bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of whole-body and regional body fat using abdominal quantitative computed tomography in Chinese women and men
Authors: Mai Jinci , Wu Qiulian , Wu Huanhua , Zeng Chunyuan , Li Yingxin , Shang Jingjie , Wu Biao , Cai Qijun , Du Junbi , Gong Jian 
Published: February 2024

Abstract
Background
Being overweight or obese has become a serious public health concern, and accurate assessment of body composition is particularly important. More precise indicators of body fat composition include visceral adipose tissue (VAT) mass and total body fat percentage (TBF%). Study objectives included examining the relationships between abdominal fat mass, measured by quantitative computed tomography (QCT), and the whole-body and regional fat masses, measured by dual energy X-ray absorptiometry (DXA), as well as to derive equations for the prediction of TBF% using data obtained from multiple QCT slices.

Methods
Whole-body and regional fat percentage were quantified using DXA in Chinese males (n = 68) and females (n = 71) between the ages of 24 and 88. All the participants also underwent abdominal QCT measurement, and their VAT mass and visceral fat volume (VFV) were assessed using QCT and DXA, respectively.

Results
DXA-derived TBF% closely correlated with QCT abdominal fat percentage (r = 0.89–0.93 in men and 0.76–0.88 in women). Stepwise regression showed that single-slice QCT data were the best predictors of DXA-derived TBF%, DXA android fat percentage and DXA gynoid fat percentage. Cross-validation analysis showed that TBF% and android fat percentage could be accurately predicted using QCT data in both sexes. There were close correlations between QCT-derived and DXA-derived VFV (r = 0.97 in men and 0.93 in women).

Conclusion
Clinicians can assess the TBF% and android and gynoid fat percentages of Chinese women and men by analysing existing abdominal CT-derived data using the QCT technique.
Tissue-plasminogen activator effects on the phenotype of splenic myeloid cells in acute inflammation
Authors: Seillier Célia , Lesec Léonie , Hélie Pauline , Marie Charlotte , Vivien Denis , Docagne Fabian , Le Mauff Brigitte , Toutirais Olivier 
Published: February 2024

AbstractTissue-plasminogen activator (tPA) is a serine protease well known for its fibrinolytic function. Recent studies indicate that tPA could also modulate inflammation via plasmin generation and/or by receptor mediated signalling in vitro. However, the contribution of tPA in inflammatory processes in vivo has not been fully addressed. Therefore, using tPA-deficient mice, we have analysed the effect of lipopolysaccharide (LPS) challenge on the phenotype of myeloid cells including neutrophils, macrophages and dendritic cells (DCs) in spleen. We found that LPS treatment upregulated the frequency of major histocompatibility class two (MHCII+) macrophages but also, paradoxically, induced a deep downregulation of MHCII molecule level on macrophages and on conventional dendritic cells 2 (cDC2). Expression level of the CD11b integrin, known as a tPA receptor, was upregulated by LPS on MHCII+ macrophages and cDC2, suggesting that tPA effects could be amplified during inflammation. In tPA−/− mice under inflammatory conditions, expression of costimulatory CD86 molecules on MHCII+ macrophages was decreased compared to WT mice, while in steady state the expression of MHCII molecules was higher on macrophages. Finally, we reported that tPA deficiency slightly modified the phenotype of DCs and T cells in acute inflammatory conditions. Overall, our findings indicate that in vivo, LPS injection had an unexpectedly bimodal effect on MHCII expression on macrophages and DCs that consequently might affect adaptive immunity. tPA could also participate in the regulation of the T cell response by modulating the levels of CD86 and MHCII molecules on macrophages.
Physical activity and sleep pattern in relation to incident Parkinson’s disease: a cohort study
Authors: Chen Li-Hua , Sun Shi-Yu , Li Guijie , Gao Xiang , Luo Weifeng , Tian Haili , Zhang Xuanhao , Yin Xi , Liu Ziwei , Chen Guo-Chong , Xu Guangfei , Liu Tong , Li Fu-Rong 
Published: February 2024

Abstract
Background
How physical activity (PA) and different sleep traits and overall sleep pattern interact in the development of Parkinson’s disease (PD) remain unknown.

Objective
To prospectively investigate the joint associations of PA and sleep pattern with risk of PD.

Methods
Included were 339,666 PD-free participants from the UK Biobank. Baseline PA levels were grouped into low (< 600 MET-mins/week), medium (600 to < 3000 MET-mins/week) and high (≥ 3000 MET-mins/week) according to the instructions of the UK Biobank. Healthy sleep traits (chronotype, sleep duration, insomnia, snoring, and daytime sleepiness) were scored from 0 to 5 and were categorized into “ideal sleep pattern” (≥ 3 sleep scores) and “poor sleep pattern” (0–2 sleep scores). Hazard ratios (HRs) and 95% confidence intervals (CIs) of PD were estimated by Cox proportional hazards models.

Results
During a median of 11.8 years of follow-up, 1,966 PD events were identified. The PD risk was lower in participants with high PA (HR = 0.73; 95% CI: 0.64, 0.84), compared to those with low PA; and participants with ideal sleep pattern also had a lower risk of PD (HR = 0.78; 95% CI: 0.69, 0.87), compared to those with poor sleep pattern. When jointly investigating the combined effect, participants with both high PA and ideal sleep pattern had the lowest risk of incident PD (HR = 0.55; 95% CI: 0.44, 0.69), compared to those with low PA and poor sleep pattern; notably, participants with high PA but poor sleep pattern also gained benefit on PD risk reduction (HR = 0.74; 95% CI: 0.55, 0.99).

Conclusions
Both high PA and ideal sleep pattern were independently associated with lower risk of developing PD, and those with both high PA level and ideal sleep pattern had the lowest risk. Our results suggest that improving PA levels and sleep quality may be promising intervention targets for the prevention of PD.
Tubulointerstitial nephritis antigen-like 1 from cancer-associated fibroblasts contribute to the progression of diffuse-type gastric cancers through the interaction with integrin β1
Authors: Lee Dagyeong , Ham In-Hye , Oh Hye Jeong , Lee Dong Min , Yoon Jung Hwan , Son Sang-Yong , Kim Tae-Min , Kim Jae-Young , Han Sang-Uk , Hur Hoon 
Published: February 2024

Abstract
Background
Tumor cells of diffuse-type gastric cancer (DGC) are discohesive and infiltrate into the stroma as single cells or small subgroups, so the stroma significantly impacts DGC progression. Cancer-associated fibroblasts (CAFs) are major components of the tumor stroma. Here, we identified CAF-specific secreted molecules and investigated the mechanism underlying CAF-induced DGC progression.

Methods
We conducted transcriptome analysis for paired normal fibroblast (NF)-CAF isolated from DGC patient tissues and proteomics for conditioned media (CM) of fibroblasts. The effects of fibroblasts on cancer cells were examined by transwell migration and soft agar assays, western blotting, and in vivo. We confirmed the effect of blocking tubulointerstitial nephritis antigen-like 1 (TINAGL1) in CAFs using siRNA or shRNA. We evaluated the expression of TINAGL1 protein in frozen tissues of DGC and paired normal stomach and mRNA in formalin-fixed, paraffin-embedded (FFPE) tissue using RNA in-situ hybridization (RNA-ISH).

Results
CAFs more highly expressed TINAGL1 than NFs. The co-culture of CAFs increased migration and tumorigenesis of DGC. Moreover, CAFs enhanced the phosphorylation of focal adhesion kinase (FAK) and mesenchymal marker expression in DGC cells. In an animal study, DGC tumors co-injected with CAFs showed aggressive phenotypes, including lymph node metastasis. However, increased phosphorylation of FAK and migration were reduced by blocking TINAGL1 in CAFs. In the tissues of DGC patients, TINAGL1 was higher in cancer than paired normal tissues and detected with collagen type I alpha 1 chain (COL1A1) in the same spot. Furthermore, high TINAGL1 expression was significantly correlated with poor prognosis in several public databases and our patient cohort diagnosed with DGC.

Conclusions
These results indicate that TINAGL1 secreted by CAFs induces phosphorylation of FAK in DGC cells and promotes tumor progression. Thus, targeting TINAGL1 in CAFs can be a novel therapeutic strategy for DGC.
Differences in upper body posture between patients with lumbar spine syndrome and healthy individuals under the consideration of sex, age and BMI
Authors: Holzgreve Fabian , Nazzal Celine , Nazzal Rasem , Golbach Rejane , Groneberg David A. , Maurer-Grubinger Christian , Wanke Eileen M. , Ohlendorf Daniela 
Published: February 2024

Abstract
Background
Work-related forced postures, such as prolonged standing work, can lead to complaints in the lower back. Current research suggests that there is increased evidence of associations between patients with low back pain (LBP) and reduced lordosis in the lumbar spine and generally less spinal tilt in the sagittal plane. The aim of this study is to extend the influence of LBP to other parameters of upper body posture in standing, taking into account the rotational and frontal planes.

Methods
The study included a no-LBP group (418 males, 412 females, aged 21–65 years) and an LBP group (138 subjects: 80 females, 58 males, aged 18–86 years) with medically diagnosed lumbar spine syndrome (LSS). The “ABW BodyMapper” back scanner from ABW GmbH in Germany was used for posture assessment using video raster stereography. Statistical analyses employed two-sample t-tests or Wilcoxon-Mann-Whitney-U tests to assess the relationship between the LBP/no-LBP groups and back posture parameters. Linear and logarithmic regressions were used with independent variables including group, sex, height, weight and body mass index (BMI). Significance level: α = 0.05 (95% confidence).

Results
The regression analysis showed that sagittal parameters of the spine (sagittal trunk decline, thoracic and lumbar bending angle, kyphosis and lordosis angles) depend primarily on sex, age, BMI, height and/or weight but not on group membership (LBP/no-LBP). In the shoulder region, a significant dependency between group membership and scapular rotation was found. In the pelvic region, there were only significant dependencies in the transverse plane, particularly between pelvic torsion and BMI, weight, height and between pelvic rotation and group membership, age and sex.

Conclusion
No difference between the patients and healthy controls were found. In addition, sex appears to be the main influencing factor for upper body posture. Other influencing factors such as BMI, height or weight also seem to have a significant influence on upper body posture more frequently than group affiliation.
Unifying duplication episode clustering and gene-species mapping inference
Authors: Górecki Paweł , Rutecka Natalia , Mykowiecka Agnieszka , Paszek Jarosław 
Published: February 2024

AbstractWe present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC). This problem is particularly relevant in metagenomics, where incomplete data often poses a challenge in the accurate reconstruction of gene histories. To solve MetaEC, we propose a polynomial time dynamic programming (DP) formulation that verifies the existence of a set of duplication episodes from a predefined set of episode candidates. In addition, we design a method to infer distributions of gene-species mappings. We then demonstrate how to use DP to design an algorithm that solves MetaEC. Although the algorithm is exponential in the worst case, we introduce a heuristic modification of the algorithm that provides a solution with the knowledge that it is exact. To evaluate our method, we perform two computational experiments on simulated and empirical data containing whole genome duplication events, showing that our algorithm is able to accurately infer the corresponding events.
Enhancing surgical performance in cardiothoracic surgery with innovations from computer vision and artificial intelligence: a narrative review
Authors: Constable Merryn D. , Shum Hubert P. H. , Clark Stephen 
Published: February 2024

AbstractWhen technical requirements are high, and patient outcomes are critical, opportunities for monitoring and improving surgical skills via objective motion analysis feedback may be particularly beneficial. This narrative review synthesises work on technical and non-technical surgical skills, collaborative task performance, and pose estimation to illustrate new opportunities to advance cardiothoracic surgical performance with innovations from computer vision and artificial intelligence. These technological innovations are critically evaluated in terms of the benefits they could offer the cardiothoracic surgical community, and any barriers to the uptake of the technology are elaborated upon. Like some other specialities, cardiothoracic surgery has relatively few opportunities to benefit from tools with data capture technology embedded within them (as is possible with robotic-assisted laparoscopic surgery, for example). In such cases, pose estimation techniques that allow for movement tracking across a conventional operating field without using specialist equipment or markers offer considerable potential. With video data from either simulated or real surgical procedures, these tools can (1) provide insight into the development of expertise and surgical performance over a surgeon’s career, (2) provide feedback to trainee surgeons regarding areas for improvement, (3) provide the opportunity to investigate what aspects of skill may be linked to patient outcomes which can (4) inform the aspects of surgical skill which should be focused on within training or mentoring programmes. Classifier or assessment algorithms that use artificial intelligence to ‘learn’ what expertise is from expert surgical evaluators could further assist educators in determining if trainees meet competency thresholds. With collaborative efforts between surgical teams, medical institutions, computer scientists and researchers to ensure this technology is developed with usability and ethics in mind, the developed feedback tools could improve cardiothoracic surgical practice in a data-driven way.
Perceval sutureless bioprosthesis versus Perimount sutured bioprosthesis for aortic valve replacement in patients with aortic stenosis: a retrospective, propensity-matched study
Authors: Kapadia Sharan J , Salmasi Mohammed Yousuf , Zientara Alicja , Roussin Isabelle , Quarto Cesare , Asimakopoulos George 
Published: February 2024

Abstract
Background
Rapid-deployment aortic valve replacement (RDAVR) is an alternative to conventional AVR (cAVR) for aortic stenosis. Benefits include a reduction in operative times, facilitation of minimal access surgery and superior haemodynamics compared to conventional valves. However, further evidence is required to inform guidelines, preferably in the form of propensity-matched studies that include mid-term follow-up data.

Methods
This was a single-centre, retrospective, propensity-matched cohort study comparing the Perceval and conventional Perimount Magna Ease valve for short- and mid-term clinical parameters and size-matched mid-term echocardiographic parameters (n = 102 in both groups) from 2014 to 2020. Data were extracted from a nationally managed dataset.

Results
There were no demographic differences between the matched groups. The Perceval group had shorter cross-clamp time (Perceval 62 [49–81] minutes; Perimount 79 [63–102] minutes, P < 0.001), shorter bypass time (Perceval 89 [74–114] minutes; Perimount 104 [84–137] minutes, P < 0.001), and more frequent minimally-invasive approaches (Perceval 28%; Perimount 5%, P < 0.001). Size-matched haemodynamics showed initially higher gradients in the Perceval group, but haemodynamics equalised at 12 + months. The Perceval group had a more favourable % change in the left ventricular posterior wall dimension at 2 + years (Perceval − 4.8 ± 18; Perimount 17 ± 2).

Conclusions
The Perceval facilitated shorter operations, which may benefit intermediate-high-risk, elderly patients with comorbidities requiring concomitant procedures. It also facilitated minimally invasive surgery. Size-matched haemodynamic performance was similar at mid-term follow-up, with the Perceval possibly better facilitating regression of left ventricular hypertrophy.
Record of strep throat infections in Italy: what is needed to know about penicillin allergy? The point of view from the Italian Society of Pediatric Allergy and Immunology (SIAIP)
Authors: De Filippo Maria , Klain Angela , Brambilla Ilaria , Caimmi Silvia , Castagnoli Riccardo , Indolfi Cristiana , Dinardo Giulio , Licari Amelia , Martelli Alberto , Tosca Maria Angela , Votto Martina , Marseglia Gian Luigi , del Giudice Michele Miraglia 
Published: February 2024

AbstractNotifications of invasive group A streptococcal (iGAS) infections have significantly increased in many European Countries compared to the previous season. In Italy, there has been an increase in streptococcal pharyngitis and scarlet fever cases since January 2023, which sparked concerns about a GAS epidemic in the pediatric population. This rise may be ascribed to the GAS infection season that began earlier than usual (off-season outbreak) and the increase in the spread of respiratory viruses and viral coinfections that raised the risk of iGAS disease. Moreover, this phenomenon was also facilitated by increased travel after reduced GAS circulation during the COVID-19 pandemic.The increase in cases of GAS disease has raised some critical issues regarding the potential reactions to administering amoxicillin, the first-line antibiotic therapy, many of which have been erroneously labeled as “allergy."For these reasons, the Italian Society of Pediatric Allergy and Immunology (SIAIP) intends to provide simple clinical indications to help pediatricians manage GAS pharyngitis, discerning the allergic from non-allergic drug hypersensitivity.
Long-term effects of SARS-CoV-2 infection in hospitalized children: findings from an Italian single-center study
Authors: Calcaterra Valeria , Tagi Veronica Maria , D’Auria Enza , Lai Alessia , Zanelli Sara , Montanari Chiara , Biganzoli Elia Maria , Marano Giuseppe , Borghi Elisa , Massa Valentina , Riva Agostino , Zuccotti Gianvincenzo 
Published: February 2024

Abstract
Background
Limited evidence exists regarding the association between COVID-19 and Long COVID manifestations in children, particularly concerning variants of concern (VOCs). We aimed to characterize a cohort of pediatric patients hospitalized with confirmed acute SARS-CoV-2 and monitor them for Long COVID symptoms. Additionally, it seeks to explore any potential correlations between VOCs and clinical symptoms.

Methods
We conducted a prospective study involving children hospitalized from November 2021 to March 2023, with confirmed acute SARS-CoV-2 infection. A telephone survey was conducted at 3-6-12 months after discharge.

Results
We included 167 patients (77 F/90 M). Upon hospital admission, 95.5% of patients presented as symptomatic. Regarding patients for whom it was feasible to determine the SARS-CoV-2 variant (n = 51), the Delta variant was identified in 11 children (21.6%) and Omicron variant in the remaining 40 patients (78.4%: 27.5% BA.1 variant; 15% BA.2 variant; 57.5% BA.5 variant). 19 patients (16.5%) reported experiencing at least one symptom indicative of Long COVID (weight loss 31.6%, inappetence 26.3%, chronic cough 21.1%, fatigue 21.1%, and sleep disturbances, wheezing, abdominal pain and mood disorders 15.8%). In only 4 patients with Long COVID we could identified a specific SARS-CoV-2 variant (3 Omicron: 2 BA.1 and 1 BA.2; 1 Delta).

Conclusions
this study underscores that long COVID is a significant concern in the pediatric population. Our data reinforce the importance of continuously monitoring the impact of long-COVID in infants, children, and adolescents. A follow-up following SARS-CoV-2 infection is therefore advisable, with symptom investigation tailored to the patient’s age.
Genome sequencing as a generic diagnostic strategy for rare disease
Authors: Schobers Gaby , Derks Ronny , den Ouden Amber , Swinkels Hilde , van Reeuwijk Jeroen , Bosgoed Ermanno , Lugtenberg Dorien , Sun Su Ming , Corominas Galbany Jordi , Weiss Marjan , Blok Marinus J. , Olde Keizer Richelle A. C. M. , Hofste Tom , Hellebrekers Debby , de Leeuw Nicole , Stegmann Alexander , Kamsteeg Erik-Jan , Paulussen Aimee D. C. , Ligtenberg Marjolijn J. L. , Bradley Xiangqun Zheng , Peden John , Gutierrez Alejandra , Pullen Adam , Payne Tom , Gilissen Christian , van den Wijngaard Arthur , Brunner Han G. , Nelen Marcel , Yntema Helger G. , Vissers Lisenka E. L. M. 
Published: February 2024

Abstract
Background
To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline genetic diagnosis for rare disease.

Methods
We performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across different workflows, representative of our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide variants and indels < 50 bp), large variants (copy number variants and short tandem repeats) and other variants (structural variants and aneuploidies). Variant calling format files were queried per variant, from which workflow-specific true positive rates (TPRs) for detection were determined. A TPR of ≥ 98% was considered the threshold for transition to GS. A GS-first scenario was generated for our laboratory, using diagnostic efficacy and predicted false negative as primary outcome measures. As input, we modeled the diagnostic path for all 24,570 individuals referred in 2022, combining the clinical referral, the transition of the underlying workflow(s) to GS, and the variant type(s) to be detected.

Results
Overall, 95% (1206/1271) of variants were detected. Detection rates differed per variant category: small variants in 96% (826/860), large variants in 93% (341/366), and other variants in 87% (39/45). TPRs varied between workflows (79–100%), with 7/10 being replaceable by GS. Models for our laboratory indicate that a GS-first strategy would be feasible for 84.9% of clinical referrals (750/883), translating to 71% of all individuals (17,444/24,570) receiving GS as their primary test. An estimated false negative rate of 0.3% could be expected.

Conclusions
GS can capture clinically relevant germline variants in a ‘GS-first strategy’ for the majority of clinical indications in a genetics diagnostic lab.