bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of case detection strategies on the prognosis of tuberculosis patients in the state of São Paulo, Brazil, 2010–19: A retrospective cohort study
Authors: da Silva José Mário Nunes , Diaz‐Quijano Fredi Alexander 
Published: December 2024

AbstractBackgroundDespite existing recommendations, there is still a scarcity of evidence on the impact of active case finding strategies versus passive case finding strategies, especially with regard to the mortality of tuberculosis patients. Therefore, our aim was to estimate the effect of case detection strategies on the prognosis of tuberculosis patients.MethodsWe conducted a retrospective cohort study of 160,384 new cases of tuberculosis patients diagnosed between 1 January 2010 and 31 August 2019 in the state of São Paulo, Brazil. We classified exposure into: passive case finding (emergency room, outpatient clinics or hospital settings) and active case finding (institutions, community or contact investigation). The primary outcome was all‐cause mortality, and the secondary outcome was a composite outcome with treatment outcomes. We investigated associations using logistic regression, allowing for municipality‐level random effects.ResultsCompared with outpatient passive case finding, passive case finding in the emergency room and in the hospital showed higher odds of death (adjusted odds ratio [OR] 3.69; 95% CI: 3.47–3.93 and 4.47; 95% CI: 4.22–4.74, respectively) and unfavourable treatment outcomes (1.92; 95% CI: 1.84–1.99 and 2.06; 95% CI: 1.98–2.14, respectively). By contrast, patients detected through community‐based active case finding and contact investigation showed lower odds of death (0.77; 95% CI: 0.61–0.97 and 0.71; 95% CI: 0.54–0.92, respectively) and unfavourable treatment outcomes (0.85; 95% CI: 0.77–0.95 and 0.82; 95% CI: 0.74–0.91, respectively).ConclusionCommunity‐based active case finding and contact investigation were associated with better prognosis than passive strategies in tuberculosis patients. Our results highlight the importance of strengthening active case finding as a fundamental part of mitigating the disease burden and controlling tuberculosis.
Pseudovibriamides from
Pseudovibrio
marine sponge bacteria promote flagellar motility via transcriptional modulation
Authors: Dai Yitao , Lourenzon Vitor , Ióca Laura P. , Al-Smadi Dua , Arnold Lydia , McIntire Ian , Berlinck Roberto G. S. , Eustáquio Alessandra S. 
Published: December 2024

ABSTRACT

Pseudovibrio
α-Proteobacteria have been repeatedly isolated from marine sponges and proposed to be beneficial to the host. Bacterial motility is known to contribute to host colonization. We have previously identified pseudovibriamides A and B, produced in culture by
Pseudovibrio brasiliensis
Ab134, and shown that pseudovibriamide A promotes flagellar motility. Pseudovibriamides are encoded in a hybrid nonribosomal peptide synthetase-polyketide synthase gene cluster that also includes several accessory genes. Pseudovibriamide A is a linear heptapeptide and pseudovibriamide B is a nonadepsipeptide derived from pseudovibriamide A. Here, we define the borders of the pseudovibriamides gene cluster, assign function to biosynthetic genes using reverse genetics, and test the hypothesis that pseudovibriamides impact motility by modulating gene transcription. RNA-sequencing transcriptomic analyses of strains having different compositions of pseudovibriamides suggested that both pseudovibriamides A and B affect genes potentially involved in motility, and that a compensatory mechanism is at play in mutants that produce only pseudovibriamide A, resulting in comparable flagellar motility as the wild type. The data gathered suggest that pseudovibriamides A and B have opposite roles in modulating a subset of genes, with pseudovibriamide B having a primary effect in gene activation, and pseudovibriamide A on inhibition. Finally, we observed many differentially expressed genes (up to 29% of the total gene number) indicating that pseudovibriamides have a global effect on transcription that goes beyond motility.

IMPORTANCE

Marine sponges are found throughout the oceans from tropical coral reefs to polar sea floors, playing crucial roles in marine ecosystems.
Pseudovibrio
bacteria have been proposed to contribute to sponge health. We have previously shown that pseudovibriamides produced by
Pseudovibrio brasiliensis
promote bacterial motility, a behavior that is beneficial to bacterial survival and host colonization. The gene cluster that encodes pseudovibriamide biosynthesis is found in two-thirds of
Pseudovibrio
genomes. This gene cluster is also present in
Pseudomonas
bacteria that interact with terrestrial plants and animals. Here, we first assign functions to pseudovibriamide biosynthetic genes using reverse genetics. We then show that pseudovibriamides play a major role in transcriptional regulation, affecting up to 29% of
P. brasiliensis
genes, including motility genes. Thus, this work gives insights into pseudovibriamide biosynthesis and provides evidence that they are signaling molecules relevant to bacterial motility and to other yet-to-be-identified phenotypes.
HIV-1 transcription start sites usage and its impact on unspliced RNA functions in people living with HIV
Authors: Islam Saiful , Maldarelli Frank , Nikolaitchik Olga A. , Cheng Zetao , Gorelick Robert , Nikolaitchik Maria A. , Pathak Vinay K. , Hu Wei-Shau 
Published: December 2024

ABSTRACT

HIV-1 unspliced RNA serves two distinct functions during viral replication: it is packaged into particles as the viral genome, and it is translated to generate Gag/Gag-Pol polyproteins required for virus assembly. Recent studies have demonstrated that in cultured cells, HIV-1 uses multiple transcription start sites to generate several unspliced RNA species, including two major transcripts with three and one 5′ guanosine, referred to as 3G and 1G RNA, respectively. Although nearly identical, 1G RNA is selected over 3G RNA to be packaged as the virion genome, indicating that these RNA species are functionally distinct. Currently, our understanding of HIV-1 transcription start site usage and the functions of RNA species is based on studies using cultured cells. Here, we examined samples from people living with HIV to investigate HIV-1 transcription start site usage and its impact on RNA function. Using paired samples collected from the same participants on the same date, we examined the HIV-1 unspliced RNA species in infected cells (PBMC) and in viruses (plasma). Our findings demonstrate that in people living with HIV, the virus uses multiple transcription start sites to generate several unspliced transcripts, including 3G and 1G RNA. Furthermore, we observed an enrichment of 1G RNA in the paired plasma samples, indicating a preferential packaging of 1G RNA
in vivo
. Our study illustrates the complex regulation of HIV-1 unspliced RNA in people living with HIV and provides valuable insights into how HIV-1 unspliced RNAs serve their functions
in vivo
.

IMPORTANCE
HIV-1 virions must contain unspliced RNA and its translation products to maintain infectivity. How HIV-1 unspliced RNA fulfills these two essential and yet distinct roles in viral replication has been a long-standing question in the field. In this report, we demonstrate that in people living with HIV, the virus uses multiple transcription start sites to generate several unspliced RNA species that are 99% identical in sequence but differ functionally. One of the RNA species, 1G RNA, is selected over other HIV-1 unspliced RNAs to be packaged into viral particles. These findings are consistent with previous cell-culture-based observations and provide insights into how HIV-1 regulates its unspliced RNA function in people living with HIV.
Complete genome sequence of
Pseudomonas brenneri
strain JD2-26, a potential pollutant-reducing bacterium isolated from a municipal solid waste landfill facility
Authors: Han Kook-Il , Nam Young Ho , Kang Hye Kyeong , Jin Hyun Mi , Kim Eui-Jin 
Published: December 2024

ABSTRACT

We report here the complete genome sequence of
Pseudomonas brenneri
strain JD2-26 isolated from a municipal solid waste landfill facility. The genome consists of a 6.32-Mbp chromosome and a plasmid having a total of 6,100 genes, including 5,914 coding sequences.
First complete genome sequence of
Tenacibaculum maritimum
serotype O4, a rising threat in marine aquaculture
Authors: Escribano M. Pilar , Salvador-Clavell Rubén , Balado Miguel , Magariños Beatriz , Amaro Carmen , Lemos Manuel L. 
Published: December 2024

ABSTRACT

Tenacibaculum maritimum
is a Gram-negative marine fish pathogen. Here, we present the complete genome sequence of strain SP9.1, representing the emerging serotype O4. Selected as a model for pathogenesis studies, this genome provides valuable insights into the genetic basis of virulence and adaptation, complementing existing data for serotype O1.
Draft genome sequences of
Schizosaccharomyces pombe
strain I-540 isolated from grape must
Authors: Vasyagin Egor A. , Beletsky Alexey V. , Ivanova Elena V. , Shalamitskiy Maxim Yu. , Mardanov Andrey V. , Ravin Nikolai V. 
Published: December 2024

ABSTRACT

Schizosaccharomyces pombe
is a non-Saccharomyces yeast that is widely used in winemaking due to its ability to ferment malic acid, thus improving organoleptic properties of wine. We report the draft genome sequence of
S. pombe
strain I-540, isolated from grape must in Russia.
Draft genome sequences of
Kluyveromyces marxianus
strain U848 isolated from
Agave sisalana
Authors: Vasyagin Egor A. , Beletsky Alexey V. , Shalamitskiy Maxim Yu. , Semenova Karina A. , Ravin Nikolai V. , Mardanov Andrey V. 
Published: December 2024

ABSTRACT

Kluyveromyces marxianus
is a yeast widely used in the dairy industry and frequently isolated from vineyards and wineries. Its capacity to metabolize diverse sugars makes it highly promising for winemaking applications. We report the draft genome sequence of the
K. marxianus
strain U848.
Spatiotemporal distribution characteristics and impact factors of hepatitis C in Chongqing, China, 2014–2020
Authors: Chen Saijuan , Wang Qiuting , An Yunyi , Chen Ying , Liu Hua , Tan Weijie , Zhou Xinyun , Xing Dianguo , Zhang Yan 
Published: December 2024

Objectives
This study aimed to explore the spatial and temporal distribution of hepatitis C and its influencing factors in Chongqing, providing a scientific basis for the relevant departments to formulate targeted preventive measures for the high prevalence of hepatitis C in the region and population.

Design
We collected data on hepatitis C cases in Chongqing (located in the southwest of China) from 2014 to 2020, and analysed the spatiotemporal heterogeneity of hepatitis C incidence in different populations and identified factors that might influence the incidence of hepatitis C by constructing a Bayesian spatiotemporal model.

Settings
The study subjects included clinically diagnosed cases and confirmed cases of hepatitis C with current address in Chongqing and onset date between 1 January 2014 and 31 December 2020.

Participants
The study used aggregated data, including 33 900 clinically diagnosed cases and confirmed cases of hepatitis C.

Results
From 2014 to 2020, the high-risk areas of hepatitis C were primarily concentrated in the main and new urban areas of Chongqing. In contrast, the low-risk areas were mainly found in southeast and northeast Chongqing. There was also an increasing trend in the risk of incidence in the low-risk areas. Analysis of different populations revealed that men aged 45–59 years had a higher risk of developing hepatitis C in the main urban area compared with other age groups. Additionally, the risk for this population group showed an increasing trend in the southeast and northeast of Chongqing as well as the main urban area. Among women, the rising trend of hepatitis C risk was stronger for those aged 30–44 years in southeast Chongqing and for those aged 45–59 years in northeast Chongqing compared with other age groups. The analysis of influencing factors found that gross domestic product per capita, population density and the proportion of tertiary industry were associated with an increased risk of hepatitis C.

Conclusions
High-risk areas for hepatitis C virus were mainly located in the main and new urban areas of Chongqing, where the male prime-age population was the focus of prevention and treatment. In the future, the relevant authorities should concentrate on high-risk areas and at the same time strengthen screening and serological surveys for hepatitis C in low-risk areas and various populations, and raise public awareness of prevention, so as to reduce the incidence of hepatitis C.
ChatGPT (GPT-4) versus doctors on complex cases of the Swedish family medicine specialist examination: an observational comparative study
Authors: Arvidsson Rasmus , Gunnarsson Ronny , Entezarjou Artin , Sundemo David , Wikberg Carl 
Published: December 2024

BackgroundRecent breakthroughs in artificial intelligence research include the development of generative pretrained transformers (GPT). ChatGPT has been shown to perform well when answering several sets of medical multiple-choice questions. However, it has not been tested for writing free-text assessments of complex cases in primary care.ObjectivesTo compare the performance of ChatGPT, version GPT-4, with that of real doctors.Design and settingA blinded observational comparative study conducted in the Swedish primary care setting. Responses from GPT-4 and real doctors to cases from the Swedish family medicine specialist examination were scored by blinded reviewers, and the scores were compared.ParticipantsAnonymous responses from the Swedish family medicine specialist examination 2017–2022 were used.Outcome measuresPrimary: the mean difference in scores between GPT-4’s responses and randomly selected responses by human doctors, as well as between GPT-4’s responses and top-tier responses by human doctors. Secondary: the correlation between differences in response length and response score; the intraclass correlation coefficient between reviewers; and the percentage of maximum score achieved by each group in different subject categories.ResultsThe mean scores were 6.0, 7.2 and 4.5 for randomly selected doctor responses, top-tier doctor responses and GPT-4 responses, respectively, on a 10-point scale. The scores for the random doctor responses were, on average, 1.6 points higher than those of GPT-4 (p<0.001, 95% CI 0.9 to 2.2) and the top-tier doctor scores were, on average, 2.7 points higher than those of GPT-4 (p<0.001, 95 % CI 2.2 to 3.3). Following the release of GPT-4o, the experiment was repeated, although this time with only a single reviewer scoring the answers. In this follow-up, random doctor responses were scored 0.7 points higher than those of GPT-4o (p=0.044).ConclusionIn complex primary care cases, GPT-4 performs worse than human doctors taking the family medicine specialist examination. Future GPT-based chatbots may perform better, but comprehensive evaluations are needed before implementing chatbots for medical decision support in primary care.
Postnatal foot length measurement as a proxy to identify low birth weight for frontline health workers in rural Sindh Province, Pakistan: a diagnostic accuracy study
Authors: Tikmani Shiyam Sunder , Brown Nick , Inayat Ali Alijaan , Martensson Andreas , Saleem Sarah , Martensson Thomas 
Published: December 2024

ObjectiveTo assess the diagnostic accuracy of postnatal foot length (FL) measurements as a proxy to identify low birth weight (LBW) for frontline healthcare workers in rural Sindh Province, Pakistan.DesignA community-based cross-sectional study.SettingThis study was conducted in the catchment area of Global Network’s Maternal and Newborn Health Registry, Thatta, Sindh Province, Pakistan, from January to June 2023.ParticipantsSingleton live births irrespective of gestational age at birth.Reference standardBirth weight was measured using calibrated digital weighing scales in grams based on the average of three readings with minimal clothing.Index testFL was measured within 48 hours of birth using a rigid transparent plastic ruler in centimetres based on the average of three measurements.Primary outcomeSensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), receiver operating characteristics curve and area under the curve with 95% CI were calculated. Euclidean distance was used to identify the cutoff of FL to identify LBW. A simple linear equation was created to predict the birth weight.ResultsOut of 336 analysed newborns, 179 (53.3%) were male and 157 (46.7%) were female. The median birth weight was 2801 g (IQR: 2465–3057), of whom 88 (26.2%) were LBW. The median foot length was 7.9 cm (IQR: 7.6–8.1). For identifying LBW, the foot length cutoff was ≤7.6 cm with 90.3% sensitivity, 81.8% specificity, 63.8% PPV and 96.0% NPV. A FL of 7.6 cm predicted birth weight of 2459.4 g.ConclusionPostnatal FL cutoff of ≤7.6 cm has adequate predictive value served as a simple, low-cost and reliable method to identify LBW for frontline healthcare providers in the rural settings of Thatta without calibrated weighing scales to triage LBW newborns in need of higher-level care.Trial registration numberNCT05515211.
Identifying the population to be targeted in a lung cancer screening programme in Denmark
Authors: Fernández Montejo María Del Pilar , Saghir Zaigham , Bødtger Uffe , Jepsen Randi , Lynge Elsebeth , Lophaven Søren 
Published: December 2024

IntroductionWe assessed the impact of recruitment criteria on lung cancer detection in a future Danish screening programme with low-dose CT.MethodsWe combined data from two Danish population-based health examination surveys with eligibility criteria from seven randomised controlled trials on lung cancer screening. Incident lung cancers were identified by linkage with the National Pathology Data Bank (Patobank). For an average of 4.4 years of follow-up, we calculated sensitivity, specificity, efficient frontier and number needed to screen (NNS) for lung cancer detection.ResultsWhen applying the different eligibility criteria to the 48 171 persons invited to the two surveys, the number of lung cancer cases identified in the target groups varied from 46 to 68. The National Lung Screening Trial (NLST) criteria had the highest sensitivity of 62.6% (95% CI 52.7 to 71.8) and the Dutch-Belgian NEderlands-Leuvens Screening ONderzoek (NELSON) criteria had the highest specificity 81.6% (95% CI 81.0 to 82.1). Sensitivity was higher for men than for women (NLST criteria 71.7% (95% CI 57.7 to 83.2) and 53.7% (95% CI 39.6 to 67.4), respectively). The NLST criteria identified the target population obtaining the lowest NNS with 46.3. The application of the NLST criteria showed that the higher the sensitivity, the lower the number of false-negative cases and, thus, the lower the NNS.ConclusionsThis study highlights the impact of the definition of the at-risk population on lung cancer screening efficacy. We found lower sensitivity among women regardless of screening criteria used. This should be carefully addressed in a possible screening programme.
Deployment to bases with open burn pits and mortality of US Military Veterans
Authors: Hoover Christian , Trivedi Amal N , Bello Anila , Culpepper William J , Gasper Joseph , Gaither Rachel , Jiang Lan , Rennix Christopher , Schneiderman Aaron , Wellenius Gregory A , Woskie Susan R , Savitz David A 
Published: December 2024

Introduction
Five million US Veterans had possible exposure to open burn pits used for waste disposal through service in Iraq (2003–2011) and Afghanistan (2001–2014). Burn pits generate toxic exposures that may be associated with adverse health outcomes. We examined all-cause and cause-specific mortality in relation to deployment to bases with open burn pits.

Methods
We analysed a cohort of 474 634 Veterans who received some healthcare from the Veterans Health Administration, linked to Department of Defense deployment records to identify assignments to bases with burn pits. In multivariable logistic regression models, we assessed the association between duration of deployment to bases with burn pits and all-cause mortality and cause-specific mortality from the six most common causes among this population of Veterans.

Results
Duration of deployment to bases with burn pits was modestly related to all-cause mortality, with adjusted ORs of 1.07 (95% CI 0.99 to 1.15), 1.08 (95% CI 1.00 to 1.16) and 1.16 (95% CI 1.06 to 1.27) across tertiles, but not associated with mortality due to cancer, heart disease or chronic liver disease/cirrhosis. Positive associations were also found for unintentional injuries, suicide and stroke.

Discussion
These data are suggestive of an association between duration of deployment to bases with burn pits and overall mortality, but not from cancer or heart disease. Unexpected associations with injury and suicide call for a more detailed evaluation. Conclusions are restricted by the broad aggregations of causes of death, a limited number of deaths in this relatively young cohort and the lack of more detailed information on exposure to burn pits.
Casimir–Lifshitz adhesion between Si and Ru measured by the method of adhered cantilever
Authors: Postnikov Alexander V. , Uvarov Ilia V. , Morozov Oleg V. , Svetovoy Vitaly B. 
Published: December 2024

Measurements of the Casimir–Lifshitz (dispersion) forces at distances below 50 nm are difficult due to the snap-in effect, and precision is poor due to increasing relative uncertainty in the distance. In this paper, a method of adhered cantilever that avoids the loss of stability is used to measure the interaction energy between Si and Ru surfaces in direct contact. Background capillary and short-range interactions are strongly suppressed because surface roughness significantly deviates from a normal distribution. Electrostatic interaction is not fully compensated, but the potential is limited to a value less than 29.8[Formula: see text]mV. Adhesion energy is measured directly, and the average equilibrium distance is predicted theoretically. The ability to achieve high precision in this type of experiment is demonstrated.
EFFECTS OF BALANCE TRAINING EXERCISE ON PAIN INTENSITY AND DISABILITY IN CHRONIC LOW BACK PAIN INDIVIDUALS: A CLINICAL TRIAL
Authors: Dinesh R. , Antony Leo Aseer P. , Soundararajan K. 
Published: December 2024

Background: Chronic Low Back Pain (CLBP) has been the leading cause of disability globally for at least three decades. Totally, 10% to 20% of people who experience acute lower back pain episodes often develop CLBP. In CLBP, there is an altered sensorimotor pathway which impairs body the balance. There are lacunae in studies prescribing balance exercise to CLBP individuals. This study aims to determine the effects of balance exercises on pain intensity, back physical performance, trunk extensor muscle endurance, and disability in CLBP individuals. Methods: A qualified therapist unaware of the study assessed all outcome measures (Visual Analogue scale– VAS, Oswestry Disability Index — ODI, Back Performance Scale — BPS, Biering Sorenson test — BST) at baseline, end of 4th week, and 8th week. All participants underwent balance exercise intervention for 30 min/day, 3 days a week, for 8 weeks. Repeated measures ANOVA was performed at [Formula: see text] < 0.05. Results: Out of 65 screened participants, 40 (24 females, 16 males) fulfilled the study criteria and performed the balance exercise. The BPS score for back physical performance, VAS score for patient-reported pain intensity, BST value for trunk extensor muscle endurance, and ODI score for low back disability domains significantly improved after the balance exercise intervention at the end of 4th week and 8th week ([Formula: see text] < 0.05). Conclusions: Balance exercise effectively improves back physical performance, reducing pain and back-related impairments. Further, the controlled trial is warranted to add the level of evidence.