bluuebunny/crossref_metadata_2025_split huggingface dataset:
NSP6 inhibits the production of ACE2-containing exosomes to promote SARS-CoV-2 infectivity
Authors: Lv Xi , Chen Ran , Liang Taizhen , Peng Haojie , Fang Qiannan , Xiao Shiqi , Liu Sen , Hu Meilin , Yu Fei , Cao Lixue , Zhang Yiwen , Pan Ting , Xi Zhihui , Ding Yao , Feng Linyuan , Zeng Tao , Huang Wenjing , Zhang Hui , Ma Xiancai 
Published: February 2024

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global pandemic, which severely endangers public health. Our and others’ works have shown that the angiotensin-converting enzyme 2 (ACE2)-containing exosomes (ACE2-exos) have superior antiviral efficacies, especially in response to emerging variants. However, the mechanisms of how the virus counteracts the host and regulates ACE2-exos remain unclear. Here, we identified that SARS-CoV-2 nonstructural protein 6 (NSP6) inhibits the production of ACE2-exos by affecting the protein level of ACE2 as well as tetraspanin-CD63 which is a key factor for exosome biogenesis. We further found that the protein stability of CD63 and ACE2 is maintained by the deubiquitination of proteasome 26S subunit, non-ATPase 12 (PSMD12). NSP6 interacts with PSMD12 and counteracts its function, consequently promoting the degradation of CD63 and ACE2. As a result, NSP6 diminishes the antiviral efficacy of ACE2-exos and facilitates the virus to infect healthy bystander cells. Overall, our study provides a valuable target for the discovery of promising drugs for the treatment of coronavirus disease 2019.

IMPORTANCE
The outbreak of coronavirus disease 2019 (COVID-19) severely endangers global public health. The efficacy of vaccines and antibodies declined with the rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutants. Angiotensin-converting enzyme 2-containing exosomes (ACE2-exos) therapy exhibits a broad neutralizing activity, which could be used against various viral mutations. Our study here revealed that SARS-CoV-2 nonstructural protein 6 inhibited the production of ACE2-exos, thereby promoting viral infection to the adjacent bystander cells. The identification of a new target for blocking SARS-CoV-2 depends on fully understanding the virus-host interaction networks. Our study sheds light on the mechanism by which the virus resists the host exosome defenses, which would facilitate the study and design of ACE2-exos-based therapeutics for COVID-19.
Time-resolved RNA-seq analysis to unravel the
in vivo
competence induction by
Streptococcus pneumoniae
during pneumonia-derived sepsis
Authors: Oh Myung Whan , Lin Jingjun , Chong Sook Yin , Lew Shi Qian , Alam Tauqeer , Lau Gee W. 
Published: February 2024

ABSTRACT

Competence development in
Streptococcus pneumoniae
(pneumococcus) is tightly intertwined with virulence. In addition to genes encoding genetic transformation machinery, the competence regulon also regulates the expression of allolytic factors, bacteriocins, and cytotoxins. Pneumococcal competence system has been extensively interrogated
in vitro
where the short transient competent state upregulates the expression of three distinct phases of “early,” “late,” and “delayed” genes. Recently, we have demonstrated that the pneumococcal competent state develops naturally in mouse models of pneumonia-derived sepsis. To unravel the underlying adaptive mechanisms driving the development of the competent state, we conducted a time-resolved transcriptomic analysis guided by the spatiotemporal live
in vivo
imaging system of competence induction during pneumonia-derived sepsis. Mouse lungs infected by the serotype 2 strain D39 expressing a competent state-specific reporter gene (D39-
ssbB-luc
) were subjected to RNA sequencing guided by monitoring the competence development at 0, 12, 24, and, at the moribund state, >40 hours post-infection (hpi). Transcriptomic analysis revealed that the competence-specific gene expression patterns
in vivo
were distinct from those under
in vitro
conditions. There was significant upregulation of early, late, and some delayed phase competence-specific genes as early as 12 hpi, suggesting that the pneumococcal competence regulon is important for adaptation to the lung environment. Additionally, members of the histidine triad (
pht
) gene family were sharply upregulated at 12 hpi followed by a steep decline throughout the rest of the infection cycle, suggesting that Pht proteins participate in the early adaptation to the lung environment. Further analysis revealed that Pht proteins execute a metal ion-dependent regulatory role in competence induction.

IMPORTANCE

The induction of pneumococcal competence for genetic transformation has been extensively studied
in vitro
but poorly understood during lung infection. We utilized a combination of live imaging and RNA sequencing to monitor the development of a competent state during acute pneumonia. Upregulation of competence-specific genes was observed as early as 12 hour post-infection, suggesting that the pneumococcal competence regulon plays an important role in adapting pneumococcus to the stressful lung environment. Among others, we report novel finding that the pneumococcal histidine triad (
pht
) family of genes participates in the adaptation to the lung environment and regulates pneumococcal competence induction.
Pseudomonas
-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda (
Ailuropoda melanoleuca
)
Authors: Ning Ruihong , Li Caiwu , Xia Maohua , Zhang Yu , Gan Yunong , Huang Yan , Zhang Tianyou , Song Haitao , Zhang Siyuan , Guo Wei 
Published: February 2024

ABSTRACT

Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda’s gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and
p
-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically,
Pseudomonas
, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three
Pseudomonas
-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability
in vitro
. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism.

IMPORTANCE

Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and
p
-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically,
Pseudomonas
, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein,
Pseudomonas
-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via
Pseudomonas
, as the main lignin-degrading bacteria.
Explainable machine learning for breast cancer diagnosis from mammography and ultrasound images: a systematic review
Authors: Gurmessa Daraje kaba , Jimma Worku 
Published: February 2024

BackgroundBreast cancer is the most common disease in women. Recently, explainable artificial intelligence (XAI) approaches have been dedicated to investigate breast cancer. An overwhelming study has been done on XAI for breast cancer. Therefore, this study aims to review an XAI for breast cancer diagnosis from mammography and ultrasound (US) images. We investigated how XAI methods for breast cancer diagnosis have been evaluated, the existing ethical challenges, research gaps, the XAI used and the relation between the accuracy and explainability of algorithms.MethodsIn this work, Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist and diagram were used. Peer-reviewed articles and conference proceedings from PubMed, IEEE Explore, ScienceDirect, Scopus and Google Scholar databases were searched. There is no stated date limit to filter the papers. The papers were searched on 19 September 2023, using various combinations of the search terms ‘breast cancer’, ‘explainable’, ‘interpretable’, ‘machine learning’, ‘artificial intelligence’ and ‘XAI’. Rayyan online platform detected duplicates, inclusion and exclusion of papers.ResultsThis study identified 14 primary studies employing XAI for breast cancer diagnosis from mammography and US images. Out of the selected 14 studies, only 1 research evaluated humans’ confidence in using the XAI system—additionally, 92.86% of identified papers identified dataset and dataset-related issues as research gaps and future direction. The result showed that further research and evaluation are needed to determine the most effective XAI method for breast cancer.ConclusionXAI is not conceded to increase users’ and doctors’ trust in the system. For the real-world application, effective and systematic evaluation of its trustworthiness in this scenario is lacking.PROSPERO registration numberCRD42023458665.
Single session of interpretation bias modification helped to improve fear of COVID-19 and COVID-19-related post-traumatic stress symptoms
Authors: Zhang Fan , Xu Huijing , Liu Qian , Sun Yingchao , Yan Wenjie , Ouyang Hui , Liu Weizhi 
Published: February 2024

BackgroundPost-traumatic stress symptoms (PTSS) are frequently observed in those who have experienced trauma events like the COVID-19 outbreak. The cognitive model of PTSS highlights the relationship between PTSS and negative interpretation bias.ObjectiveThe present study aimed to modify interpretation bias and to improve PTSS as well as PTSS-related fear.Methods59 participants with high PTSS levels were recruited and randomly allocated to either the interpretation modification programme (IMP) intervention group or the interpretation control condition (ICC) control group. PTSS, negative interpretation bias, fear of COVID-19, and depression and anxiety symptoms were assessed before and after training.FindingsIntention-to-treat analyses showed that compared with ICC, participants receiving IMP generated fewer negative interpretations for ambiguous scenarios, and the group-by-time interaction effect was significant. IMP also illustrated a more significant change in fear after training compared with ICC. Although no effects of training conditions were found on PTSS, the interaction of training conditions with fear reduction could predict PTSS improvement.ConclusionsIMP could improve negative interpretations and fear related to COVID-19 and might help to ameliorate PTSS.Clinical implicationsThe role of PTSS-related emotion should be considered when exploring the effectiveness of IMP. IMP is a flexible approach that can be tailored to the specific characteristics of the traumatic event, which makes it suitable for a broader range of traumatised individuals.
Perceptions and attitudes of women in the perinatal period towards male midwives in a rural district of Ghana: a descriptive, exploratory qualitative study
Authors: Boakye Dorothy Serwaa , Amoah Vida Maame Kissiwaa , Amoah Christian , Damte Felix Kofi Kofi , Poku Adjoa Afriyie , Boateng Edward Appiah , Ataara Naomi , Gyekye Sandra Twum , Dzomeku Veronica 
Published: February 2024

ObjectiveThe study sought to explore the perceptions and attitudes of women in the perinatal period towards the reproductive health services of male midwives.DesignThe study adopted an in-depth exploratory descriptive design for data collection and themes extracted using thematic analysis.SettingAntenatal and postpartum units of two primary healthcare facilities in the Kwabre-East District of Ghana.Participants20 women in the perinatal period who were receiving antenatal care and delivery services from the facilities included in the study were recruited through purposive sampling.FindingsDivergent views emerged among our participants regarding the acceptability and utilisation of perinatal services provided by male midwives. Some participants perceived male midwives as patient, supportive, caring, compassionate and skilful at their work while the negative attitude related to some participants perceiving their interactions with male midwives as an opportunity for sexual violation. Positive attitudes emanated from male midwives’ empathetic behaviour, reception, privacy and confidentiality of information. Conversely, negative attitudes arose from a lack of awareness of the changing female gender domination in midwifery, fear and misconceptions. Finally, participants faced various challenges, rooted in culture, which impacted their acceptance of male midwifery services.ConclusionsFactors influencing participants’ negative perceptions and attitudes towards male midwives were born out of culturally motivated and gender-sensitive stereotyping rather than male professional midwifery competencies. The study outcome provides the basis and the need for a community-based intervention to effect changes in the perception and attitude of women in the perinatal period towards male midwifery practice in the affected communities. Increasing awareness of the existence of male midwives in the communities would contribute to increasing acceptance and utilisation of their services among women in the perinatal period in Ghana.
What might make nurses stay? A protocol for discrete choice experiments to understand NHS nurses’ preferences at early-career and late-career stages
Authors: Ejebu Ourega-Zoé , Turnbull Joanne , Atherton Iain , Rafferty Anne Marie , Palmer Billy , Philippou Julia , Prichard Jane , Jamieson Michelle , Rolewicz Lucina , Williams Matthew , Ball Jane 
Published: February 2024

IntroductionLike many countries, England has a national shortage of registered nurses. Employers strive to retain existing staff, to ease supply pressures. Disproportionate numbers of nurses leave the National Health Services (NHS) both early in their careers, and later, as they near retirement age. Research is needed to understand the job preferences of early-career and late-career nurses working in the NHS, so tailored policies can be developed to better retain these two groups.Methods and analysisWe will collect job preference data for early-career and late-career NHS nurses, respectively using two separate discrete choice experiments (DCEs). Findings from the literature, focus groups, academic experts and stakeholder discussions will be used to identify and select the DCE attributes (ie, job features) and levels. We will generate an orthogonal, fractional factorial design using the experimental software Ngene. The DCEs will be administered through online surveys distributed by the regulator Nursing and Midwifery Council. For each group, we expect to achieve a final sample of 2500 registered NHS nurses working in England. For early-career nurses, eligible participants will be registered nurses who graduated in the preceding 5 years (ie, 2019–2023). Eligible participants for the late-career survey will be registered nurses aged 55 years and above. We will use conditional and mixed logit models to analyse the data. Specifically, study 1 will estimate the job preferences of early-career nurses and the possible trade-offs. Study 2 will estimate the retirement preferences of late-career NHS nurses and the potential trade-offs.Ethics and disseminationThe research protocol was reviewed and approved by the host research organisation Ethics Committees Research Governance (University of Southampton, number 80610) (https://www.southampton.ac.uk/about/governance/regulations-policies/policies/ethics). The results will be disseminated via conference presentations, publications in peer-reviewed journals and annual reports to key stakeholders, the Department of Health and Social Care, and NHS England/Improvement retention leaders.Registration detailsRegistration on OSFhttp://doi.org/10.17605/OSF.IO/RDN9G.
Systematic review of best practices for GPS data usage, processing, and linkage in health, exposure science and environmental context research
Authors: Pearson Amber L , Tribby Calvin , Brown Catherine D , Yang Jiue-An , Pfeiffer Karin , Jankowska Marta M 
Published: February 2024

Global Positioning System (GPS) technology is increasingly used in health research to capture individual mobility and contextual and environmental exposures. However, the tools, techniques and decisions for using GPS data vary from study to study, making comparisons and reproducibility challenging.ObjectivesThe objectives of this systematic review were to (1) identify best practices for GPS data collection and processing; (2) quantify reporting of best practices in published studies; and (3) discuss examples found in reviewed manuscripts that future researchers may employ for reporting GPS data usage, processing and linkage of GPS data in health studies.DesignA systematic review.Data sourcesElectronic databases searched (24 October 2023) were PubMed, Scopus and Web of Science (PROSPERO ID: CRD42022322166).Eligibility criteriaIncluded peer-reviewed studies published in English met at least one of the criteria: (1) protocols involving GPS for exposure/context and human health research purposes and containing empirical data; (2) linkage of GPS data to other data intended for research on contextual influences on health; (3) associations between GPS-measured mobility or exposures and health; (4) derived variable methods using GPS data in health research; or (5) comparison of GPS tracking with other methods (eg, travel diary).Data extraction and synthesisWe examined 157 manuscripts for reporting of best practices including wear time, sampling frequency, data validity, noise/signal loss and data linkage to assess risk of bias.ResultsWe found that 6% of the studies did not disclose the GPS device model used, only 12.1% reported the per cent of GPS data lost by signal loss, only 15.7% reported the per cent of GPS data considered to be noise and only 68.2% reported the inclusion criteria for their data.ConclusionsOur recommendations for reporting on GPS usage, processing and linkage may be transferrable to other geospatial devices, with the hope of promoting transparency and reproducibility in this research.PROSPERO registration numberCRD42022322166.
Experiences and opinions of general practitioners with patient online record access: an online survey in England
Authors: Blease Charlotte R , Kharko Anna , Dong Zhiyong , Jones Ray B , Davidge Gail , Hagglund Maria , Turner Andrew , DesRoches Catherine , McMillan Brian 
Published: February 2024

ObjectiveTo describe the experiences and opinions of general practitioners (GPs) in England regarding patients having access to their full online GP health records.DesignConvenience sample, online survey.Participants400 registered GPs in England.Main outcome measuresInvestigators measured GPs’ experiences and opinions about online record access (ORA), including patient care and their practice.ResultsA total of 400 GPs from all regions of England responded. A minority (130, 33%) believed ORA was a good idea. Most GPs believed a majority of patients would worry more (364, 91%) or find their GP records more confusing than helpful (338, 85%). Most GPs believed a majority of patients would find significant errors in their records (240, 60%), would better remember their care plan (280, 70%) and feel more in control of their care (243, 60%). The majority believed they will/already spend more time addressing patients’ questions outside of consultations (357, 89%), that consultations will/already take significantly longer (322, 81%) and that they will be/already are less candid in their documentation (289, 72%) after ORA. Nearly two-thirds of GPs believed ORA would increase their litigation (246, 62%).ConclusionsSimilar to clinicians in other countries, GPs in our sample were sceptical of ORA, believing patients would worry more and find their records more confusing than helpful. Most GPs also believed the practice would exacerbate work burdens. However, the majority of GPs in this survey also agreed there were multiple benefits to patients having online access to their primary care health records. The findings of this survey also contribute to a growing body of contrastive research from countries where ORA is advanced, demonstrating clinicians are sceptical while studies indicate patients appear to derive multiple benefits.
Clinical characteristics and outcomes of traumatic brain injury in patients admitted to surgical ward of Jimma Medical Center, Southwest Ethiopia: a prospective observational follow-up study
Authors: Dibera Gemechis Belay , Yizengaw Mengist Awoke , Yadeta Gemechu Lemi , Iticha Dinka Dugassa , Gamachu Busha , Legesse Bruck Tesfaye 
Published: February 2024

ObjectiveTo assess the Clinical Characteristics and Outcomes of Traumatic Brain Injury in Patients Admitted to the Surgical Ward of Jimma Medical Center, Southwest Ethiopia from January to July 2022.Design and settingA hospital-based prospective observational study was conducted among 175 patients admitted with Traumatic Brain Injury at Jimma Medical Center from January to July 2022. Data were collected by structured questionnaires and a convenient sampling technique was used. For data entry, Epidata V.4.6.0.5 software was used and exported to Stata V.14.0.2 for analysis. The Cox regression model was fitted to evaluate the predictors of mortality and variables with a p value <0.05 at 95% CI were taken as statistically significant predictors.ResultsThe incidence of in-hospital mortality was 22 (12.6%). The mean length of hospital stay was 6 days. In-hospital complications were recorded in 32.0% of patients. A Glasgow Coma Scale (GCS) score of <8 on admission (adjusted HR (AHR)=6.2, 95% CI 0.75 to 51), hyperthermia (AHR: 1.7, 95% CI 1.02 to 3.05) and lack of prehospital care (AHR: 3.2, 95% CI 2.2 to 8.07) were predictors of mortality in patients with traumatic brain injury.ConclusionIn-hospital mortality was recorded in over one-tenth of patients with traumatic brain injury. The GCS score of <8 on admission, hyperthermia and lack of prehospital care positively affected the outcome of patients with traumatic brain injury. Screening of patients for hyperthermia and antipsychotics should be strengthened to reduce death. However, a multicentred study is needed for further evidence. Giving priority to the patients with those predictors will decrease the number of deaths.