bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Contamination of Donor Blood Units in a Ghanaian Blood Bank: A Critical Concern for Transfusion Safety
Authors: Aidoo N B 
Published: October 2024

Abstract

Introduction/Objective
Background: Blood transfusions, while life-saving, pose a significant risk to patient safety, with transfusion-associated bacterial sepsis emerging as a persistent and potentially fatal threat. The prevalence and severity of bacterial contamination in donor blood units necessitate regular surveillance to ensure safe and effective transfusion therapy.

Aim
This study aimed to identify and assess the susceptibility of bacterial isolates in whole blood donor units at the blood bank of Cape Coast Teaching Hospital in the Central Region of Ghana.

Methods/Case Report
Method(s): One hundred and three (103) units of stored whole blood units, declared safe for transfusion (testing negative for HIV I&II, HBsAg, HCV, and syphilis), were inoculated into Brain Heart Infusion Broth and incubated for 24 hours. The inoculated broths were then cultured on MacConkey agar (MAC), Chocolate agar (CHOC), and Blood agar. Gram-negative and Gram-positive isolates were identified using standard biochemical tests. Antimicrobial susceptibility testing was performed using the disc diffusion method.

Results (if a Case Study enter NA)
Results: Of the 103 donor blood units tested, 33 (32.03%) were found to have bacterial isolates. Gram-positive organisms accounted for 67.14% of the isolates, including Coagulase negative Staphylococcus, Bacillus spp, and S. aureus. Gram-negative bacteria constituted 32.86% of the isolates, with Citrobacter freundii, Serratia marcescens, E. coli, and Providencia stuartii identified. Notably, 62.9% of the bacterial isolates were skin commensals, while 25.7% were of enteric origin and 11.4% were of nosocomial origin. Resistance to commonly used antibiotics varied among isolates, with Coagulase-negative Staphylococcus exhibiting resistance to amoxicillin (92.86%) and erythromycin (76.19%), while Citrobacter freundii showed resistance to levofloxacin (75.00%) and ofloxacin (75.00%).

Conclusion
Conclusion(s): The high incidence of bacterial contamination in donor blood units highlights the need for improved phlebotomy procedures and decontamination practices at blood banks in Ghana to reduce the risk of sepsis in transfusion recipients. Furthermore, this study provides valuable information regarding antibiotic resistance patterns in bacterial isolates, emphasizing the importance of antibiotic stewardship in Ghana.
In conclusion, this study underscores the urgency of addressing bacterial contamination in donor blood units in Ghanaian blood banks to enhance transfusion safety.
Comparison of low-density lipoprotein cholesterol (LDL-c) estimates by in-lab and point-of-care devices in the context of emerging LDL-c equations
Authors: Hubler Zita , Roper Stephen 
Published: October 2024

Abstract
Low-density lipoprotein cholesterol (LDL-c) and lipid measurements are used for hyperlipidemia diagnosis, cardiovascular disease risk classification, and medication management. Millions of lipid panels are performed annually. Given the widespread need for lipid testing, there are two CLIA-waived point-of-care (POC) lipid testing devices. These devices were FDA-approved using the Friedewald equation to estimate LDL-c based on measurements of (triglycerides (TG), high-density lipoprotein cholesterol (HDL-c), and total cholesterol (TC). By contrast, for laboratory-based LDL-c estimation, the Friedewald equation is being replaced by newer, more accurate equations such as the NIH-Sampson equation. These equations use the same lipid panel results to estimate LDL-c and only differ in the arithmetic of the estimation. This study evaluates how differences between the in-clinic POC machines and in-laboratory lipid measurements affect the estimated LDL-c results and are compounded by differences in the equations used for LDL-c estimation. This retrospective observational study collected deidentified lipid results (TG, HDL-c, TC, LDL-c) and demographic data (age, gender) for all samples that had lipid panel results from in-lab and POC within twenty-four hours of each other in a single hospital system between 2014 and 2023. Three hundred twenty samples were identified; samples with non-numerical values or results outside of the reportable range for TG, HDL-c, or TC were not included in subsequent LDL-c calculations using the Friedewald and NIH-Sampson equations (69 results). Patients under the age of 18 were excluded (2 results). Two hundred and forty-nine samples met inclusion criteria; this cohort showed non-significant differences in lipid, age, and gender distributions relative to all POC results tested in the same time frame. Consistent with prior reports, we observed discordance between POC and the in-lab lipid measurements, particularly for TG (Bland-Altman: bias:-23.04 mg/dL, standard deviation:61.3 mg/dL). These analytical differences may not change clinical management if the cardiovascular risk classification using estimated LDL-c is unchanged. However, the risk classification based on the in-lab versus in-clinic testing differed for 20% of patients. The most pronounced difference in LDL-c estimation occurred when the POC machine used Friedewald and in-lab testing used NIH-Sampson, and resulted in 5% more patients differentially classified. Regardless of testing platform, more patients are categorized as higher risk on an individual and population-based level with the NIH-Sampson equation. This study highlights the need for transparency in lipid panel reports regarding which LDL-c equation is used in both POC and in-lab testing formats, and the need for readily available tools for conversion between different LDL-c estimation equations.
Effect of Pre-Analytical Line Settings on Artefactually Elevated Anion Gap Results
Authors: Cooke Tyler , Cullen Regina , D’Ambrosia Christopher , Hod Eldad 
Published: October 2024

Abstract

Introduction
When the core lab at a large tertiary care hospital introduced an automated laboratory system from a major manufacturer, the automated line aliquoted patient serum into open cups for all chemistry testing. It was subsequently discovered that if sample testing was delayed, electrolyte abnormalities could be introduced from evaporation, resulting in an increased anion gap (presumably due to a loss of bicarbonate with evaporation of carbon dioxide). To address this issue, the core lab changed the sample processing protocol in April 2023 from an open cup system to testing primary tubes on the analyzers. The purpose of this study was to evaluate the impact of switching to a primary tube testing system on artefactually elevated anion gap results.

Methods
Equivalent ten-week blocks of anion gap, creatinine and sample turnaround time (from receipt on the line to analyzer perform time) results from pre- to post-primary tube conversion were collected from the laboratory information system. Data from weekend testing and from repeat samples from the same patient were excluded. Data was cleaned and analyzed using R.

Results
Multivariable linear regression showed that when adjusted for the turnaround time and creatinine result, the open cup system was significantly associated (p&lt;0.0001) with a 0.95 [95% CI 0.69-1.21] increase in anion gap. There was a positive relationship between turnaround time and anion gap, with a slope of 0.017 (i.e., a 0.017 increase in anion gap per minute delay; p&lt;0.0001). Overall, the proportion of abnormal results (defined as anion gap &gt;=16) decreased from 26% to 10% after switching to a primary tube testing system. Furthermore, there was an association between the times of day in which the lines were overloaded with specimens, turnaround time, and an increase in abnormal anion gap results. Overall, the mean anion gap decreased by 1 with a turnaround time of one hour and 2 after two hours by switching to the primary tube system. This trend in anion gap was largely driven by a corresponding decrease in bicarbonate. Sodium and chloride levels did not show any relationship with turnaround time.

Conclusions
Using an open cup system for electrolyte testing can cause spuriously elevated anion gap levels, especially with testing delays. Switching to a primary tube testing system largely resolved the issue; however, the data still showed a weakly positive relationship between turnaround time and anion gap for the primary tube testing system, so additional work is needed to identify potential causes of this relationship.
scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering
Authors: Zhang Tianjiao , Zhang Hongfei , Ren Jixiang , Wu Zhenao , Zhao Zhongqian , Wang Guohua 
Published: October 2024

Abstract

Motivation
Cell clustering is foundational for analyzing the heterogeneity of biological tissues using single-cell sequencing data. With the maturation of single-cell multi-omics sequencing technologies, we can integrate multiple omics data to perform cell clustering, thereby overcoming the limitations of insufficient information from single omics data. Existing methods for cell clustering often only consider the differences in data patterns during the analysis of multi-omics data, but the dependencies between omics features of different cell types also significantly influence cell clustering. Moreover, the high dropout rates in scRNA-seq and scATAC-seq data can impact the performance of cell clustering.

Results
We propose a cell clustering model based on a masked autoencoder, scDRMAE. Utilizing a masking mechanism, scDRMAE effectively learns the relationships between different features and imputes false zeros caused by dropout events. To differentiate the importance of various omics data in cell clustering, we dynamically adjust the weights of different omics data through an attention mechanism. Finally, we use the K-means algorithm for cluster analysis of the fused multi-omics data. On commonly used sets of 15 multi-omics datasets, our method demonstrates superior cell clustering performance on multiple metrics compared to other computational methods. In addition, when datasets exhibit varying degrees of dropout noise, our method shows better performance and stronger stability on multiple metrics compared to other methods. Moreover, by analyzing the cell clusters classified by scDRMAE, we identified several biologically significant biomarkers that have been validated, further confirming the effectiveness of scDRMAE in cell clustering from a biological perspective.
SurvBal: compositional microbiome balances for survival outcomes
Authors: Li Ying , Lee Teresa , Marin Kai , Hua Xing , Srinivasan Sujatha , Fredricks David N , Lee John R , Ling Wodan 
Published: October 2024

Abstract

Summary
Identification of balances of bacterial taxa in relation to continuous and dichotomous outcomes is an increasingly frequent analytic objective in microbiome profiling experiments. SurvBal enables the selection of balances in relation to censored survival or time-to-event outcomes which are of considerable interest in many biomedical studies. The most commonly used survival models—the Cox proportional hazards and parametric survival models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e. the ratio of the geometric means of two groups of taxa’s relative abundances.

Availability and implementation
The SurvBal R package and Shiny app can be accessed at https://github.com/yinglia/SurvBal and https://yinglistats.shinyapps.io/shinyapp-survbal/.
Future implications of artificial intelligence in lung cancer screening: a systematic review
Authors: Quirk Joseph , Mac Donnchadha Conor , Vaantaja Jonathan , Mitchell Cameron , Marchi Nicolas , AlSaleh Jasmine , Dalton Bryan 
Published: October 2024

Abstract

Objectives
The aim of this study was to systematically review the literature to assess the application of AI-based interventions in lung cancer screening, and its future implications.

Methods
Relevant published literature was screened using PRISMA guidelines across three databases: PubMed, Scopus, and Web of Science. Search terms for article selection included “artificial intelligence,” “radiology,” “lung cancer,” “screening,” and “diagnostic.” Included studies evaluated the use of AI in lung cancer screening and diagnosis.

Results
Twelve studies met the inclusion criteria. All studies concerned the role of AI in lung cancer screening and diagnosis. The AIs demonstrated promising ability across four domains: (1) detection, (2) characterization and differentiation, (3) augmentation of the work of human radiologists, (4) AI implementation of the LUNG-RADS framework and its ability to augment this framework. All studies reported positive results, demonstrating in some cases AI’s ability to perform these tasks to a level close to that of human radiologists.

Conclusions
The AI systems included in this review were found to be effective screening tools for lung cancer. These findings hold important implications for the future use of AI in lung cancer screening programmes as they may see use as an adjunctive tool for lung cancer screening that would aid in making early and accurate diagnosis.

Advances in knowledge
AI-based systems appear to be powerful tools that can assist radiologists with lung cancer screening and diagnosis.
Comparison of homocysteine, vitamin B12 and folic acid between rural and urban ageing Indians and its association with mild cognitive impairment and cardiovascular risk factors: a cross-sectional analysis
Authors: Mallikarjun Divya N , Malo Palash Kumar , Mensegere Abhishek , Partha Ajith , Sundarakumar Jonas S , Issac Thomas Gregor , Diwakar Latha 
Published: October 2024

Abstract
The relationship between blood levels of homocysteine (HCY), vitamin B12, folic acid and cognitive impairment is inconclusive. Since HCY is an independent risk factor for cardiovascular diseases, understanding its association with Framingham risk score (FRS) may provide insight into the shared underlying mechanism between cardiovascular disease and cognitive impairment. Cross-sectional analyses utilized baseline data from two ongoing longitudinal studies: the Tata Longitudinal Study of Ageing (n = 923), an urban cohort, and Srinivaspura Ageing, NeuroSenescence and COGnition (n = 4239), a rural cohort. The study compared the HCY, vitamin B12 and folic acid levels across cohorts and normal versus mild cognitive impairment (MCI) participants. The association between HCY and cognitive status was established using regression models. Three models were analysed: model 1—unadjusted; model 2—adjusted for age, gender, smoking, alcohol consumption, diet, hypertension, cardiac illness, diabetes; and model 3—adjusted for variables in model 2 plus vitamin B12 and folic acid. Correlation was calculated between HCY and FRS. The urban cohort exhibited a significantly higher level of HCY [median (IQR) (17.70 (10.2) versus 14.70 (9.7); P &lt; 0.001)], vitamin B12 (251 (231) versus 219 (138); P &lt; 0.001) and folic acid (8.21 (8) versus 5.48 (4); P &lt; 0.001) levels compared to rural cohort. HCY, vitamin B12 and folic acid levels did not differ significantly between normal and MCI participants in the urban cohort. In the rural cohort, among the age-gender matched MCI-normal, participants with normal cognition had higher levels of vitamin B12 (≥60 years) [227 (152) versus 217 (175); P = 0.03] and folic acid (&lt;60 years) [5.91 (4) versus 5.40 (4); P = 0.04] compared to MCI. There was no association between HCY and cognitive status in both the cohorts, but there was a significant positive relationship between vitamin B12 deficiency and Clinical Dementia Rating—Sum of the Boxes (CDR-SOB), as well as folic acid deficiency and CDR-SOB in rural and urban cohorts, respectively, within a specific age group. A significant correlation was observed between FRS and HCY in the rural cohort (r = 0.17, P &lt; 0.001), but not in the urban cohort. This study revealed significant differences in HCY, vitamin B12 and folic acid levels between the cohorts. In the rural cohort, participants with MCI had lower vitamin B12 and folic acid levels in a certain age group. Association between HCY and cognitive status was insignificant in both the cohorts. A small significant correlation between FRS and HCY was seen in the rural cohort.
Valvular and perivalvular thrombosis following self-expandable aortic valve replacement: analysis of 100 multi-detector computed tomography scans
Authors: Moscarelli Marco , Zaccone Gregorio , Zlahoda-Huzior Adriana , Pernice Vincenzo , Milo Sabrina , Violante Francesco , Trizzino Francesca , Dudek Dariusz , Speziale Giuseppe , Lancellotti Patrizio , Fattouch Khalil 
Published: October 2024

Abstract

Aims
Subclinical thrombosis may represent an early stage of prosthesis structural disease. Most of the available evidence on the incidence, location, predictors, and consequences of thrombosis comes from studies that have employed balloon-expandable valves. We aimed to describe the different localisations of valvular and perivalvular thrombosis and analyse prosthesis-host multi-detector computed tomography predictors in the context of self-expandable prosthesis. Additionally, we aimed to assess the impact of valvular and perivalvular thrombosis on prosthesis performance and subsequent clinical outcomes.

Methods and results
This analysis includes 100 consecutive patients with normal renal function who underwent transcatheter aortic valve replacement using Evolut R and received multi-detector computed tomography and transthoracic bi-dimensional echocardiography at the 6 month follow-up. Leaflet thrombosis was detected in 18 (18%) patients; 6 (6%) had at least one leaflet with severe thrombosis. Thrombosis of the anatomic sinus was detected in 24 patients (24%) and was more prevalent in the non-coronary sinus. Subvalvular thrombosis with partial or complete circumferential involvement of the prosthesis inner skirt was diagnosed in 23 patients (23%). Bicuspid valve was the predictor with highest association with hypoattenuated lesions [least absolute shrinkage and selection operator coefficient 0.35, 95%, confidence interval (CI) 0.21–0.68]. There was no difference in terms of haemodynamic structural valve dysfunction, neurological events, and re-hospitalisation between the groups with and without thrombosis (hazard ratio: 0.86, 95% CI: 0.24–3.06, P = 0.82).

Conclusion
This study showed that in a relatively low-risk population, valvular and perivalvular thrombosis were not rare phenomena following transcatheter aortic valve replacement at early follow-up. Bicuspid valve showed the strongest association with post-implant thrombosis.
Autonomic reactivity to mental stress is associated with cardiovascular mortality
Authors: Shah Anish S , Vaccarino Viola , Moazzami Kasra , Almuwaqqat Zakaria , Garcia Mariana , Ward Laura , Elon Lisa , Ko Yi-An , Sun Yan V , Pearce Brad D , Raggi Paolo , Bremner J Douglas , Lampert Rachel , Quyyumi Arshed A , Shah Amit J 
Published: October 2024

Abstract

Aims
The mechanisms linking acute psychological stress to cardiovascular disease (CVD) mortality are incompletely understood. We studied the relationship of electrocardiographic measures of autonomic dysfunction during acute mental stress provocation and CVD death.

Methods and results
In a pooled cohort of 765 participants with stable CVD from two related studies, we collected Holter data during standardized laboratory-based mental stress testing with a speech task and followed them for events. We assessed autonomic function using low-frequency (LF) heart rate variability (HRV) in 5-min intervals before, during, and after stress induction, and specifically examined changes from rest to stress. We employed cause-specific survival models to examine its association with CVD and all-cause mortality, controlling for demographic and CVD risk factors. The mean (SD) age was 58 (10) years, 35% were women, and 44% self-identified as Black. After a median follow-up of 5.6 years, 37 (5%) died from CVD causes. A stress-induced LF HRV decrease (67% of sample), vs. increase, was associated with a hazard ratio (HR) of 3.48 (95% confidence interval—3.25, 3.73) for CVD mortality. Low rest LF HRV (bottom quartile) was also independently associated with CVD mortality, HR = 1.75 (1.58, 1.94), vs. normal rest LF HRV (upper three quartiles). The combination of stress-induced LF HRV decrease and low rest LF HRV was associated with HR = 5.73 (5.33, 6.15) vs. the normal stress/rest LF HRV reference. We found similar results with HF HRV.

Conclusion
Stress-induced LF HRV decrease and low rest LF HRV are both independently and additively associated with a higher CVD mortality risk. Additional research is needed to assess whether targeting autonomic dysfunction may improve CVD outcomes.
“What Does ‘Age-Friendly’ Mean to You?”: The Role of Microaggressions in a Retirement and Assisted Living Community
Authors: Kilaberia Tina R , Chang E-Shien , Padgett Deborah K , Lachs Mark , Rosen Tony 
Published: October 2024

Abstract

Background and Objectives
In conversations about expanding age-friendly ecosystems, the concept of “age-friendliness” has not been explored in relation to residential settings.

Research Design and Methods
This multiple-case study compared four residents’ perspectives on the age-friendliness of a retirement and assisted living community, combining individual semi-structured interviews with observational data and organizational document analyses in a contextualist thematic examination.

Results
Three themes depict (A) existing experiences of the setting as “age-friendly” and the tension of the built design vs. identity; (B) resident-to-resident microaggressions, delineated into 4 subthemes including identity-related, intergenerational, condition-related microaggressions, and their influence on social isolation; and (C) desired experiences of the setting as “age-friendly” reflecting the social design. In cases of visibly perceptible diversity (white cane, darker skin tone), residents fared worse in experiencing microaggressions stemming from ableism, racism, and age differences. Conversely, in cases of visibly imperceptible diversity, residents had more positive or entirely positive experiences. Although the setting met many environmental and healthcare needs, it lacked design factors prioritizing meaningful social relationships among residents, affecting social isolation.

Discussion and Implications
Resident-to-resident social relationships were key in the experience of a retirement and assisted living community as age-friendly. Resident-to-resident microaggressions undermined perceptions of the community as age-friendly, and influenced social isolation. We reflect on the organizational role in mitigating against negative social relationships and social isolation to maximize dignity.