bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model
in vivo
responses
Authors: Davis Kathleen P. , Morales Yoelkys , Ende Rachel J. , Peters Ryan , McCabe Anne L. , Mecsas Joan , Aldridge Bree B. 
Published: February 2024

ABSTRACT

The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Here, we tested the hypothesis that drug-drug interactions vary in different media, and determined which
in vitro
models best predict drug interactions in the lungs. We systematically studied pair-wise antibiotic interactions in three different media, CAMHB, (a rich lab medium standard for antibiotic susceptibility testing), a urine mimetic medium (UMM), and a minimal medium of M9 salts supplemented with glucose and iron (M9Glu) with three Gram-negative ESKAPE pathogens,
Acinetobacter baumannii
(Ab),
Klebsiella pneumoniae
(Kp), and
Pseudomonas aeruginosa
(Pa). There were pronounced differences in responses to antibiotic combinations between the three bacterial species grown in the same medium. However, within species, PaO1 responded to drug combinations similarly when grown in all three different media, whereas Ab17978 and other Ab clinical isolates responded similarly when grown in CAMHB and M9Glu medium. By contrast, drug interactions in Kp43816, and other Kp clinical isolates poorly correlated across different media. To assess whether any of these media were predictive of antibiotic interactions against Kp in the lungs of mice, we tested three antibiotic combination pairs.
In vitro
measurements in M9Glu, but not rich medium or UMM, predicted
in vivo
outcomes. This work demonstrates that antibiotic interactions are highly variable across three Gram-negative pathogens and highlights the importance of growth medium by showing a superior correlation between
in vitro
interactions in a minimal growth medium and
in vivo
outcomes.

IMPORTANCE
Drug-resistant bacterial infections are a growing concern and have only continued to increase during the SARS-CoV-2 pandemic. Though not routinely used for Gram-negative bacteria, drug combinations are sometimes used for serious infections and may become more widely used as the prevalence of extremely drug-resistant organisms increases. To date, reliable methods are not available for identifying beneficial drug combinations for a particular infection. Our study shows variability across strains in how drug interactions are impacted by growth conditions. It also demonstrates that testing drug combinations in tissue-relevant growth conditions for some strains better models what happens during infection and may better inform combination therapy selection.
Draft genome sequences of three rhodopsin possessing
Croceitalea
sp. strains, isolated from the sea surface microlayer in Japan
Authors: Takada Mako , Jiang Chunqi , Sugai Youta , Hasegawa-Takano Masumi , Fujiwara Takayoshi , Tsukamoto Yuya , Nakajima Yu , Nishimura Yosuke , Yoshizawa Susumu 
Published: February 2024

ABSTRACT

Here, we present the draft genome sequences of three
Croceitalea
sp. strains containing microbial rhodopsins, isolated from the Japanese coastal sea surface microlayer, which is exposed to intense sunlight. This study will contribute to the understanding of the genus
Croceitalea
and the diversity of microbial rhodopsins.
Evaluation of CHROMagar
Candida
Plus for the detection of
C. auris
with a panel of 206 fungal isolates and 83 colonization screening skin-swabs
Authors: Bentz Meghan L. , Le Ngoc , Min Brian , Nunnally Natalie S. , Sullivan Vickie , Tran Mike , Lockhart Shawn R. , Litvintseva Ana , Berkow Elizabeth L. , Sexton D. Joseph 
Published: February 2024

ABSTRACT

CHROMagar
Candida
Plus is a new formulation of chromogenic media designed for the detection and differentiation of major clinical
Candida
species, including
Candida auris
. The objective of this study is to evaluate CHROMagar
Candida
Plus when used according to manufacturer’s instructions with a panel of 206 fungal isolates and 83 skin-swab specimens originally collected for
C. auris
colonization screening. Of the 68
C
.
auris
isolates tested, 66/68 displayed the expected light-blue colony morphology and blue halo within 48 h. None of the remaining 138 non-
auris
isolates appeared similar to
C. auris
. CHROMagar
Candida
Plus was, therefore, inclusive to 97% of 68
C
.
auris
isolates tested and supported visual exclusion of 100% of the 138 non-
C
.
auris
isolates tested. For the 83 colonization screening specimens, direct plating onto CHROMagar
Candida
Plus was 60% sensitive and 100% specific when compared to the enrichment broth gold-standard reference method. In sum, these findings demonstrate the utility of this media when working with isolates but also notable limitations when working with primary skin-swabs specimens when competing yeast species are present.

IMPORTANCE

Candida auris
is an emerging fungal pathogen of public health concern. As it continues to spread, it is important to publish evaluations of new diagnostic tools. In this study, we share our experience with a new chromogenic media which can help distinguish
C. auris
from related species.
Assessing the medical reasoning skills of GPT-4 in complex ophthalmology cases
Authors: Milad Daniel , Antaki Fares , Milad Jason , Farah Andrew , Khairy Thomas , Mikhail David , Giguère Charles-Édouard , Touma Samir , Bernstein Allison , Szigiato Andrei-Alexandru , Nayman Taylor , Mullie Guillaume A , Duval Renaud 
Published: February 2024

Background/aimsThis study assesses the proficiency of Generative Pre-trained Transformer (GPT)-4 in answering questions about complex clinical ophthalmology cases.MethodsWe tested GPT-4 on 422Journal of the American Medical AssociationOphthalmology Clinical Challenges, and prompted the model to determine the diagnosis (open-ended question) and identify the next-step (multiple-choice question). We generated responses using two zero-shot prompting strategies, including zero-shot plan-and-solve+ (PS+), to improve the reasoning of the model. We compared the best-performing model to human graders in a benchmarking effort.ResultsUsing PS+ prompting, GPT-4 achieved mean accuracies of 48.0% (95% CI (43.1% to 52.9%)) and 63.0% (95% CI (58.2% to 67.6%)) in diagnosis and next step, respectively. Next-step accuracy did not significantly differ by subspecialty (p=0.44). However, diagnostic accuracy in pathology and tumours was significantly higher than in uveitis (p=0.027). When the diagnosis was accurate, 75.2% (95% CI (68.6% to 80.9%)) of the next steps were correct. Conversely, when the diagnosis was incorrect, 50.2% (95% CI (43.8% to 56.6%)) of the next steps were accurate. The next step was three times more likely to be accurate when the initial diagnosis was correct (p<0.001). No significant differences were observed in diagnostic accuracy and decision-making between board-certified ophthalmologists and GPT-4. Among trainees, senior residents outperformed GPT-4 in diagnostic accuracy (p≤0.001 and 0.049) and in accuracy of next step (p=0.002 and 0.020).ConclusionImproved prompting enhances GPT-4’s performance in complex clinical situations, although it does not surpass ophthalmology trainees in our context. Specialised large language models hold promise for future assistance in medical decision-making and diagnosis.
Mpox (monkeypox) risk and mortality associated with HIV infection: a national case–control study in Nigeria
Authors: Yinka-Ogunleye Adesola , Dalhat Mahmood , Akinpelu Afolabi , Aruna Olusola , Garba Fatima , Ahmad Adama , Adeleye Adesola , Botson Iliya , Oluwafemi Bamidele , Ogunbode Oladipo , Amao Lateefat , Ekripo Udeme , Aliyu Gambo Gumel , Adetifa Ifedayo , Ihekweazu Chikwe , Abubakar Ibrahim 
Published: February 2024

IntroductionRecent outbreaks of mpox are characterised by changes in the natural history of the disease, the demographic and clinical characteristics of the cases, and widening geographical distribution. We investigated the role of HIV and other sexually transmitted infections (STIs) coinfection among cases in the re-emergence of mpox to inform national and global response.MethodsWe conducted a national descriptive and case–control study on cases in the 2017–2019 Nigerian mpox outbreak. Mpox cases were age, sex and geographical area matched each with two randomly selected controls from a representative national HIV/AIDS survey. Logistic regression was used to investigate the association between HIV infection and the risk of mpox acquisition and death.ResultsAmong 204 suspected mpox cases, 86 were confirmed (median age 31 years (IQR 27–38 years), mostly males (61 cases, 70.9%). Three-fifths of mpox cases had serological evidence of one or more STIs with 27.9% (24/86) coinfected with HIV. The case fatality rate was 9.4% (8/86) and 20.8% (5/24) overall and in HIV positive cases respectively. Mpox cases were more likely to have HIV coinfection compared with an age, gender and geography-matched control group drawn from the general population (OR 45 (95% CI 6.1 to 333.5, p=0.002) and when compared with non mpox rash cases (7.29 (95% CI 2.6 to 20.5, p<0.0001)). HIV coinfection and young age were associated with mortality among mpox cases (aOR 13.66 (95% CI 1.88 to 98.95, p=0.010) and aOR 0.90 (0.82–0.97, p=0.008), respectively).ConclusionHIV infection was associated with a higher risk of contracting and dying from mpox. Children are also at high risk of death. STIs in mpox cases may be suggestive of high-risk sexual behaviours among these individuals.
Age at menarche and risk of ovarian hyperstimulation syndrome in women undergoing IVF/ICSI cycles: a retrospective cohort study
Authors: Wang Qiaofeng , Tang Xiaojun , Lv Xingyu , Meng Xiangqian , Geng Lihong , Zhong Zhaohui , Ding Yubin , Li Tian , Wan Qi 
Published: February 2024

ObjectivesWe aimed to explore the association between age at menarche (AAM) and ovarian hyperstimulation syndrome (OHSS) in fresh in vitro fertilisation (IVF)/intracytoplasmic sperm injection (ICSI) cycles.DesignA retrospective cohort study.SettingData were collected from a large obstetrics and gynaecology hospital in Sichuan, China.ParticipantsThis study included 17 419 eligible women aged ≤40 years who underwent the first IVF/ICSI cycles from January 2015 to December 2021. Women were divided into three groups according to their AAM: ≤12 years (n=5781), 13–14 years (n=9469) and ≥15 years (n=2169).ResultsThe means of age at recruitment and AAM were 30.4 years and 13.1 years, respectively. Restricted cubic spline models suggested that early menarche age increased the risk of OHSS. The multivariable logistic analysis showed that women with menarche age ≤12 years were more likely to suffer from OHSS (OR 1.321, 95% CI 1.113 to 1.567) compared with those aged 13–14 years among the whole cohort. This significant relationship remained in women administered with different ovarian stimulation protocols and gonadotrophin doses. When stratified by female age, this correlation was presented only in patients aged ≤30 years (OR 1.362, 95% CI 1.094 to 1.694). And the mediation analysis showed that the relationship between AAM and OHSS was totally mediated by antral follicle counts (AFC).ConclusionMenarche age earlier than 12 years may increase the OHSS risk in women aged ≤30 years through the mediation of AFC. More prospective studies are required to verify the results.
Quality of locally designed surveys in a quality improvement collaborative: review of survey validity and identification of common errors
Authors: Reed Julie E , Johnson Julie K , Zanni Robert , Messier Randy , Asfour Fadi , Godfrey Marjorie M 
Published: February 2024

ObjectiveSurveys are a commonly used tool in quality improvement (QI) projects, but little is known about the standards to which they are designed and applied. We aimed to investigate the quality of surveys used within a QI collaborative, and to characterise the common errors made in survey design.MethodsFive reviewers (two research methodology and QI, three clinical and QI experts) independently assessed 20 surveys, comprising 250 survey items, that were developed in a North American cystic fibrosis lung transplant transition collaborative. Content Validity Index (CVI) scores were calculated for each survey. Reviewer consensus discussions decided an overall quality assessment for each survey and survey item (analysed using descriptive statistics) and explored the rationale for scoring (using qualitative thematic analysis).Results3/20 surveys scored as high quality (CVI >80%). 19% (n=47) of survey items were recommended by the reviewers, with 35% (n=87) requiring improvements, and 46% (n=116) not recommended. Quality assessment criteria were agreed upon. Types of common errors identified included the ethics and appropriateness of questions and survey format; usefulness of survey items to inform learning or lead to action, and methodological issues with survey questions, survey response options; and overall survey design.ConclusionSurvey development is a task that requires careful consideration, time and expertise. QI teams should consider whether a survey is the most appropriate form for capturing information during the improvement process. There is a need to educate and support QI teams to adhere to good practice and avoid common errors, thereby increasing the value of surveys for evaluation and QI. The methodology, quality assessment criteria and common errors described in this paper can provide a useful resource for this purpose.
Reducing use of seclusion on a male medium secure forensic ward
Authors: Rowsell Kathryn Amy , Akinbola Ayodele , Hancock Mark , Nyambayo Tsitsi , Jackson Zoe , Hunt David Francis 
Published: February 2024

The reduction of restrictive practices is a priority for mental health inpatient services. Often such practices are considered to increase patients’ feelings of anger, loneliness, hopelessness and vulnerability. Moreover, such approaches are counterintuitive to both recovery-orientated and trauma-informed practice.Our project, based in a male 15-bed secure forensic ward, aimed to reduce the duration (outcome measure) and frequency (balancing measure) of the use of seclusion by 10% over 6 months. Following the analysis of our local data systems and feedback from both patients and staff, we identified the high levels of use of seclusion, and reluctance to terminate it. These included a lack of awareness of the effective and appropriate use of such a facility, a hesitancy to use de-escalation techniques and an over-reliance on multidisciplinary team and consultant decision making.We subsequently designed and implemented three tests of change which reviewed seclusion processes, enhanced de-escalation skills and improved decision making. Our tests of change were applied over a 6-month period. During this period, we surpassed our original target of a reduction of frequency and duration by 10% and achieved a 33% reduction overall. Patients reported feeling safer on the ward, and the team reported improvements in relationships with patients.Our project highlights the importance of relational security within the secure setting and provides a template for other wards wishing to reduce the frequency and duration of seclusions.
Complaint behaviour among healthcare users: self-reported complaint experience and complaint proneness in adult men
Authors: Birkeland Søren , Bismark Marie , Barry Michael J , Möller Sören 
Published: February 2024

AimsWhen patients are harmed by, or dissatisfied with, healthcare, only a minority will lodge a complaint or file a claim for compensation. This survey aimed to investigate complaint behaviour and inequalities in complaints using self-reports and hypothetical case vignettes.MethodsCross-sectional, web-based survey among 6755 Danish men aged 45–70 years (response rate=30%). Participants reported their lifetime complaint experience and the likelihood that they would complain in response to hypothetical case vignettes.ResultsOverall, 4.8% of participants had complained about healthcare. Predictors were younger age (OR 2.08, 95% CI 1.32 to 3.27, p=0.002 45–50 years compared with 65–70 years), chronic illness (OR 1.49, 95% CI 1.12 to 1.98, p=0.006), rural residence (OR 2.11, 95% CI 1.20 to 3.73, p=0.010 comparing least and most populated areas), high healthcare utilisation (OR 1.55, 95% CI 1.18 to 2.03, p=0.002 primary care, and OR 1.97, 95% CI 1.52 to 2.55, p=0.000 hospital care) and decreased agreeableness on the 10-item Big Five personality inventory (OR 0.91, 95% CI 0.83 to 0.99, p=0.034). Complaint experience was associated with increased wish to complain about the treatment in the hypothetical vignettes (p=0.006).ConclusionsRoughly 1 in 20 men reported having complained about healthcare. Complaints were more common among men who were younger, living in rural areas, diagnosed with chronic illness and high users of healthcare services. Prior complaint experience may be associated with a higher proclivity for complaining about future healthcare. Findings suggest differences in the way healthcare users respond to care experiences, pointing to the importance of aligning expectations and providing clear information about treatment options.
Social media as a public health tool during the UK mpox outbreak: a qualitative study of stakeholders’ experiences
Authors: Garcia-Iglesias Jaime , May Tom , Pickersgill Martyn , Williams Jeremy , Nagington Maurice , Buijsen Sophie , McHugh Ciara , Horwood Jeremy 
Published: February 2024

Objectives
This rapid response research explored the experiences of key stakeholder groups during the 2022–2023 mpox outbreak in the UK, and in particular, the use of social media as a tool of health promotion. The project sought to identify key lessons learnt for future epidemic and pandemic preparedness.

Methods
The qualitative study employed online focus groups and interviews with key stakeholder communities, including activists, clinicians, policy actors and individuals with lived experience of mpox. N=29 stakeholders participated. Data were subject to framework analysis, with findings discussed and conclusions reached through a face-to-face analysis workshop.

Results
Participants emphasised the significant role of social media, particularly Twitter (now called X), in the response to the mpox outbreak. Several benefits were highlighted, including disseminating relevant information, tackling stigma and generating/advancing advocacy and collaboration. However, participants also pointed out challenges associated with social media; in particular, its reliance on pre-existing networks and associated dynamics of exclusion, and the presence of misinformation.

Conclusion
Social media played an important role in informal and purposive health promotion during the 2022–2023 mpox outbreak, while also presenting significant challenges regarding misinformation and exclusion. We recommend that preparedness for infectious disease outbreaks must consider the role of social media as key tools for not only the dissemination of health promotion messages, but also for real-time collaboration on message development. Special attention should be paid to ensuring collaboration and dissemination strategies are explicitly orientated towards promoting the inclusion of underserved groups.
Serum biomarker signature is predictive of the risk of hepatocellular cancer in patients with cirrhosis
Authors: El-Serag Hashem , Kanwal Fasiha , Ning Jing , Powell Hannah , Khaderi Saira , Singal Amit G , Asrani Sumeet , Marrero Jorge A , Amos Christopher I , Thrift Aaron P , Luster Michelle , Alsarraj Abeer , Olivares Luis , Skapura Darlene , Deng Jenny , Salem Emad , Najjar Omar , Yu Xian , Duong Hao , Scheurer Michael E , Ballantyne Christie M , Kaochar Salma 
Published: February 2024

BackgroundInflammatory and metabolic biomarkers have been associated with hepatocellular cancer (HCC) risk in phases I and II biomarker studies. We developed and internally validated a robust metabolic biomarker panel predictive of HCC in a longitudinal phase III study.MethodsWe used data and banked serum from a prospective cohort of 2266 adult patients with cirrhosis who were followed until the development of HCC (n=126). We custom designed a FirePlex immunoassay to measure baseline serum levels of 39 biomarkers and established a set of biomarkers with the highest discriminatory ability for HCC. We performed bootstrapping to evaluate the predictive performance using C-index and time-dependent area under the receiver operating characteristic curve (AUROC). We quantified the incremental predictive value of the biomarker panel when added to previously validated clinical models.ResultsWe identified a nine-biomarker panel (P9) with a C-index of 0.67 (95% CI 0.66 to 0.67), including insulin growth factor-1, interleukin-10, transforming growth factor β1, adipsin, fetuin-A, interleukin-1 β, macrophage stimulating protein α chain, serum amyloid A and TNF-α. Adding P9 to our clinical model with 10 factors including AFP improved AUROC at 1 and 2 years by 4.8% and 2.7%, respectively. Adding P9 to aMAP score improved AUROC at 1 and 2 years by 14.2% and 7.6%, respectively. Adding AFP L-3 or DCP did not change the predictive ability of the P9 model.ConclusionsWe identified a panel of nine serum biomarkers that is independently associated with developing HCC in cirrhosis and that improved the predictive ability of risk stratification models containing clinical factors.
Clinical implications of discordance between anti-dsDNA antibodies by multiplex flow immunoassay andCrithidia luciliaeassay in a multiethnic racial cohort of patients with SLE
Authors: Zaminski Devyn , Saxena Amit , Izmirly Peter , Buyon Jill P , Belmont H Michael 
Published: February 2024

ObjectiveAnti-dsDNA antibodies (anti-dsDNA) are a component of all classification schemes in SLE and comprise one of the domains in validated activity indices. Anti-dsDNA is frequently measured commercially by an enzyme immunoassay (EIA) orCrithidia luciliaeimmunofluorescence test (CLIFT). To address the clinical impact of measuring these antibodies by two different assays, this study leveraged a well-phenotyped multiethnic/racial cohort.MethodsAll patients fulfilled the classification criteria for SLE by at least one of the validated schemes: American College of Rheumatology, Systemic Lupus Erythematosus International Collaborating Clinics and/or American College of Rheumatology/European League Against Rheumatism classification criteria. Patients with one or more simultaneously paired anti-dsDNA by multiplex EIA and CLIFT were identified. Analysis of concordance or discordance, titre comparability of assays and association with hybrid SLE Disease Activity Index score, prevalence of lupus nephritis (LN), ability to predict a flare and classification criteria was performed.Results207 patients were simultaneously tested by EIA and CLIFT at least once for anti-dsDNA, generating 586 paired results. 377 pairs were concordant and 209 were discordant. 41 of 207 patients always had discordant paired results and 39 patients always had results with titre discordance. In 100 patients with LN, 60 were positive by EIA and 72 by CLIFT. Sensitivities and specificities for patients with LN versus patients without LN were EIA 60% and 47%, and CLIFT 72% and 37%, respectively. 42 patients had flare assessment within 90 days of their paired result. Six of seven patients with mild flares and all four patients with severe flares had concordant positive results.ConclusionOur data demonstrate that discordance of positivity between both assays for anti-dsDNA is relatively common, occurring in a fifth of patients overall and a third of visits. EIA positivity is associated with LN less often than CLIFT positivity. With the significant discordance of results between anti-dsDNA assays, obtaining both CLIFT and EIA assays may be beneficial for classification and routine monitoring of SLE.