bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helping students see bacteria in 3D: cellular models increase student learning about cell size and diffusion
Authors: Wollmuth Emily M. , Correa Alberto , Alvarado Obando Manuela , Smith Michelle K. , Buckley Daniel H. , Hefferon Kathleen L. , Angert Esther R. 
Published: October 2023

ABSTRACT
In the microbial world, cell size and shape impact physiology, but students struggle to visualize spatial relationships between cells and macromolecules. In prokaryotic cells, cell size is limited by reliance on diffusion for nutrient uptake and the transport of nutrients within the cell. Cells must also meet a minimum size threshold to accommodate essential cellular components such as ribosomes and DNA. Using 3D printing allows for the creation of custom models that can be influential teaching tools in the biology classroom. This lesson uses 3D cell models to teach students enrolled in an introductory microbiology course about bacterial cell size and the biological importance of surface-area-to-volume ratio. During the lesson, students interact with 3D cell models and discuss a series of questions in small groups. Student learning was assessed using quantitative and qualitative student response data collected pre- and post-lesson. Student achievement of learning objectives, and their confidence in their knowledge of these concepts, improved post-lesson, and these gains were statistically significant. Our findings suggest that interacting with 3D-printed cell models improves student understanding about bacterial cell size and diffusion.
Recurrent copy number variations in the human fungal pathogen
Candida parapsilosis
Authors: Selmecki Anna 
Published: October 2023

ABSTRACT

Candida parapsilosis
is an opportunistic fungal pathogen with increasing incidence in hospital settings worldwide; however, we lack a comprehensive understanding of the mechanisms promoting its virulence and drug resistance. Bergin et al. systematically quantify the frequency and effect of copy number variation (CNV) across 170 diverse clinical and environmental isolates of
C. parapsilosis
(Bergin SA, Zhao F, Ryan AP, Müller CA, Nieduszynski CA, Zhai B, Rolling T, Hohl TM, Morio F, Scully J, Wolfe KH, Butler G, 2022, mBio,
https://doi.org/10.1128/mbio.01777-22
). Using a combination of both short- and long-read whole genome sequencing techniques, they determine the structure and copy number of two CNVs that arose recurrently throughout the evolution of these isolates. Each CNV predominantly amplifies one coding sequence (
ARR3
or
RTA3
); however, the amplitude and recombination breakpoints are variable across the isolates. Amplification of
RTA3
correlates with drug resistance and deletion causes drug susceptibility. This study highlights the need for further research into the mechanisms and dynamics of CNV formation and the impact of these CNVs on virulence and drug resistance across diverse fungal pathogens.
Complete genome sequence of
Mycolicibacterium mageritense
strain H4_3_1 isolated from a hybrid biological-inorganic system reactor
Authors: Feng Xiang , Kazama Daichi , Sato Kozo , Kobayashi Hajime 
Published: October 2023

ABSTRACT

We report the complete genome of
Mycolicibacterium mageritense
strain H4_3_1, which was isolated from a reactor of a hybrid biological-inorganic system. This genome will provide useful information about hydrogen-oxidizing bacteria as well as mycolicibacteria in non-host environments.
Draft whole-genome sequences of
Bacillus
strains of potential probiotic for poultry
Authors: Ma Li Maria , Lopez Nicolas , Zhang Guodong 
Published: October 2023

ABSTRACT

Bacillus
species have been widely selected and used as probiotics for humans and animals. In this article, we reported draft whole-genome sequences of four
Bacillus
strains isolated from sourdough and chicken cecum and previously selected as potential probiotics for poultry. These genome sequences will provide a foundation for further characterization and understanding of their probiotic attributes.
The multidrug efflux pump regulator AcrR directly represses motility in
Escherichia coli
Authors: Maldonado Jessica , Czarnecka Barbara , Harmon Dana E. , Ruiz Cristian 
Published: October 2023

ABSTRACT

Efflux and motility are two key biological functions in bacteria. Recent findings have shown that efflux impacts flagellum biosynthesis and motility in
Escherichia coli
and other bacteria. AcrR is known to be the major transcriptional repressor of AcrAB-TolC, the main multidrug efflux pump in
E. coli
and other
Enterobacteriaceae
. However, the underlying molecular mechanisms of how efflux and motility are co-regulated remain poorly understood. Here, we have studied the role of AcrR in direct regulation of motility in
E. coli
. By combining bioinformatics, electrophoretic mobility shift assays (EMSAs), gene expression, and motility experiments, we have found that AcrR represses motility in
E. coli
by directly repressing transcription of the
flhDC
operon, but not the other flagellum genes/operons tested.
flhDC
encodes the master regulator of flagellum biosynthesis and motility genes. We found that such regulation primarily occurs by direct binding of AcrR to the
flhDC
promoter region containing the first of the two predicted AcrR-binding sites identified in this promoter. This is the first report of direct regulation by AcrR of genes unrelated to efflux or detoxification. Moreover, we report that overexpression of AcrR restores to parental levels the increased swimming motility previously observed in
E. coli
strains without a functional AcrAB-TolC pump, and that such effect by AcrR is prevented by the AcrR ligand and AcrAB-TolC substrate ethidium bromide. Based on these and prior findings, we provide a novel model in which AcrR senses efflux and then co-regulates efflux and motility in
E. coli
to maintain homeostasis and escape hazards.

IMPORTANCE

Efflux and motility play a major role in bacterial growth, colonization, and survival. In
Escherichia coli
, the transcriptional repressor AcrR is known to directly repress efflux and was later found to also repress flagellum biosynthesis and motility by Kim et al. (J Microbiol Biotechnol 26:1824–1828, 2016, doi: 10.4014/jmb.1607.07058). However, it remained unknown whether AcrR represses flagellum biosynthesis and motility directly and through which target genes, or indirectly because of altering the amount of efflux. This study reveals that AcrR represses flagellum biosynthesis and motility by directly repressing the expression of the
flhDC
master regulator of flagellum biosynthesis and motility genes, but not the other flagellum genes tested. We also show that the antimicrobial, efflux pump substrate, and AcrR ligand ethidium bromide regulates motility via AcrR. Overall, these findings support a novel model of direct co-regulation of efflux and motility mediated by AcrR in response to stress in
E. coli
.
Joining the bacterial conversation: increasing the cultivation efficiency of soil bacteria with acyl-homoserine lactones and cAMP
Authors: Lopez Marin Marco A. , Strejcek Michal , Uhlik Ondrej 
Published: October 2023

ABSTRACTBacteria need to be isolated in pure culture to gain access to the wide array of interesting functions they conceal. This is challenging because they do not live in isolation but instead in communities where they actively communicate and interact with each other. In this study, we aimed to increase the culturability of soil bacteria using three different signaling molecules: N-(3-oxohexanoyl)-L-homoserine lactone, N-octanoyl-L-homoserine lactone, and 3',5'-cyclic adenosine monophosphate (cAMP). The signals were added individually to soils suspended in PBS buffer to a final concentration of 5 µM. Soil suspensions were agitated for 24 hours, after which they were serially diluted and plated on tenfold-diluted Reasoner’s 2A agar that either contained or did not contain the same signaling molecule used during the extraction step. DNA was isolated from both soil suspensions and grown cultures and, after a high-throughput amplicon sequencing, differences in bacterial abundances and diversity were determined across treatments. To further explain the action of the signaling molecules on the treated soil communities, their metagenomic functions were predicted using the software PICRUSt2. N-octanoyl-L-homoserine lactone was found to increase the diversity observed on solid media, while N-(3-oxohexanoyl)-L-homoserine lactone and cAMP were not. Potentially novel isolates aided by the signaling molecules were affiliated with the generaPseudomonasandNocardioides.IMPORTANCEMicroorganisms are a repository of interesting metabolites and functions. Therefore, accessing them is an important exercise for advancing not only basic questions about their physiology but also to advance technological applications. In this sense, increasing the culturability of environmental microorganisms remains an important endeavor for modern microbiology. Because microorganisms do not live in isolation in their environments, molecules can be added to the cultivation strategies to “inform them” that they are present in growth-permissive environmental conditions. Signaling molecules such as acyl-homoserine lactones and 3',5'-cyclic adenosine monophosphate belong to the plethora of molecules used by bacteria to communicate with each other in a phenomenon called quorum sensing. Therefore, including quorum sensing molecules can be an incentive for microorganisms, specifically soil bacteria, to increase their numbers on solid media.
Effect of multi-level interventions on mental health outcomes among adolescents in sub-Saharan Africa: a systematic review
Authors: Mthiyane Nondumiso , Rapulana Antony M , Harling Guy , Copas Andrew , Shahmanesh Maryam 
Published: October 2023

ObjectiveIn sub-Saharan Africa (SSA), multiple factors contribute to the considerable burden of mental health disorders among adolescents, highlighting the need for interventions that address underlying risks at multiple levels. We reviewed evidence of the effectiveness of community or family-level interventions, with and without individual level interventions, on mental health disorders among adolescents in SSA.DesignSystematic review using the Grades of Recommendation, Assessment, Development and Evaluation approach.Data sourcesA systematic search was conducted on Cochrane Library, MEDLINE, EMBASE, PSYCINFO and Web of Science up to 31 March 2021.Eligibility criteriaStudies were eligible for inclusion in the review if they were randomised controlled trials (RCTs) or controlled quasi-experimental studies conducted in sub-Saharan African countries and measured the effect of an intervention on common mental disorders in adolescents aged 10–24 years.Data extraction and synthesisWe included studies that assessed the effect of interventions on depression, anxiety, post-traumatic stress disorder and substance abuse. Substance abuse was only considered if it was measured alongside mental health disorders. The findings were summarised using synthesis without meta-analysis, where studies were grouped according to the type of intervention (multi-level, community-level) and participants.ResultsOf 1197 studies that were identified, 30 studies (17 RCTs and 3 quasi-experimental studies) were included in the review of which 10 delivered multi-level interventions and 20 delivered community-level interventions. Synthesised findings suggest that multi-level interventions comprise economic empowerment, peer-support, cognitive behavioural therapy were effective in improving mental health among vulnerable adolescents. Majority of studies that delivered interventions to community groups reported significant positive changes in mental health outcomes.ConclusionsThe evidence from this review suggests that multi-level interventions can reduce mental health disorders in adolescents. Further research is needed to understand the reliability and sustainability of these promising interventions in different African contexts.PROSPERO registration numberCRD42021258826.
Silver linings of ADHD: a thematic analysis of adults’ positive experiences with living with ADHD
Authors: Nordby Emilie S. , Guribye Frode , Nordgreen Tine , Lundervold Astri J. 
Published: October 2023

ObjectivesTo identify and explore positive aspects of attention deficit hyperactivity disorder (ADHD) as reported by adults with the diagnosis.DesignThe current study used a qualitative survey design including the written responses to an open-ended question on positive aspects of ADHD. The participants’ responses were analysed using thematic analysis.SettingThe participants took part in trial of a self-guided internet-delivered intervention in Norway. As part of the intervention, the participants were asked to describe positive aspects of having ADHD.ParticipantsThe study included 50 help-seeking adults with an ADHD diagnosis.ResultsThe participants described a variety of positive aspects related to having ADHD. The participants’ experiences were conceptualised and thematically organised into four main themes: (1) the dual impact of ADHD characteristics; (2) the unconventional mind; (3) the pursuit of new experiences and (4) resilience and growth.ConclusionsHaving ADHD was experienced as both challenging and beneficial, depending on the context and one’s sociocultural environment. The findings provide arguments for putting a stronger emphasis on positive aspects of ADHD, alongside the challenges, in treatment settings.Trial registration numberNCT04511169
Comparing persistence of new biologics to conventional anti-TNF alphas in adult patients with inflammatory bowel disease: a systematic review and meta-analysis protocol
Authors: Yiu Tsz Hong , Ko Yanna , Pudipeddi Aviv , Natale Patrizia , Leong Rupert W 
Published: October 2023

BackgroundBiological therapy is a cornerstone of managing moderate-to-severe inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn’s disease (CD). New biologics have been evolving over the past 20 years and selection of an agent remains challenging.Drug persistence measures the duration of time from initiation to discontinuation of a therapy, which can be a surrogate marker of drug tolerance and efficacy.ObjectivesThe study aimed to compare drug persistence of new generation biologics for the treatment of UC and CD (vedolizumab, ustekinumab, certolizumab, tofacitinib, natalizumab and golimumab) with conventional anti-tumor necroisis factor alphas (anti-TNF alphas) (adalimumab and infliximab) in adult patients with IBD. Results of the study may provide guidance on the preferred first and subsequent lines of biological treatments in patients with IBD.Methods and analysisSearch via electronic databases including EMBASE, MEDLINE, PubMed and clinical trial databases will be conducted on 10 March 2023 with eligible studies included from inception of 2017 to 2023. The primary outcomes are 1-year persistence of individual biologics with comparison of new biologics versus conventional anti-TNF alphas. A meta-analysis will be conducted using Review Manager V.5 and outcome will be presented as relative risk. Heterogeneity will be assessed with forest plot, χ2and I2, followed with sensitivity analysis and subgroup analysis. Finally, the Grading of Recommendations Assessment, Development and Evaluation system will be used to assess the quality of evidence.Ethics and disseminationEthical approval is not required as no private information of participants will be used. Results of the present study will be disseminated in a peer-reviewed journal or conference presentation.PROSPERO registration numberCRD42023392236.
Correlation of drug exposure and bacterial susceptibility with treatment response forMycobacterium avium complexlung disease: protocol for a prospective observational cohort study
Authors: Zheng Xubin , Wang Li , Davies Forsman Lina , Zhang Yangyi , Chen Yuhang , Luo Xuejiao , Liu Yidian , Bruchfeld Judith , Hu Yi , Alffenaar Jan-Willem C , Sha Wei , Xu Biao 
Published: October 2023

IntroductionThe burden ofMycobacterium avium complex(MAC) lung disease is increasing globally and treatment outcome is in general poor. Therapeutic drug monitoring has the potential to improve treatment outcome by ensuring adequate drug exposure. However, very limited population-based studies exist for MAC lung disease. This study aims to describe the distribution of drug exposure for key antimycobacterial drugs at population level, and to analyse them in relationship to treatment outcome in patients with MAC lung disease.Methods and analysisA prospective cohort aiming to include 100 adult patients diagnosed with and treated for MAC lung disease will be conducted in Shanghai Pulmonary Hospital, China. Blood samples will be collected after 1 month MAC treatment for measurement of macrolides, rifamycin, ethambutol, amikacin and/or fluoroquinolones, using a validated liquid-chromatography tandem mass spectrometry method. Respiratory samples will be collected at inclusion and once every 3 months for mycobacterial culture until treatment completion. Minimum inhibitory concentration (MIC) determination will be performed using a commercial broth microdilution plate. In addition to mycobacterial culture, disease severity and clinical improvement will be assessed from the perspective of lung function, radiological presentation and self-reported quality of life. Whole genome sequencing will be performed for any longitudinal isolates with significant change of MIC to explore the emergence of drug resistance-conferring mutations. The relationship between drug exposure and treatment outcome will be analysed and potential confounders will be considered for adjustment in multivariable models. Meanwhile, the associations between drug exposure in relation to MIC and markers of treatment response will be explored using Cox proportional hazards or binary logistic regression models, as appropriate.Ethics and disseminationThis study has been approved by the ethics committee of Shanghai Pulmonary Hospital (No. K22-149Z). Written and oral informed consent will be obtained from all participants. The study results will be submitted to a peer-reviewed journal.Trial registeration numberNCT05824988.
Improving the quality of the fracture liaison service through the implementation of a structured health record
Authors: Djuv Ane , Harboe Knut , Nysted Hege , Kirkhus Toril Kristin , Horpestad Oda , Birkeland Fredrik Holten , Mehl Birgitte Wågsæther , Johnsen Erlend , Paulsen Aksel 
Published: October 2023

ObjectiveAccording to the best practice framework for secondary fracture prevention, all patients aged ≥50 years with a fracture should be assessed for osteoporosis within the fracture liaison service (FLS). The framework includes an FLS quality registry database to ensure quality. The input of data into our FLS registry was time-consuming and required entering data twice: into both the journal record and the registry. A ‘3-in-1’ solution was required: (1) developing a structured health record (SHR) to provide decision-support to FLS nurses during patient consultations; (2) making a structured journal record from the SHR and (3) exporting data to the quality registry database. The SHR needed to be web based, secure and available for use all over the world.DesignOne provider at Stavanger University Hospital met all the criteria for further development of the record (CheckWare). An interdisciplinary working group was established, following the Plan–Do–Study–Act working model. Depending on the answers given, the FLS nurses were provided decision-making support. A significant loss of height (≥4 cm) was highlighted as one of the process quality indicators. All clinically relevant data were summarised in a report, which was exported to the health record software. Data were exported to the FLS quality registry.ResultsAll fracture patients in need of a dual-energy X-ray absorptiometry scan received an appointment at the FLS outpatient clinic and 96% attended. The minimum standard was met for the three quality indicators 1–3). In particular, the use of SHRs increased the number of patients investigated for vertebral fractures with a height loss ≥4 cm from 67% to 93%.ConclusionThe SHR was successful in regard to the ‘3-in-1’ solution: providing decision support to FLS nurses, developing structured journal records and exporting data to the FLS quality registry. After implementation, all FLS registry quality indicators improved.
Are we achieving the standards of good nutritional care for older people in hospital with fragility fractures?
Authors: Sahota Amunpreet , Marsh Kirandeep , Avery Amanda , Sahota Opinder 
Published: October 2023

Malnutrition is common in older people with fragility fractures and is associated with poor clinical outcomes and increased risk of complications. The UK National Health Service has published national standards for food and drink for patients, staff and visitors, in hospitals. These standards describe the methods to ensure quality and sustainability.We assessed these standards and report the nutritional status of older (70 years of age) patients admitted to hospital with fragility fracture, and weighed food trolley and plate waste after lunch and supper for five days.There were 19 older patients with fragility fractures on the trauma and orthopaedic ward. The mean intake for 'nutritionally well' was 1592 kcal/day and 65.7 g/day protein; the mean intake for 'nutritionally vulnerable' was 643 kcal/day and 24.8 g/day protein.Although all key characteristics of good nutrition and hydration care for patients in hospital were achieved, energy and protein intake was poor in the nutritionally vulnerable group. Further interventions are necessary to improve dietary intake in hospital, particularly in those who are nutritionally vulnerable.
Preventing the next fragility fracture: a cross-sectional survey of secondary fragility fracture prevention services worldwide
Authors: Singh Sonia , van den Berg Peter , Fergusson Kim , Martins Pinto Juliana , Koerner-Bungey Tasha , Chan Ding-Chen (Derrick) , Boonnasa Wararat , Javaid Muhaamad K , Speerin Robyn 
Published: October 2023

BackgroundThere has been an increasing awareness of the public health impact of fragility fractures due to osteoporosis and the imperative of addressing this health burden with well-designed secondary fragility fracture prevention services (SFFPS). The objectives of this survey, conducted within the international membership of the Fragility Fracture Network (FFN), were to identify gaps in services and identify the needs for further training and mentorship to improve the quality of SFFPS provided to patients who sustain fragility fractures.MethodsWe conducted an electronic cross-sectional survey of FFN Secondary Fracture Prevention Special Interest Group (SIG) members from April 2021 to June 2021 using SurveyMonkey. The survey questions were developed by four SIG members from New Zealand, Australia, Canada and the Netherlands, who have experience in developing, implementing and evaluating SFFPS. The sampling framework was convenience sampling of all 1162 registered FFN Secondary Fracture Prevention SIG members. Descriptive analyses were performed for all variables and presented as frequencies and percentages.Results69 individuals participated in the survey, from 34 different countries over six continents, with a response rate of 6% (69/1162). Almost one-third of respondents (22/69) were from 15 countries within the European continent. Key findings included: (1) 25% of SFFPS only included patients with hip fracture; (2) less than 5% of SFFPS had any mandatory core competencies for training; (3) 38.7% of SFFPS were required to collect key performance indicators; and (4) 9% were collecting patient-reported outcome measures.ConclusionsThis survey identified key areas for improving SFFPS, including: expanding the reach of SFFPS to more patients with fragility fracture, developing international core competencies for health provider training, using key performance indicators to improve SFFPS and including the patient voice in SFFPS development. These findings will be used by the FFN to support SFFPS development internationally.