important pathogen that causes severe systemic infections in domestic ducks, resulting in substantial economic losses for China’s waterfowl industry. Controlling
R. anatipestifer
with antibiotics is extremely challenging due to its multidrug resistance. Notably, large-scale studies on antimicrobial resistance (AMR) and the corresponding genetic determinants in
R. anatipestifer
remain scarce. To solve this dilemma, more than 400 nonredundant
R. anatipestifer
isolates collected from 22 provinces in China between 1994 and 2021 were subjected to broth dilution antibiotic susceptibility assays, and their resistance-associated genetic determinants were characterized by whole-genome sequencing. While over 90% of the isolates was resistant to sulfamethoxazole, kanamycin, gentamicin, ofloxacin, norfloxacin, and trimethoprim, 88.48% of the isolates was resistant to the last-resort drug (tigecycline). Notably,
R. anatipestifer
resistance to oxacillin, norfloxacin, ofloxacin, and tetracycline was found to increase relatively over time. Genome-wide analysis revealed the alarmingly high prevalence of
bla
OXA
-like (93.05%) and
tet
(X) (90.64%) genes and the uneven distribution of resistance genes among lineages. Overall, this study reveals a serious AMR situation regarding
R. anatipestifer
in China, with a high prevalence and high diversity of antimicrobial resistance genes, providing important data for the rational use of antibiotics in veterinary practice.

IMPORTANCE

Riemerella anatipestifer (R. anatipestifer
), an important waterfowl pathogen, has caused substantial economic losses worldwide, especially in China. Antimicrobial resistance (AMR) is a major challenge in controlling this pathogen. Although a few studies have reported antimicrobial resistance in
R. anatipestifer
, comprehensive data remain a gap. This study aims to address the lack of information on
R. anatipestifer
AMR and its genetic basis. By analyzing more than 400 isolates collected over two decades, this study reveals alarming levels of resistance to several antibiotics, including drugs of last resort. The study also revealed the lineage-specificity of resistance profiles and resistance gene profiles. Overall, this study provides new insights and updated data support for understanding AMR and its genetic determinants in
R. anatipestifer
.
Mechanisms of nitrogen isotope fractionation at an ancient black smoker in the 2.7 Ga Abitibi greenstone belt, Canada
Authors: Martin A.N. , Stüeken E.E. , Michaud J.A.-S. , Münker C. , Weyer S. , van Hees E.H.P. , Gehringer M.M. 
Published: January 2024

Abstract
The biological nitrogen (N) cycle on early Earth is enigmatic because of limited data from Archean (meta-)sediments and the potential alteration of primary biotic signatures. Here we further investigate unusual 15N enrichments reported in 2.7 Ga meta-sediments from the Abitibi greenstone belt, Canada, purportedly related to a 15N-enriched Archean atmosphere. Given that sediments from this region are contemporaneous with large-scale volcanogenic massive sulfide deposits, we utilize Cu and Zn contents to trace the effects of hydrothermal circulation on N isotope fractionation. We show that high δ15Nbulk values as high as +23‰ are associated with Cu-Zn mineralization, whereas unmineralized organic-rich shales exhibit much lower δ15Nbulk and δ15Nkerogen values. Moreover, we find a large offset between δ15Nbulk and δ15Nkerogen of as much as 17‰ and relate this to the addition of organic-bound N during the late-stage emplacement of organic-rich veins. We conclude that the previously reported high δ15N values are most parsimoniously explained by biotic and abiotic mechanisms rather than a 15N-enriched atmosphere. Crucially, both mechanisms require the presence of NH4+ in hydrothermal fluids, supporting the hypothesis that hydrothermal discharge was an important nutrient source for Neoarchean marine life.
Clinical decision support systems to improve drug prescription and therapy optimisation in clinical practice: a scoping review
Authors: Armando Lucrezia Greta , Miglio Gianluca , de Cosmo Pierluigi , Cena Clara 
Published: January 2024

ObjectiveClinical decision support systems (CDSSs) can reduce medical errors increasing drug prescription appropriateness. Deepening knowledge of existing CDSSs could increase their use by healthcare professionals in different settings (ie, hospitals, pharmacies, health research centres) of clinical practice. This review aims to identify the characteristics common to effective studies conducted with CDSSs.Materials and methodsThe article sources were Scopus, PubMed, Ovid MEDLINE and Web of Science, queried between January 2017 and January 2022. Inclusion criteria were prospective and retrospective studies that reported original research on CDSSs for clinical practice support; studies should describe a measurable comparison of the intervention or observation conducted with and without the CDSS; article language Italian or English. Reviews and studies with CDSSs used exclusively by patients were excluded. A Microsoft Excel spreadsheet was prepared to extract and summarise data from the included articles.ResultsThe search resulted in the identification of 2424 articles. After title and abstract screening, 136 studies remained, 42 of which were included for final evaluation. Most of the studies included rule-based CDSSs that are integrated into existing databases with the main purpose of managing disease-related problems. The majority of the selected studies (25 studies; 59.5%) were successful in supporting clinical practice, with most being pre–post intervention studies and involving the presence of a pharmacist.Discussion and conclusionA number of characteristics have been identified that may help the design of studies feasible to demonstrate the effectiveness of CDSSs. Further studies are needed to encourage CDSS use.
Measures of socioeconomic advantage are not independent predictors of support for healthcare AI: subgroup analysis of a national Australian survey
Authors: Frost Emma Kellie , O’Shaughnessy Pauline , Steel David , Braunack-Mayer Annette , Aquino Yves Saint James , Carter Stacy M 
Published: January 2024

Objectives:Applications of artificial intelligence (AI) have the potential to improve aspects of healthcare. However, studies have shown that healthcare AI algorithms also have the potential to perpetuate existing inequities in healthcare, performing less effectively for marginalised populations. Studies on public attitudes towards AI outside of the healthcare field have tended to show higher levels of support for AI among socioeconomically advantaged groups that are less likely to be sufferers of algorithmic harms. We aimed to examine the sociodemographic predictors of support for scenarios related to healthcare AI.Methods:The Australian Values and Attitudes toward AI survey was conducted in March 2020 to assess Australians’ attitudes towards AI in healthcare. An innovative weighting methodology involved weighting a non-probability web-based panel against results from a shorter omnibus survey distributed to a representative sample of Australians. We used multinomial logistic regression to examine the relationship between support for AI and a suite of sociodemographic variables in various healthcare scenarios.Results:Where support for AI was predicted by measures of socioeconomic advantage such as education, household income and Socio-Economic Indexes for Areas index, the same variables were not predictors of support for the healthcare AI scenarios presented. Variables associated with support for healthcare AI included being male, having computer science or programming experience and being aged between 18 and 34 years. Other Australian studies suggest that these groups may have a higher level of perceived familiarity with AI.Conclusion:Our findings suggest that while support for AI in general is predicted by indicators of social advantage, these same indicators do not predict support for healthcare AI.
Women’s health service access and associated factors in Ethiopia: application of geographical information system and multilevel analysis
Authors: Demsash Addisalem Workie , Walle Agmasie Damtew 
Published: January 2024

ObjectivesWomen’s access to healthcare services is challenged by various factors. This study aimed to assess women’s health service access and identify associated factors.MethodsA cross-sectional study design with a two-stage stratified sampling technique, and 12 945 women from the 2016 Ethiopia Demographic and Health Survey dataset were used. The spatial hotspot analysis and purely Bernoulli-based model scan statistics were used to highlight hot and cold spot areas, and to detect significant local clusters of women’s health service access. A multilevel logistic regression analysis was used to assess factors that affect women’s access to health services. A variable with a p<o.o5 was considered as a significant factor.ResultsOverall, 29.8%% of women had health services access. 70.2% of women had problems with health services access such as: not wanting to go alone (42%), distance to health facilities (51%), getting the money needed for treatment (55%) and getting permission to go for medical care (32.3%). The spatial distribution of health service access in Ethiopia was clustered, and low health service access was observed in most areas of the country. Women who lived in primary, secondary and tertiary clusters were 96%, 39% and 72% more likely to access health services. Educational status, rich wealth status, media exposure and rural residence were statistically significant factors.ConclusionsIn Ethiopia, women have problems with health services access. The spatial distribution of health services access was non-random, and hotspot areas of women’s health service access were visualised in parts of Benishangul Gumez, Amhara, Afar, DireDawa, Harari, and Somali regions. Creating job opportunities, public health promotion regarding maternal health service utilisation and constructing nearby health facilities are required for better healthcare service access for women.
A natural language processing approach to categorise contributing factors from patient safety event reports
Authors: Tabaie Azade , Sengupta Srijan , Pruitt Zoe M , Fong Allan 
Published: January 2024

ObjectivesThe objective of this study was to explore the use of natural language processing (NLP) algorithm to categorise contributing factors from patient safety event (PSE). Contributing factors are elements in the healthcare process (eg, communication failures) that instigate an event or allow an event to occur. Contributing factors can be used to further investigate why safety events occurred.MethodsWe used 10 years of self-reported PSE reports from a multihospital healthcare system in the USA. Reports were first selected by event date. We calculated χ2values for each ngram in the bag-of-words then selected N ngrams with the highest χ2values. Then, PSE reports were filtered to only include the sentences containing the selected ngrams. Such sentences were called information-rich sentences. We compared two feature extraction techniques from free-text data: (1) baseline bag-of-words features and (2) features from information-rich sentences. Three machine learning algorithms were used to categorise five contributing factors representing sociotechnical errors: communication/hand-off failure, technology issue, policy/procedure issue, distractions/interruptions and lapse/slip. We trained 15 binary classifiers (five contributing factors * three machine learning models). The models’ performances were evaluated according to the area under the precision-recall curve (AUPRC), precision, recall, and F1-score.ResultsApplying the information-rich sentence selection algorithm boosted the contributing factor categorisation performance. Comparing the AUPRCs, the proposed NLP approach improved the categorisation performance of two and achieved comparable results with baseline in categorising three contributing factors.ConclusionsInformation-rich sentence selection can be incorporated to extract the sentences in free-text event narratives in which the contributing factor information is embedded.
Willingness of diabetes mellitus patients to use mHealth applications and its associated factors for self-care management in a low-income country: an input for digital health implementation
Authors: Walle Agmasie Damtew , Ferede Tigist Andargie , Shibabaw Adamu Ambachew , Wubante Sisay Maru , Guadie Habtamu Alganeh , Yehula Chalachew Msganaw , Demsash Addisalem Workie 
Published: January 2024

BackgroundAlthough mHealth applications are becoming more widely available and used, there is no evidence about why people are willing to use them. Therefore, this study aimed to assess the willingness of patients with diabetes to use mHealth applications and associated factors for self-care management in Ethiopia.MethodsAn institutional cross-sectional study was conducted among 422 patients with diabetes. Data were collected using pretested interviewer-administered questionnaire. Epi Data V.4.6 for entering the data and STATA V.14 for analysing the data were used. A multivariable logistic regression analysis was carried out to identify factors associated with patient’s willingness to use mobile health applications.ResultsA total of 398 study participants were included in the study. About 284 (71.4%) 95% CI (66.8% to 75.9%)). Of participants were willing to use mobile health applications. Patients below 30 years of age (adjusted OR, AOR 2.21; 95% CI (1.22 to 4.10)), urban residents (AOR 2.12; 95% CI (1.12 to 3.98)), internet access (AOR 3.91; 95% CI (1.31 to 11.5)), favourable attitude (AOR 5.20; 95% CI (2.60 to 10.40)), perceived ease of use (AOR 2.57; 95% CI (1.34 to 4.85)) and perceived usefulness (AOR 4.67; 95% CI (1.95 to 5.77)) were significantly associated with patients’ willingness to use mobile health applications.ConclusionsOverall, diabetes patients’ willingness to use mobile health applications was high. Patients’ age, place of residence, internet access, attitude, perceived ease of use and perceived usefulness were significant factors concerning their willingness to use mobile health applications. Considering these factors could provide insight for developing and adopting diabetes management applications on mobile devices in Ethiopia.
Twenty-year follow-up of promising clinical studies reported in highly circulated newspapers: a meta-epidemiological study
Authors: Tajika Aran , Tsujimoto Yasushi , Onishi Akira , Tsutsumi Yusuke , Funada Satoshi , Ogawa Yusuke , Takeshima Nozomi , Hayasaka Yu , Iwakami Naotsugu , Furukawa Toshi A 
Published: January 2024

ObjectivesResearchers have identified cases in which newspaper stories have exaggerated the results of medical studies reported in original articles. Moreover, the exaggeration sometimes begins with journal articles. We examined what proportion of the studies quoted in newspaper stories were confirmed.MethodsWe identified newspaper stories from 2000 that mentioned the effectiveness of certain treatments or preventions based on original studies from 40 main medical journals. We searched for subsequent studies until June 2022 with the same topic and stronger research design than each original study. The results of the original studies were verified by comparison with those of subsequent studies.ResultsWe identified 164 original articles from 1298 newspaper stories and randomly selected 100 of them. Four studies were not found to be effective in terms of the primary outcome, and 18 had no subsequent studies. Of the remaining studies, the proportion of confirmed studies was 68.6% (95% CI 58.1% to 77.5%). Among the 59 confirmed studies, 13 of 16 studies were considered to have been replicated in terms of effect size. However, the results of the remaining 43 studies were not comparable.DiscussionIn the dichotomous judgement of effectiveness, about two-thirds of the results were nominally confirmed by subsequent studies. However, for most confirmed results, it was impossible to determine whether the effect sizes were stable.ConclusionsNewspaper readers should be aware that some claims made by high-quality newspapers based on high-profile journal articles may be overturned by subsequent studies within the next 20 years.