bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a multivariable prediction model of central venous catheter-tip colonization in a cohort of five randomized trials
Authors: Iachkine Jeanne , Buetti Niccolò , de Grooth Harm-Jan , Briant Anaïs R. , Mimoz Olivier , Mégarbane Bruno , Mira Jean-Paul , Ruckly Stéphane , Souweine Bertrand , du Cheyron Damien , Mermel Leonard A. , Timsit Jean-François , Parienti Jean-Jacques 
Published: July 2022

Abstract
Background
The majority of central venous catheters (CVC) removed in the ICU are not colonized, including when a catheter-related infection (CRI) is suspected. We developed and validated a predictive score to reduce unnecessary CVC removal.

Methods
We conducted a retrospective cohort study from five multicenter randomized controlled trials with systematic catheter-tip culture of consecutive CVCs. Colonization was defined as growth of ≥103 colony-forming units per mL. Risk factors for colonization were identified in the training cohort (CATHEDIA and 3SITES trials; 3899 CVCs of which 575 (15%) were colonized) through multivariable analyses. After internal validation in 500 bootstrapped samples, the CVC-OUT score was computed by attaching points to the robust (> 50% of the bootstraps) risk factors. External validation was performed in the testing cohort (CLEAN, DRESSING2 and ELVIS trials; 6848 CVCs, of which 588 (9%) were colonized).

Results
In the training cohort, obesity (1 point), diabetes (1 point), type of CVC (dialysis catheter, 1 point), anatomical insertion site (jugular, 4 points; femoral 5 points), rank of the catheter (second or subsequent, 1 point) and catheterization duration (≥ 5 days, 2 points) were significantly and independently associated with colonization . Area under the ROC curve (AUC) for the CVC-OUT score was 0.69, 95% confidence interval (CI) [0.67–0.72]. In the testing cohort, AUC for the CVC-OUT score was 0.60, 95% CI [0.58–0.62]. Among 1,469 CVCs removed for suspected CRI in the overall population, 1200 (82%) were not colonized. The negative predictive value (NPV) of a CVC-OUT score < 6 points was 94%, 95% CI [93%–95%].

Conclusion
The CVC-OUT score had a moderate ability to discriminate catheter-tip colonization, but the high NPV may contribute to reduce unnecessary CVCs removal. Preference of the subclavian site is the strongest and only modifiable risk factor that reduces the likelihood of catheter-tip colonization and consequently the risk of CRI.

Clinical Trials Registration: NCT00277888, NCT01479153, NCT01629550, NCT01189682, NCT00875069.
scSTEM: clustering pseudotime ordered single-cell data
Authors: Song Qi , Wang Jingtao , Bar-Joseph Ziv 
Published: July 2022

AbstractWe develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metrics to summarize the expression of genes and assigns ap-value to clusters enabling the identification of significant profiles and comparison of profiles across different paths. Application of scSTEM to several scRNA-seq datasets demonstrates its usefulness and ability to improve downstream analysis of biological processes. scSTEM is available athttps://github.com/alexQiSong/scSTEM.
Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance
Authors: Yang Minglei , Lin Chenghao , Wang Yanni , Chen Kang , Zhang Haiyue , Li Weizhong 
Published: July 2022

Abstract
Background
Immune checkpoint blockade (ICB) therapy has revolutionized the treatment of lung squamous cell carcinoma (LUSC). However, a significant proportion of patients with high tumour PD-L1 expression remain resistant to immune checkpoint inhibitors. To understand the underlying resistance mechanisms, characterization of the immunosuppressive tumour microenvironment and identification of biomarkers to predict resistance in patients are urgently needed.

Methods
Our study retrospectively analysed RNA sequencing data of 624 LUSC samples. We analysed gene expression patterns from tumour microenvironment by unsupervised clustering. We correlated the expression patterns with a set of T cell exhaustion signatures, immunosuppressive cells, clinical characteristics, and immunotherapeutic responses. Internal and external testing datasets were used to validate the presence of exhausted immune status.

Results
Approximately 28 to 36% of LUSC patients were found to exhibit significant enrichments of T cell exhaustion signatures, high fraction of immunosuppressive cells (M2 macrophage and CD4 Treg), co-upregulation of 9 inhibitory checkpoints (CTLA4, PDCD1, LAG3, BTLA, TIGIT, HAVCR2, IDO1, SIGLEC7, and VISTA), and enhanced expression of anti-inflammatory cytokines (e.g. TGFβ and CCL18). We defined this immunosuppressive group of patients as exhausted immune class (EIC). Although EIC showed a high density of tumour-infiltrating lymphocytes, these were associated with poor prognosis. EIC had relatively elevated PD-L1 expression, but showed potential resistance to ICB therapy. The signature of 167 genes for EIC prediction was significantly enriched in melanoma patients with ICB therapy resistance. EIC was characterized by a lower chromosomal alteration burden and a unique methylation pattern. We developed a web application (http://lilab2.sysu.edu.cn/tex & http://liwzlab.cn/tex) for researchers to further investigate potential association of ICB resistance based on our multi-omics analysis data.

Conclusions
We introduced a novel LUSC immunosuppressive class which expressed high PD-L1 but showed potential resistance to ICB therapy. This comprehensive characterization of immunosuppressive tumour microenvironment in LUSC provided new insights for further exploration of resistance mechanisms and optimization of immunotherapy strategies.
Clinical mobility metrics estimate and characterize physical activity following lower-limb amputation
Authors: Seth Mayank , Pohlig Ryan Todd , Hicks Gregory Evan , Sions Jaclyn Megan 
Published: July 2022

Abstract
Background
Regular physical activity following a lower-limb amputation is essential for maintaining health and a high quality of life. Most adults with a lower-limb amputation, however, participate in insufficient daily physical activity, and thus, are predisposed to poor health outcomes. Estimating physical activity after lower-limb amputation via common mobility metrics may aid in clinical decisions regarding treatment prioritization and prosthesis prescription. The objectives of this study were (a) to examine associations between daily physical activity and patient-reported and performance-based mobility metrics among adults with lower-limb amputation, and (b) to determine whether patient-reported and performance-based mobility metrics can distinguish between physical activity status [i.e., sedentary (< 5000 steps/day) or non-sedentary (≥ 5000 steps/day)] of adults with lower-limb amputation.

Methods
A cross-sectional study involving 35 adults with a unilateral transtibial (N = 23; 63.0 ± 10.4 years) or transfemoral amputation (N = 12; 58.8 ± 9.5 years) was conducted. Participants completed patient-reported (Prosthesis Evaluation Questionnaire-Mobility Subscale) and performance-based mobility metrics (L-Test, 10-m Walk Test, 6-min Walk Test). Physical activity, i.e., average steps/day, was measured with an accelerometer.

Results
Patient-reported and performance-based mobility metrics were associated with daily physical activity (p < 0.050). Prosthesis Evaluation Questionnaire-Mobility Subscale scores, L-Test time, 10-m Walk Test speed and 6-min Walk Test distance independently explained 11.3%, 31.8%, 37.6% and 30.7% of the total variance in physical activity. Receiver operating characteristic curves revealed patient-reported and performance-based mobility metrics significantly distinguish between physical activity status, i.e., sedentary (< 5000 steps/day) versus non-sedentary (≥ 5000 steps/day). Preliminary cut-points for mobility metrics to classify physical activity status were determined.

Conclusions
Following a lower-limb amputation, patient-reported and performance-based mobility metrics may estimate daily physical activity, thereby aiding clinical decisions regarding treatment prioritization as well as prosthesis selection.
Lactobacilli displacement and Candida albicans inhibition on initial adhesion assays: a probiotic analysis
Authors: Rodríguez-Arias Robert Josue , Guachi-Álvarez Bryan Omar , Montalvo-Vivero Dominique Esther , Machado António 
Published: July 2022

AbstractObjectiveThis study evaluates the probiotic activity of three vaginalLactobacillus gasseri(H59.2, IMAUFB014, and JCM1131) and one non-vaginalL. plantarumATCC14917 against threeCandida albicans(ATCC10231, candidiasis, and healthy vaginal microbiota). Displacement of lactobacilli and adhesion inhibition ofC. albicanswere evaluated on an abiotic surface through adhesion assays with different experimental settings (ES) through low (1.0E + 03 CFU/ml) and high (1.00E + 09 CFU/ml) levels of colonization. ES simulated dysbiosis (ES1 and ES4), candidiasis (ES2), and healthy vaginal microbiota (ES3).ResultsAt ES2 and ES3,L. gasseriH59.2 showed discrepant inhibition values amongC. albicansisolates (ES2:P = 0.008, ES3:P = 0.030; two‐way ANOVA).L. plantarumwas only displaced by 23%, 31%, 54%, and 94% against low and high levels ofC. albicansATCC10231.L. plantarumwas less displaced, when compared toL. gasseristrains (ES1: 61–84%, ES2: 82–96%, ES3: 83–95%, and ES4: 73–97%), showing multiple statistical differences (ES1:P =  < 0.001, ES2:P = 0.003, and ES3:P =  < 0.001; two‐way ANOVA).L. plantarumalso showed a superior inhibition ofC. albicansATCC10231 in ES1 (81%) and ES2 (58%) when compared toL. gasseristrains (ES1: 27–73%,P < 0.001; and ES2:1–49%,P < 0.001; two‐way ANOVA).
AutoClassWeb: a simple web interface for Bayesian clustering of omics data
Authors: Poulain Pierre , Camadro Jean-Michel 
Published: July 2022

Abstract
Objective
Data clustering is a common exploration step in the omics era, notably in genomics and proteomics where many genes or proteins can be quantified from one or more experiments. Bayesian clustering is a powerful unsupervised algorithm that can classify several thousands of genes or proteins. AutoClass C, its original implementation, handles missing data, automatically determines the best number of clusters but is not user-friendly.

Results
We developed an online tool called AutoClassWeb, which provides an easy-to-use and simple web interface for Bayesian clustering with AutoClass. Input data are entered as TSV files and quality controlled. Results are provided in formats that ease further analyses with spreadsheet programs or with programming languages, such as Python or R. AutoClassWeb is implemented in Python and is published under the 3-Clauses BSD license. The source code is available at https://github.com/pierrepo/autoclassweb along with a detailed documentation.
Conditions for uptake of evidence-based knowledge in municipal care for older people in Sweden: a developmental evaluation
Authors: Hultqvist Sara , Ekstam Lisa , Andersson Janicke , Nilsson Maria H. , Overton Marieclaire , Zingmark Magnus , Iwarsson Susanne 
Published: July 2022

Abstract
Objective
The objective of this paper is to describe the initial phase of a long-term collaboration initiative between a municipality and the Faculty of Medicine at a university in Sweden. The overall ambition of the collaboration is to strengthen the quality of care for older people. The concrete goal is to equip academically trained registered health care professionals (HCP) with tools for transferring evidence-based knowledge into practice. As municipal healthcare for older people is mainly carried out by staff lacking academic education, reg. HCP are key actors to bring in and consolidate an evidence-based approach in this setting. Developmental evaluation (DE) has been used to evaluate four separate activities in the initial phase. The activities where sequenced in a cumulative design to provide knowledge for further development of adequate tools.

Results
The cumulative design originally planned did not fit the internal logic of the municipality. Therefore, workflow and pace adjustments were made to proceed towards the joint ambition; the creation of fruitful conditions for the uptake of evidence-based knowledge. Long-term collaboration between academia and organizations outside academia demands a sensitive and flexible research approach, recognizing that collaboration implies mutuality and restricts the sovereignty of academia in designing research.
Chidamide and venetoclax synergistically exert cytotoxicity on multiple myeloma by upregulating BIM expression
Authors: Cao Liqin , Chen Qingxiao , Gu Huiyao , Li Yi , Cao Wen , Liu Yang , Qu Jianwei , Hou Yifan , Chen Jing , Zhang Enfan , He Jingsong , Cai Zhen 
Published: July 2022

Abstract
Background
Multiple myeloma (MM) is the second most common hematologic malignancy with almost all patients eventually having relapse or refractory MM (RRMM), thus novel drugs or combination therapies are needed for improved prognosis. Chidamide and venetoclax, which target histone deacetylase and BCL2, respectively, are two promising agents for the treatment of RRMM.

Results
Herein, we found that chidamide and venetoclax synergistically exert an anti-myeloma effect in vitro in human myeloma cell lines (HMCLs) with a combination index (CI) < 1. Moreover, the synergistic anti-myeloma effect of these two drugs was demonstrated in primary MM cells and MM xenograft mice. Mechanistically, co-exposure to chidamide and venetoclax led to cell cycle arrest at G0/G1 and a sharp increase in DNA double-strand breaks. In addition, the combination of chidamide and venetoclax resulted in BCL-XL downregulation and BIM upregulation, and the latter protein was proved to play a critical role in sensitizing HMCLs to co-treatment.

Conclusion
In conclusion, these results proved the high therapeutic potential of venetoclax and chidamide combination in curing MM, representing a potent and alternative salvage therapy for the treatment of RRMM.
Synthetic MRI in children with tuberous sclerosis complex
Authors: Coban Gokcen , Gumeler Ekim , Parlak Safak , Konuskan Bahadir , Karakaya Jale , Yalnizoglu Dilek , Anlar Banu , Oguz Kader K. 
Published: July 2022

AbstractObjectiveThe generation of numerous sequences and quantitative data in a short scanning time is the most potential advantage of Synthetic MRI (SyMRI). We aimed to test detection of the tubers and to determine underlying tissue characteristics, and morphometric alterations in the brain of pediatric tuberous sclerosis complex (TSC) patients, using SyMRI.MethodsConventional brain MRI (cMRI) and SyMRI were prospectively obtained from 10 TSC patients and 18 healthy control subjects (HCs). Two neuroradiologists independently evaluated tubers on both scans. Additionally, automatically segmented volume calculation and myelin quantification, including the subcortical part of the tubers and normal-appearing brain parenchyma (NABP) of patients, were carried out using SyMRI.ResultsThe cMRI and SyMRI comparison showed a very good correlation on the detection of the tubers (k = 0.82–0.94). Automatic segmentation of Non-gray matter/white matter/cerebrospinal fluid (Non), %Non/brain parenchymal volume, and %Non/intracranial volume was significantly higher; however, %Myelin/intracranial volume and %Myelin/brain parenchymal volume were significantly lower in the TSC patients (p < 0.05). The proton density values were significantly increased, and myelin fraction volume and myelin-correlated compound values were significantly decreased in the NABP in TSC patients on myelin maps (p < 0.05). The white-matter volume, myelin and white-matter fractional volume, longitudinal relaxation rate, transverse relaxation rate, and myelin-correlated compound values were significantly decreased in the subcortical part of tubers on quantification maps (p < 0.001) in TSC patients.ConclusionSyMRI enables the detection of cortical tubers and is a developing tool in the quantification of morphometric and tissue alterations in pediatric TSC patients with a rational scanning time.
Promoting the use of the PRECISE score for prostate MRI during active surveillance: results from the ESOR Nicholas Gourtsoyiannis teaching fellowship
Authors: Giganti Francesco , Aupin Laurene , Thoumin Camille , Faouzi Ingrid , Monnier Hippolyte , Fontaine Matthieu , Navidi Alexandre , Ritvo Paul-Gydéon , Ong Valentin , Chung Cecile , Bibi Imen , Lehrer Raphaële , Hermieu Nicolas , Barret Eric , Ambrosi Alessandro , Kasivisvanathan Veeru , Emberton Mark , Allen Clare , Kirkham Alex , Moore Caroline M. , Renard-Penna Raphaële 
Published: July 2022

Abstract
Objectives
The PRECISE criteria for serial multiparametric magnetic resonance imaging (MRI) of the prostate during active surveillance recommend the use of a dedicated scoring system (PRECISE score) to assess the likelihood of clinically significant radiological change. This pilot study assesses the effect of an interactive teaching course on prostate MRI during active surveillance in assessing radiological change in serial imaging.

Methods
Eleven radiology fellows and registrars with different experience in prostate MRI reading participated in a dedicated teaching course where they initially evaluated radiological change (based on their previous training in prostate MRI reading) independently in fifteen patients on active surveillance (baseline and follow-up scan), and then attended a lecture on the PRECISE score. The initial scans were reviewed for teaching purposes and afterwards the participants re-assessed the degree of radiological change in a new set of images (from fifteen different patients) applying the PRECISE score. Receiver operating characteristic analysis was performed. Confirmatory biopsies and PRECISE scores given in consensus by two radiologists (involved in the original draft of the PRECISE score) were the reference standard.

Results
There was a significant improvement in the average area under the curve (AUC) for the assessment of radiological change from baseline (AUC: 0.60 [Confidence Intervals: 0.51–0.69] to post-teaching (AUC: 0.77 [0.70–0.84]). This was an improvement of 0.17 [0.016–0.28] (p = 0.004).

Conclusions
A dedicated teaching course on the use of the PRECISE score improves the accuracy in the assessment of radiological change in serial MRI of the prostate.
Fibrin glue injection method for complex fistula after laparoscopic distal pancreatectomy: a case report
Authors: Izumi Hideki , Yoshii Hisamichi , Abe Rin , Mukai Masaya , Nomura Eiji , Makuuchi Hiroyasu 
Published: July 2022

Abstract
Background
Pancreatic fistula is the most problematic complication in pancreatectomy. Although drainage can be used to relieve this complication, pancreatic surgeons often encounter refractory pancreatic fistula. Fibrin glue injection, with the use of a twofold diluted solution B and a double-lumen tube, was found effective in treating this complicated pancreatic fistula.

Case presentation
We report the case of a 64-year-old Japanese man who underwent laparoscopic distal pancreatectomy for pancreatic tail cancer. After initial drainage of the pancreatic fistula diagnosed 4 days postoperatively, on day 134, refractory pancreatic fistula was observed using contrast-enhanced computed tomography. We used fibrin glue injection, with a twofold diluted solution containing thrombin and calcium chloride and a double-lumen tube, for treating the refractory fistula; the fluid drainage was almost stopped with no fever or abdominal pain. No recurrence of pancreatic cancer has been observed since the procedure.

Conclusions
Fibrin glue injection was effective for complicated pancreatic fistula after distal pancreatectomy. Using a twofold diluted solution B containing thrombin and calcium chloride and a double-lumen tube makes possible the thorough injection of fibrin glue.
Sex differences in cardiac remodeling post myocardial infarction with acute cigarette smoking
Authors: Kaplan Abdullah , Abidi Emna , Diab Reine , Ghali Rana , Al-Awassi Hiam , Booz George W. , Zouein Fouad A. 
Published: July 2022

Abstract
Background
Whether cigarette smoking affects the heart post-myocardial infarction (MI) in a sex-dependent way remains controversial. Using a mouse model, we investigated cardiac remodeling under the influence of acute cigarette smoke (CS) exposure following ischemic injury in both sexes.

Methods
Ten cigarettes were smoked twice daily for 2 weeks followed by MI and then 1 additional week post permanent LAD ligation. Cardiac function, histology, and infarct size were assessed, and inflammatory markers quantified by RT–PCR. Statistical comparisons were performed using an unpaired t test or ANOVA followed by Tukey post hoc test.

Results
We observed that cigarette smoking exacerbated both left and right ventricular remodeling only in males at an early stage of post-MI. Females did not display a significant structural and/or functional alteration within 7 days of cardiac remodeling post-MI upon CS exposure. Worsened right ventricular remodeling in males was independent of pulmonary congestion. CS-exposed males exhibited enhanced increases in left ventricular end systolic and diastolic volumes, as well as reductions in ejection fraction and fractional area changes of left ventricular base. At day 7, infarct size was increased by cigarette smoking in males only, which was accompanied by enhanced collagen deposition in both the infarcted and peri-infarcted areas. Both IL-6 and TNF-α mRNA expression significantly increased in CS-exposed MI male group only at day 7 post-MI suggestive of prolonged inflammation.

Conclusions
These findings indicate that CS exposure worsens the progression of cardiac remodeling post-MI in male sex in a significant manner compared to female sex at least at early stages.
Sex-related differences in left ventricular remodeling and outcome after alcohol septal ablation in hypertrophic obstructive cardiomyopathy: insights from cardiovascular magnetic resonance imaging
Authors: Chen You-Zhou , Zhao Xing-Shan , Yuan Jian-Song , Zhang Yan , Liu Wei , Qiao Shu-Bin 
Published: July 2022

Abstract
Background
Alcohol septal ablation (ASA) has been proven to reverse left ventricular (LV) remodeling in hypertrophic cardiomyopathy (HCM). However, there are no studies on the effect of sex on LV remodeling after ASA. We aimed to investigate whether sex differences affect the process of LV remodeling and outcome after ASA.

Methods
A total of 107 patients with obstructive HCM (54 men and 53 women, mean age 51 ± 8 years) were recruited. Cardiovascular magnetic resonance (CMR) was performed at baseline and 16 months after ASA. The extent of late gadolinium enhancement (LGE) was measured.

Results
Women had a higher indexed LV mass and smaller indexed LV end-systolic volumes than men at the time of ASA. After ASA, both men and women exhibited a regression of LV mass, and the percentage of mass regression was greater in men than women (15.3% ± 4.3% vs. 10.7% ± 1.8%, p < 0.001). In multivariable analysis, male sex, higher reduction of LV outflow tract (LVOT) gradient and lower baseline LV mass index were independently associated with greater LV mass regression after ASA. Kaplan–Meier analysis showed significantly higher cardiovascular events in women than in men (p = 0.015). Female sex [hazard ratio (HR) 3.913, p = 0.038] and LV mass preablation (HR, 1.019, p = 0.010) were independent predictors of cardiovascular outcomes.

Conclusions
Males with HCM had favorable reverse remodeling with greater LV mass regression post-ASA than female patients. This favorable LV reverse remodeling might provide a mechanistic explanation for the survival advantage in men.