bluuebunny/crossref_metadata_2025_split huggingface dataset:
Veno-venous Extracorporeal Membrane Oxygenation in Patients with Traumatic Brain Injuries and Severe Respiratory Failure: A Single-Center Retrospective Analysis
Authors: Austin Samuel E. , Galvagno Samuel M. , Podell Jamie E. , Teeter William A. , Kundi Rishi , Haase Daniel J. , Taylor Bradley S. , Betzold Richard , Stein Deborah M. , Scalea Thomas M. , Powell Elizabeth K. 
Published: October 2023

Abstract

Background
Veno-venous extracorporeal membrane oxygenation (VV ECMO) can support trauma patients with severe respiratory failure. Use in traumatic brain injury (TBI) may raise concerns of worsening complications from intracranial bleeding. However, VV ECMO can rapidly correct hypoxemia and hypercarbia, possibly preventing secondary brain injury. We hypothesize that adult trauma patients with TBI on VV ECMO have comparable survival to trauma patients without TBI.

Methods
Single center, retrospective cohort study involving review of electronic medical records of trauma admissions between July 1, 2014 to August 30, 2022 with discharge diagnosis of TBI who were placed on VV ECMO during their hospital course

Results
Seventy-five trauma patients were treated with VV ECMO; 36 (48%) had TBI. Of those with TBI, 19 (53%) had a hemorrhagic component. Survival was similar between patients with and without a TBI (72% v 64%, p = 0.45). TBI survivors had a higher admission Glasgow Coma Scale (7 v 3, p < 0.001) than non-survivors. Evaluation of prognostic scoring systems on initial head CT demonstrated TBI VV ECMO survivors were more likely to have a Rotterdam Score of 2 (62% v 20%, p = 0.03) and no survivors had a Marshall score ≥ 4. Twenty-nine (81%) patients had a repeat head CT on VV ECMO with one incidence of expanding hematoma and one new focus of bleeding. Neither patient with a new/worsening bleed received anticoagulation. Survivors demonstrated favorable neurologic outcomes at discharge and outpatient follow-up, based on their mean Rancho Los Amigos Scale (RLAS) (6.5, SD 1.2), median Cerebral Performance Category (CPC) (2, IQR 1-2), and median Glasgow Outcome Scale-Extended (GOS-E) (7.5, IQR 7-8).

Conclusions
In this series, the majority of TBI patients survived and had good neurologic outcomes despite a low admission GCS. VV ECMO may minimize secondary brain injury and may be considered in select patients with TBI.

Level of Evidence
Level IV, Prognostic/Epidemiological
Survivor’s Remorse
Authors: Douglas Anthony , Rogers Selwyn 
Published: October 2023

Abstract
In urban, large metropolitan trauma centers we are accustomed to seeing the most gruesome morbidity and mortality in medicine. By far the most devastating morbidity and mortality to observe is that inflicted on one human being to another. Gun violence is pervasive in this industrialized country, and it impacts us all. Staff, residents, and faculty in trauma centers bear the brunt of this trauma, second only to the families and communities which suffer the loss of loved ones. This burden is especially heavy for health care workers who share the same ethnic background of those who are disproportionately affected by interpersonal gun violence. Survivors of gun violence exist on a spectrum of chronic illness. An illness that ranges in physical and mental morbidity and social disruption in loss of wages and capabilities. This disease not only infects those wounded or killed, but it also transmits through communities and generations. Urban violence exists because of historic and systematic racism. It continues to persist because racism creates inequities in the quality of education, housing, and investment in urban environments, exacerbated by residential segregation. For two providers, a trainee and a faculty member of African descent, conscious of the determinants which create gun violence, it is overwhelming. We, as health care providers must tell our stories and the stories of those whose voices are not empowered. We can hope that by sharing these experiences we stimulate action and change by raising the moral conscious of those unaware of the tragedies we witness every day.
Caregiver Perceptions of Social Risk Screening in Pediatric Liver Transplantation: From the Multicenter SOCIAL-Tx Study
Authors: Wadhwani Sharad I. , Kruse Gina , Squires James , Ebel Noelle , Gupta Nitika , Campbell Kathleen , Hsu Evelyn , Zielsdorf Shannon , Vittorio Jennifer , Desai Dev M. , Bucuvalas John C. , Gottlieb Laura M. , Lai Jennifer C. 
Published: October 2023

Background.
The social determinants of health contribute to adverse post–liver transplant outcomes. Identifying unmet social risks may enable transplant teams to improve long-term outcomes for at-risk children. However, providers may feel uncomfortable asking about household-level social risks in the posttransplant period because they might make their patients/families uncomfortable.

Methods.
We conducted a mixed-methods analysis of caregiver participants (ie, parents/guardians of pediatric liver transplant recipients) in the Social and Contextual Impact on Children Undergoing Liver Transplantation study to assess their perceptions of provider-based social risk screening. Participants (N = 109) completed a 20-min social determinants of health questionnaire that included questions on the acceptability of being asked intimate social risk questions. A subset of participants (N = 37) engaged in an in-depth qualitative interview to share their perceptions of social risk screening.

Results.
Of 109 participants across 9 US transplant centers, 60% reported financial strain and 30% reported at least 1 material economic hardship (eg, food insecurity, housing instability). Overall, 65% of respondents reported it very or somewhat appropriate and 25% reported being neutral to being screened for social risks in a liver transplant setting. In qualitative analyses, participants reported trust in the providers and a clear understanding of the intention of the screening as prerequisites for liver transplant teams to perform social risk screening.

Conclusions.
Only a small minority of caregivers found social risk screening unacceptable. Pediatric liver transplant programs should implement routine social risk screening and prioritize the patient and family voices when establishing a screening program to ensure successful implementation.
Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature
Authors: LaFlamme Christy W. , Rastin Cassandra , Sengupta Soham , Pennington Helen E. , Russ-Hall Sophie J. , Schneider Amy L. , Bonkowski Emily S. , Almanza Fuerte Edith P. , Galey Miranda , Goffena Joy , Gibson Sophia B. , Allan Talia J. , Nyaga Denis M. , Lieffering Nico , Hebbar Malavika , Walker Emily V. , Darnell Daniel , Olsen Scott R. , Kolekar Pandurang , Djekidel Nahdir , Rosikiewicz Wojciech , McConkey Haley , Kerkhof Jennifer , Levy Michael A. , Relator Raissa , Lev Dorit , Lerman-Sagie Tally , Park Kristen L. , Alders Marielle , Cappuccio Gerarda , Chatron Nicolas , Demain Leigh , Genevieve David , Lesca Gaetan , Roscioli Tony , Sanlaville Damien , Tedder Matthew L. , Hubshman Monika Weisz , Ketkar Shamika , Dai Hongzheng , Worley Kim Carlyle , Rosenfeld Jill A. , Chao Hsiao-Tuan ,   Undiagnosed Diseases Network, Neale Geoffrey , Carvill Gemma L. ,   University of Washington Center for Rare Disease Research, Wang Zhaoming , Berkovic Samuel F. , Sadleir Lynette G. , Miller Danny E. , Scheffer Ingrid E. , Sadikovic Bekim , Mefford Heather C. 
Published: October 2023

ABSTRACTSequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations (“epivariants”) can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct “episignature” biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature forCHD2using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights intoCHD2pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
Dehydration inducedAePer50regulates midgut infection inAe. aegypti
Authors: Accoti Anastasia , Becker Margaret , Abu Angel Elma I. , Vulcan Julia , Yun Ruimei , Widen Steven , Sylla Massamba , Popov Vsevolod L. , Weaver Scott C. , Dickson Laura B. 
Published: October 2023

AbstractIn the face of climate change, mosquitoes will experience evolving climates including longer periods of drought. An important physiological response to dry environments is the protection against water loss or dehydration, here defined as desiccation tolerance. Various environmental factors including temperature are known to alter interactions between the mosquito,Aedes aegypti, and the arboviruses it transmits, but little is known about how low humidity impacts arboviral infection. Here, we report that a gene upregulated in response to desiccation is important for controlling midgut infection. We have identified two genetically diverse lines ofAe. aegyptiwith marked differences in desiccation tolerance. To understand if the genetic basis underlying desiccation tolerance is the same between the contrasting lines, we compared gene expression profiles between desiccant treated and non-desiccant treated individuals in both the desiccation tolerant and susceptible lines by RNAseq. Gene expression analysis demonstrates that different genes are differentially expressed in response to desiccation stress between desiccation tolerant and susceptible lines. The most highly expressed transcript under desiccation stress in the desiccation susceptible line encodes a peritrophin protein,AePer50. Peritrophins play a crucial role in peritrophic matrix formation after a bloodmeal. Gene silencing ofAePer50 by RNAi demonstrates that expression ofAePer50 is required for survival of the desiccation susceptible line under desiccation stress, but not for the desiccation tolerant line. Moreover, the knockdown ofAePer50 results in higher infection rates and viral replication rates of ZIKV and higher infection rates of CHIKV. Finally, following a bloodmeal, the desiccation susceptible line develops a thicker peritrophic matrix than the desiccation tolerant line. Together these results provide a functional link between the protection against desiccation and midgut infection which has important implications in predicting how climate change will impact mosquito-borne viruses.
Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: Transmission dynamics and epidemiological insights
Authors: de Rioja Víctor López , Perramon Aida , Alonso Sergio , Andrés Cristina , Antón Andrés , Bordoy Antoni E. , Càmara Jordi , Cardona Pere-Joan , Català Marti , López Daniel , Marti Sara , Martró Elisa , Saludes Verónica , Prats Clara , Alvarez-Lacalle Enrique 
Published: October 2023

AbstractBackgroundCountries across Europe have faced similar evolutions of SARS-CoV-2 VOCs, including the Alpha, Delta, and Omicron variants.Materials and MethodsWe used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants across Europe over a period of more than two years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility (∆β) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants.ResultsOur model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated ∆β between variants, revealing that: (i) ∆β increased progressively from the Alpha to the Omicron variant; (ii) ∆βshowed a high degree of variability within Omicron variants; (iii) a higher ∆βwas associated with a later emergence of the variant within a country; (iv) a higher degree of immunization of the population against previous variants was associated with a higher ∆βfor the Delta variant; (v) larger countries exhibited smaller ∆β, suggesting regionally diverse outbreaks within the same country; and finally (vi) the model reliably captures the dynamics of competing variants, even in complex scenarios.ConclusionsThe use of mathematical models allows for the precise and reliable estimation of daily cases of each variant. By quantifying ∆β, we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. On the other hand, we have shown that the country-level increases in transmissibility can always be influenced by the geographical characteristics of the country and the timing of the emergence of the variant.
A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease
Authors: Eoli A. , Ibing S. , Schurmann C. , Nadkarni G.N. , Heyne H.O. , Böttinger E. 
Published: October 2023

AbstractChronic kidney disease (CKD) is a complex disorder that causes a gradual loss of kidney function, affecting approximately 9.1% of the world’s population. Here, we use a soft-clustering algorithm to deconstruct its genetic heterogeneity. First, we selected 322 CKD-associated independent genetic variants from published genome-wide association studies (GWAS) and added association results for 229 traits from the GWAS catalog. We then applied nonnegative matrix factorization (NMF) to discover overlapping clusters of related traits and variants. We computed cluster-specific polygenic scores and validated each cluster with a phenome-wide association study (PheWAS) on the BioMe biobank (n=31,701). NMF identified nine clusters that reflect different aspects of CKD, with the top-weighted traits signifying areas such as kidney function, type 2 diabetes (T2D), and body weight. For most clusters, the top-weighted traits were confirmed in the PheWAS analysis. Results were found to be more significant in the cross-ancestry analysis, although significant ancestry-specific associations were also identified. While all alleles were associated with a decreased kidney function, associations with CKD-related diseases (e.g., T2D) were found only for a smaller subset of variants and differed across genetic ancestry groups. Our findings leverage genetics to gain insights into the underlying biology of CKD and investigate population-specific associations.
Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 – 07/2023
Authors: Bundschuh Christian , Weidner Niklas , Klein Julian , Rausch Tobias , Azevedo Nayara , Telzerow Anja , Mallm Jan-Philipp , Kim Heeyoung , Steiger Simon , Seufert Isabelle , Börner Kathleen , Bauer Katharina , Hübschmann Daniel , Jost Katharina Laurence , Parthé Sylvia , Schnitzler Paul , Boutros Michael , Rippe Karsten , Müller Barbara , Bartenschlager Ralf , Kräusslich Hans-Georg , Benes Vladimir 
Published: October 2023

SummaryAt the beginning of 2021 the monitoring of the circulating variants of SARS-CoV-2 was established in Germany in accordance with the Corona Surveillance Act (discontinued after July 2023) to allow a better containment of the pandemic, because certain amino acid exchanges (especially) in the spike protein lead to higher transmission as well as a reduced vaccination efficacy.Therefore, our group performed whole genome sequencing applying the ARTIC protocol (currently V4) on Illumina’s NextSeq 500 platform (and starting in May 2023 on the MiSeq DX platform) for SARS-CoV-2 positive specimen from patients of the Heidelberg University Hospital (and associated hospitals) as well as the Public health office in Rhine-Neckar/Heidelberg region.Our group sequenced a total of 26,795 SARS-CoV-2-positive samples between January 2021 and July 2023 - valid sequences, according to the requirements for sequence upload to the German electronic sequencing data hub (DESH) operated by the Robert Koch Institute (RKI), could be determined for 24,852 samples, while the lineage/clade could be identified for 25,912 samples.While the year 2021 was very dynamic and changing regarding the circulating variants in the Rhine-Neckar/Heidelberg region with the initial non-variant of concerns, followed by A.27.RN and the rise of B.1.1.7 in winter/spring and its displacement by B.1.617.2 in spring/summer, which remained almost exclusive until the beginning of December and the first B.1.1.529 incidences, which rose to a proportion of 40 percent by the end of 2021 (and superseded B.1.617.2 by January 2022 with a proportion of over 90 percent). The years 2022 and 2023 were then dominated by B.1.1.529 and its numerous sublineages, especially BA.5 and BA.2, and more recently by the rise of recombinant variants, such as XBB.1.5. By the end of July 2023 (and since calendar week 20) the proportion of the recombinant variants amounted to 100 percent of all circulating variants in the Rhine-Neckar/Heidelberg region.
The impact of COVID-19 on non-communicable disease patients in sub-Saharan African countries: systematic review
Authors: Basa Muluken , De Vries Jan , McDonagh David , Comiskey Catherine 
Published: October 2023

AbstractBackgroundCOVID-19 and its prevention measures have had a significant impact on patients with non-communicable diseases (NCDs) by disrupting routine healthcare service and increasing risk factors. These challenges were expected to be more severe in sub-Saharan Africa due to the lack of physical infrastructure and inadequate resources. The quantity of studies conducted was limited, and there was a lack of published systematic reviews in the specified region. This systematic review aimed to comprehensively assess the impact of COVID-19 on NCD patients in sub-Saharan Countries.MethodThis systematic review adheres to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines and is registered with PROSPERO (ID CRD42023387755). Extensive searches were conducted in MEDLINE, EMBASE, and CINAHL databases in November 2022, supplemented by a manual search of references, grey literature, and the WHO COVID-19 database. Inclusion criteria encompassed studies that reported on the impact of COVID-19 on NCD patients in sub-Saharan African countries, focusing on access to care, health outcomes, and factors related to NCDs. Critical appraisal of study quality was performed using the Joanna Briggs Institute (JBI) analytical cross-sectional studies critical appraisal tool. Data were extracted and synthesized, highlighting the main findings and relevant limitations.FindingsThis review included 26 primary studies with a cumulative sample size of 15,722 participants, conducted in six sub-Saharan African countries. Findings of these studies identified that the COVID-19 pandemic caused a disruption of 76% to 80% of regular NCDs patient care provision. The studies also identified a reduction in patient health-seeking behavior and reduced medication adherence (39.0%-63%), leading to poor treatment outcome (35.66%-55.8%). Furthermore, the pandemic and related lockdowns have been implicated in the increased prevalence of substance use, decreased physical exercise, and increased mental health problems.ConclusionThis systematic review identified the complex challenges faced by NCD patients in sub-Saharan Africa during the COVID-19 pandemic. It also underlines the need to consider the indirect impact on vulnerable populations while developing pandemic prevention and control strategies for the future. The current NCD management strategies should prioritize the restoration of access to essential healthcare services while considering the multifaceted risks posed by decreased physical activity, poor dietary practices, and increased substance use.The main limitation of this review was the study design and setting. All of the studies included in this review employed a cross-sectional design, which may result in a low quality of evidence. This study identified research conducted in only six countries among the 46 UN-classified sub-Saharan nations, which may impair the generalizability of the result.
New POCT instrument, GBTsol ICA system for HIV monitoring by CD4 and CD8 enumeration in resource-poor settings
Authors: Sung Stephe , Kim Hyon-Suk , Song Jaewoo , Lee Jaeyoung , Aghamoradi Shabnam , Baek Seungrim 
Published: October 2023

AbstractAccording to WHO report 39.0 million (33.1–45.7 million) people around the world were living with HIV infection till Dec of 2022. One method that we need for treatment and monitoring of HIV patients is CD4 counting and CD4/CD8 ratio. For this purpose, there are many different laboratory test with technical complexity and in other hand most of them are time consuming, expensive or cannot be used in resource limited places.This work demonstrates POCT microchip platform for enumerating leukocytes, CD4+ T- lymphocytes, and CD8+ T lymphocytes from whole blood, using fluorochrome-conjugated primary antibodies as a detection method.This device and its method omits all obstacles for WBC and CD4, CD8 T lymphocytes and it offers fast, cost effective and easy absolute WBC and CD4, CD8 T lymphocytes count for monitoring HIV patients’ immune situation with high accuracy which can be implemented insource limited stings or doctors’ office.We incubated Phycoerythrin (PE) conjugated primary antibodies specific to CD4 and CD8 antigens to enumerate CD4+ and CD8+ T cells, respectively. Comparison studies were performed with FACS count to evaluate total leukocytes, CD4+T cell number, and CD8+T cell number in whole blood samples for monitoring the immune systems of patients with human immunodeficiency virus (HIV)/AIDS. Statistical analyses for precision, correlation, and agreement were performed. Coefficients of variation (CV) ranging from 0.67% to 12.78%, 0.81 to 13.68%, and 0.29% to 8.33% were obtained for CD4, CD8 and leukocyte recovery respectively. A significant correlation was found between the two assays for CD4 count and CD8 count, with correlation coefficients of 0.90 and 0.91, respectively. Using Bland-Altman plots, a mean bias of 23, 38, and 490 cells/µL (95% CI, n=113) was obtained for CD4, CD8, and total leukocyte count, respectively. These data show that the GBTsol ICA (Immune Cell Analyzer) is comparable to the FACS count platform method for measuring the amounts of CD4 T cells, CD8 T cells, and total leukocytes in blood samples for the purpose of monitoring HIV/AIDS patients with cheap, easy and fast way.