bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical advancement of patients infected with SARS-CoV-2 Omicron variant in Shanghai, China
Authors: Shao Jiasheng , Fan Rong , Zhang Tiejun , Lee Catherine , Huang Xuyuan , Wang Fei , Liang Haiying , Jin Ye , Jiang Ying , Gu Yanhua , Hu Jianrong , Huang Gang 
Published: July 2022

ABSTRACTBackgroundStudies on the Omicron variant infection have generally been restricted to descriptions of its initial clinical and epidemiological characteristics. We investigated the timeline-related advancement in individuals with Omicron variant.MethodsWe conducted a retrospective, single-centered study including 226 laboratory-confirmed cases with Omicron variant between April 6th and May 11th, 2022 in Shanghai, China. Final date of follow-up was May 30, 2022.ResultsAmong 226 enrolled patients, the median age was 52 years old, and 118 (52.2%) were female. The duration from onset of symptoms to hospitalization was 3 days (interquartile range [IQR]: 2-4 days) for symptomatic patients. Cough occurred in 168 patients (74.3%). The median interval to negative reverse-transcriptase PCR tests of nasopharynx swab was 10 days ([IQR]: 8-13 days). No radiographic progressions were found in 196 patients on the 7th day after onset of symptoms. The median duration of fever in all participants was 5 days (IQR: 4–6 days). The median PCR conversion time of Paxlovid-treated patients was 8 days (IQR: 7-10 days) compared with that of Lianhuaqingwen (10 days, IQR: 8-13 days) (p=0.00056). Booster vaccination can significantly decrease the severity of Omicron infection when compared with unvaccinated, partially or fully vaccinated patients (p=0.009). The median time of PCR conversion in individuals aged under 14 recovered significantly faster than older patients (median 8 days versus 11 days, P < 0.0001). In multivariate logistic analysis, erythrocyte sedimentation rate (ESR) (OR=1.05) was independently related to the severity of the infection.ConclusionsThe majority clinical symptoms of Omicron infection were not severe. Early and aggressive administration of Paxlovid can significantly reduce the PCR conversion time. Booster vaccination should also be highly recommended in population over 14 years old.
Quantitative G6PD point-of-care test can be used reliably on cord blood to identify male and female newborns at increased risk of neonatal hyperbilirubinaemia: a mixed method study
Authors: Bancone Germana , Gilder Mary Ellen , Win Elsie , Gornsawun Gornpan , Penpitchaporn Penporn , Moo Paw Khu , Archasuksan Laypaw , Wai Nan San , Win Sylverine , Aung Ko Ko , Hashmi Ahmar , Hanboonkunupakarn Borimas , Nosten Francois , Carrara Verena I , McGready Rose 
Published: July 2022

ABSTRACTIntroductionNew point-of-care (POC) quantitative G6PD testing devices developed to provide safe radical cure for P. vivax malaria may be used to diagnose G6PD deficiency in newborns at risk of severe neonatal hyperbilirubinaemia, improving clinical care, and preventing related morbidity and mortality. Methods: We conducted a mixed-methods study analyzing technical performance and usability of the “STANDARD G6PD” Biosensor when used by trained midwives on cord blood samples at two rural clinics on the Thailand-Myanmar border.ResultsIn 307 cord blood samples, the Biosensor had a sensitivity of 1.000 (95%CI 0.859-1.000) and a specificity of 0.993 (95% CI 0.971-0.999) as compared to gold standard spectrophotometry to diagnose G6PD deficient newborns using a receiving operator characteristic (ROC) analysis-derived threshold of ≤4.8IU/gHb. The Biosensor had a sensitivity of 0.727 (95%CI: 0.498-0.893) and specificity of 0.933 (95%CI: 0.876-0.969) for 30-70% activity range in females using ROC analysis-derived range of 4.9 to 9.9IU/gHb. These thresholds allowed identification of all G6PD deficient neonates and 80% of female neonates with intermediate phenotypes.Need of phototherapy treatment for neonatal hyperbilirubinaemia was higher in neonates with deficient and intermediate phenotypes as diagnosed by either reference spectrophotometry or Biosensor.Focus group discussions found high levels of learnability, willingness, satisfaction, and suitability for the Biosensor in this setting. The staff valued the capacity of the Biosensor to identify newborns with G6PD deficiency early (“We can know that early, we can counsel the parents about the chances of their children getting jaundice”) and at the POC, including in more rural settings (“Because we can know the right result of the G6PD deficiency in a short time. Especially for the clinic which does not have a lab”). Conclusions: The Biosensor is a suitable tool in this resource-constrained setting to identify newborns with abnormal G6PD phenotypes at increased risk of neonatal hyperbilirubinaemia.
The association between diabetes and mortality among patients hospitalized with COVID-19: Cohort Study of Hospitalized Adults in Ontario, Canada and Copenhagen, Denmark
Authors: Bogler Orly , Raissi Afsaneh , Colacci Michael , Beaman Andrea , Biering-Sørensen Tor , Cressman Alex , Detsky Allan , Gosset Alexi , Højbjerg Lassen Mats , Kandel Chris , Khaykin Yaariv , Barbosa David , Shaw Lauren Lapointe , MacFadden Derek R. , Pearson Alexander , Perkins Bruce , Rothman Kenneth J. , Skaarup Kristoffer Grundtvig , Weagle Rachael , Yarnell Chris , Sholzberg Michelle , Hodzic-Santor Bena , Lovblom Erik , Zipursky Jonathan , Quinn Kieran L. , Fralick Mike 
Published: July 2022

AbstractImportanceDiabetes has been reported to be associated with an increased risk of death among patients with COVID-19. However, available studies lack detail on COVID illness severity and measurement of relevant comorbidities.Design, Setting, and ParticipantsWe conducted a multicenter, retrospective cohort study of patients over the age of 18 years who were hospitalized with COVID-19 between January 1, 2020 and November 30, 2020 in Ontario, Canada and Copenhagen, Denmark. Chart abstraction emphasizing co-morbidities and disease severity was performed by trained research personnel. The association between diabetes and death was measured using Poissson regression.Main Outcomes and Measureswithin hospital 30-day risk of death.ResultsOur study included 1018 hospitalized patients with COVID-19 in Ontario and 305 in Denmark, of whom 405 and 75 patients respectively had pre-existing diabetes. In both Ontario and Denmark, patients with diabetes were more likely to be older, have chronic kidney disease, cardiovascular disease, higher troponin levels, and to receive antibiotics compared with adults who did not have diabetes. In Ontario, the crude mortality rate ratio among patients with diabetes was 1.60 [1.24 – 2.07 95% CI] and in the adjusted regression model was 1.19 [0.86 – 1.66 95% CI]. In Denmark, the crude mortality rate ratio among patients with diabetes was 1.27 (0.68 – 2.36 95% CI) and in the adjusted model was 0.87 (0.49 – 1.54 95% CI)]. Meta-analyzing the two rate ratios from each region resulted in a crude mortality rate ratio of 1.55 (95% CI 1.22,1.96) and an adjusted mortality rate ratio of 1.11 (95% CI 0.84, 1.47).ConclusionsPresence of diabetes was not strongly associated with in-hospital COVID mortality independent of illness severity and other comorbidities.
Caregiving in a Tertiary Health Institution in North Central Nigeria: Support Types and Financial Burden
Authors: Akande Oluwatosin Wuraola , Fasiku Mojirola Martina , Bolarinwa Oladimeji Akeem , Akande Tanimola Makanjuola 
Published: July 2022

AbstractBackgroundCaregivers play an important role in informal patient management. Identification of the support types and the challenges faced by caregivers will provide information on strategies to ease this burden. This study aimed to describe the support types and financial burden among caregivers in a tertiary hospital in North Central Nigeria.MethodsThis was a cross-sectional study conducted among caregivers of in-patients admitted in a tertiary hospital in North Central Nigeria. Data was collected using a pre-tested interviewer-administered questionnaire. Data was analysed using the Statistical Package for Social Sciences package version 23. Results were reported in frequencies and proportions, and presented in prose, tables and charts.ResultsA total of 400 caregivers were recruited. Mean age was 38.32 ± 12.82 years and most (66.0%) were females. Caregivers supported their patients by running errands (96.3%) and 85.3% reported caregiving as stressful. The reported errands were purchase of medications (92.3%), supply of non-medical needs (63.3%), submission of laboratory samples and collection of results (52.3%) and service payment (47.5%). About two thirds (63.2%) reported loss of income while caregiving and about half (50.8%) provided financial support to the patients.ConclusionThis study suggests that majority of caregivers experience significant physical and financial burden while caregiving. This burden can be eased off by the simplification of payment and laboratory processes, and employment of more staff to support patients admitted in the wards. The financial burden experienced by caregivers reinforces the need to encourage more Nigerians to enrol in a health insurance scheme.
AI-based image quality assessment in CT
Authors: Edenbrandt Lars , Trägårdh Elin , Ulén Johannes 
Published: July 2022

ABSTRACTMedical imaging, especially computed tomography (CT), is becoming increasingly important in research studies and clinical trials and adequate image quality is essential for reliable results. The aim of this study was to develop an artificial intelligence (AI)-based method for quality assessment of CT studies, both regarding the parts of the body included (i.e. head, chest, abdomen, pelvis), and other image features (i.e. presence of hip prosthesis, intravenous contrast and oral contrast).Approach1, 000 CT studies from eight different publicly available CT databases were retrospectively included. The full dataset was randomly divided into a training (n= 500), a validation/tuning (n= 250), and a testing set (n= 250). All studies were manually classified by an imaging specialist. A deep neural network network was then trained to directly classify the 7 different properties of the image.ResultsThe classification results on the 250 test CT studies showed accuracy for the anatomical regions and presence of hip prosthesis in the interval 98.4% to 100.0%. The accuracy for intravenous contrast was 89.6% and for oral contrast 82.4%.ConclusionsWe have shown that it is feasible to develop an AI-based method to automatically perform a quality assessment regarding if correct body parts are included in CT scans, with a very high accuracy.
A Qualitative Study Exploring the Consumer Experience of Receiving Self-Initiated Polygenic Risk Scores from a Third-Party Website
Authors: Lowes Kiara , Borle Kennedy , Folkersen Lasse , Austin Jehannine 
Published: July 2022

ABSTRACTThe number of people accessing their own polygenic risk scores (PRSs) online is rapidly increasing, yet little is known about why people are doing this, how they react to the information, and what they do with it. We conducted a qualitative interview-based study with people who pursued PRSs through Impute.me, to explore their motivations for seeking PRS information, their emotional reactions, and actions taken in response to their results. Using interpretive description, we developed a theoretical model describing the experience of receiving PRSs in a direct-to-consumer (DTC) context. Dissatisfaction with healthcare was an important motivator for seeking PRS information. Participants described having medical concerns dismissed, and experiencing medical distrust, which drove them to self-advocate for their health, which in turn ultimately led them to seek PRSs. Polygenic risk scores were often empowering for participants, but could be distressing when PRS information did not align with participants’ perceptions of their personal or family histories. Behavioural changes made in response to PRS results included dietary modifications, changes in vitamin supplementation and talk-based therapy. Our data provides the first qualitative insight into how people’s lived experience influence their interactions with DTC PRSs.
Association between skull bone mineral density and periodontitis: evidence from the National Health and Nutrition Examination Survey (2011-2014)
Authors: Jin Fuqian , Song Jukun , Luo Yi , Wang Beichuan , Ding Ming , Hu Jiaxin , Chen Zhu 
Published: July 2022

AbstractBackground and ObjectiveBone mineral density (BMD) and periodontitis have been the subject of many studies. However, the relationship between skull (including mandible) BMD and periodontitis has not been extensively studied. An objective of this cross-sectional study was to examine the relationship between skull BMD and periodontitis using data from the National Health and Nutrition Examination Surveys (NHANES) for 2011-2012 and 2013-2014.Materials and MethodsFrom 19,931 participants, 3,802 were screened and included with no missing values in the study. We examined the distribution of variables by grouping the skull BMD levels into quartiles. Periodontitis is defined by the Centers for Disease Control and Prevention (CDC) and the American Periodontal Association (AAP) in 2012. An interaction test was conducted using stratified and adjusted logistic regression models, and multivariate logistic regression analysis was performed, along with curve fitting and a threshold effect analysis were performed on the relationship between skull BMD and periodontitis.ResultsThe results showed a negatively relationship between skull BMD and the risk of periodontitis. Although the inflection point was found (the skull BMD= 2.89g/cm2), it was not statistically significant, indicating that the skull BMD and periodontitis are linearly related, which 1 unit increase in the skull BMD (g/cm2) was associated with a 30% (OR=0.70; CI=0.57, 0.87; p=0.0010) reduction in the risk of periodontitis events.ConclusionsPeriodontal disease may be related to low skull BMD, for those people, oral hygiene and health care should be more closely monitored. Validation of our findings will require further research.
A Bayesian nonparametric method for detecting rapid changes in disease transmission
Authors: Creswell Richard , Robinson Martin , Gavaghan David , Parag Kris V , Lei Chon Lok , Lambert Ben 
Published: July 2022

AbstractWhether an outbreak of infectious disease is likely to grow or dissipate is determined through the time-varying reproduction number,Rt. Real-time or retrospective identification of changes inRtfollowing the imposition or relaxation of interventions can thus contribute important evidence about disease transmission dynamics which can inform policymaking. Here, we present a method for estimating shifts inRtwithin a renewal model framework. Our method, which we call EpiCluster, is a Bayesian nonparametric model based on the Pitman-Yor process. We assume thatRtis piecewise-constant, and the incidence data and priors determine when or whetherRtshould change and how many times it should do so throughout the series. We also introduce a prior which induces sparsity over the number of changepoints. Being Bayesian, our approach yields a measure of uncertainty inRtand its changepoints. EpiCluster is fast, straightforward to use, and we demonstrate that it provides automated detection of rapid changes in transmission, either in real-time or retrospectively, for synthetic data series where theRtprofile is known. We illustrate the practical utility of our method by fitting it to case data of outbreaks of COVID-19 in Australia and Hong Kong, where it finds changepoints coinciding with the imposition of non-pharmaceutical interventions. Bayesian nonparametric methods, such as ours, allow the volume and complexity of the data to dictate the number of parameters required to approximate the process and should find wide application in epidemiology.HighlightsIdentifying periods of rapid change in transmission is important for devising strategies to control epidemics.We assume that the time-varying reproduction number,Rt, is piecewise-constant and transmission is determined by a Poisson renewal model.We develop a Bayesian nonparametric method, called EpiCluster, which uses a Pitman Yor process to infer changepoints inRt.Using simulated incidence series, we demonstrate that our method is adept at inferring changepoints.Using real COVID-19 incidence series, we infer abrupt changes in transmission at times coinciding with the imposition of non-pharmaceutical interventions.
Drivers of Mortality in COVID ARDS Depend on Patient Sub-Type
Authors: Cheyne Helen , Gandomi Amir , Vajargah Shahrzad Hosseini , Catterson Victoria M. , Mackoy Travis , Mccullagh Lauren , Musso Gabriel , Hajizadeh Negin 
Published: July 2022

AbstractBackgroundThe most common cause of death in people with COVID-19 is acute respiratory distress syndrome (ARDS). ARDS is a heterogeneous syndrome, however, subgroups that have been identified among non-COVID-19 ARDS patients do not clearly apply to COVID-19 ARDS patients. Additionally, studies of COVID-19 ARDS have been limited by sample size.MethodsWe applied an iterative clustering and machine learning framework to electronic health record data from thousands of hospitalized COVID-19 ARDS patients with the goal of defining and characterizing clinically-relevant COVID-19 ARDS subgroups (phenoclusters). We then applied a supervised model to identify risk factors for hospital mortality for each phenocluster and compared these between phenoclusters and the entire cohort.FindingsRisk factors that predict mortality in the overall cohort of COVID-19 ARDS patients do not necessarily predict mortality in phenoclusters. In fact, some risk factors increase the risk of hospital mortality in some phenoclusters, but decrease mortality in others.InterpretationThese phenocluster-specific risk factors would not have been observed with a single predictive model. Heterogeneity in phenoclusters of COVID-19 ARDS as well as drivers of mortality may partially explain challenges in finding effective treatments when applied to all patients with ARDS.FundingThis work was supported by philanthropic funds to the Feinstein Institutes for Medical Research. The funding source did not control any aspect of the study and did not review the results. All authors had full access to the full data in the study and accept responsibility to submit for publication.
Functional genomics for curation of variants in telomere biology disorder associated genes, a systematic review
Authors: Nelson Niles , Feurstein Simone , Niaz Aram , Truong Jia , Holien Jessica K. , Lucas Sionne , Fairfax Kirsten , Dickinson Joanne , Bryan Tracy M. 
Published: July 2022

AbstractBackgroundPatients with an underlying telomere biology disorder (TBD) have variable clinical presentations and can be challenging to diagnose clinically. A genomic diagnosis for patients presenting with TBD is vital for optimal treatments. Unfortunately, many variants identified during diagnostic testing are variants of uncertain significance (VOUS). This complicates management decisions, delays treatment and risks non-uptake of a potentially curative therapies. Improved application of functional genomic evidence may reduce VOUS classifications.MethodsWe systematically searched the literature for published functional assays interrogating TBD gene variants. Where possible, established likely benign/benign and likely pathogenic/pathogenic variants were used to estimate the assay sensitivity, specificity, positive predictive value, negative predictive value and odds of pathogenicity.Results3131 articles were screened and 152 met inclusion criteria. Sufficient data to enable a PS3/BS3 recommendation was available forTERTvariants only. We recommend PS3 and BS3 can be applied at a moderate and supportive level respectively. PS3/BS3 application was limited by a lack of assay standardisation and limited inclusion of benign variants.ConclusionsFurther assay standardisation and assessment of benign variants is required for optimal use of the PS3/BS3 criterion for TBD gene variant classification.
FOXA2 controls the anti-oxidant response in FH-deficient cells
Authors: Rogerson Connor , Sciacovelli Marco , Maddalena Lucas A , Valcarcel-Jimenez Lorea , Schmidt Christina , Yang Ming , Ivanova Elena , Kent Joshua , Mora Ariane , Cheeseman Danya , Carroll Jason S , Kelsey Gavin , Frezza Christian 
Published: July 2022

AbstractHereditary Leiomyomatosis and renal cell cancer (HLRCC) is a cancer syndrome caused by inactivating germline mutations in fumarate hydratase (FH) and subsequent accumulation of fumarate. Fumarate accumulation leads to the activation of an anti-oxidant response via nuclear translocation of the transcription factor NRF2. The activation of the anti-oxidant response is key for cellular survival in FH-deficient cells, yet the extent to which chromatin remodelling shapes the anti-oxidant response is currently unknown. Here, we explored the global effects of FH loss on the chromatin landscape to identify transcription factor networks involved in the highly remodelled chromatin landscape of FH-deficient cells. We identify FOXA2 as a key transcription factor which directly regulates anti-oxidant response genes and subsequent metabolic rewiring. Moreover, we also find that FOXA2 regulates anti-oxidant genes independent of the canonical anti-oxidant regulator NRF2. The identification of FOXA2 as an anti-oxidant regulator provides new insights into the molecular mechanisms behind cell responses to fumarate accumulation, and potentially provides new avenues for therapeutic intervention for HLRCC.
Monoallelic CRMP1 gene variants cause neurodevelopmental disorder
Authors: Ravindran Ethiraj , Arashiki Nobuto , Becker Lena-Luise , Takizawa Kohtaro , Lévy Jonathan , Rambaud Thomas , Makridis Konstantin L. , Goshima Yoshio , Li Na , Vreeburg Maaike , Demeer Bénédicte , Dickmanns Achim , Stegmann Alexander P.A , Hu Hao , Nakamura Fumio , Kaindl Angela M. 
Published: July 2022

AbstractCollapsing response mediator proteins (CRMPs) are key for brain development and function. Here, we link CRMP1 to a neurodevelopmental disorder. We report heterozygous de novo variants in the CRMP1 gene in three unrelated individuals with muscular hypotonia, intellectual disability and/or autism spectrum disorder. Based on in silico analysis these variants are predicted to affect the CRMP1 structure. We further analyzed the effect of the variants on the protein structure/levels and cellular processes. We showed that the human CRMP1 variants are dominant-negative and impact the oligomerization of CRMP1 proteins. Moreover, overexpression of mutant-CRMP1 variants affect neurite outgrowth of murine cortical neurons. While altered CRMP1 levels have been reported in psychiatric diseases, genetic mutation in CRMP1 gene has never been linked to human disease. We report for the first-time mutations in the CRMP1 gene and emphasize its key role in brain development and function by linking directly to a human neurodevelopmental disease.