bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for long COVID among healthcare workers, Brazil, 2020–2022
Authors: Marra Alexandre R. , Sampaio Vanderson Souza , Ozahata Mina Cintho , da Silva Rafael Lopes Paixão , Brito Anderson , Bragatte Marcelo , Kalil Jorge , Miraglia João Luiz , Malheiros Daniel Tavares , Guozhang Yang , Teich Vanessa Damazio , Victor Elivane da Silva , Pinho João Renato Rebello , Cypriano Adriana , Vieira Laura Wanderly , Polonio Miria , de Oliveira Solange Miranda , Ricardo Victória Catharina Volpe , Maezato Aline Miho , Callado Gustavo Yano , Schettino Guilherme de Paula Pinto , de Oliveira Ketti Gleyzer , Santana Rúbia Anita Ferraz , Malta Fernanda de Mello , Amgarten Deyvid , Boechat Ana Laura , Kobayashi Takaaki , Perencevich Eli , Edmond Michael B. , Rizzo Luiz Vicente 
Published: January 2023

ABSTRACTObjectivesWe aimed to determine risk factors for the development of long coronavirus disease (COVID) in healthcare workers (HCWs).MethodsWe conducted a case-control study among HCWs who had confirmed COVID-19 infection working in a Brazilian healthcare system between March 1, 2020 and July 15, 2022. Cases were defined as those having long COVID per the Centers for Disease Control and Prevention definition. Controls were defined as HCWs who had documented COVID-19 infection but did not develop long COVID. Multiple logistic regression was used to assess the association between exposure variables and long COVID during 180 days of follow-up.ResultsOf 7,051 HCWs diagnosed with COVID-19 infection, 1,933 (27.4%) who developed long COVID were compared to 5,118 (72.6%) who did not. The majority of those with long COVID (51.8%) had 3 or more symptoms. Factors associated with development of long COVID were female sex (OR 1.21 [CI95 1.05-1.39]), age (OR 1.01 [CI95 1.00-1.02]), and two or more COVID-19 infections (1.27 [CI95 1.07-1.50]). Those infected with the Delta variant (OR 0.30 [CI95 0.17-0.50]) or the Omicron variant (OR 0.49 [CI95 0.30-0.78]), and those receiving four COVID-19 vaccine doses prior to infection (OR 0.05 [CI95 0.01-0.19]) were significantly less likely to develop long COVID.ConclusionsLong COVID can be prevalent among HCWs. We found that acquiring more than one COVID-19 infection was a major risk factor for long COVID, while maintenance of immunity via vaccination was highly protective.
Deciphering microbiota of acute upper respiratory infections: a comparative analysis of PCR and mNGS methods for lower respiratory trafficking potential
Authors: Almas Sadia , Carpenter Rob E. , Singh Anuradha , Rowan Chase , Tamrakar Vaibhav K. , Sharma Rahul 
Published: January 2023

AbstractAlthough it is clinically important for acute respiratory tract (co)infections to have rapid and accurate diagnosis, it is critical that respiratory medicine understand the advantages of current laboratory methods. In this study we tested nasopharyngeal samples (n=29) with a commercially available PCR assay and compared the results with hybridization capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct<35 and for mNGS samples >40% target coverage, median depth of 1X and RPKM>10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positive 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterize the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify® Platform for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompetent respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndromic-based tests and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration—with promise to reduce morbidity and mortality.HighlightsWhat are the main findings?Although there was a high concordance between methodologies, a hybridization capture-based mNGS workflow was able to detect 29 additional upper respiratory microorganisms versus PCR.Identified microorganisms were rapidly characterized into three phenotypic groups for infectivity and trafficking potential.What is the implication of the main finding?A hybridization capture-based mNGS workflow can provide a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infectionDeciphering upper respiratory microbiota with phenotypic grouping has potential to provide respiratory medicine a tool to better manage immunocompetent and complex respiratory cases.
Non-steroidal anti-inflammatories for analgesia in critically ill patients: a systematic review and meta-analysis of randomized control trials
Authors: Ma Chen-Hsiang , Tworek Kimberly B. , Kung Janice Y. , Kilcommons Sebastian , Wheeler Kathleen , Parker Arabesque , Senaratne Janek , Macintyre Erika , Sligl Wendy , Karvellas Constantine J. , Zampieri Fernando G , Kutsogiannis Demetrios Jim , Basmaji John , Lewis Kimberley , Chaudhuri Dipayan , Sharif Sameer , Rewa Oleksa G. , Rochwerg Bram , Bagshaw Sean M. , Lau Vincent I. 
Published: January 2023

AbstractPurposeWhile opioids are part of usual care for analgesia in the intensive care unit (ICU), there are concerns regarding excess use. This is a systematic review of non-steroidal anti-inflammatories (NSAIDs) use in critically ill adult patients.MethodsWe conducted a systematic search of MEDLINE, EMBASE, CINAHL, and Cochrane Library. We included randomized control trials (RCTs) comparing NSAIDs alone or as an adjunct to opioids for analgesia. The primary outcome was opioid utilization. We reported mean difference for continuous outcomes and relative risk for dichotomous outcomes with 95% confidence intervals (CIs). We evaluated study risk of bias using the Cochrane risk of bias tool and evidence certainty using GRADE.ResultsWe included 15 RCTs (n=1621 patients). Adjunctive NSAID therapy to opioids reduced 24-hour oral morphine equivalent consumption by 21.4mg (95% CI: 11.8-31.0mg reduction, high certainty) and probably reduced pain scores (measured by visual analogue scale) by -6.1mm (95% CI: -12.2 to +0.1, moderate certainty). Adjunctive NSAIDs probably had no impact on duration of mechanical ventilation (-1.6 hours, 95% CI: -0.4 to -2.7 hours, moderate certainty) and may have no impact on ICU length of stay (-2.1 hours, 95% CI: -6.1 to +2.0 hours, low certainty). Variability in reporting of adverse outcomes (e.g. gastrointestinal bleeding, acute kidney injury) precluded their meta-analysis.ConclusionIn critically ill adult patients, NSAIDs reduced opioid use, probably reduced pain scores, but were uncertain for duration of mechanical ventilation or ICU length of stay. Further research is required to characterize the prevalence of NSAID-related adverse outcomes.Take-Home MessageIn this systematic review and meta-analysis of 15 randomized control trials that included 1621 critically ill adult patients, the addition of non-steroidal anti-inflammatories to an opioid analgesic strategy reduced 24-hour opioid use and modestly reduced pain with no impact on duration of mechanical ventilation or ICU length of stay.
Alternative epidemic indicators for COVID-19: a model-based assessment of COVID-19 mortality ascertainment in three settings with incomplete death registration systems
Authors: McCabe Ruth , Whittaker Charles , Sheppard Richard J. , Abdelmagid Nada , Ahmed Aljaile , Alabdeen Israa Zain , Brazeau Nicholas F. , Abd Elhameed Abd Elhameed Ahmed , Bin-Ghouth Abdulla Salem , Hamlet Arran , AbuKoura Rahaf , Barnsley Gregory , Hay James A. , Alhaffar Mervat , Besson Emilie Koum , Saje Semira Mitiku , Sisay Binyam Girma , Gebreyesus Seifu Hagos , Sikamo Adane Petros , Worku Aschalew , Ahmed Yakob Seman , Mariam Damen Haile , Sisay Mitike Molla , Checchi Francesco , Dahab Maysoon , Endris Bilal Shikur , Ghani Azra C. , Walker Patrick G. T. , Donnelly Christl A. , Watson Oliver J. 
Published: January 2023

AbstractNot all COVID-19 deaths are officially reported and, particularly in low-income and humanitarian settings the magnitude of such reporting gaps remain sparsely characterised. Alternative data sources, including burial site worker reports, satellite imagery of cemeteries and social-media-conducted surveys of infection, may offer solutions. By merging these data with independently conducted, representative serological studies within a mathematical modelling framework, we aim to better understand the range of under-reporting using the example of three major cities: Addis Ababa (Ethiopia), Aden (Yemen) and Khartoum (Sudan) during 2020. We estimate 69% - 100%, 0.8% - 8.0% and 3.0% - 6.0% of COVID-19 deaths were reported in these three settings, respectively. In future epidemics, and in settings where vital registrations systems are absent or limited, using multiple alternative data sources could provide critically-needed, improved estimates of epidemic impact. However, ultimately, functioning vital registration systems are needed to ensure that, in contrast to COVID-19, the impact of future pandemics or other drivers of mortality are reported and understood worldwide.One sentence summaryWe demonstrate the suitability of alternative data sources to assess the under-ascertainment of COVID-19 mortality.
Promoting Sleep Duration in the Pediatric Setting Using a Mobile Health Platform: A Randomized Optimization Trial
Authors: Mitchell Jonathan A. , Morales Knashawn H. , Williamson Ariel A. , Jawahar Abigail , Juste Lionola , Vajravelu Mary Ellen , Zemel Babette S. , Dinges David F. , Fiks Alexander G. 
Published: January 2023

AbstractObjectiveDetermine the optimal combination of digital health intervention component settings that increase average sleep duration by ≥30 minutes per weeknight.MethodsOptimization trial using a 25factorial design. The trial included 2 week run-in, 7 week intervention, and 2 week follow-up periods. Typically developing children aged 9-12y, with weeknight sleep duration <8.5 hours were enrolled (N=97). All received sleep monitoring and performance feedback. The five candidate intervention components (with their settings to which participants were randomized) were: 1) sleep goal (guideline-based or personalized); 2) screen time reduction messaging (inactive or active); 3) daily routine establishing messaging (inactive or active); 4) child-directed loss-framed financial incentive (inactive or active); and 5) caregiver-directed loss-framed financial incentive (inactive or active). The primary outcome was weeknight sleep duration (hours per night). The optimization criterion was: ≥30 minutes average increase in sleep duration on weeknights.ResultsAverage baseline sleep duration was 7.7 hours per night. The highest ranked combination included the core intervention plus the following intervention components: sleep goal (either setting was effective), caregiver-directed loss-framed incentive, messaging to reduce screen time, and messaging to establish daily routines. This combination increased weeknight sleep duration by an average of 39.6 (95% CI: 36.0, 43.1) minutes during the intervention period and by 33.2 (95% CI: 28.9, 37.4) minutes during the follow-up period.ConclusionsOptimal combinations of digital health intervention component settings were identified that effectively increased weeknight sleep duration. This could be a valuable remote patient monitoring approach to treat insufficient sleep in the pediatric setting.
Determinants of wasting, stunting, and undernutrition among children under five years: Cross-sectional study in southern Punjab, Pakistan
Authors: Saleem Javeria , Zakar Rubeena , Aadil Rana Muhammad , Butt Muhammad Salman , Mushtaq Faisal , Bukhari Gul Mehar Javaid , Fischer Florian 
Published: January 2023

AbstractBackgroundMalnutrition is a serious concern globally and may lead to early death if it remains untreated. Prevalence of malnutrition is high in South Asian countries. Therefore, this study aims to evaluate the determinants of wasting, stunting, and undernutrition in under-five children of southern Punjab, Pakistan.MethodsWe conducted a cross-sectional study among 185 children. Anthropometric measures were done by nutritional experts and pediatricians. Data were analyzed with SPSS version 25.0. A p-value <0.05 was considered statistically significant.ResultsSignificant determinants of wasting (weight-for-height) were family monthly earnings (β=-0.14; 95% CI: -0.89 to -0.04; p=0.03) and complementary feeding practices (β=-0.21; 95% CI: -1.14 to 0.19; p<0.001). For stunting (length/height-for-age), the significant determinants were tuberculosis (TB) contact history (β=-0.15; 95% CI: -0.97 to -0.03; p=0.03) and non-use of exclusive breastfeeding practices (β=-0.19; 95% CI: -1.40 to 0.16; p=0.01). For undernutrition, significant determinants were monthly income (β=0.28; 95% CI: 0.11 to 0.62; p=0.02) and exclusive breastfeeding practices (β=0.22; 95% CI: 0.17 to 0.39; p=0.02).ConclusionSocial determinants such as family earnings, family food security, practices of exclusive breastfeeding and proper complementary feeding, number of under-five siblings, and history of TB contact have a strong association with malnutrition and undernutrition. Concerted and comprehensive strategies are needed for the improvement of associated factors to combat malnutrition as well as undernutrition among children.
Biological diagnosis and characterization of occult hepatitis B virus infection in Burkina Faso
Authors: Doumbia Boubacar , Diarra Birama , Kone Bourahima , Djigma Florencia , Baya Bocar , Simpore Jacque 
Published: January 2023

AbstractIntroduction/objectiveThe occult infection by the hepatitis B virus (OBI) characterized by the undetectable (HBs Ag) negative antigen in the serum and the presence of viral DNA, constitutes a major public health problem and a major challenge for clinical forms of hepatitis worldwide. The persistence of OBI very often leads to hepatocellular carcinoma (HCC) and immunodeficiency. The aim of this study was to estimate the prevalence of OBI and to characterize the incriminated genotypes of the virus.Material and methodThe plasmas of 252 HBsAg-negative volunteers were used for highlighting the viral DNA by PCR classic. PCR Multiplex using specific primers of 6 genotypes (A to F) was used for characterization.ResultsA prevalence of 11.9% (30/252) of OBI was obtained with 7.5% in women and 4.4% for men. Genotypes E (60.0%) and A3 (23.3%) were present and genotypes B, C, D, and F were absent. A mixed infection with E/A3 genotypes (16.7%) was observed. AC Anti-HBc was present in 80% of cases OBI.Discussion/ConclusionThe prevalence of 11.9% of OBI could be related to the level of endemicity of the study area, Burkina Faso being a country with a prevalence of more than 14% of HBV infection. These infections are dominated by the A3 and E genotypes, confirming their importance in chronic HBV infections. The absence of genotypes B and C in cases of OBI constitutes a positive predictive value since their presence is linked to a more rapid evolution of the infection towards HCC.
The immediate treatment outcomes and cost estimate for managing clinical measles in children admitted at Mulago Hospital: a retrospective cohort study
Authors: Namugga Barbara , Malande Ombeva , Kitonsa Jonathan , Banura Cecily , Mupere Ezekiel 
Published: January 2023

AbstractBackgroundOver the recent years, the Ministry of Health in Uganda has reported multiple measles outbreaks in various districts despite the availability of a safe cost effective vaccine. Measles, especially among the unvaccinated, can lead to serious complications including death, while its management heavily burdens the family and health care delivery system. Whereas the cost of measles vaccination is known, the cost of treating measles is unknown. Knowledge of this can inform policy and planning for healthcare services.MethodA retrospective single cohort study using records review was conducted to determine the immediate treatment outcomes and estimate the health care delivery cost of managing measles among children 0-12 years admitted at Mulago hospital throughout 2018. Demographics, complications, vaccination status, discharge status, duration of hospital stay, type of treatment, supplies used and investigations done were abstracted from the patient charts. The costs of treatment were obtained from the hospital pharmacy price list while the unit cost of utilities, human resource, food and security were obtained from the hospital accounts department. Patients’ characteristics were summarized descriptively. For all cost information, we reported the mean with standard deviation (SD) and range, and costs information was stratified and presented as direct health care (blood test, radiology and treatment) and direct non health care.ResultsOut of 536 patient charts, 267 were chosen, 51% were for females and the median age was 1.0 (IQR 0.75-2) years. Sixty-three patients (24%) were immunised, 79 (29%) were not immunized, 56 (21%) were not due for immunisation at the time of hospitalisation while the status of 69 (26%) was not recorded. Median length of hospital stay was 4.0 days (IQR 3.0-7.0) with majority (n=207, 77%) staying < 7 days. There were 30 deaths (11%) with mortality highest among the unimmunised (n= 13, 44%) and severe pneumonia (39.5%) was the commonest complication.The average cost estimate to the health care delivery system to treat a child with measles was (114.5 USD). Human resource (79.33USD, SD 4.63) and treatment costs (21.98USD, SD 22.77) were the largest expenses.ConclusionsMortality among children with measles was high and occurrence of complications common. The estimated average direct health care cost of treating a measles case in the National Referral Hospital was considerably high. Further research is required to estimate the cost to the family and society in managing a child with measles.
Filopodial protrusion driven by density-dependent Ena-TOCA-1 interactions
Authors: Blake Thomas C. A. , Fox Helen M. , Urbančič Vasja , Wolowczyk Adam , Allgeyer Edward S. , Mason Julia , Gallop Jennifer L. 
Published: January 2023

AbstractFilopodia are narrow actin-rich protrusions with important roles in neuronal development. The neuronally-enriched TOCA-1/CIP4 family of F-BAR and SH3 domain adaptor proteins have emerged as upstream regulators that link membrane interactions to actin binding proteins in lamellipodia and filopodia, including WAVE and N-WASP nucleation promoting factors and formins. Here, we demonstrate a direct interaction between TOCA-1 and Ena/VASP actin filament elongators that is mediated by clustered SH3 domain interactions. UsingXenopusretinal ganglion cell axonal growth cones, where Ena/VASP proteins have a native role in filopodia extension, we show that TOCA-1 localises to filopodia and lamellipodia, with a retrograde flow of puncta, and correlates with filopodial protrusion. Two-colour single molecule localization microscopy of TOCA-1 and Ena supports their nanoscale association. TOCA-1 clusters coalesce at advancing lamellipodia and filopodia and operate synergistically with Ena to promote filopodial protrusion dependent on a functional SH3 domain. In analogous yet distinct ways to lamellipodin and IRSp53, we propose that transient TOCA-1 clusters recruit and promote Ena activity to orchestrate filopodial protrusion.
Optimization of molecular methods for detection and quantification of specific duckweed-bacteria interactions
Authors: Acosta Kenneth , Sorrels Shawn , Chrisler William , Huang Weijuan , Gilbert Sarah , Brinkman Thomas , Michael Todd P. , Lebeis Sarah , Lam Eric 
Published: January 2023

AbstractBacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains as well as in the context of complex bacterial communities. Quantitative studies that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study specific duckweed-bacteria interactions. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacteria interactions, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacteria interactions present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe interactions within plant-microbial communities.
Label-free single-cell live imaging reveals fast metabolic switch in T lymphocytes
Authors: Paillon Noémie , Ung Thi Phuong Lien , Dogniaux Stéphanie , Stringari Chiara , Hivroz Claire 
Published: January 2023

ABSTRACTT cell activation induces a metabolic switch generating energy required for proliferation, survival, and fueling their functions. Thus, it is essential to monitor metabolism associated to subcellular functional and structural changes. We used non-invasive label-free two-photon fluorescence lifetime microscopy (2P-FLIM) to map the spatial and temporal dynamics of the metabolic NADH co-enzyme during T lymphocyte activation. 2P-FLIM measurements of the protein-bound and free NADH ratios provides a readout of the redox state (NAD+/ NADH) of the cells, and thus of their OXPHOS and glycolysis rates. Using this method, we followed the dynamics of fraction of bound NADH (fb NADH) in live single cells. Comparing fb NADH between resting and activated T cells, we show that T cell activation induces a rapid switch toward glycolysis. The switch takes only 10 minutes and remains stable for at least one hour. Three-dimensional (3D) analysis revealed that the intracellular distribution of fb NADH is symmetrically distributed in resting cells, whereas increases at the contact zone in activated cells. Finally, we show that fb NADH negatively correlates with spreading of activated T cells, suggesting a link between actin remodeling and metabolic changes. This study shows that 2P-FLIM measurement of fb NADH is well suited to follow a fast metabolic switch in 3D, in single T lymphocytes with subcellular resolution.