bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complex case of the calcareous sponge Leucosolenia complicata (Porifera: Calcarea): hidden diversity in Boreal and Arctic regions with description of a new species
Authors: Lavrov Andrey , Ekimova Irina , Schepetov Dimitry , Koinova Alexandra , Ereskovsky Alexander 
Published: October 2023

Abstract
In this study, we present the first integrative revision of the Boreal and Arctic calcareous sponges of the genus Leucosolenia with a specific focus on its biodiversity in the White Sea. The material for this work included a combination of newly collected specimens from different regions of the North-East Atlantic and the White Sea and historical museum collections. An integrative analysis was implemented based on vast morphological data (light microscopy, scanning and transmission electron microscopy), microbiome observations, ecological data, accompanied by molecular phylogenetic and species’ delimitation analyses based on three nuclear markers (28S rRNA, 18S rRNA, and histone 3). We demonstrate that Leucosolenia complicata, previously reported from Arctic waters, is restricted to the North-East Atlantic, while in the Arctic, Leucosolenia diversity is represented by at least four species: Leucosolenia corallorrhiza, Leucosolenia variabilis, and two new species, one of which is described herein under the name Leucosolenia creepae sp. nov.. The molecular phylogeny analysis supports the species identity of these species. In addition to conventional morphological characters, new informative fine morphological characters (skeleton and oscular crown organization; cytological structure, including morphotypes of symbiotic bacteria) were found, providing a baseline for further revision of this group in other regions.
The novel peptide DR4penA attenuates the bleomycin‐ and paraquat‐induced pulmonary fibrosis by suppressing the TGF‐β/Smad signaling pathway
Authors: Wang Dan , Deng Bochuan , Cheng Lu , Li Jieru , Guo Xiaomin , Zhang Jiao , Zhang Xiang , Su Ping , Li Guofeng , Miao Xiaokang , Yang Wenle , Xie Junqiu , Wang Rui 
Published: October 2023

AbstractPulmonary fibrosis (PF), which is caused by continuous alveolar epithelial cell injury and abnormal repair, is referred to as a difficult disease of the lung system by the World Health Organization due to its rapid progression, poor prognosis, and high mortality rate. However, there is still a lack of ideal therapeutic strategies. The peptide DR8 (DHNNPQIR‐NH2), which is derived from rapeseed, exerted antifibrotic activity in the lung, liver, and kidney in our previous studies. By studying the structure–activity relationship and rational design, we introduced an unnatural hydrophobic amino acid (α‐(4‐pentenyl)‐Ala) into DR8 and screened the novel peptide DR4penA (DHNα‐(4‐pentenyl)‐APQIR‐NH2), which had higher anti‐PF activity, higher antioxidant activity and a longer half‐life than DR8. Notably, DR4penA attenuated bleomycin‐ and paraquat‐induced PF, and the anti‐PF activity of DR4penA was equivalent to that of pirfenidone. Additionally, DR4penA suppressed the TGF‐β/Smad pathway in TGF‐β1‐induced A549 cells and paraquat‐induced rats. This study demonstrates that the novel peptide DR4penA is a potential candidate compound for PF therapy, and its antifibrotic activity in different preclinical models of PF provides a theoretical basis for further study.
Early Albumin Infusion Is Associated With Greater Survival to Discharge Among Patients With Sepsis/Septic Shock Who Develop Severe Acute Kidney Injury Among Patients With Sepsis/Septic Shock Who Develop Severe Acute Kidney Injury
Authors: Raghunathan Karthik , Kempker Jordan A. , Davis E. Anne , Sindhwani Navreet S. , Telang Santosh , Lodaya Kunal , Martin Greg S. 
Published: October 2023

Importance:
Adults hospitalized with sepsis/septic shock commonly develop acute kidney injury (AKI) which imposes a significant burden on the healthcare system. The administration of early human albumin in this patient population may yield more efficient healthcare resource utilization.

Objectives:
To examine the association between early use of albumin and time to discharge in adults who develop severe AKI while hospitalized with sepsis/septic shock.

Design:
Retrospective cohort study using de-identified electronic health records from a national database (Cerner Health Facts; Cerner Corp., Kansas City, MO).

Setting and Participants:
Patients (n = 2,829) hospitalized between January 2013 and April 2018 with a diagnosis of sepsis/septic shock (identified using International Classification of Diseases, 9th Revision and 10th Revision codes) who developed severe AKI (stage 3 according to Kidney Disease Improving Global Outcomes criteria) during hospitalization (n = 2,845 unique encounters).

Main Outcomes and Measures:
Patients were grouped according to timing of albumin exposure: within less than or equal to 24 hours of admission (“early albumin”) or unexposed/exposed late (“nonearly albumin”). A cause-specific hazard model, censoring for death/discharge to hospice, was used to examine the association between “early albumin” and the rate of hospital discharge with clinical stability.

Results:
Albumin was administered early in 8.6% of cases. Cases with early albumin administration had a median time to discharge of 13.2 days compared with 17.0 in the nonearly group (Log-rank p < 0.0001). An adjusted analysis showed that the rate of hospital discharge with clinical stability increased by 83% in the early albumin group compared with the nonearly group (hazard ratio, 1.832; 95% CI, 1.564–2.146; p < 0.001 nonearly group.

Conclusions and Relevance:
The use of albumin within 24 hours of hospital admission was associated with a shorter time to discharge and a higher rate of discharge with clinical stability, suggesting an improvement in healthcare resource utilization among patients with sepsis/septic shock who developed stage 3 AKI during hospitalization.
Optimized Arterial Line Artifact Identification Algorithm Cleans High-Frequency Arterial Line Data With High Accuracy in Critically Ill Patients
Authors: Khan Jasmine M. , Maslove David M. , Boyd J. Gordon 
Published: October 2023

OBJECTIVES:
High-frequency data streams of vital signs may be used to generate individualized hemodynamic targets for critically ill patients. Central to this precision medicine approach to resuscitation is our ability to screen these data streams for errors and artifacts. However, there is no consensus on the best method for data cleaning. Our goal was to determine whether an error-checking algorithm developed for intraoperative use could be applied to high volumes of arterial line data in an ICU population.

DESIGN:
Multicenter observational study.

SETTING:
ICUs across Ontario, Canada.

PATIENTS:
Nested cohort of ICU patients with shock and/or respiratory failure requiring invasive mechanical ventilation.

INTERVENTIONS:
High-frequency blood pressure data was analyzed. Systolic, diastolic, and mean arterial pressure minute averages were calculated. For manual analysis, a trained researcher retrospectively reviewed mean arterial pressure data, removing values that were deemed nonphysiological. The algorithm was implemented and identified artifactual data.

MEASUREMENTS AND MAIN RESULTS:
Arterial line data was extracted from 15 patients. A trained researcher manually reviewed 40,798 minute-by-minute data points, then subsequently analyzed them with the algorithm. Manual review resulted in the identification of 119 artifacts (0.29%). The optimized algorithm identified 116 (97%) of these artifacts. Five hundred thirty-seven data points were erroneously removed or modified. Compared with manual review, the modified algorithm incorporating absolute thresholds of greater than 30 and less than 200 mm Hg had 97.5% sensitivity, 98.7% specificity, and a Matthew correlation coefficient of 0.41.

CONCLUSIONS:
The error-checking algorithm had high sensitivity and specificity in detecting arterial line blood pressure artifacts compared with manual data cleaning. Given the growing use of large datasets and machine learning in critical care research, methods to validate the quality of high-frequency data is important to optimize algorithm performance and prevent spurious associations based on artifactual data.
Safety and Outcome of High-Flow Nasal Oxygen Therapy Outside ICU Setting in Hypoxemic Patients With COVID-19*
Authors: Janssen Matthijs L. , Türk Yasemin , Baart Sara J. , Hanselaar Wessel , Aga Yaar , van der Steen-Dieperink Mariëlle , van der Wal Folkert J. , Versluijs Vera J. , Hoek Rogier A.S. , Endeman Henrik , Boer Dirk P. , Hoiting Oscar , Hoelters Jürgen , Achterberg Sefanja , Stads Susanne , Heller-Baan Roxane , Dubois Alain V.F. , Elderman Jan H. , Wils Evert-Jan ,   on behalf of the Dutch HFNO COVID-19 Study Group
Published: October 2023

OBJECTIVE:
High-flow nasal oxygen (HFNO) therapy is frequently applied outside ICU setting in hypoxemic patients with COVID-19. However, safety concerns limit more widespread use. We aimed to assess the safety and clinical outcomes of initiation of HFNO therapy in COVID-19 on non-ICU wards.

DESIGN:
Prospective observational multicenter pragmatic study.

SETTING:
Respiratory wards and ICUs of 10 hospitals in The Netherlands.

PATIENTS:
Adult patients treated with HFNO for COVID-19-associated hypoxemia between December 2020 and July 2021 were included. Patients with treatment limitations were excluded from this analysis.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Outcomes included intubation and mortality rate, duration of hospital and ICU stay, severity of respiratory failure, and complications. Using propensity-matched analysis, we compared patients who initiated HFNO on the wards versus those in ICU. Six hundred eight patients were included, of whom 379 started HFNO on the ward and 229 in the ICU. The intubation rate in the matched cohort (n = 214 patients) was 53% and 60% in ward and ICU starters, respectively (p = 0.41). Mortality rates were comparable between groups (28-d [8% vs 13%], p = 0.28). ICU-free days were significantly higher in ward starters (21 vs 17 d, p < 0.001). No patient died before endotracheal intubation, and the severity of respiratory failure surrounding invasive ventilation and clinical outcomes did not differ between intubated ward and ICU starters (respiratory rate-oxygenation index 3.20 vs 3.38; Pao
2:Fio
2 ratio 65 vs 64 mm Hg; prone positioning after intubation 81 vs 78%; mortality rate 17 vs 25% and ventilator-free days at 28 d 15 vs 13 d, all p values > 0.05).

CONCLUSIONS:
In this large cohort of hypoxemic patients with COVID-19, initiation of HFNO outside the ICU was safe, and clinical outcomes were similar to initiation in the ICU. Furthermore, the initiation of HFNO on wards saved time in ICU without excess mortality or complicated course. Our results indicate that HFNO initiation outside ICU should be further explored in other hypoxemic diseases and clinical settings aiming to preserve ICU capacity and healthcare costs.
Screening for Comorbidity of Sleep Disorders in Career Firefighters
Authors: Hamilton Nancy A. , Russell Julia , Hamadah Kareem , Youngren Westley , Toon Addie , Nguyen Thu A. , Joles Kevin 
Published: October 2023

Background
The purpose of this study was to assess the prevalence and sequelae of insomnia, obstructive sleep apnea (OSA), and comorbid OSA and insomnia (COMISA).

Method
In the morning, after a shift end, Midwest career firefighters (N = 89) in a midsized city completed an electronic battery of questionnaire to screen for OSA, daytime sleepiness, insomnia, presleep arousal, nightmares, mental and physical health symptoms, and a one-night sleep diary.

Results
Prevalence of firefighters exceeding screening thresholds: OSA: 54%; insomnia: 30%; COMISA: 17%; four or more nightmares per month: 15%. Firefighters who met criteria for COMISA had shorter total sleep time, less restful and worse sleep quality, higher depression and anxiety symptoms, and presleep arousal symptoms than firefighters without self-reported sleep problems.

Conclusions
Many firefighters are at elevated risk of individual behavioral sleep disorders, COMISA, and daytime dysfunction.
Relationship between uric acid to albumin ratio and in-stent restenosis in patients with coronary artery disease undergoing drug-eluting stenting
Authors: Liu Wenquan , Ding Kun , Bao Jiaqi , Hu Yilan , Gui Yang , Ye Lifang , Wang Lihong 
Published: October 2023

Background
In-stent restenosis (ISR) in patients undergoing percutaneous coronary intervention (PCI) to treat coronary artery disease (CAD) is an urgent issue in clinical practice. Recent studies have highlighted uric acid-albumin ratio (UAR) as a new marker for evaluating inflammation and oxidative stress, capable of predicting cardiovascular ailments. We aimed to examine the correlation between UAR levels and ISR in patients who underwent drug-eluting stent (DES) implantation.

Methods
We included 503 patients with CAD who underwent initial DES implantation and angiography during the follow-up period. Based on coronary angiographic findings, the patients were categorized into ISR (n = 73) and non-ISR groups (n = 430). Before angiography, laboratory parameters were measured for all enrolled patients. To ascertain the influential factors linked to ISR, multivariate logistic regression analysis was performed. The predictive capability of UAR in determining ISR was assessed using receiver operating characteristic (ROC) curve analysis. Statistical significance was set at P < 0.05.

Results
Multivariate logistic regression analysis revealed that diabetes mellitus, stent length, UAR, albumin levels, and C-reactive protein levels independently predicted ISR. ROC curve analysis revealed that UAR had an area under the curve of 0.767 (95% CI: 0.709 – 0.826) for predicting ISR and demonstrated that UAR outperformed the individual predictive abilities of uric acid and albumin for ISR.

Conclusion
UAR was associated with ISR in patients with CAD undergoing PCI with DES implantation. Moreover, ROC curve analysis demonstrated that UAR exhibited superior predictive accuracy for ISR compared with evaluating uric acid and albumin levels separately.
Delayed tranexamic acid after traumatic brain injury impedes learning and memory: Early tranexamic acid is favorable but not in sham animals
Authors: Culkin Matthew C. , Coons Michael , Bele Priyanka , Thaploo Advait , Georges Anastasia P. , Anderson Erin , Browne Kevin D. , Jacovides Christina , Santos Patricia , Kaplan Lewis J. , Meaney David F. , Smith Douglas H. , Pascual Jose L. 
Published: October 2023

BACKGROUND
Early but not late tranexamic acid (TXA) after TBI preserves blood-brain-barrier integrity, but it is unclear if and how dose timing affects cognitive recovery beyond hours postinjury. We hypothesized that early (1 hour post-TBI) but not late (24 hours post-TBI) TXA administration improves cognitive recovery for 14 days.

METHODS
CD1 male mice (n = 25) were randomized to severe TBI (injury [I], by controlled cortical impact) or sham craniotomy (S) followed by intravenous saline at 1 hour (placebo [P1]) or 30 mg/kg TXA at 1 hour (TXA1) or 24 hours (TXA24). Daily body weights, Garcia Neurological Test scores, brain/lung water content, and Morris water maze exercises quantifying swimming traffic in the platform quadrant (zone [Z] 1) and platform area (Z5) were recorded for up to 14 days.

RESULTS
Among injured groups, I-TXA1 demonstrated fastest weight gain for 14 days and only I-TXA1 showed rapid (day 1) normalization of Garcia Neurological Test (p = 0.01 vs. I-P1, I-TXA24). In cumulative spatial trials, compared with I-TXA1, I-TXA24 hindered learning (distance to Z5 and % time in Z1, p < 0.05). Compared with I-TXA1, I-TXA24 showed poorer memory with less Z5 time (0.51 vs. 0.16 seconds, p < 0.01) and Z5 crossing frequency. Unexpectedly, TXA in uninjured animals (S-TXA1) displayed faster weight gain but inferior learning and memory.

CONCLUSION
Early TXA appears beneficial for cognitive and behavioral outcomes following TBI, although administration 24 hours postinjury consistently impairs cognitive recovery. Tranexamic acid in sham animals may lead to adverse effects on cognition.
Pipeline for RNA sequencing data analysis by combination of Nextflow and R
Authors: Qu Jia-Hua 
Published: October 2023

AbstractWith the development of high-throughput technologies, RNA sequencing (RNA-seq) has become a widely used technology in biological studies and thus a large number of RNA-seq data are emerging and remain to be analyzed. Although there are many different options for analysis methods and tools, a unified pipeline for RNA-seq data analysis is always necessary for a laboratory. Given the update of new methods and tools, I summarized my customized analysis codes to generate an updated pipeline for RNA-seq data analysis. During aging, gene mutations accumulate, and hormone regulation is disrupted, which may exacerbate age-related diseases. Therefore, we generated a dataset from mice with a gene mutation or not and under different hormone treatments to study the effects of two factors, i.e., hormone and gene mutation, on the transcriptome. Based on the Nextflow nf-core rnaseq pipeline, this project established this pipeline consisting of three stages: (1) upstream analysis containing quality control of fastq files before and after trimming, trimming, alignment, and quantification; (2) midstream analysis containing count normalization, differentially expressed genes analysis, and visualization via boxplot, PCA, t-SNE, sample distance heatmap, MA plot, volcano plot, and gene expression heatmap; and (3) downstream analysis containing functional enrichments of KEGG pathways and GO terms. Results showed distinct effects of the single factor as well as interactive effects of the two factors. Codes are also provided for readers who want to customize their analysis pipeline adapted from this pipeline easily.
The Efficacy of Multimodal Physiotherapy versus Usual Care in Chronic Whiplash-Associated Disorders With Facet-Mediated Pain Undergoing Platelet Rich Plasma treatment: A Series of Single Case Experimental Designs
Authors: Smith Ashley , Gupta Arun , Stone Jacqui , Habberfield Jeff , Schneider Geoff 
Published: October 2023

ABSTRACTPurposeChronic whiplash-associated disorders (WAD) is a heterogeneous condition with limited effective treatment options available. This study evaluated the effectiveness of multimodal physiotherapy versus usual care in chronic WAD with facet-mediated pain receiving platelet-rich plasma (PRP) injections to determine if pain interference and confidence completing activities in the presence of neck pain could be improved.Materials and MethodsA multiple-baseline, single-case experimental design was used to evaluate the 6-week effect of physiotherapy or usual care in two groups of three participants each.ResultsAll six participants demonstrated a significant reduction in pain interference, and three participants showed improved confidence to perform daily activities when in pain. Weighted Tau-U demonstrated a significant reduction of pain interference with large to very large effect sizes (> 0.75) for both interventions in all participants irrespective of treatment allocation with no significant group difference demonstrated. Similar effects were demonstrated for the confidence to perform daily activities with neck pain (ES > 0.46), although this was only evident in three participants (two PT and one UC). Generalization measures also showed improvements in pain and disability, psychological and quality of life outcomes. No adverse events were reported.ConclusionsBoth physiotherapy and usual care demonstrated improvements in pain interference and confidence to perform activities of daily living with neck pain in people with chronic WAD following cervical facet joint PRP.Trial RegistrationThe trial was registered withClinicalTrials.gov(Protocol Number:NCT03949959)
Probing Human Heart TCA Cycle Metabolism and Response to Glucose Load using Hyperpolarized [2-13C]Pyruvate MR Spectroscopy
Authors: Chen Hsin-Yu , Gordon Jeremy W. , Dwork Nicholas , Chung Brian T. , Riselli Andrew , Sivalokanathan Sanjay , Bok Robert A. , Slater James B. , Vigneron Daniel B. , Abraham M. Roselle , Larson Peder E.Z. 
Published: October 2023

Abstract SummaryIntroductionThe normal heart has remarkable metabolic flexibility that permits rapid switching between mitochondrial glucose oxidation and fatty acid (FA) oxidation to generate ATP. Loss of metabolic flexibility has been implicated in the genesis of contractile dysfunction seen in cardiomyopathy. Metabolic flexibility has been imaged in experimental models, using hyperpolarized (HP) [2-13C]pyruvate MRI, which enables interrogation of metabolites that reflect tricarboxylic acid (TCA) cycle flux in cardiac myocytes. This study aimed to develop methods, demonstrate feasibility for [2-13C]pyruvate MRI in the human heart for the first time, and assess cardiac metabolic flexibility.MethodsGood Manufacturing Practice [2-13C]pyruvic acid was polarized in a 5T polarizer for 2.5-3 hours. Following dissolution, QC parameters of HP pyruvate met all safety and sterility criteria for pharmacy release, prior to administration to study subjects. Three healthy subjects each received two HP injections and MR scans, first under fasting conditions, followed by oral glucose load. A 5cm axial slab-selective spectroscopy approach was prescribed over the left ventricle and acquired at 3s intervals on a 3T clinical MRI scanner.ResultsThe study protocol which included HP substrate injection, MR scanning and oral glucose load, was performed safely without adverse events. Key downstream metabolites of [2-13C]pyruvate metabolism in cardiac myocytes include the glycolytic derivative [2-13C]lactate, TCA-associated metabolite [5-13C]glutamate, and [1-13C]acetylcarnitine, catalyzed by carnitine acetyltransferase (CAT). After glucose load,13C-labeling of lactate, glutamate, and acetylcarnitine from13C-pyruvate increased by 39.3%, 29.5%, and 114%, respectively in the three subjects, that could result from increases in lactate dehydrogenase (LDH), pyruvate dehydrogenase (PDH), and CAT enzyme activity as well as TCA cycle flux (glucose oxidation).ConclusionsHP [2-13C]pyruvate imaging is safe and permits non-invasive assessment of TCA cycle intermediates and the acetyl buffer, acetylcarnitine, which is not possible using HP [1-13C]pyruvate. Cardiac metabolite measurement in the fasting/fed states provides information on cardiac metabolic flexibility and the acetylcarnitine pool.Graphical Abstract