bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of pulsatile Versus nonpulsatile cardiopulmonary bypass on renal function in patients undergoing coronary artery bypass graft surgery, a randomized controlled trial
Authors: Khademi Saeed , Jahromi Marzieh Zamani , Ghazinoor Mohammad , Farrokhi Amirmohammad , Bahmani Kazerooni Mohamad Hosein , Najafi Masoud 
Published: February 2023

AbstractBackgroundCoronary artery bypass grafting is of the most major surgeries performed around the world. Even though advances are achieved in the surgical technique, a relatively high complication rate regarding circulation is still observed. These complications are believed to be related to cardiopulmonary bypass flow types, pulsatile and nonpulsatile. With renal complications being one of the most important ones, we aim to evaluate the effect of choice of these two flow types on patients’ renal function in a randomized controlled trial.MethodThe study is a double blind randomized clinical trial. Patients with left ventricular dysfunction who were candidates for CABG and were between the ages of 40 to 75 were included in this study. The patients then were randomly assigned into two groups of intraoperative pulsatile and nonpulsatile flow type. The patients renal function markers such as 24-hour urine output, blood urea nitrogen and serum creatinine levels and creatinine clearance were evaluated before and CABG and afterwards in the ICU ward. The results were then analyzed using SPSS 23 software.Resultsof the initial 80 patients enrolled in this study, 16 patients were dropped due to unwillingness to continue follow-up and limitation of data gathering. Patients demographic data between two groups did not differ significantly. No statistically significant difference was observed between the 24 patients undergoing surgery with pulsatile flow and 40 with nonpulsatile flow regarding renal function. Both groups had a decrease in creatinine clearance during their ICU stay. Patients in the pulsatile flow group had less intubation time, less need for blood transfusion but more bleeding after the surgery.ConclusionOur study indicated that there is no difference between the use of pulsatile versus nonpulsatile flow regarding patients’ renal outcome. Our participants had a relatively broader age range than similar studies, including younger patients. This plus having an acceptable number of patients evaluated may illustrate that the differences in these two flow types may be dependent on other risk factors depending on the studied population. Further investigations with focal groups could lead us towards a better understanding how these two flow types differ.
Major outbreak of endophthalmitis after cataract surgery: a retrospective cohort in northern Brazil
Authors: Perez da Silva Pereira Priscilla , Carvalho Sabini Andriely Alayne , Ferreira de Almeida Rosa Maria , Oliveira Pontes Daniela , Bezerra Mororó Alves Márcia Maria , Alves de Sousa Viviane , da Silva Azevedo Magzan , de Souza Botelho Adalgiza , Freire Ramalhaes Surlange , Batista da Silva Edilson 
Published: February 2023

SummaryBackgroundEndophthalmitis is one of the most important adverse events after cataract surgery as it can lead to total vision loss. The aim of this study was to describe the occurrence of endophthalmitis after phacoemulsification with intraocular lens implantation among patients assisted during a joint effort in Porto Velho, Rondônia, Brazil.MethodThis is a retrospective cohort study, carried out from a bank with 649 medical records of patients who underwent surgery. Descriptive analysis and multiple analysis using Robust Poisson Regression were performed to estimate relative risks (RR) and 95% confidence intervals (95%CI). A statistical analysis was performed using the statistical program Stata® version 16.0 (College Station, Texas, USA).ResultsThe incidence of postoperative endophthalmitis confirmed by culture was 10.88%, the highest ever recorded in the world. A higher risk for endophthalmitis was found, in probable cases, among males (RR: 1.88; 95%CI:1.03; 3.44) and brown and yellow skin color (RR: 2.78; 95 %CI %: 1.17; 6.60). For confirmed and probable cases, bilateral surgery and specific lens model were also risk factors. The predominant etiological agents were gram-negative and the main clinical manifestation was corneal edema. The average number of days to start treatment was eight days and 27.12% used antibiotics.ConclusionSpecific protocols are needed for cataract surgeries that encompass hiring, performing and monitoring these services to ensure good practices and patient safety.
Sarcopenia, adiposity, and discrepancies in cystatin C versus creatinine-based eGFR in patients with cancer: a cross-sectional study
Authors: Hanna Paul E. , Ouyang Tianqi , Tahir Ismail , Katz-Agranov Nurit , Wang Qiyu , Mantz Lea , Strohbehn Ian , Moreno Daiana , Harden Destiny , Dinulos James E. , Cosar Duru , Seethapathy Harish , Gainor Justin F. , Shah Sachin J. , Gupta Shruti , Leaf David E. , Fintelman Florian J. , Sise Meghan E. 
Published: February 2023

AbstractPurposeCreatinine-based estimated glomerular filtration rate (eGFRCRE) may overestimate kidney function in patients with sarcopenia. While Cystatin C-based eGFR (eGFRCYS) is less affected by muscle mass, it may underestimate kidney function in patients with obesity. We sought to evaluate the relationship between body composition and discrepancies between creatinine and eGFRCREand eGFRCYSin patients with cancer.MethodsWe conducted a cross-sectional study of consecutive adults with cancer who had an abdominal CT scan performed within 90 days of simultaneous eGFRCREand eGFRCYSmeasurements between May 2010-January 2022. Sarcopenia was defined using independent sex-specific cutoffs for skeletal muscle index (SMI) at the level of the third lumbar vertebral body (<39 cm2/m2for women,<55 cm2/m2for men). High adiposity was defined as the highest sex-specific quartile of total (visceral plus subcutaneous) adiposity index in the cohort. The primary outcome was eGFR discrepancy, defined by eGFRCYS>30% lower than eGFRCRE. We estimated the odds of eGFR discrepancy using multivariable logistic regression modeling.ResultsOf 545 included patients (mean age 63 ±14 years, 300 [55%] females, 440 [80.7%] non-Hispanic white), 320 (58.7%) met the criteria for sarcopenia and 136 (25%) had high adiposity. After adjustment for potential confounders, sarcopenia and high adiposity were both associated with >30% eGFR discrepancy (adjusted odds ratio [aOR] 1.90, 95% confidence interval [CI] 1.12–3.24; aOR 2.01, 95% CI 1.15–3.52, respectively).ConclusionDiscrepancies in eGFRCREand eGFRCYSare common in adult patients with cancer, and sarcopenia and high adiposity are both independently associated with large eGFR discrepancies.Significance statementSerum creatinine may overestimate glomerular filtration rate (GFR) in patients with muscle loss, which is particularly common among patients with cancer. Serum cystatin C may perform better than creatinine in such patients, but its accuracy is affected by obesity. We performed body composition analysis using computed tomography scans in 545 adult patients with cancer and found that both sarcopenia and high adiposity were independently associated with greater discrepancies in serum creatinine-vs. cystatin C-based estimated GFR. These findings highlight the need for future studies to improve and personalize GFR assessment in patients with cancer, particularly in those who will receive renally cleared medications and anti-neoplastic therapies with a narrow therapeutic index.
Comparing in-person, blended and virtual training interventions; a real-world evaluation of HIV capacity building programs in 16 countries in sub-Saharan Africa
Authors: Kiguli-Malwadde E , Forster M , Eliaz A , Celentano J , Chilembe E , Couper ID , Dassah ET , De Villiers MR , Gachuno O , Haruzivishe C , Khanyola J , Martin S , Motlhatlhedi K , Mubuuke R , Mteta K A , Moabi P , Rodrigues A , Sears D , Semitala F , von Zinkernagel D , Reid MJA , Suleman F 
Published: February 2023

AbstractIntroductionWe sought to evaluate the impact of transitioning a multi-country HIV training program from in-person to online by comparing digital training approaches implemented during the pandemic with in-person approaches employed before COVID-19.MethodsWe evaluated mean changes in pre-and post-course knowledge scores and self-reported confidence scores for learners who participated in (1) in-person workshops (between October 2019 and March 2020), (2) an entirely asynchronous, Virtual Workshops [VW] (between May 2021 and January 2022), and (3) a blended Online Course [OC] (between May 2021 and January 2022) across 16 SSA countries. Learning objectives and evaluation tools were the same for all three groups.ResultsAcross 16 SSA countries, 3023 participants enrolled in the in-person course, 2193 learners participated in the virtual workshop and 527 in the online course. The proportions of women who participated in the VW and OC were greater than the proportion who participated in the in-person course (60.1% and 63.6%, p<0.001). Nursing and midwives constituted the largest learner group overall (1145 [37.9%] vs. 949 [43.3%] vs. 107 [20.5%]).Across all domains of HIV knowledge and self-perceived confidence, there was a mean increase between pre- and post-course assessments, regardless of how training was delivered. The greatest percent increase in knowledge scores was among those participating in the in-person course compared to VW or OC formats (13.6% increase vs. 6.0% and 7.6%, p<0.001). Gains in self-reported confidence were greater among learners who participated in the in-person course compared to VW or OC formats, regardless of training level (p<0.001) or professional cadre (p<0.001).ConclusionsIn this multi-country capacity HIV training program, in-person, online synchronous and blended synchronous/asynchronous strategies were effective means of training learners from diverse clinical settings. Online learning approaches facilitated participation from more women and more diverse cadres. However, gains in knowledge and clinical confidence were greater among those participating in in-person learning programs.
Uncovering the Heritable Components of Multimorbidities and Disease Trajectories: A Nationwide Cohort Study
Authors: Westergaard David , Jørgensen Frederik Hytting , Waaben Jens , Lademann Mette , Hansen Thomas Folkmann , Cremers Jolien , Ostrowski Sisse Rye , Vesterager Pedersen Ole Birger ,   Danish Blood Donor Study Genomic Consortium, Requant Roc , Jørgensen Isabella Friis , Fitzgerald Tom , Birney Ewan , Banasik Karina , Mortensen Laust , Brunak Søren 
Published: February 2023

AbstractQuantifying the contribution of genetics and environmental effects on disease initiation and progression, as well as the shared genetics of different diseases, is vital for the understanding of the disease etiology of multimorbidities. In this study, we leverage nationwide Danish registries to provide a granular atlas of the genetic origin of disease phenotypes for a cohort of all Danes 1978-2018 with partially known pedigree (n = 6.3 million). We estimate the heritability and genetic correlation between thousands of disease phenotypes using a novel approach that can be scaled to nationwide data. Our findings confirm the importance of genetics for a number of known associations and increase the resolution of heritability by adding numerous novel associations, some of which point to shared biologically origin of different phenotypes. We also establish the heritability of disease trajectories and the importance of sex-specific genetic contributions.
Effectiveness of bivalent mRNA booster vaccination against SARS-CoV-2 Omicron infection in the Netherlands, September to December 2022
Authors: Huiberts Anne J. , de Gier Brechje , Hoeve Christina E. , de Melker Hester E. , Hahné Susan J.M. , Hartog Gerco den , van de Wijgert Janneke H.H.M. , van den Hof Susan , Knol Mirjam J. 
Published: February 2023

AbstractWe used data of 32,542 prospective cohort study participants who previously received primary and one or two monovalent booster COVID-19 vaccinations. Between 26 September and 19 December 2022, relative effectiveness of bivalent Original/Omicron BA.1 vaccination against self-reported Omicron SARS-CoV-2 infection was 31% in 18-59-year-olds and 14% in 60-85-year-olds. Protection was higher after prior Omicron infection than after bivalent vaccination without prior infection. Although bivalent booster vaccination increases protection against COVID-19 hospitalizations, we found limited added benefit in preventing SARS-CoV-2 infection.
Characteristics and Outcomes of COVID-19 Patients Presumed to be Treated with Sotrovimab in NHS Hospitals in England
Authors: Patel Vishal , Levick Bethany , Boult Stephen , Gibbons Daniel C. , Drysdale Myriam , Lloyd Emily J. , Singh Moushmi , Birch Helen J. 
Published: February 2023

ABSTRACTIntroductionThere is limited real-world evidence describing the effectiveness of early treatments for Coronavirus disease 2019 (COVID-19) during the period where Omicron was the dominant variant. Here we describe characteristics and acute clinical outcomes in patients with COVID-19 treated with a monoclonal antibody (mAb; presumed to be sotrovimab) across six distinct periods covering the emergence and subsequent dominance of Omicron subvariants (BA.1, BA.2 and BA.5) in England.MethodsRetrospective cohort study using data from Hospital Episode Statistics database between 1stJanuary – 31stJuly 2022. Included patients were aged ≥12 years and received a mAb delivered by a National Health Service (NHS) hospital as a day-case, for which the primary diagnosis was COVID-19. Patients were presumed to have received sotrovimab on the basis of available NHS data showing that 99.98% of individuals who received COVID-19 treatment during the period covered by the study were actually treated with sotrovimab. COVID-19-attributable hospitalisations were reported overall and across six distinct periods of Omicron sub-variant prevalence. A multivariate Poisson regression model was used to estimate incidence rate ratios for each period. Subgroup analyses were conducted in patients with severe renal disease and active cancer.ResultsIn total, 10,096 patients were included. The most common high-risk comorbidities were Immune-Mediated Inflammatory Disorders (43.0%;n= 4,337), severe renal disease (14.1%;n= 1,422), rare neurological conditions (10.4%;n= 1,053) and active cancer (9.0%;n= 910). The proportions of patients with a COVID-19-attributable hospitalisation was 1.0% (n= 96), or with a hospital visit due to any cause was 4.6% (n= 465) during the acute period. The percentage of patients who died due to any cause during the acute study period was 0.3% (n= 27). COVID-19-attributable hospitalisation rates were consistent among subgroups and no significant differences (p-values ranged from 0.13 to 0.64) were observed across periods of Omicron subvariants.ConclusionLow levels of COVID-19-attributable hospitalisations and deaths were recorded in mAb-treated patients. Results were consistent for patients with severe renal disease and active cancer. No evidence of differences in hospitalisation rates were observed whilst Omicron BA.1, and BA.2 or BA.5 subvariants were predominant, despite reported reductions in in vitro neutralisation activity of sotrovimab against BA.2 and BA.5.
Predicting hospital readmissions in patients receiving novel-dose Sacubitril/Valsartan therapy: A competing-risk, causal mediation analysis
Authors: Hou Changchun , Hao Xinxin , Sun Ning , Luo Xiaolin , Wang Luyu , Yang Enpu , Gao Zhichun , Chen Ling , Wang Zebi , Cui Yun , Zhong Jing , Yang Juhao , Liu Xi , Qin Zhexue 
Published: February 2023

AbstractBackgroundThe effects of novel-dose Sacubitril/Valsartan (S/V) in patients with heart failure (HF) in the real world have not been adequately studied. We examined the risk for all-cause re-admission in the patients with HF taking novel-dose S/V and the possible mediator role of left ventricular reverse remodeling (LVRR).Methods and ResultsThere were 464 patients recruited from December 2017 to September 2021 in our hospital with a median follow-up of 660 days (range, 17-1494). Model 1 and 2 were developed based on the results of univariable competing risk analysis, least absolute shrinkage and selection operator approach, backward stepwise regression and multivariable competing risk analysis. The internal verification (data-splitting method) indicated that Model 1 had better discrimination, calibration, and clinical utility. The corresponding nomogram showed that patients aged 75 years and above, or taking the lowest-dose S/V (≤50mg twice a day), or diagnosed with ventricular tachycardia, or valvular heart disease, or chronic obstructive pulmonary disease, or diabetes mellitus were at the highest risk of all-cause readmission. In the causal mediation analysis, LVRR was considered as a critical mediator that negatively affected the difference of novel-dose S/V in readmission.ConclusionsA significant association was detected between novel-dose S/V and all-cause readmission in HF patients, in part negatively mediated by LVRR. The web-based nomogram could provide individual prediction of all-cause readmission in HF patients receiving novel-dose S/V. The effects of different novel-dose S/V are still needed to be explored further in the future.
Cross-sectional association between blood cholesterol and calcium levels in genetically diverse strains of mice
Authors: Cousineau Cody M. , Loftus Kaelin , Churchill Gary A. , Bridges Dave 
Published: February 2023

AbstractGenetically diverse outbred mice allow for the study of genetic variation in the context of high dietary and environmental control. Using a machine learning approach we investigated clinical and morphometric factors that associate with serum cholesterol levels in 840 genetically unique mice of both sexes, and on both a control chow and high fat high sucrose diet. We find expected elevations of cholesterol in male mice, those with elevated serum triglycerides and/or fed a high fat high sucrose diet. The third strongest predictor was serum calcium which correlated with serum cholesterol across both diets and sexes (r=0.39-0.48). This is in-line with several human cohort studies which show associations between calcium and cholesterol, and calcium as an independent predictor of cardiovascular events.
Adaptive Digital Tissue Deconvolution
Authors: Görtler Franziska , Mensching-Buhr Malte , Skaar Ørjan , Schrod Stefan , Sterr Thomas , Schäfer Andreas , Beißbarth Tim , Joshi Anagha , Zacharias Helena U. , Grellscheid Sushma Nagaraja , Altenbuchinger Michael 
Published: February 2023

AbstractMotivationThe inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular archetypes which serve as a reference; e.g., a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and that pre-specified cell archetypes can distort the inference of cellular compositions.ResultsWe propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts prototypic reference profiles to the molecular environment of the cells, which further resolves cell-type specific gene regulation from bulk transcriptomics data. We verify this in simulation studies and demonstrate that ADTD improves existing approaches in estimating cellular compositions. In an application to bulk transcriptomics data from breast cancer patients, we demonstrate that ADTD provides insights into cell-type specific molecular differences between breast cancer subtypes.Availability and implementationA python implementation of ADTD and a tutorial are available at Gitlab and zenodo (doi:10.5281/zenodo.7548362).Contactmichael.altenbuchinger@bioinf.med.uni-goettingen.deandsushma.grellscheid@uib.noSupplementary informationSupplementary material is available atBioinformaticsonline.
Coadaptation of coexisting plants enhances productivity in an agricultural system
Authors: Schmutz Anja , Schöb Christian 
Published: February 2023

AbstractGrowing crops in more diverse crop systems (i.e. intercropping) is one way to produce food more sustainably. Even though intercropping, compared to average monocultures, is generally more productive, the full yield potential of intercropping might not yet have been achieved as modern crop cultivars are bred to be grown in monoculture. Breeding plants for more familiarity in mixtures, i.e. plants that are adapted to more diverse communities (i.e.adaptation) or even to coexist with each other (i.e.coadaptation) might have the potential to sustainably enhance productivity.In this study, the productivity benefits of familiarity throughevolutionary adaptation, where one species adapts to its neighbourhood, andcoevolutionary coadaptation, where two or more species adapt to each other, were disentangled in a crop system through an extensive common garden experiment. Furthermore, evolutionary and coevolutionary effects on species-level and community-level productivity were linked to corresponding changes in functional traits.We found evidence for higher productivity and trait convergence with increasing familiarity of the plants composing the community. Furthermore, our results provide evidence forcoevolutionof plants in mixtures leading to higher productivity of coadapted species. However, with the functional traits measured in our study we could not fully explain the productivity benefits found uponcoevolution.Our study is, to our knowledge, the first study that investigatedcoevolutionamong randomly interacting plants and was able to demonstrate thatcoadaptationthroughcoevolutionof coexisting species in mixtures promote ecosystem functioning (i.e. higher productivity). This result is particularly relevant for the diversification of agricultural and forest ecosystems, demonstrating the added value of artificially selecting plants for the communities they are familiar with.