bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next‐Generation Sequencing‐Based Strategy
Authors: Chen Xi , He Yuxuan , Zhou Linke , Li Xingtong , Jiang Meiling , Wu Min , Li Jing , Chen Li , Xu Huan , Gui Li , Zhou Zhenhua 
Published: September 2024

Background
Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.

Methods and Results

Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next‐generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large‐artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large‐artery atherosclerosis showed a significantly higher relative abundance of
Ralstonia insidiosa
among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.

Conclusions
This study, based on the approach of metagenomic next‐generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large‐artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.
Computed Tomography Imaging Measurements as a Surrogate for Clinical Outcomes After Surgical Management of Acute Type A Aortic Dissection: A Systematic Review
Authors: Vo Thin X. , Rahmouni Kenza , Visintini Sarah , Guo Ming H. , Ouzounian Maral , Chu Michael W. A. , Boodhwani Munir , Appoo Jehangir J. , Tucker Katherine , Al‐Atassi Talal ,   the Canadian Thoracic Aortic Collaborative (CTAC)
Published: September 2024

Background
Postoperative computed tomography imaging surveillance is an essential component of care after acute type A aortic dissection (ATAAD) repair. Prognostic imaging factors after ATAAD repair have not been systematically reviewed.

Methods and Results
We performed a systematic review to summarize postoperative computed tomography measurements including aortic diameter, cross‐sectional area, volume, growth rate, and false lumen thrombosis in addition mid‐ to long‐term clinical outcomes after ATAAD repair. Searches were conducted in Medline, Embase, and CENTRAL in October 2022. Studies were included if they reported clinical outcomes such as mortality or aortic reintervention after 1 year and included aforementioned computed tomography findings. Studies of chronic aortic dissection and studies of exclusive patient populations such as those with connective tissue diseases were excluded. Risk of bias was assessed with the Newcastle‐Ottawa Scale. Searches retrieved 6999 articles. Sixty‐eight studies met inclusion criteria (7885 patients). Extended repairs were associated with improved false lumen thrombosis, decreased aortic growth rate, and decreased rates of reintervention but not improved survival. Growth rates of the aorta post‐ATAAD repair were highest in the descending thoracic aorta. The most frequent prognostic imaging factors reported were a patent/partially thrombosed false lumen and postoperative aortic diameter >40 to 45 mm.

Conclusions
Established measurements of positive aortic remodeling, including complete false lumen thrombosis and stabilization of postoperative aortic diameter and growth are the most studied prognostic indicators for improved clinical outcomes after ATAAD repair. Growth rate of the aorta remains significant after ATAAD repair. Future studies should prospectively evaluate and compare prognostic factors for improved surveillance and management.
Significance of an Early Repeat Troponin Measurement Upon Presentation to the Hospital for Acute Heart Failure
Authors: Horiuchi Yu , Maisel Alan S. , van Veldhuisen Dirk J. , Mueller Christian , Hogan Christopher , Kontos Michael C. , Cannon Chad M. , Müller Gerhard A. , Taub Pam , Vilke Gary M. , Duff Stephen , McDonald Kenneth , Mahon Niall , Nuñez Julio , Briguori Carlo , Passino Claudio , Murray Patrick T. , Wettersten Nicholas 
Published: September 2024

Background
Higher cardiac troponin is associated with worse outcomes in patients with acute heart failure. The significance of repeat measurements over hours remains unclear. We assessed whether a repeat measurement and the Δ between measurements of high‐sensitivity cardiac troponin I (hs‐cTnI) were associated with outcomes in hypervolemic patients with acute heart failure without acute coronary syndrome.

Methods and Results
We analyzed 582 individuals from AKINESIS (Acute Kidney Injury Neutrophil Gelatinase‐Associated Lipocalin Evaluation of Symptomatic Heart Failure Study) with hs‐cTnI measured ≤12 hours from admission and repeated ≤6 hours thereafter. Associations between hs‐cTnI levels and their Δ with short‐term (death, intensive care unit admission, receipt of inotropes, or positive pressure ventilation during hospitalization) and long‐term (death or heart failure readmission within 1 year) outcomes were assessed. The average age was 69±13 years, 62% were men, 65% were White, 46% had coronary artery disease, and 22% had chest pain. Median hs‐cTnI levels were 27 (interquartile range [IQR], 13–62) ng/L initially and 28 (IQR, 14–68) ng/L subsequently, with a Δ of 0 [IQR, −2 to 4] ng/L over 3.4±1 hours. Only the second measurement was associated with short‐term outcomes (odds ratio, 1.14 per 2‐fold higher [95% CI, 1.02–1.28]). Both individual measurements and the Δ were associated with long‐term outcomes (hazard ratios, 1.09, 1.12, and 1.16 for first, second, and Δ, respectively). Associated risk for the first and second measurements were not constant over the year but highest early after being measured and decreased over 1 year.

Conclusions
Repeat measurements of hs‐cTnI over hours can identify individuals with acute heart failure without acute coronary syndrome at risk for short‐ and long‐term outcomes.
Investigating the Relative Contribution from Tropical Indo-Pacific SST to Asian Monsoon Precipitation Variability Using LIM
Authors: Guderian Erin , Han Weiqing , Webster Peter , Zhang Lei , Di Lorenzo Emanuele 
Published: September 2024

Abstract
A critical issue is determining the factors that control the year-to-year variability in precipitation over southern Asia. In this study, we employ a cyclostationary linear inverse model (CS-LIM) to quantify the relative contribution of tropical Pacific and Indian Ocean sea surface temperature anomalies (SSTAs) to the interannual variability of the Asian monsoon, especially Indian summer monsoon rainfall (ISMR). Through a series of CS-LIM experiments, we isolate the impacts of the direct forcing from Pacific SSTAs, Indian Ocean SSTAs, and their interaction on Asian monsoon rainfall variability. Our results reveal distinct patterns of influence with the direct forcing from the Pacific (Indian) Ocean tending to enhance (reduce) the magnitude of precipitation variability, while the Indo-Pacific interaction acts to strongly damp the variability of Asian monsoon precipitation, especially over India. We further investigate these specific impacts on ISMR by analyzing the relationship between tropical Indo-Pacific SSTAs and the leading three empirical orthogonal functions (EOFs) of ISMR. The results from our CS-LIM experiments indicate that the direct forcing from El Niño–Southern Oscillation (ENSO) enhances the variability of the first and third EOFs, while the Indian Ocean SSTA opposes ENSO’s effects, which is consistent with previous studies. Our new results show that the tropical Indo-Pacific interaction strongly damps ISMR variability, which is due to the ENSO-induced Indian Ocean dipole (IOD) opposing the direct impacts from ENSO on ISMR. Additionally, reduced ENSO amplitude and duration associated with the Indo-Pacific interaction may also contribute to the damping effect on ISMR, but this requires further study to understand the relevant mechanisms.
A Systematic Local View of the Long-Term Changes in the Atmospheric Energy Cycle
Authors: Liu Zhen , Franzke Christian L. E. , Novak Lenka , Tailleux Remi , Lembo Valerio 
Published: September 2024

Abstract
The global climatology and long-term changes in the atmospheric energy cycle in the boreal winter are analyzed using a local available potential energy framework using the fifth-generation ECMWF reanalysis data during 1979–2021. In contrast to the classic Lorenz energy cycle, this local framework provides the local information of available potential energy (APE) and its interactions with kinetic energy (KE), allowing the systematic study of barotropic and baroclinic processes. A further systematic decomposition of the APE and KE reservoirs into high- and low-frequency components is conducted to investigate the source and sink terms that account for their spatial variations and long-term changes. The climatology of the local energetic budget terms shows that the interplay between low-frequency APE and KE is mostly over the tropical and polar regions associated with the thermally direct circulation there. Interactions involving high-frequency components are mainly located in the storm-track regions. We show that under recent global warming, a prominent dipolar trend of changes is present over the Asia–Pacific region for all energy forms. The long-term changes in the energy budget reveal how high-frequency APE intensification is due to a stronger conversion from low-frequency APE upstream of the storm track and that this intensification can be compensated by eddy advection away from the storm track, rather than conversion to kinetic energy in the proximity of the mean jet. This provides evidence that a warmer climate substantially affects the energy cycle and, thus, the atmospheric circulation.

Significance Statement
Potential and kinetic energies are major components of atmospheric circulation. Those energies and their generation, dissipation, and conversions provide insight into the dynamics of atmospheric circulation. The Lorenz energy cycle, based on a global framework, has been fundamental in deepening our understanding of the atmosphere. However, here we use a systematic local framework to gain a better understanding of atmospheric circulation changes and how global warming has affected them. Our study finds a general intensification of the local energy cycle over the last few decades.
Estimating the In Situ Stratification via Remotely Sensed Internal Wave Speeds
Authors: Fang Chufan , Simpson Alexandra J. , Lerczak James A. , Haller Merrick C. 
Published: September 2024

Abstract
This work tests a methodology for estimating the ocean stratification gradient using remotely sensed, high temporal and spatial resolution field measurements of internal wave propagation speeds. The internal wave (IW) speeds were calculated from IW tracks observed using a shore-based, X-band marine radar deployed at a field site on the south-central coast of California. An inverse model, based on the work of Kar and Guha, utilizes the linear internal wave dispersion relation, assuming a constant vertical density gradient is the basis for the inverse model. This allows the vertical gradient of density to be expressed as a function of the internal wave phase speed, local water depth, and a background average density. The inputs to the algorithm are the known cross-shore bathymetry, the background ocean density, and the remotely sensed cross-shore profiles of IW speed. The estimated density gradients are then compared to the synchronously measured vertical density profiles collected from an in situ instrument array. The results show a very good agreement offshore in deeper water (∼50–30 m) but more significant discrepancies in shallow water (20–10 m) closer to shore. In addition, a sensitivity analysis is conducted that relates errors in measured speeds to errors in the estimated density gradients.

Significance Statement
The propagation speed of ocean internal waves inherently depends on the vertical structure of the water density, which is termed stratification. In this work, we evaluate and test with real field observations a technique to infer the ocean density stratification from internal wave propagation speeds collected from remote sensing images. Such methods offer a way to monitor ocean stratification without the need for extensive in situ measurements.
Lived-in Experience Among Caregivers of Autistic Children: A Qualitative Study from South India
Authors: Ray Aishwarya , Alphonsa K. K.  , Chandran Suhas 
Published: September 2024

Background: Autism is a developmental disorder that impairs the skills related to behavior, communication, interaction, and learning. This study was undertaken to understand the difficulties faced by caregivers in various aspects of life while taking care of children with autism and their unique life experiences. Methods: After obtaining ethical approval, the study was conducted in a tertiary care hospital in Bangalore, India. An informed consent and a subject information sheet were taken to obtain permission from the subjects. A baseline proforma was prepared for collecting the demographic data for both autistic children and the caregivers. An in-depth, face-to-face, semi-structured interview that consisted of around 10 questions was conducted for 30 minutes. The interview was recorded, later transcribed verbatim, and extracted into specific themes and subthemes. Results: The lived-in experiences throw light on many emotional, social, psychological, and physical distress the caregivers go through on a day-to-day basis. The daily hassles of every caregiver are unique and challenging. Five themes and corresponding subthemes were extracted as follows: emotional meltdown, change in family dynamics, spiritual transition, perceived social burden, and perception of a child’s future. Conclusion: The caregivers of children with autism faced various challenges such as physical and emotional turmoil, financial constraints, and the deprivation of a healthy social life almost every day. Interventional measures such as nurse-led clinics, counseling measure, and planning training sessions for nurses to deal with the various issues faced by the caregivers could be taken up to address the growing concerns of caregivers of children with autism.
Improving Mental Health Literacy and Stigma Among the Hmong
Authors: Vang-Kue Mayche , McNeill Cynthera , Stephens Umeika 
Published: September 2024

Introduction: One in five adults in the United States suffers from mental illness. Negative social influences in the Hmong community stigmatize those who have mental health challenges and mental health outcomes are impacted by poor mental health literacy. Language barriers, conflicting traditional beliefs, and Western concepts of health contribute to low mental health literacy and willingness to seek professional mental health services among the Hmong. Aims: The aim of this project was to successfully implement Mental Health First Aid (MHFA) to a group of 30 or more Hmong adult church leaders in a faith-based setting. Methods: A pretest posttest project design was used. The project implementation process was guided by the Plan-Do-Study-Act (PDSA) model and took place from June 2023 to August 2023. Participants were recruited from three local Detroit Hmong churches. Indicator measures included the Mental Health Literacy Scale (MHLS) and Community Attitudes toward Mental Illness (CAMI) Scale before and immediately after training. One final survey was administered at 6 weeks post MHFA training to measure information retention, stigma, and utilization of MHFA skills. Results: Results reflect the existing body of literature regarding MHFA and the positive impacts on mental health literacy, confidence level, mental health awareness, and decreasing stigma. Conclusion: MHFA continues to demonstrate successful implementation across many settings and populations, especially for this project among Hmong adult church leaders. More research is needed to expand on mental health and the Hmong.
Deep Learning Based Micro-RNA Analysis of Lipopolysaccharide Exposed Periodontal Ligament Stem Cells Exosomes Reveal Apoptotic and Inflammasome Derived Pathway Activation
Authors: Yadalam Pradeep Kumar , Anegundi Raghavendra Vamsi , Thilagar Sivasankari , Arumuganainar Deepavalli , Shrivastava Deepti , Heboyan Artak 
Published: September 2024

Background: The production of inflammatory factors in periodontium is increased by LPS, particularly from P. gingivalis, and the damage to periodontal tissues is exacerbated. Exosomes from periodontal ligament stem cells change regeneration and repair brought on by bacterial LPS. MiRNAs are carried by exosomes to recipient cells to affect epigenetic functions. Thus, this study aims to utilize deep learning algorithms to uncover novel micro-RNA biomarkers in bacterial LPS-exposed PDLSC stem cells to understand the activation pathway. Methods: Using NCBI GEO DATA SET GSE163489, the most differentially expressed micro RNAs were found to differ between healthy and LPS-induced PDLSC cells. Deep learning analysis, employing a Random Forest, Artificial Neural Network c, a Support Vector Machine (SVM), and a Linear Regression model implemented within the orange data mining toolkit, identified novel microRNA biomarkers. The orange data mining toolkit was utilized for deep learning analysis of microRNA expression data, providing a user-friendly environment for machine learning tasks like classification, regression, and clustering. Results: Random Forest emerged as the superior model, achieving the highest R2 score (.985) and the lowest RMSE (0.189) compared to Neural Networks ( R2 = .952, RMSE = 0.332), Linear Regression ( R2 = .949, RMSE = 0.343), and SVM ( R2 = .931, RMSE = 0.398). This suggests its superior ability to capture the underlying patterns in the microRNA expression data. Given its robust performance, Random Forest holds promise for identifying novel biomarkers, developing more accurate diagnostic tools, and potentially guiding the stratification of patients for targeted therapeutic interventions in periodontal disease. Conclusion: The current study utilizes deep learning analysis of microRNA expression data to identify novel biomarkers associated with inflammasome activation and anti-apoptotic pathways. These findings hold promise for guiding the development of novel therapeutic strategies for periodontal disease. However, future studies are warranted to validate these biomarkers using independent datasets and experimental methods.
Comparative outcomes between cryopreserved cadaveric saphenous vein and spliced autogenous vein for infrainguinal bypass
Authors: Montoya Christopher , Yuan Fang , Tordjman Lea , Challa Akashara , Chow Christopher , Kang Naixin , Shao Tony , Kenel-Pierre Stefan , Rey Jorge , Bornak Arash 
Published: September 2024

Objective Cryopreserved greater saphenous vein (CV) and spliced autogenous veins (SV) serve as alternative conduits for lower extremity revascularization when a single-segment autogenous saphenous vein is not available. This study compares the outcomes of infrainguinal bypasses using CV and two-segment SV as conduits. Methods We conducted a retrospective review of data on all lower extremity bypasses performed using CV or SV at our institution. Patients undergoing revascularization for atherosclerotic occlusive disease were included in the statistical analysis, while those with primary acute embolic and/or traumatic causes were excluded. Primary outcomes included limb loss. Secondary outcomes included primary, primary assisted, and secondary patency at one and 3 years. Results 56 patients were included in the analysis, 25 had CV bypass and 31 had SV. The groups did not significantly differ in demographics and comorbidities except for age (mean age 68 CV vs 62 SV, p = .03), and prior coronary artery bypass graft (32% CV vs 6.5% SV, p = .01). There was no statistically significant difference between CV and SV at one- and three-years in limb salvage (54.4% CV vs 61.7% SV, p = .96 and 48.3% CV vs 50.2% SV, p = .94), and bypass abandonment (44.2% CV vs 61.7% SV, p = .83 and 44.2% CV vs 44% SV, p = .85). Despite lower one and 3-year primary patency for CV compared to SV (33.3% CV vs 54.9% SV, p = .29, and 27.7% CV vs 48% SV, p = .27), the difference was statistically not significant. CV and SV had also similar one and 3-year primary assisted (41.8% CV vs 57.8% SV, p = .72 and 41.8% CV vs 44.9% SV, p = .71), and secondary patency (43.9% CV vs 61.7% SV, p = .8 and 43.9% CV vs 44% SV, p = .88), with no statistically significant difference. Conclusion In patients for whom single-segment autologous saphenous vein bypass is not an option, CV and SV show comparable limb salvage up to 3 years. SV may be a more durable option with higher patency, this was however not statistically significant in our cohort likely due to sample size.
Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free
Authors: Chang Jia Jin Marc , Ip Yin Cheong Aden , Neo Wan Lin , Mowe Maxine A. D. , Jaafar Zeehan , Huang Danwei 
Published: September 2024

Abstract
Background
DNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.

Results
We show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~ 4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤ 1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12–15 h of sequencing.

Conclusion
Our results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.