bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel mechanism of hydrogen peroxide for promoting efficient natamycin synthesis in
Streptomyces
Authors: Zong Gongli , Cao Guangxiang , Fu Jiafang , Zhang Peipei , Chen Xi , Yan Wenxiu , Xin Lulu , Wang Zhongxue , Xu Yan , Zhang Rongzhen 
Published: September 2023

ABSTRACT

The mechanism of regulation of natamycin biosynthesis by Streptomyces in response to oxidative stress is unclear. Here, we first show cholesterol oxidase SgnE, which catalyzes the formation of H
2
O
2
from sterols, triggered a series of redox-dependent interactions to stimulate natamycin production in
S. gilvosporeus
. In response to reactive oxygen species, residues Cys212 and Cys221 of the H
2
O
2
-sensing consensus sequence of OxyR were oxidized, resulting in conformational changes in the protein: OxyR extended its DNA-binding domain to interact with four motifs of promoter p

sgnM

. This acted as a redox-dependent switch to turn on/off gene transcription of
sgnM
, which encodes a cluster-situated regulator, by controlling the affinity between OxyR and p

sgnM

, thus regulating the expression of 12 genes in the natamycin biosynthesis gene cluster. OxyR cooperates with SgnR, another cluster-situated regulator and an upstream regulatory factor of SgnM, synergistically modulated natamycin biosynthesis by masking/unmasking the −35 region of p

sgnM

depending on the redox state of OxyR in response to the intracellular H
2
O
2
concentration.

IMPORTANCE

Cholesterol oxidase SgnE is an indispensable factor, with an unclear mechanism, for natamycin biosynthesis in
Streptomyces
. Oxidative stress has been attributed to the natamycin biosynthesis. Here, we show that SgnE catalyzes the formation of H
2
O
2
from sterols and triggers a series of redox-dependent interactions to stimulate natamycin production in
S. gilvosporeus
. OxyR, which cooperates with SgnR, acted as a redox-dependent switch to turn on/off gene transcription of
sgnM
, which encodes a cluster-situated regulator, by masking/unmasking its −35 region, to control the natamycin biosynthesis gene cluster. This work provides a novel perspective on the crosstalk between intracellular ROS homeostasis and natamycin biosynthesis. Application of these findings will improve antibiotic yields via control of the intracellular redox pressure in
Streptomyces
.
The Fourier-transform infrared spectroscopy-based method as a new typing tool for
Candida parapsilosis
clinical isolates
Authors: De Carolis Elena , Posteraro Brunella , Falasca Benedetta , Spruijtenburg Bram , Meis Jacques F. , Sanguinetti Maurizio 
Published: September 2023

ABSTRACT

The Fourier-transform infrared spectroscopy-based IR Biotyper is a straightforward typing tool for bacterial species, but its use with
Candida
species is limited. We applied IR Biotyper to
Candida parapsilosis
, a common cause of nosocomial bloodstream infection (BSI), which is aggravated by the intra-hospital spread of fluconazole-resistant isolates. Of 59
C
.
parapsilosis
isolates studied,
n
= 56 (48 fluconazole-resistant and 8 fluconazole-susceptible) and
n
= 3 (2 fluconazole-resistant and 1 fluconazole-susceptible) isolates, respectively, had been recovered from BSI episodes in 2 spatially distant Italian hospitals. The latter isolates served as an outgroup. Of fluconazole-resistant isolates,
n
= 40 (including one outgroup) harbored the Y132F mutation alone and
n
= 10 (including one outgroup) harbored both Y132F and R398I mutations in the
ERG11
-encoded azole-target enzyme. Using a microsatellite typing method, which relies on the amplification of genomic short tandem repeats (STR), two major clusters were obtained based on the mutation(s) (Y132F or Y132F/R398I) present in the isolates. Regarding IR Biotyper, each isolate was analyzed in quintuplicate using an automatic (i.e., proposed by the manufacturer’s software) or tentative (i.e., proposed by us) cutoff value. In the first case, four clusters were identified, with clusters I and II formed by Y132F or Y132F/R398I isolates, respectively. In the second case, six subclusters (derived by the split of clusters I and II) were identified. This allowed to separate the outgroup isolates from other isolates and to increase the IR Biotyper typeability. The agreement of IR Biotyper with STR ranged from 47% to 74%, depending on type of cutoff value used in the analysis.

IMPORTANCE

Establishing relatedness between clinical isolates of
Candida parapsilosis
is important for implementing rapid measures to control and prevent nosocomial transmission of this
Candida
species. We evaluated the FTIR-based IR Biotyper, a new typing method in the
Candida
field, using a collection of fluconazole-resistant
C. parapsilosis
isolates supposed to be genetically related due to the presence of the Y132F mutation. We showed that IR Biotyper was discriminatory but not as much as the STR method, which is still considered the method of choice. Further studies on larger series of
C. parapsilosis
isolates or closely related
Candida
species will be necessary to confirm and/or extend the results from this study.
Investigation of machine learning algorithms for taxonomic classification of marine metagenomes
Authors: Park Helen , Lim Shen Jean , Cosme Jonathan , O'Connell Kyle , Sandeep Jilla , Gayanilo Felimon , Cutter Jr. George R. , Montes Enrique , Nitikitpaiboon Chotinan , Fisher Sam , Moustahfid Hassan , Thompson Luke R. 
Published: September 2023

ABSTRACT
Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut microbiomes of invertebrates, fish, reptiles, and mammals. Assessments of marine microbial diversity are therefore critical to understanding spatiotemporal variations in microbial community structure and function in ocean ecosystems. With recent advances in DNA shotgun sequencing for metagenome samples and computational analysis, it is now possible to access the taxonomic and genomic content of ocean microbial communities to study their structural patterns, diversity, and functional potential. However, existing taxonomic classification tools depend upon manually curated phylogenetic trees, which can create inaccuracies in metagenomes from less well-characterized communities, such as from ocean water. Herein, we explore the utility of deep learning tools—DeepMicrobes and a novel Residual Network architecture—that leverage natural language processing and convolutional neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups) without reliance on a curated taxonomic tree. We trained both models using metagenomic reads simulated from marine microbial genomes in the MarRef database. The performance of both models (accuracy, precision, and percent microbe predicted) was compared with the standard taxonomic classification tool Kraken2 using 10 complex metagenomic data sets simulated from MarRef. Our results demonstrate that time, compute power, and microbial genomic diversity still pose challenges for machine learning (ML). Moreover, our results suggest that high genome coverage and rectification of class imbalance are prerequisites for a well-trained model, and therefore should be a major consideration in future ML work.

IMPORTANCE
Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.
Association between engagement in cultural activities and use of general practitioner consultations: 7-year follow-up of adults from the HUNT study, Norway.
Authors: Løkken Bente Irene , Sund Erik R , Krokstad Steinar , Bjerkeset Ottar , Rangul Vegar 
Published: September 2023

ObjectiveAssess whether engagement in a range of cultural activities, both ‘passive’ and ‘active’ (ie, receptive and creative) participation, is associated with later demand for general practitioner (GP) consultations.DesignLongitudinal prospective cohort study.SettingData from the population-based the third Survey of Trøndelag Health Study (2006–2008) in Norway was linked to an administrative register including service information from all GP offices nationwide.ParticipantsThis study included 17 396 (54.6%) women and 14 451 (45.4%) men aged 30–79 years.Main outcome measuresMultilevel negative binomial regression models assessed the relationship between cultural engagement and GP consultations, and reported as rate ratios.ResultsA mean of 3.57 GP visits per patient was recorded during the 7 years of follow-up. Participation in creative activities and a combination of both receptive and creative activities was associated with lower number of GP consultation. Gender-specific analyses suggest that these effects were attributable to men. The rate ratio of GP consultations among men taking part in creative activities less than once, twice and more than twice (<9 times) per week is 0.90, 0.89 and 0.87 times lower, respectively, compared with non-participants. Whereas weekly frequency of receptive and creative activity engagement showed a 0.92, 0.87 and 0.83 times lower rate ratio among engaged men. The variety of activities shows a similar pattern and participation in creative activities lowers the rate ratio among men. Engagement in a wide range/variety of activities, compared with non-engagement, was associated with lower numbers of GP consultations in men, but not women.ConclusionsEngagement in creative or combined receptive and creative cultural activities was associated with lower numbers of GP consultations among men. Thus, facilitating and promoting a culturally engaged lifestyle, particularly in men, may affect primary healthcare use. However, this study design gives no evidence of a causal relationship between cultural engagement and use of GP consultations.
Randomised controlled trial on the effect of video-conference cognitive behavioural therapy for patients with schizophrenia: a study protocol
Authors: Katsushima Masayuki , Nakamura Hideki , Hanaoka Hideki , Shiko Yuki , Komatsu Hideki , Shimizu Eiji 
Published: September 2023

IntroductionCognitive behavioural therapy for psychosis (CBTp) has demonstrated effectiveness in reducing positive symptoms, improving depression, enhancing coping skills and increasing awareness of illness. However, compared with cognitive behavioural therapy for depression and anxiety, the spread of CBTp in clinical practice is minimal. The present study designed a randomised controlled trial (RCT) research protocol to evaluate whether real-time remote video-conference CBTp (vCBTp) could facilitate access to psychosocial interventions and effectively improve symptoms compared with usual care (UC) for patients with schizophrenia.Methods and analysisThis exploratory RCT will consist of two parallel groups (vCBTp+UC and UC alone) of 12 participants (n=24) diagnosed with schizophrenia, schizoaffective disorder or paranoid disorder, who remain symptomatic following pharmacotherapy. Seven 50-min weekly vCBTp interventions will be administered to test efficacy. The primary outcome will be the positive and negative syndrome scale score at week 8. The secondary outcome will be the Beck Cognitive Insight Scale to assess insight, the Patient Health Questionnaire-9 to assess depression, the Generalised Anxiety Disorder-7 to assess anxiety, the 5-level EuroQol 5-dimensional questionnaire to assess quality of life and the Impact of Event Scale-Revised to assess subjective distress about a specific stressful life event. We will take all measurements at 0 weeks (baseline) and at 8 weeks (post-intervention), and apply intention-to-treat analysis.Ethics and disseminationWe will conduct this study in the outpatient department of Cognitive Behavioral Therapy Center at Chiba University Hospital. Further, all participants will be informed of the study and will be asked to sign consent forms. We will report according to the Consolidated Standards of Reporting Trials.Trial registration numberUMIN000043396.
A nomogram for predicting hospital mortality of critical ill patients with sepsis and cancer: a retrospective cohort study based on MIMIC-IV and eICU-CRD
Authors: Yuan Zhen-nan , Xue Yu-juan , Wang Hai-jun , Qu Shi-ning , Huang Chu-lin , Wang Hao , Zhang Hao , Xing Xue-zhong 
Published: September 2023

ObjectiveSepsis remains a high cause of death, particularly in immunocompromised patients with cancer. The study was to develop a model to predict hospital mortality of septic patients with cancer in intensive care unit (ICU).DesignRetrospective observational study.SettingMedical Information Mart for Intensive Care IV (MIMIC IV) and eICU Collaborative Research Database (eICU-CRD).ParticipantsA total of 3796 patients in MIMIC IV and 549 patients in eICU-CRD were included.Primary outcome measuresThe model was developed based on MIMIC IV. The internal validation and external validation were based on MIMIC IV and eICU-CRD, respectively. Candidate factors were processed with the least absolute shrinkage and selection operator regression and cross-validation. Hospital mortality was predicted by the multivariable logistical regression and visualised by the nomogram. The model was assessed by the area under the curve (AUC), calibration curve and decision curve analysis curve.ResultsThe model exhibited favourable discrimination (AUC: 0.726 (95% CI: 0.709 to 0.744) and 0.756 (95% CI: 0.712 to 0.801)) in the internal and external validation sets, respectively, and better calibration capacity than Acute Physiology and Chronic Health Evaluation IV in external validation.ConclusionsDespite that the predicted model was based on a retrospective study, it may also be helpful to predict the hospital morality of patients with solid cancer and sepsis.
Pharmacists’ approaches to vaccination consultations in Switzerland: a qualitative study comparing the roles of complementary and alternative medicine (CAM) and biomedicine
Authors: Zimmermann Clara , Jusufoska Meliha , Tolic Josipa , Abreu de Azevedo Marta , Tarr Philip E , Deml Michael J 
Published: September 2023

BackgroundMany community pharmacies in Switzerland provide complementary and alternative medicine (CAM) approaches in addition to providing biomedical services, and a few pharmacies specialise in CAM. A common perception is that CAM providers are sceptical towards, or opposed to, vaccination.ObjectivesKey objectives of this study are to examine the potential roles of biomedically oriented and CAM-specialised pharmacists regarding vaccine counselling and to better understand the association between vaccine hesitancy and CAM.DesignWe conducted semistructured, qualitative interviews. Transcripts were coded and analysed using thematic analysis. Interview questions were related to: type of pharmaceutical care practised, views on CAM and biomedicine, perspectives on vaccination, descriptions of vaccination consultations in community pharmacies and views on vaccination rates.SettingQualitative interviews in three language regions of Switzerland (German, French and Italian).ParticipantsWe interviewed 18 pharmacists (N=11 biomedically oriented, N=7 CAM specialised).ResultsPharmacist participants expressed generally positive attitudes towards vaccination. Biomedically oriented pharmacists mainly advised customers to follow official vaccination recommendations but rarely counselled vaccine-hesitant customers. CAM-specialised pharmacists were not as enthusiastic advocates of the Swiss vaccination recommendations as the biomedically oriented pharmacists we interviewed. Rather, they considered that each customer should receive individualised, nuanced vaccination advice so that customers can reach their own decisions. CAM-specialised pharmacists described how mothers in particular preferred getting a second opinion when they felt insufficiently advised by biomedically oriented paediatricians.ConclusionsVaccination counselling in community pharmacies represents an additional option to customers who have unmet vaccination consultation needs and who seek reassurance from healthcare professionals (HCPs) other than physicians. By providing individualised vaccination counselling to vaccine-hesitant customers, CAM-specialised pharmacists are likely meeting specific needs of vaccine-hesitant customers. As such, research and implementation efforts should more systematically involve pharmacists as important actors in vaccination provision. CAM-specialised pharmacists particularly should not be neglected as they are important HCPs who counsel vaccine-hesitant customers.
Effects of mass casualty incidents on anxiety, depression and PTSD among doctors and nurses: a systematic review protocol
Authors: Uddin Helal , Hasan Md Khalid , Castro-Delgado Rafael 
Published: September 2023

IntroductionBoth doctors and nurses showed a greater risk of being exposed to different mental health conditions following mass casualties. This systematic review aims to synthesise the existing evidence on the prevalence of anxiety, depression and post-traumatic stress disorder and their associated risk factors among doctors and nurses following mass casualty incidents.Methods and analysisSeven electronic databases (PubMed, PsycINFO, MEDLINE Ovid, Embase, CINAHL, Web of Science and Nursing & Allied Health database) will be searched from 2010 to 2022 with peer-reviewed articles in English language using the predefined keywords. Two reviewers will independently screen the titles and abstracts, as well as review the full texts using the eligibility criteria, then extract data independently. The National Institutes of Health Quality Assessment Tools (NIH-QAT) for quantitative studies, the Critical Appraisal Skills Programme (CASP) Checklist for qualitative studies and the Mixed-Methods Appraisal Tool (MMAT) for mixed-method studies will be used to measure the quality appraisal of eligible studies. A third reviewer will resolve the discrepancies when the two reviewers cannot reach an agreement in any step. The result from the eligible studies will be described following narrative synthesis with the key characteristics and findings of the included studies, and meta-analysis will be performed, if applicable.Ethics and disseminationThis systematic review deals with existing published studies without any personally identifiable information of participants. Therefore, ethical approval from the research committee is not required. Findings from this review will be disseminated in peer-reviewed journals and presented at relevant international conferences.PROSPERO registration numberCRD42023412852.
Patient experiences of Cytosponge: a qualitative study
Authors: Neilson Laura Jane , Fitzgerald Rebecca C , Deane Jennifer , Debiram-Beecham Irene , Gulle Halime , Rees Colin , Sharp Linda 
Published: September 2023

ObjectiveCytosponge is a novel technology for oesophageal pathology diagnosis. Uses include diagnosis of Barrett’s oesophagus and as a triage tool to prioritise upper gastrointestinal endoscopy. Patient experience is a key component of quality care. Previous work has developed endoscopy patient-reported experience measures. An appropriate tool to measure patient experience of Cytosponge is required. The aim of this work was to describe the patient experience of Cytosponge.Design/MethodIndividuals aged 18 years or over, who had undergone Cytosponge from September 2020 to March 2021, were invited to participate in a semi-structured interview. Interviews were audio-recorded, transcribed verbatim and anonymised. Thematic analysis was undertaken. Themes were organised into two overarching areas relating to patient experiences and patient perceptions of the test.Results19 patients underwent interview (aged 37–80 years, 13 male). In terms of patient experiences of Cytosponge, five themes were identified: emotional reaction; expectations; environment and physical process; sensory experience; communication and information. All themes were present across all procedural phases, aside from sensory experience which was only present during the test. With regard to perception of the test, two major themes were identified: test novelty (encompassing patient awareness of the test and reaction to the new test) and trusting the test results.ConclusionPatients must remain central to novel technologies such as Cytosponge. Measuring patient experience is essential to achieve that. This study demonstrates five major themes which describe the patient experience of this procedure. These have been used to adapt the Newcastle ENDOPREM for use in Cytosponge.
Preoperative cerebral angiography nearly doubles the rate of diffusion-weighted imaging lesion detection following minimally invasive surgery for intracerebral hemorrhage
Authors: Rossitto Christina P , Vasan Vikram , Downes Margaret H , Yildiz Sema , Smith Colton J , Liang John W , Schupper Alexander J , Hardigan Trevor , Liu Xinyan , Ali Muhammad , Chapman Emily K , Devarajan Alex , Odland Ian C , Kellner Christopher P , Mocco J 
Published: September 2023

BackgroundDiffusion-weighted imaging (DWI) lesions have been linked to poor outcomes after intracerebral hemorrhage (ICH). We aimed to assess the impact of cerebral digital subtraction angiography (DSA) on the presence of DWI lesions in patients who underwent minimally invasive surgery (MIS) for ICH.MethodsRetrospective chart review was performed on ICH patients treated with MIS in a single health system from 2015 to 2021. One hundred and seventy consecutive patients who underwent postoperative MRIs were reviewed. Univariate analyses were conducted to determine associations. Variables with p<0.05 were included in multivariate analyses.ResultsDWI lesions were present in 88 (52%) patients who underwent MIS for ICH. Of the 83 patients who underwent preoperative DSA, 56 (67%) patients demonstrated DWI lesions. In this DSA cohort, older age, severe leukoaraiosis, larger preoperative hematoma volume, and increased presenting National Institutes of Health Stroke Score (NIHSS) were independently associated with DWI lesion identification (p<0.05). In contrast, of 87 patients who did not undergo DSA, 32 (37%) patients demonstrated DWI lesions on MRI. In the non-DSA cohort, presenting systolic blood pressure, intraventricular hemorrhage, and NIHSS were independently associated with DWI lesions (p<0.05). Higher DWI lesion burden was independently associated with poor modified Rankin Scale (mRS) at 6 months on a univariate (p=0.02) and multivariate level (p=0.02).ConclusionsIn this cohort of ICH patients who underwent minimally invasive evacuation, preprocedural angiography was associated with the presence of DWI lesions on post-ICH evacuation MRI. Furthermore, the burden of DWI lesions portends a worse prognosis after ICH.