bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Candida albicans
reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates filamentation, biofilm formation, and oral commensalism
Authors: Glazier Virginia E. , Kramara Juraj , Ollinger Tomye , Solis Norma V. , Zarnowski Robert , Wakade Rohan S. , Kim Min-Ju , Weigel Gabriel J. , Liang Shen-Huan , Bennett Richard J. , Wellington Melanie , Andes David R. , Stamnes Mark A. , Filler Scott G. , Krysan Damian J. 
Published: September 2023

ABSTRACT

Candida albicans
is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effect of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of
C. albicans
. The
C. albicans
reference strain SC5314 is a
ROB1
heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946, resulting in a serine- or proline-containing isoform. An analysis of 224 sequenced
C. albicans
genomes indicates that SC5314 is the only
ROB1
heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the
ROB1
alleles are functionally distinct, and the rare

ROB1
946S

allele supports increased filamentation
in vitro
and increased biofilm formation
in vitro
and
in vivo
, suggesting it is a phenotypic gain-of-function allele. SC5314 is among the most highly filamentous and invasive strains characterized to date. Introduction of the

ROB1
946S

allele into a poorly filamenting clinical isolate increases filamentation, and conversion of an SC5314 laboratory strain to a

ROB1
946S

homozygote increases
in vitro
filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant

ROB1
946P

allele establishes a commensal state while the

ROB1
946S

phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of
C. albicans
phenotypic heterogeneity.

IMPORTANCE

Candida albicans
is a commensal fungus that colonizes the human oral cavity and gastrointestinal tract but also causes mucosal as well as invasive disease. The expression of virulence traits in
C. albicans
clinical isolates is heterogeneous and the genetic basis of this heterogeneity is of high interest. The
C. albicans
reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These findings explain, in part, the outlier phenotype of the reference strain and highlight the role heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
Genome sequence of bacteriophage Aoka, a cluster FO phage isolated using
Arthrobacter globiformis
Authors: Sasaoka Aidan , Arellano Olivia , Hatch Xavier R. , Garcia Costas Amaya M. 
Published: September 2023

ABSTRACT

We report the discovery and genome sequence of bacteriophage Aoka, an actinobacteriophage isolated from a soil sample in Pueblo, Colorado using
Arthrobacter globiformis
, B2880-SEA. Its genome length is 36,744 base pairs with 54 protein-coding genes. Based on gene content similarity to other actinobacteriophages, Aoka is assigned to cluster FO.
Fourier-transform infrared spectroscopy for typing of vancomycin-resistant
Enterococcus faecium
: performance analysis and outbreak investigation
Authors: Scheier T. C. , Franz J. , Boumasmoud M. , Andreoni F. , Chakrakodi B. , Duvnjak B. , Egli A. , Zingg W. , Ramette A. , Wolfensberger A. , Kouyos R. D. , Brugger S. D. 
Published: September 2023

ABSTRACT

Vancomycin-resistant Enterococci, mainly
Enterococcus faecium
(VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day.

IMPORTANCE

Vancomycin-resistant Enterococci, mainly
Enterococcus faecium
(VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.
Assessing the transmission risk of red sea bream iridovirus (RSIV) in environmental water: insights from fish farms and experimental settings
Authors: Kawato Yasuhiko , Takada Yuzo , Mizuno Kaori , Harakawa Shogo , Yoshihara Yusaku , Nakagawa Yukihiro , Kurobe Tomofumi , Kawakami Hidemasa , Ito Takafumi 
Published: September 2023

ABSTRACT

Aquatic animal viruses are considered to be transmitted via environmental water between fish farms. This study aimed to understand the actual transmission risk of red sea bream iridovirus (RSIV) through environmental water among fish farms. An environmental DNA (eDNA) method using iron-based flocculation coupled with large-pore filtration was used to monitor RSIV DNA copies in seawater from fish farms and from an experimental infection model. RSIV dispersion in seawater from a net pen where the disease outbreak occurred was visualized by the inverse distance weighting method using multiple-sampling data sets from a fish farm. The analysis demonstrated that the center of the net pen had a high viral load, and RSIV seemed to be quickly diluted by the tidal current. To evaluate the transmission risk of RSIV in environmental water, the red sea bream
Pagrus major
(approximately 10 g) was exposed to RSIV-contained seawater (10
3
, 10
4
, 10
5
, 10
6
, and 10
7
copies/L) for 3 days, which mimicked field exposure. A probit analysis of the challenge test indicated that the inferred infection rates of seawater containing 10
5.9
copies/L and 10
3.1
copies/L of RSIV were 50% and 0.0001%, respectively. In the surveillance for 3 years at 10 fixed points (
n
= 306), there were only seven samples in which the viral load exceeded 10
4
copies/L in seawater. These results suggest that the transmission of RSIV among fish farms via seawater is highly associated with the distance between the net pens, and the environmental water is not always an infection source for the transmission of RSIV between fish farms.

IMPORTANCE

Our surveillance of viral loads for red sea bream iridovirus (RSIV) by monitoring environmental DNA in fish farms suggested that the viral loads in the seawater were low, except for the net pens where RSIV outbreaks occurred. Furthermore, our experimental infection model indicated that the infection risk of RSIV-contained seawater with less than 10
3
copies/L was extremely low. The limited risk of environmental water for transmission of RSIV gives an insight that RSIV could be partly transmitted between fish farms due to the movement of equipment and/or humans from the fish farm where the disease outbreaks. Since our data suggest that seawater can function as a potential wall to reduce the transmission of RSIV, biosecurity management, such as disinfection of equipment associated with fish farms could be effective, even in the semi-open system aquaculture that the environmental water can be freely transferred, to reduce the risk of RSIV outbreaks.
Taxonomic characterization of
Pseudomonas hygromyciniae
sp. nov., a novel species discovered from a commercially purchased antibiotic
Authors: Turner Timothy L. , Mitra Sumitra D. , Kochan Travis J. , Pincus Nathan B. , Lebrun-Corbin Marine , Cheung Bettina H. , Gatesy Samuel W. , Afzal Tania , Nozick Sophie H. , Ozer Egon A. , Hauser Alan R. 
Published: September 2023

ABSTRACT

In an attempt to identify novel bacterial species, microbiologists have examined a wide range of environmental niches. We describe the serendipitous discovery of a novel gram-negative bacterial species from a different type of extreme niche: a purchased vial of antibiotic. The vial of antibiotic hygromycin B was found to be factory contaminated with a bacterial species, which we designate
Pseudomonas hygromyciniae
sp. nov. The proposed novel species belongs to the
P. fluorescens
complex and is most closely related to
P. brenneri
,
P. proteolytica
, and
P. fluorescens
. The type strain
Pseudomonas hygromyciniae
sp. nov.

strain SDM007
T

(SDM007
T
) harbors a novel 250 kb megaplasmid which confers resistance to hygromycin B and contains numerous other genes predicted to encode replication and conjugation machinery. SDM007
T
grows in hygromycin concentrations of up to 5 mg/mL but does not use the antibiotic as a carbon or nitrogen source. While unable to grow at 37°C ruling out its ability to infect humans, it grows and survives at temperatures between 4 and 30°C. SDM007
T
can infect plants, as demonstrated by the lettuce leaf model, and is highly virulent in the
Galleria mellonella
infection model but is unable to infect mammalian A549 cells. These findings indicate that commercially manufactured antibiotics represent another extreme environment that may support the growth of novel bacterial species.

IMPORTANCE

Physical and biological stresses in extreme environments may select for bacteria not found in conventional environments providing researchers with the opportunity to not only discover novel species but to uncover new enzymes, biomolecules, and biochemical pathways. This strategy has been successful in harsh niches such as hot springs, deep ocean trenches, and hypersaline brine pools. Bacteria belonging to the
Pseudomonas
species are often found to survive in these unusual environments, making them relevant to healthcare, food, and manufacturing industries. Their ability to survive in a variety of environments is mainly due to the high genotypic and phenotypic diversity displayed by this genus. In this study, we discovered a novel
Pseudomonas
sp. from a desiccated environment of a sealed antibiotic bottle that was considered sterile. A close genetic relationship with its phylogenetic neighbors reiterated the need to use not just DNA-based tools but also biochemical characteristics to accurately classify this organism.
Relationship between daytime napping with the occurrence and development of diabetes: a systematic review and meta-analysis
Authors: Liu Mengdie , Liu Minhui , Wang Shuo , Sun Yumei , Zhou Fang , Sun Hongyu 
Published: September 2023

ObjectiveTo determine the relationship of napping with incident diabetes risk and glycaemic control in people with diabetes.DesignSystematic review and meta-analysis.Data sourcesMEDLINE (PubMed), EMBASE, Web of Science and the Cochrane Library were searched for studies published from database inception to 9 May 2023.Eligibility criteriaObservational studies reporting the relationship of napping with diabetes or glycaemic control in patients with diabetes in adult populations were included.Data extraction and synthesisTwo reviewers independently screened the literature, extracted data and assessed the quality of the included studies. The results were reported as ORs and 95% CIs, which were pooled by using fixed and random effects models, and subgroup analyses were performed. The Grading of Recommendations Assessment, Development and Evaluation method was used to assess the quality of the evidence.ResultsForty studies were included in our review. Habitual napping was associated with an increased diabetes risk (OR 1.20, 95% CI 1.14 to 1.27) and poor glycaemic control in patients with diabetes (OR 2.05, 95% CI 1.55 to 2.73). Nap durations less than 30 min were unrelated to diabetes (OR 1.05, 95% CI 0.97 to 1.14). Nap durations of 30–60 min were associated with diabetes risk (OR 1.09, 95% CI 1.02 to 1.17), but there were differences in the subgroup analysis results. Nap durations of more than 60 min significantly increased the risk of diabetes (OR 1.31, 95% CI 1.20 to 1.44).ConclusionsNapping is associated with increased diabetes risk and poor glycaemic control, and future research will need to confirm whether there are sex and regional differences. Nap durations of more than 60 min significantly increases the risk of diabetes, and the relationship between nap duration and glycaemic control in patients with diabetes needs to be further explored in the future.PROSPERO registration numberCRD42021292103.
Effect of robotic-assisted gait training on gait and motor function in spinal cord injury: a protocol of a systematic review with meta-analysis
Authors: Wang Lei , Peng Jin-lin , Chen Ai-lian 
Published: September 2023

IntroductionRobotic-assisted gait training (RAGT) has been reported to be effective in rehabilitating patients with spinal cord injury (SCI). However, studies on RAGT showed different results due to a varied number of samples. Thus, summarising studies based on robotic-related factors is critical for the accurate estimation of the effects of RAGT on SCI. This work aims to search for strong evidence showing that using RAGT is effective in treating SCI and analyse the deficiencies of current studies.Methods and analysisThe following publication databases were electronically searched in December 2022 without restrictions on publication year: MEDLINE, Cochrane Library, Web of Science, Embase, PubMed, the Cochrane Central Register of Controlled Trials and China National Knowledge Infrastructure. Various combinations of keywords, including ‘motor disorders’, ‘robotics’, ‘robotic-assisted gait training’, ‘Spinal Cord Injuries’, ‘SCI’ and ‘gait analysis’ were used as search terms. All articles on randomised controlled trials (excluding retrospective trials) using RAGT to treat SCI that were published in English and Chinese and met the inclusion criteria were included. Outcomes included motor function, and gait parameters included those assessed by using the instrumented gait assessment, the Berg Balance Scale, the 10-m walk speed test, the 6-min walk endurance test, the functional ambulation category scale, the Walking index of SCI and the American Spinal Injury Association assessment scale. Research selection, data extraction and quality assessment were conducted independently by two reviewers to ensure that all relevant studies were free from personal bias. In addition, the Cochrane risk-of-bias assessment tool was used to assess the risk of bias. Review Manager V.5.3 software was used to produce deviation risk maps and perform paired meta-analyses.Ethics and disseminationEthics approval is not required for systematic reviews and network meta-analyses. The results will be submitted to a peer-reviewed journal or presented at a conference.PROSPERO registration numberCRD42022319555.
Multiple chemical sensitivity scoping review protocol: overview of research and MCS construct
Authors: Hempel Susanne , Danz Margie , Robinson Karen A , Bolshakova Maria , Rodriguez Jesus , Mears Alanna , Pham Cindy , Yagyu Sachi , Motala Aneesa , Tolentino Danica , Akbari Omid , Johnston Jill 
Published: September 2023

IntroductionMultiple chemical sensitivity (MCS) has been characterised by reported adverse responses to environmental exposures of common chemical agents (eg, perfumes, paint, cleaning products and other inhaled or ingested agents) in low doses considered non-toxic for the general population. There is currently no consensus on whether MCS can be established as a distinct disorder.Methods and analysisThe scoping review of the literature will be guided by five questions: How is MCS defined and which diagnostic criteria have been proposed? What methods are used to report prevalence and incidence estimates of MCS? What are the characteristics of the body of scientific evidence that addresses whether MCS is a distinct disorder or syndrome? What underlying mechanisms for MCS have been proposed in the scientific literature? Which treatment and management approaches for MCS have been evaluated in empirical research studies? We will conduct a comprehensive search in 14 research databases. Citation screening will be supported by machine learning algorithms. Two independent reviewers will assess eligibility of full-text publications against prespecified criteria. Data abstraction will support concise evidence tables. A formal consultation exercise will elicit input regarding the review results and presentation. The existing research evidence will be documented in a user-friendly visualisation in the format of an evidence map.Ethics and disseminationDetermined to be exempt from review (UP-22-00516). Results will be disseminated through a journal manuscript and data will be publicly accessible through an online data repository.Registration detailsThe protocol is registered in Open Science Framework (osf.io/4a3wu).
Exploring HPV vaccine knowledge, attitudes, barriers and information sources among parents, health professionals and teachers in Kazakhstan: a mixed-methods study protocol
Authors: Kassymbekova Fatima , Zhetpisbayeva Indira , Tcoy Evgeniya , Dyussenov Rassul , Davletov Kairat , Rommel Alexander , Glushkova Natalya 
Published: September 2023

IntroductionHuman papillomavirus (HPV) is a prevalent sexually transmitted infection linked to certain types of malignant neoplasms, notably cervical cancer (CC). In Kazakhstan, a high prevalence of high oncogenic HPV types (HR-HPV) has been observed, and CC ranks as the second most common malignancy among women with a crude incidence rate of 18.3 cases per 100 000 women. The HPV vaccine, developed as the primary prevention measure against HPV infection, including the most prevalent HR-HPV, received approval from the WHO in 2009. In 2014, Kazakhstan initiated HPV vaccination as a pilot project in four sub-national regions; however, it was later in 2017 discontinued due to widespread parental refusal influenced by negative media reports. This study aims to examine knowledge, attitudes, information sources, barriers to HPV vaccination and factors associated with HPV vaccination hesitancy among different target groups in Kazakhstan prior to the HPV vaccine re-launch announced by the Ministry of Health.Methods and analysisThis mixed-method-designed research comprises quantitative and qualitative components. Data on HPV awareness, attitudes towards HPV vaccination and sources of information will be collected through an online survey administered by parents and legal guardians, health professionals, and schoolteachers in the Republic of Kazakhstan between January 2023 and January 2024. Additionally, qualitative data on Kazakhstani parental beliefs and attitudes toward HPV vaccination will be collected through online focus group discussions.Ethics and dissemination of resultsThe study has been approved by the local ethics committee at the Kazakhstan Medical University “Higher School of Public Health” (KMU “KSPH”) (No. 138 of 31.05.2021). The results will be reported in publications, at conferences among researchers and healthcare and school education professionals in Kazakhstan, and internationally.
Dynamic nomogram for predicting acute kidney injury in patients with community-acquired pneumonia
Authors: Chen Dawei , Zhao Jing , Ma Mengqing , Jiang Lingling , Tan Yan , Wan Xin 
Published: September 2023

IntroductionAcute kidney injury (AKI) is a common complication in patients with community-acquired pneumonia (CAP) and negatively affects both short-term and long-term prognosis in patients with CAP. However, no study has been conducted on developing a clinical tool for predicting AKI in CAP patients. Therefore, this study aimed to develop a predictive tool based on a dynamic nomogram for AKI in CAP patients.MethodsThis retrospective study was conducted from January 2014 to May 2017, and data from adult inpatients with CAP at Nanjing First Hospital were analysed. Demographic data and clinical data were obtained. The least absolute shrinkage and selection operator (LASSO) regression model was used to select important variables, which were entered into logistic regression to construct the predictive model for AKI. A dynamic nomogram was based on the results of the logistic regression model. Calibration and discrimination were used to assess the performance of the dynamic nomogram. A decision curve analysis was used to assess clinical efficacy.ResultsA total of 2883 CAP patients were enrolled in this study. The median age was 76 years (IQR 63–84), and 61.3% were male. AKI developed in 827 (28.7%) patients. The LASSO regression analysis selected five important factors for AKI (albumin, acute respiratory failure, CURB-65 score, Cystatin C and white cell count), which were then entered into the logistic regression to construct the predictive model for AKI in CAP patients. The dynamic nomogram model showed good discrimination with an area under the receiver operating characteristics curve of 0.870 and good calibration with a Brier score of 0.129 and a calibration plot. The decision curve analysis showed that the dynamic nomogram prediction model had good clinical decision-making.ConclusionThis easy-to-use dynamic nomogram may help physicians predict AKI in patients with CAP.