bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit
Authors: Schäfer Ann-Britt , Sidarta Margareth , Abdelmesseh Nekhala Ireny , Marinho Righetto Gabriela , Arshad Aysha , Wenzel Michaela 
Published: January 2024

ABSTRACT

Phenotypic analysis assays such as bacterial cytological profiling (BCP) have become increasingly popular for antibiotic mode of action analysis. A plethora of dyes, protein fusions, and reporter strains are available and have been used for this purpose, enabling both rapid mode of action categorization and in-depth analysis of antibiotic mechanisms. However, non-expert researchers may struggle choosing suitable assays and interpreting results. This is a particular problem for antibiotics that have multiple or complex targets, such as the bacterial cell envelope. Here, we set out to curate a minimal set of accessible and affordable phenotypic assays that allow distinction between membrane and cell wall targets, can identify dual-action inhibitors, and can be implemented in most research environments. To this end, we employed BCP, membrane potential, fluidity, and cell wall synthesis assays. To assess specificity and ease of interpretation, we tested three well-characterized and commercially available reference antibiotics: the potassium ionophore valinomycin, the lipid II-binding glycopeptide vancomycin, and the dual-action lantibiotic nisin, which binds lipid II and forms a membrane pore. Based on our experiments, we suggest a minimal set of BCP, a membrane-potentiometric probe, and fluorescent protein fusions to MinD and MreB as basic assay set and recommend complementing these assays with Laurdan-based fluidity measurements and a
PliaI
reporter fusion, where indicated. We believe that our results can provide guidance for researchers who wish to use phenotypic analysis for mode of action studies but do not possess the specialized equipment or expert knowledge to employ the full breadth of possible techniques.

IMPORTANCE
Phenotypic analysis assays using specialized fluorescence fusions and dyes have become increasingly popular in antibiotic mode of action analysis. However, it can be difficult to implement these methods due to the need for specialized equipment and/or the complexity of bacterial cell biology and physiology, making the interpretation of results difficult for non-experts. This is especially problematic for compounds that have multiple or pleiotropic effects, such as inhibitors of the bacterial cell envelope. In order to make phenotypic analysis assays accessible to labs, whose primary expertise is not bacterial cell biology, or with limited equipment and resources, a set of simple and broadly accessible assays is needed that is easy to implement, execute, and interpret. Here, we have curated a set of assays and strains that does not need highly specialized equipment, can be performed in most labs, and is straightforward to interpret without knowing the intricacies of bacterial cell biology.
Post-covid-19 conditions in adults: systematic review and meta-analysis of health outcomes in controlled studies
Authors: Franco Juan Victor Ariel , Garegnani Luis Ignacio , Metzendorf Maria-Inti , Heldt Katharina , Mumm Rebekka , Scheidt-Nave Christa 
Published: January 2024

ObjectiveTo assess the impact of post-covid-19 conditions among adults.DesignSystematic review and meta-analysis of health outcomes in controlled studies.Data sourcesTwo sources were searched from database inception to 20 October 2022: Cochrane covid‐19 study register (comprising Cochrane Central Register of Controlled Trials, Medline, Embase, clinicalTrials.gov, World Health Organization's International Clinical Trials Registry Platform, medRxiv) and WHO's covid-19 research database.Eligibility criteriaCohort studies recruiting more than 100 participants with a control group and a follow-up of at least 12 weeks were included. Adults who were documented to have SARS-CoV-2 infection based on clinical, imaging, or laboratory criteria were included.Data extraction and synthesisTwo independent reviewers extracted data. The main outcomes included quality of life, functionality in daily activities, use of resources, recovery rates (cluster of symptoms), and the incidence of new medical diagnoses. Data were pooled using a random effects model. The risk of bias was assessed with the Joanna Briggs Institute critical appraisal tool for cohort studies.ResultsWe included 63 controlled cohort studies, encompassing more than 96 million participants. Based on five studies, we found a reduction in overall quality of life between individuals with confirmed SARS-CoV-2 infection versus controls at six to 24 months follow-up, although heterogeneity was very high (mean difference in EQ-5D scale −5.28 (95% confidence interval −7.88 to 2.68; I2=93.81%). Evidence from ten studies, which could not be pooled in a meta-analysis, indicated that an increased rate of functional impairment associated with SARS-CoV-2 infection. Use of care increased compared with controls at six to 24 months follow-up at intensive care units (risk ratio 2.00 (95% confidence interval 0.69 to 5.80), five studies, I2=91.96%) and in outpatient care (1.12 (1.01 to 1.24), seven studies, I2=99.51%). Regarding persistent symptoms, individuals with documented SARS-CoV-2 infection had an increased risk of having two or more persistent symptoms at follow-up, especially those related to neurological clusters (ie, risk ratio 1.51 (95% confidence interval 1.17 to 1.93), I2=98.91%). Evidence also showed an increased incidence of a wide variety of metabolic, cardiovascular, neurological, respiratory, haematological and other incident diagnoses.ConclusionEvidence suggests functional impairment after SARS-CoV-2 infection, in addition to a higher use of resources and a higher incidence of widely varying medical diagnoses. These results should be interpreted with caution, considering the high heterogeneity across studies and study limitations related to outcome measurement and attrition of participants.Systematic review registrationOpen Science Framework,osf.io/drm39
Protocol for a scoping review of how people with ME/CFS use the internet
Authors: Shortland Diane Louise , Fazil Qulsom , Hallett Nutmeg , Lavis Anna 
Published: January 2024

IntroductionMyalgic encephalomyelitis (ME) is a chronic neurological illness affecting many bodily systems, commonly the nervous and immune systems. Also known as chronic fatigue syndrome (CFS), key symptoms are extreme fatigue, post-exertional malaise, cognitive problems and sleep disturbance. With reported higher levels of online activity for people with ME/CFS than other patient groups (Westerby 2013 cited in Ytre-Arne) it is crucial to gain more knowledge of usage characteristics and experience of online use, and its integration into everyday life. This scoping review protocol details the proposed methods for gaining insight into this little known phenomenon.Methods and analysisThis review uses the methodological framework for conducting a scoping review by Arksey and O’Malley, with further guidance by Levacet al, and the Joanna Briggs Institute. It also refers to the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols reporting guidelines. The following bibliographic databases will be searched: Embase, Medline, PsychINFO, Cinahl, AMED, and ASSIA, plus Web of Science, ProQuest Dissertations and Theses Global, Scopus, and Google Scholar for grey literature. Reference lists of included papers will be studied. Two reviewers will independently screen title abstracts, and then full text of studies against inclusion criteria. Remaining studies will be quality assessed using appropriate critical appraisal tools. Findings will be charted and mapped to gain in-depth knowledge of the use of the internet in people with ME/CFS.Ethics and disseminationThe findings from this review will be disseminated through peer-reviewed publication and a report for leading charities of ME/CFS. The review will collect secondary data only and therefore does not need ethical approval.
Impact of daily cyclic enteral nutrition versus standard continuous enteral nutrition in critically ill patients: a study protocol for a randomised controlled trial in three intensive care units in France (DC-SCENIC)
Authors: Callahan Jean-Christophe , Parot-Schinkel Elsa , Asfar Pierre , Ehrmann Stephan , Tirot Patrice , Guitton Christophe 
Published: January 2024

IntroductionCurrent guidelines on clinical nutrition of ventilated patients in the intensive care unit (ICU) recommend initiating continuous enteral nutrition within 48 hours of ICU admission when feasible. However, discontinuous feeding regimens, alternating feeding and fasting intervals, may have an impact on clinical and patient centred outcomes. The ongoing "Impact of daily cyclic enteral nutrition versus standard continuous enteral nutrition in critically ill patients" (DC-SCENIC) trial aims to compare standard continuous enteral feeding with daily cyclic enteral feeding over 10 hours to evaluate if implementing a fasting-mimicking diet can decrease organ failure in ventilated patients during the acute phase of ICU management.Methods and analysisDC-SCENIC is a randomised, controlled, multicentre, open-label trial comparing two parallel groups of patients 18 years of age or older receiving invasive mechanical ventilation and having an indication for enteral nutrition through a gastric tube. Enteral feeding is continuous in the control group and administered over 10 hours daily in the intervention group. Both groups receive isocaloric nutrition with 4 g of protein per 100 mL, and have the same 20 kcal/kg/day caloric target. The primary endpoint is the change in the Sequential Organ Failure Assessment score at 7 days compared with the day of inclusion in the study. Secondary outcomes include daily caloric and protein delivery, digestive, respiratory and metabolic tolerance as well as 28-day mortality, duration of mechanical ventilation and ventilator-free days. Outcomes will be analysed on an intention-to-treat basis. Recruitment started in June 2023 in 3 French ICU’s and a sample size of 318 patients is expected by February 2026.Ethics and disseminationThis study received approval from the national ethics review board on 8 November 2022 (Comité de Protection des Personnes Sud-Est VI, registration number 2022-A00827-36). Patients are included after informed consent. Results will be submitted for publication in peer-reviewed journals.Trial registration numberNCT05627167.
Safety, efficacy and health impact of electronic nicotine delivery systems (ENDS): an umbrella review protocol
Authors: Goel Sonu , Shabil Muhammed , Kaur Jagdish , Chauhan Anil , Rinkoo Arvind Vashishta 
Published: January 2024

BackgroundElectronic nicotine delivery systems (ENDS), commonly known as e-cigarettes or vapes, have witnessed a rise in popularity, particularly among the youth. Although they were initially introduced as an alternative to traditional smoking, the design and function of ENDS vary. The potential health effects of ENDS, especially in comparison to traditional cigarettes, are a matter of ongoing debate. Given the increasing number of clinical studies and systematic reviews on this topic, there exists a demand for an umbrella review that offers a comprehensive assessment. The goal of this study is to perform an umbrella review of systematic reviews and meta-analyses to assess the safety, efficacy, health implications and potential gateway effect associated with ENDS.Methods and analysisThis umbrella review will adhere to the Joanna Briggs Institute (JBI) framework and the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. A planned literature search will be executed across databases such as OVID, PubMed/MEDLINE, EMBASE, Cochrane Library and Web of Science. The inclusion criteria are systematic reviews that discuss ENDS and e-liquids in the context of safety, efficacy and health outcomes. The exclusion criteria include narrative reviews, non-systematic reviews and studies not in English. Quality of the selected studies will be evaluated using the AMSTAR V.2 Scale. An overlap assessment will be done using the Corrected Covered Area, and data synthesis will be presented both narratively and in tabulated formsEthics and disseminationEthics approval is not required for this study, as it does not involve the collection of original data. The results will be disseminated through peer-reviewed publication. The findings will offer crucial insights for stakeholders, policy-makers and the general public, underlining the health implications and the role of ENDS in tobacco cessation.
Effectiveness of trauma-focused art therapy (TFAT) for psychological trauma: study protocol of a multiple-baseline single-case experimental design
Authors: Heijman Jackie , Wouters Hans , Schouten Karin Alice , Haeyen Suzanne 
Published: January 2024

IntroductionTreatments such as eye movement desensitisation and reprocessing and (narrative) exposure therapies are commonly used in psychological trauma. In everyday practice, art therapy is also often used, although rigorous research on its efficacy is lacking. Patients seem to benefit from the indirect, non-verbal experiential approach of art therapy. This protocol paper describes a study to examine the effectiveness of a 10-week individual trauma-focused art therapy (TFAT) intervention.Methods and analysisA mixed-methods multiple-baseline single-case experimental design will be conducted with 25–30 participants with psychological trauma. Participants will be randomly assigned to a baseline period lasting 3–5 weeks, followed by the TFAT intervention (10 weeks) and follow-up (3 weeks). Quantitative measures will be completed weekly: the Beck Depression Inventory-II, the Mental Health Continuum Short Form, the Resilience Scale, the Rosenberg Self-Esteem Scale and the Self-expression and Emotion Regulation in Art Therapy Scale. The Post-Traumatic Stress Disorder Checklist-5 will be completed at week 1 and week 10. Qualitative instruments comprise a semistructured interview with each individual patient and therapist, and a short evaluation for the referrer. Artwork will be used to illustrate the narrative findings. Quantitative outcomes will be analysed with linear mixed models using the MultiSCED web application. Qualitative analyses will be performed using thematic analysis with ATLAS.ti.Ethics and disseminationThis study has been approved by the ethics committee of the HAN University of Applied Sciences (ECO 394.0922). All participants will sign an informed consent form and data will be treated confidentially. Findings will be published open access in peer-reviewed journals.Trial registration numberNCT05593302.
Psychiatric comorbidities in epilepsy: population co-occurrence, genetic correlations and causal effects
Authors: Ahlqvist Viktor H , Dardani Christina , Madley-Dowd Paul , Forbes Harriet , Rast Jessica , Zhong Caichen , Gardner Renee M , Dalman Christina , Lyall Kristen , Newschaffer Craig , Tomson Torbjörn , Lundberg Michael , Berglind Daniel , Davies Neil M , Lee Brian K , Magnusson Cecilia , Rai Dheeraj 
Published: January 2024

BackgroundPsychiatric comorbidities are common in patients with epilepsy. Reasons for the co-occurrence of psychiatric conditions and epilepsy remain poorly understood.AimWe aimed to triangulate the relationship between epilepsy and psychiatric conditions to determine the extent and possible origins of these conditions.MethodsUsing nationwide Swedish health registries, we quantified the lifetime prevalence of psychiatric disorders in patients with epilepsy. We then used summary data from genome-wide association studies to investigate whether the identified observational associations could be attributed to a shared underlying genetic aetiology using cross-trait linkage disequilibrium score regression. Finally, we assessed the potential bidirectional relationships using two-sample Mendelian randomisation.ResultsIn a cohort of 7 628 495 individuals, we found that almost half of the 94 435 individuals diagnosed with epilepsy were also diagnosed with a psychiatric condition in their lifetime (adjusted lifetime prevalence, 44.09%; 95% confidence interval (CI) 43.78% to 44.39%). We found evidence for a genetic correlation between epilepsy and some neurodevelopmental and psychiatric conditions. For example, we observed a genetic correlation between epilepsy and attention-deficit/hyperactivity disorder (rg=0.18, 95% CI 0.09 to 0.27, p<0.001)—a correlation that was more pronounced in focal epilepsy (rg=0.23, 95% CI 0.09 to 0.36, p<0.001). Findings from Mendelian randomisation using common genetic variants did not support bidirectional effects between epilepsy and neurodevelopmental or psychiatric conditions.ConclusionsPsychiatric comorbidities are common in patients with epilepsy. Genetic correlations may partially explain some comorbidities; however, there is little evidence of a bidirectional relationship between the genetic liability of epilepsy and psychiatric conditions. These findings highlight the need to understand the role of environmental factors or rare genetic variations in the origins of psychiatric comorbidities in epilepsy.
Characteristics and trends of pediatric firepit burns: insights for prevention and safety
Authors: Fazal Maria , Chidiac Charbel , Ahmad Raheel , Issa Oussama , Hodgman Erica , Garcia Alejandro V 
Published: January 2024

IntroductionAs fire pits grow in popularity, so do the associated burn injuries. Our study examines pediatric fire pit burns characteristics to raise awareness and promote safety precautions.MethodsWe conducted a retrospective review of pediatric patients (≤21 years) with firepit burns at a tertiary care hospital from 2016 to 2021.ResultsEighty-four patients were identified, of whom 70.2% were male, with a median age of 62 months. The median percent total body surface area burned was 2% (interquartile range (IQR)=1–4). Thirty-five (41.7%) patients were admitted and 7 (8.3%) underwent grafting. Neck and trunk burns had the highest grafting rates (66% and 33%, respectively). The hands (41.7%) and the lower extremities (27.4%) were the most frequently burned body areas. The leading causes of burns were ashes/hot coals (34.5%), flames (31.0%), and direct contact (25.0%), often resulting from falling into the fire (59.5%) or running or playing in activities near it (26.2%). Thirty-five (41.7%) were admitted for inpatient management, while 49 (58.3%) were treated as outpatient. Eleven (13.2%) underwent at least one reconstructive surgery, 7 (8.4%) had at least one rehabilitation visit, and 65 (77.4%) had follow-up clinic visits. The median length of stay was 2 days (IQR=1.0–3.5). The peak months for burns were from August through October (n=40, 46.0%), with an increase observed from 10 cases in 2016 to 20 cases in 2020.ConclusionsGiven the significant proportion of firepit burns resulting from unsafe fire behaviors, it is crucial that caretakers are aware of proper firepit safety precautions.Level of evidenceIII.
#192 : Comparison of Cytokine Profiles and Th1/Th2 Ratios in the Peri-Implantation Endometrium in Recurrent Reproductive Failure Women with and Without Chronic Endometritis
Authors: Liu Yingyu , Chen Xiaoyan , Li Ruiman , Li Tin Chiu , Zhu Yuanfang 
Published: January 2024

Background and Aims: Aberrant local endometrial microenvironment in chronic endometritis (CE) may be involved in reduced endometrial receptivity and recurrent reproductive failure. Previous studies have observed some discrepancies between different types of cytokines, without showing the predominance of a specific immune response between women with miscarriage and normal pregnancy. However, exactly how CE alters the endometrial function and interferes with the process of implantation is still uncertain. Method: It was an observational retrospective study. A total of 39 women with unexplained recurrent miscarriage (RM) participated in this study. Endometrial specimens were obtained precisely 7 days after luteinization hormone surge and chronic endometritis was diagnosed by plasma cell density. In total, 24 different cytokines were examined by the Luminex technique after protein extraction and Th1/Th2 ratios are measured. Results: No significant differences in all the endometrial specimens between 14 women who found to have CE and 25 women who did not have CE. However, in the RM group, we found a significantly increased expression of IFN-[Formula: see text] (2.89 pg/mL vs. 0.75 pg/mL, [Formula: see text] = 0.027) in women with CE. In addition, an elevated Th1/Th2 ratio (IFN-[Formula: see text] /IL-4: 288.83 vs. 75.29, [Formula: see text] = 0.027) and a decreased ratio of TNF-[Formula: see text] /IL-6 (1.25 vs. 3.11, [Formula: see text] = 0.006) were observed in RM women with CE than those without CE. Moreover, the levels of VEGF-D (14.63 pg/mL vs. 9.16 pg/mL, [Formula: see text] = 0.041) and EGF (25.13 pg/mL vs. 11.98 pg/mL, [Formula: see text] = 0.023) were higher in women with live births than those women without live births in RM group and infertility group, respectively. Conclusion: In this study, altered cytokine profiles and Th1/Th2 ratios in peri-implantation endometrium is of predictive value for subsequent pregnancy outcome in women with recurrent miscarriage.
Epidemiology of Spontaneous Cervical Artery Dissection: Population-Based Study
Authors: Griffin Kim J. , Harmsen William S. , Mandrekar Jay , Brown Robert D. , Keser Zafer 
Published: January 2024

BACKGROUND:
Cervical artery dissection (CeAD) represents up to 15% to 25% of ischemic strokes in people under the age of 50 years. Noninvasive vessel imaging is increasingly used in clinical practice, but the impact on the frequency of detection of CeAD is unknown. In 2006, the yearly incidence rate of CeAD was estimated at 2.6 per 100 000 person-years, but the current incidence is unknown.

METHODS:
In this population-based retrospective observational cohort study, we utilized the resources of the Rochester Epidemiology Project to ascertain all adult residents of Olmsted County, MN, diagnosed with internal carotid artery dissection and common carotid artery dissection or vertebral artery dissection from 2002 to 2020. Patients with only intracranial involvement or CeAD following major trauma were excluded. Age-adjusted sex-specific and age- and sex-adjusted incidence rates were estimated using the US White 2010 decennial census, with rates expressed per 100 000 person-years. We assessed longitudinal trends by dividing the data into 5-year time intervals, with the last being a 4-year interval.

RESULTS:

We identified 123 patients with a diagnosis of CeAD. There were 63 patients with internal carotid artery dissection, 54 with vertebral artery dissection, 2 with concurrent internal carotid artery dissection and vertebral artery dissection, and 4 with common carotid artery dissection. There were 63 (51.2%) female patients and 60 (48.8%) male patients. The average age at diagnosis was 50.2 years (SD, 15.1 [95% CI, 20.1–90.5] years). The incidence rate of spontaneous CeAD encompassing all locations was 4.69 per 100 000 person-years (2.43 for internal carotid artery dissection and 2.01 for vertebral artery dissection). The incidence rate increased from 2.30 per 100 000 person-years from 2002 to 2006 to 8.93 per 100 000 person-years from 2017 to 2020 (
P
<0.0001). The incidence rate for female patients rose from 0.81 per 100 000 person-years from 2002 to 2006 to 10.17 per 100 000 person-years from 2017 to 2020.

CONCLUSIONS:
The incidence rate of spontaneous CeAD increased nearly 4-fold over a 19-year period from 2002 to 2020. The incidence rate in women rose over 12-fold. The increase in incidence rates likely reflects the increased use of noninvasive vascular imaging.