bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolving SARS-CoV-2 virulence among hospital and university affiliates in Spain and Greater Boston
Authors: Amer Fares , Lan Fan-Yun , Gil-Conesa Mario , Sidossis Amalia , Bruque Daniel , Iliaki Eirini , Buley Jane , Nathan Neetha , Bruno-Murtha Lou Ann , Carlos Silvia , Kales Stefanos N. , Fernandez-Montero Alejandro 
Published: November 2022

AbstractBackgroundThe COVID-19 pandemic caused by the SARS-CoV-2 virus greatly affected healthcare workers and healthcare systems. It also challenged schools and universities worldwide negatively affecting in-person education. We conducted this study is to assess the evolution of SARs-CoV-2 virulence over the course of the pandemic.MethodsA combined cohort of affiliates from the University of Navarra, two hospitals in Spain, and one healthcare system in the Greater Boston area was followed prospectively from March 8th, 2020, to January 31st, 2022 for diagnosis with COVID-19 by PCR testing and related sequelae. Follow-up time was divided into four periods according to distinct waves of infection during the pandemic. Severity of COVID-19 was measured by case-hospitalization rate. Descriptive statistics and multivariable-adjusted statistics using the Poisson mixed-effects regression model were applied.ResultsFor the last two periods of the study (January 1stto December 15th, 2021 and December 16th, 2021 to January 31st, 2022) and relative to the first period (March 8thto May 31st, 2020), the incidence rate ratios (IRRs) of hospitalization were 0.08 (95% CI, 0.03-0.17) and 0.03 (95% CI, 0.01-0.15), respectively.InterpretationThe virulence of COVID-19 and immunity of our populations evolved over time, resulting in a decrease in case severity. We found the case-hospitalization rate decreased more than 90% in our cohort despite an increase in incidence.
Exploring Views of Technology to Inform Maternal and Child Health Interventions for Black Birthing People
Authors: Jaeke Elisha , Olson Jessica , Blackwell Dalvery , Aboagye Sophia , Taylor Reiauna , Zusevics Kaija L , Stolley Melinda 
Published: November 2022

BackgroundBlack birthing people experience disproportionately higher rates of morbidity and mortality, and poorer infant health outcomes than all other racial and ethnic groups. Statewide in Wisconsin, an alarming disparity exists between Black and Non-Hispanic White (NHW) breastfeeding initiation rates (54% and 87%, respectively). For the last fourteen years, the African American Breastfeeding Network (AABN) has operated in Milwaukee County, where 70% of the state’s Black population lives. AABN’s mission is to improve maternal health and champion breastfeeding equity for Black birthing families. In 2018, AABN received more referrals than could be served by their team of doulas, lactation consultants, and advocates, leading our team to pursue ways to expand their reach through technology-based approaches. With the onset of COVID-19, the need for telehealth support increased drastically, as referrals for AABN services tripled. In this study, we explore the use of technology to support Black birthing families in Wisconsin and beyond, in the hopes of expanding the capacity of organizations like AABN.MethodsA survey was conducted amongst 21 Black women who were pregnant or had given birth in the last year, regarding perceptions of technology. Women were split equally into three focus groups to discuss survey results further and provide context. Focus groups were recorded, transcribed, and coded for themes.ResultsParticipants were “Likely” to use their phone or the internet to look for general or health-related information, but only “Somewhat Likely” to trust either general or health-related information. Participants were “Somewhat Likely” to trust the information on the phone or the internet as much as their healthcare provider (doctor, nurse, doula) in person. In the focus groups, all participants agreed that the phone or the internet was the first place looked to for information, ahead of consulting a healthcare professional. A comprehensive list of desired features was generated to guide the development of a resource to support AABN.ConclusionsStudy findings support exploring mobile technology-based approaches for breastfeeding support and education. Participants emphasized that to be relevant for them, a telehealth resource would need to: 1) Build meaningful connections between patients and providers, 2) Treat diverse opinions with trust and respect, and 3) Offer multiple sources and formats for information that can be easily cross-referenced.
Machine Learning for Antibiotic Stewardship in the Treatment of Stapholycoccus Bacterial Infections
Authors: Brokowski Trevor J. , Chiang Jeffrey N. 
Published: November 2022

AbstractAntibiotic resistance is one of the leading issues in modern healthcare due to the inability to treat common infections with available antibiotics. Many of the mechanisms of resistance have been caused by the inappropriate prescription of antibiotics to treat illnesses such as the cold or flu or the over-prescription of broad-spectrum antibiotics. Epitomizing this problem is the Staphylococcus bacteria where certain strains have become resistant to penicillin-related drugs and Vancomycin, one of the treatments for MRSA. To address this, we developed machine learning models to predict antibiotic activity and susceptibility using a patient’s entire available electronic health record. We selected patients who were suspected of having a staph infection from the Medical Information Mart for Intensive Care III (MIMIC-III) data set and utilized their microbiological culture results to identify the number of patients that were prescribed an inappropriate antibiotic and then propose suitable alternatives. In our test set, we identified that empiric prescriptions had an efficiency rate of 40 percent (the rate at which an antibiotic that would provide activity was prescribed), and the other 60 percent of cases were not susceptible to the prescribed antibiotic or the antibiotic that they were given was not tested for susceptibility against their infection. Our best models identified antibiotic susceptibility with AUROCs up to 0.9 and raw specificity up to 0.7. The models were also able to propose suitable alternatives in all but 10 cases. Overall these results demonstrate the need for implementing clinical decision support systems advising clinicians during the prescription process, and our further work will address this issue.
Persistent alveolar type 2 dysfunction and lung structural derangement in post-acute COVID-19
Authors: Rendeiro André F. , Ravichandran Hiranmayi , Kim Junbum , Borczuk Alain C. , Elemento Olivier , Schwartz Robert E. 
Published: November 2022

AbstractSARS-CoV-2 infection can manifest as a wide range of respiratory and systemic symptoms well after the acute phase of infection in over 50% of patients. Key questions remain on the long-term effects of infection on tissue pathology in recovered COVID-19 patients. To address these questions we performed multiplexed imaging of post-mortem lung tissue from 12 individuals who died post-acute COVID-19 (PC) and compare them to lung tissue from patients who died during the acute phase of COVID-19, or patients who died with idiopathic pulmonary fibrosis (IPF), and otherwise healthy lung tissue. We find evidence of viral presence in the lung up to 359 days after the acute phase of disease, including in patients with negative nasopharyngeal swab tests. The lung of PC patients are characterized by the accumulation of senescent alveolar type 2 cells, fibrosis with hypervascularization of peribronchial areas and alveolar septa, as the most pronounced pathophysiological features. At the cellular level, lung disease of PC patients, while distinct, shares pathological features with the chronic pulmonary disease of IPF. which may help rationalize interventions for PC patients. Altogether, this study provides an important foundation for the understanding of the long-term effects of SARS-CoV-2 pulmonary infection at the microanatomical, cellular, and molecular level.
Frequency of HIV serodifferent couples within TB-affected households in a setting with a high burden of HIV-associated TB
Authors: Anguzu Godwin , Gupta Amanda J , Ochom Emmanuel , Tseng Ashley S. , Zhang Meixin , Barnabas Ruanne V. , Flaxman Abraham D. , Katamba Achilles , Davis J. Lucian , Ross Jennifer M. 
Published: November 2022

AbstractBackgroundStrong epidemiological links between HIV and tuberculosis (TB) may make household TB contact investigation an efficient strategy for HIV screening and finding individuals in serodifferent partnerships at risk of HIV and linking them to HIV prevention services. We aimed to compare the proportions of HIV serodifferent couples in TB-affected households and in the general population of Kampala, Uganda.MethodsWe included data from a cross-sectional trial of HIV counselling and testing (HCT) in the context of home-based TB evaluation in Kampala, Uganda in 2016-2017. After obtaining consent, community health workers visited the homes of participants with TB to screen contacts for TB and offer HCT to household members ≥15 years. We defined index participants and their spouses and parents of the same index participant as couples, and classified couples as serodifferent if confirmed by self-reported HIV status or by HIV testing results. We used a two-sample test of proportions to compare the frequency of HIV serodifference among couples in the study to its prevalence among couples in Kampala in the 2011 Uganda AIDS Indicator Survey (UAIS).ResultsWe included 323 index TB participants and 507 household contacts aged ≥18. Most index participants (55%) were male, while most (68%) adult contacts were female. There was ≥1 couple in 115/323 (35.6%) households, with most couples (98/115, 85.2%) including the index participant and spouse. The proportion of households with HIV-serodifferent couples was 18/323 (5.6%), giving a number-needed-to-screen of 18 households. The proportion of HIV serodifference among couples identified in the trial was significantly higher than among couples in the UAIS (15.7% vs 8%, p=0.039). The 18 serodifferent couples included 14 (77.8%) where the index participant was living with HIV and the spouse was HIV-negative, and 4 (22.2%) where the index partner was HIV-negative, while the spouse was living with HIV.ConclusionsThe frequency of HIV serodifference among couples identified in TB-affected households was higher than in the general population. TB household contact investigation may be an efficient strategy for identifying people with substantial exposure to HIV and linking them to HIV prevention services.
Uptake of same-day initiation of HIV treatment in Malawi, South Africa, and Zambia: the SPRINT retrospective cohort study
Authors: Huber Amy , Hirasen Kamban , Brennan Alana T , Phiri Bevis , Tchereni Timothy , Mulenga Lloyd , Haimbe Prudence , Shakwelele Hilda , Nyirenda Rose , Matola Bilaal Wilson , Gunda Andrews , Rosen Sydney 
Published: November 2022

ABSTRACTIntroductionSince 2017 global guidelines have recommended “same-day initiation” (SDI) of antiretroviral treatment (ART) for patients considered ready for treatment on the day of HIV diagnosis. Many countries in sub-Saharan Africa have incorporated a SDI option into national guidelines, but uptake of SDI is not well documented. We estimated average time to ART initiation at 12 public healthcare facilities in Malawi, 5 in South Africa, and 12 in Zambia.MethodsWe sequentially enrolled patients who were eligible to start ART between January 2018 and June 2019 and reviewed their medical records from the point of HIV treatment eligibility (HIV diagnosis or first HIV-related interaction with the clinic) to the earlier of treatment initiation or 6 months. We estimated the proportion of patients initiating ART at their original healthcare facilities on the same day or within 7, 14, 30, or 180 days of baseline, stratified by country and gender.ResultsWe enrolled 826 patients in Malawi, 534 in South Africa, and 1,984 in Zambia. 88% of patients in Malawi, 57% in South Africa, and 91% in Zambia were offered and accepted SDI. In Malawi, most patients who did not receive SDI had also not initiated ART ≤ 6 months. In South Africa, an additional 13% of patients initiated ≤ 1 week, but 21% still had no record of initiation ≤ 6 months. Among those who did initiate within 6 months in Zambia, most started ≤ 1 week. There were no major differences by gender. Both WHO Stage III/IV and tuberculosis symptoms were associated with delays in ART initiation.DiscussionAs of 2020, uptake of same-day ART initiation was widespread, if not nearly universal, in Malawi and Zambia but was considerably less common in South Africa. Limitations of the study include pre-COVID-19 data that do not reflect pandemic adaptations and potentially missing data for Zambia. South Africa may be able to increase overall ART coverage by reducing numbers of patients who do not initiate ≤ 6 months.RegistrationClinicaltrials.govNCT04468399(Malawi),NCT04170374(South Africa), andNCT04470011(Zambia).
Trajectories of host-response biomarkers and inflammatory subphenotypes in COVID-19 patients across the spectrum of respiratory support
Authors: Lu Michael , Drohan Callie , Bain William , Shah Faraaz A. , Bittner Matthew , Evankovich John , Prendergast Niall , Hensley Matthew , Suber Tomeka , Fitzpatrick Meghan , Ramanan Raj , Murray Holt , Schaefer Caitlin , Qin Shulin , Wang Xiaohong , Zhang Yingze , Nouraie Seyed M. , Gentry Heather , Kessinger Cathy , Patel Asha , Macatangay Bernard J. , Jacobs Jana , Mellors John , Lee Janet S. , Ray Prabir , Ray Anuradha , Methé Barbara , Morris Alison , McVerry Bryan J. , Kitsios Georgios D. 
Published: November 2022

AbstractPurposeEnhanced understanding of the dynamic changes in the dysregulated inflammatory response in COVID-19 may help improve patient selection and timing for immunomodulatory therapies.MethodsWe enrolled 323 COVID-19 inpatients on different levels of baseline respiratory support: i) Low Flow Oxygen (37%), ii) Non-Invasive Ventilation or High Flow Oxygen (NIV_HFO, 29%), iii) Invasive Mechanical Ventilation (IMV, 27%), and iv) Extracorporeal Membrane Oxygenation (ECMO, 7%). We collected plasma samples upon enrollment and days 5 and 10 to measure host-response biomarkers. We classified subjects into inflammatory subphenotypes using two validated predictive models. We examined clinical, biomarker and subphenotype trajectories and outcomes during hospitalization.ResultsIL-6, procalcitonin, and Angiopoietin-2 were persistently elevated in patients at higher levels of respiratory support, whereas sRAGE displayed the inverse pattern. Patients on NIV_HFO at baseline had the most dynamic clinical trajectory, with 26% eventually requiring intubation and exhibiting worse 60-day mortality than IMV patients at baseline (67% vs. 35%, p<0.0001). sRAGE levels predicted NIV failure and worse 60-day mortality for NIV_HFO patients, whereas IL-6 levels were predictive in IMV or ECMO patients. Hyper-inflammatory subjects at baseline (<10% by both models) had worse 60-day survival (p<0.0001) and 50% of them remained classified as hyper-inflammatory on follow-up sampling at 5 days post-enrollment. Receipt of combined immunomodulatory therapies (steroids and anti-IL6 agents) was associated with markedly increased IL-6 and lower Angiopoietin-2 levels (p<0.05).ConclusionsLongitudinal study of systemic host responses in COVID-19 revealed substantial and predictive inter-individual variability, influenced by baseline levels of respiratory support and concurrent immunomodulatory therapies.
Remission and clinical patterns of systemic lupus erythematosus (SLE) in Pakistan: a retrospective cohort study
Authors: Saeed Mohammad , Pasha Aneela , Azhar Rizvi Syed Hussain , Munawar Maham , Elias Zehra Abaad , Shafi Muhammad Irfan , Gazdar Tariq , Lakhdir Maryam Ali 
Published: November 2022

AbstractObjectivesPrimary objective was to investigate clinical features and biomarkers associated with severe systemic lupus erythematosus (SLE). The secondary objective was to identify patterns of SLE remission. ’MethodsA retrospective study of 200 SLE patients (2014–20) from ImmunoCure Center was conducted. Patients fulfilled ACR criteria 1997 for SLE classification. SLEDAI-2K categories mild-moderate (score <=10) and severe (score >10) were used as outcome for the primary objective. Predictors of severe SLE were evaluated by multivariate logistic regression analysis. For the secondary objective, we evaluated 94 records with follow-up time >1year. Remission status (Yes/No) was based on DORIS criteria. Survival regression was performed using Kaplan Meier curve.ResultsSignificant predictors of severe SLE were male gender (OR 4.1; 95% CI: 1.2, 13.5), oral ulcers (OR 6.9; 95% CI: 2.8, 17.1), alopecia (OR 2.1; 95% CI 1.0-4.1), nephritis (OR 4.5; 95% CI: 1.9-11.4), ESR >30mm/hour (OR 2.3; 95% CI: 1.2-4.4) and aCL antibodies (OR 2.4, 95% CI 1.0 -5.9). The mean duration of follow-up was 41±19 months. Remission on treatment was achieved in 66% of 94 patients, while off treatment in 21% with a mean post-remission follow-up of 18±15 months. For every one-month increase in the duration of follow-up, the hazard of time to remission increased by 4% (95% CI 0.95-0.98;P<0.001). Factor analysis identified 4 SLE subtypes.ConclusionA clinical model including aCL antibodies is presented here that predicts severe SLE. Remission is possible even in severe SLE in LMIC with adequate immunosuppression and persistent follow-up.
Comparing end-tidal CO2, respiration volume per time (RVT), and average gray matter signal for mapping cerebrovascular reactivity amplitude and delay with breath-hold task BOLD fMRI
Authors: Zvolanek Kristina M. , Moia Stefano , Dean Joshua N. , Stickland Rachael C. , Caballero-Gaudes César , Bright Molly G. 
Published: November 2022

AbstractCerebrovascular reactivity (CVR), defined as the cerebral blood flow response to a vasoactive stimulus, is an imaging biomarker with demonstrated utility in a range of diseases and in typical development and aging processes. A robust and widely implemented method to map CVR involves using a breath-hold task during a BOLD fMRI scan. Recording end-tidal CO2(PETCO2) changes during the breath-hold task is recommended to be used as a reference signal for modeling CVR amplitude in standard units (%BOLD/mmHg) and CVR delay in seconds. However, obtaining reliable PETCO2recordings requires equipment and task compliance that may not be achievable in all settings. To address this challenge, we investigated two alternative reference signals to map CVR amplitude and delay in a lagged general linear model (lagged-GLM) framework: respiration volume per time (RVT) and average gray matter BOLD response (GM- BOLD). In 8 healthy adults with multiple scan sessions, we compare spatial agreement of CVR maps from RVT and GM-BOLD to those generated with PETCO2. We define a threshold to determine whether a PETCO2recording has “sufficient” quality for CVR mapping and perform these comparisons in 16 datasets with sufficient PETCO2and 6 datasets with insufficient PETCO2. When PETCO2quality is sufficient, both RVT and GM-BOLD produce CVR amplitude maps that are nearly identical to those from PETCO2(after accounting for differences in scale), with the caveat they are not in standard units to facilitate between-group comparisons. CVR delays are comparable to PETCO2with an RVT regressor but may be underestimated with the average GM- BOLD regressor. Importantly, when PETCO2quality is insufficient, RVT and GM-BOLD CVR recover reasonable CVR amplitude and delay maps, provided the participant attempted the breath-hold task. Therefore, our framework offers a solution for achieving high quality CVR maps in both retrospective and prospective studies where sufficient PETCO2recordings are not available and especially in populations where obtaining reliable measurements is a known challenge (e.g., children). Our results have the potential to improve the accessibility of CVR mapping and to increase the prevalence of this promising metric of vascular health.
Inorganic polyphosphate abets silencing of a sub-telomeric gene cluster in fission yeast
Authors: Sanchez Ana M. , Garg Angad , Schwer Beate , Shuman Stewart 
Published: November 2022

ABSTRACTInorganic polyphosphate (PolyP) is a ubiquitous polymer that plays sundry roles in cell and organismal physiology. Whereas there is evidence for polyphosphate in the cell nucleus, it is unclear whether and how physiological levels of PolyP impact transcriptional regulation in eukarya. To address this issue, we performed transcriptional profiling of fission yeastvtc4Δ cells, which lack the catalytic subunit of the Vtc4/Vtc2 polyphosphate polymerase complex and thus have no detectable intracellular PolyP. Deleting Vtc4 elicited the de-repression of four protein-coding genes –SPAC186.04c, gdt1/SPAC186.05, SPAC186.06, andSPAC750.01– located within a sub-telomeric region of the right arm of chromosome I that is known to be transcriptionally silenced by the TORC2 complex. These sub-telomeric genes were equally de-repressed invtc2Δ cells and in cells expressing polymerase-dead Vtc4, signifying that PolyP synthesis is necessary to abet TORC2-dependent locus-specific gene silencing.
Endozoicomonas-chlamydiae interactions in cell-associated microbial aggregates of the coralPocillopora acuta
Authors: Maire Justin , Tandon Kshitij , Collingro Astrid , van de Meene Allison , Damjanovic Katarina , Gøtze Cecilie Ravn , Stephenson Sophie , Philip Gayle K. , Horn Matthias , Cantin Neal E. , Blackall Linda L. , van Oppen Madeleine J. H. 
Published: November 2022

AbstractCorals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coralPocillopora acuta. Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing we show that CAMAs: (i) are located in the tentacle tips and may be intracellular; (ii) containEndozoicomonas, Kistimonas(both Gammaproteobacteria), andSimkania(Chlamydiota) bacteria; (iii)Endozoicomonasmay provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv)EndozoicomonasandSimkaniaoccur in distinct, but adjacent, CAMAs; (v)Simkaniamay rely on acetate and heme provided by neighboringEndozoicomonas. Our study provides detailed insight into coral endosymbionts, which will guide the assessment of their suitability for probiotic approaches to mitigate coral bleaching.