bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircRNA_101491 regulated the radiation sensitivity of esophageal squamous cell carcinomas via sponging miR-125a-5p
Authors: Lin Chen , Huang Xianfeng , Qian Yuchen , Li Jiayi , He Youdi , Su Huafang 
Published: June 2024

Abstract
Background
At present, it has been found that many patients have acquired resistance to radiotherapy, which greatly reduces the effect of radiotherapy and further affects the prognosis. CircRNAs is involved in the regulation of radiosensitivity of many kinds of tumor cells. Therefore, the main purpose of this study is to explore the regulatory effect of CircRNA_101491 on radiosensitivity of ESCC and its related mechanism.

Methods
We established ESCC radiation-resistant cell line (KYSE150R cell) by gradient dose method, and tested the difference of KYSE150 between KYSE150R cell and parent cell in vitro. Then, after knocking down the expression of CircRNA_101491, a series of in vitro experiments were conducted to verify the effects of CircRNA_101491 on the phenotype and radiosensitivity of KYSE150R cells, and further analyzed the related regulatory mechanism. In addition, we also used the model of transplanted tumor in nude mice to investigate the effect of CircRNA_101491 on the radiosensitivity of ESCC in vivo.

Results
According to a series of in vitro experiments, we confirmed that KYSE150R cells lost the epithelial phenotype and obtained interstitial cell-like phenotype, and found that CircRNA_101491 was highly expressed in KYSE150R cells. In addition, we found that knocking down the expression of CircRNA_101491 will lift the inhibition of miR-125a-5p, and then reverse the process of EMT, accelerate the process of apoptosis, thus play a role in radiosensitization. The in vivo experiment of transplanted tumor in nude mice also showed that knocking down the expression of CircRNA_101491 could enhance the radiosensitivity of ESCC.

Conclusion
In conclusion, we confirmed that interfering with the expression of CircRNA_101491 can relieve the inhibition of miR-125a-5p, thus reverse the process of interstitial phenotype, accelerate the process of apoptosis, and enhance the radiosensitivity of ESCC.
Development and validation of a machine learning predictive model for perioperative myocardial injury in cardiac surgery with cardiopulmonary bypass
Authors: Li Qian , Lv Hong , Chen Yuye , Shen Jingjia , shi Jia , Zhou Chenghui 
Published: June 2024

Abstract
Background
Perioperative myocardial injury (PMI) with different cut-off values has showed to be associated with different prognostic effect after cardiac surgery. Machine learning (ML) method has been widely used in perioperative risk predictions during cardiac surgery. However, the utilization of ML in PMI has not been studied yet. Therefore, we sought to develop and validate the performances of ML for PMI with different cut-off values in cardiac surgery with cardiopulmonary bypass (CPB).

Methods
This was a second analysis of a multicenter clinical trial (OPTIMAL) and requirement for written informed consent was waived due to the retrospective design. Patients aged 18–70 undergoing elective cardiac surgery with CPB from December 2018 to April 2021 were enrolled in China. The models were developed using the data from Fuwai Hospital and externally validated by the other three cardiac centres. Traditional logistic regression (LR) and eleven ML models were constructed. The primary outcome was PMI, defined as the postoperative maximum cardiac Troponin I beyond different times of upper reference limit (40x, 70x, 100x, 130x) We measured the model performance by examining the area under the receiver operating characteristic curve (AUROC), precision-recall curve (AUPRC), and calibration brier score.

Results
A total of 2983 eligible patients eventually participated in both the model development (n = 2420) and external validation (n = 563). The CatboostClassifier and RandomForestClassifier emerged as potential alternatives to the LR model for predicting PMI. The AUROC demonstrated an increase with each of the four cutoffs, peaking at 100x URL in the testing dataset and at 70x URL in the external validation dataset. However, it’s worth noting that the AUPRC decreased with each cutoff increment. Additionally, the Brier loss score decreased as the cutoffs increased, reaching its lowest point at 0.16 with a 130x URL cutoff. Moreover, extended CPB time, aortic duration, elevated preoperative N-terminal brain sodium peptide, reduced preoperative neutrophil count, higher body mass index, and increased high-sensitivity C-reactive protein levels were identified as risk factors for PMI across all four cutoff values.

Conclusions
The CatboostClassifier and RandomForestClassifer algorithms could be an alternative for LR in prediction of PMI. Furthermore, preoperative higher N-terminal brain sodium peptide and lower high-sensitivity C-reactive protein were strong risk factor for PMI, the underlying mechanism require further investigation.
Pulmonary, aorta, and coronary arteries post-arterial switch in transposition of great arteries: intermediate-term surveillance utilizing conventional echocardiography and cardiac multislice computed tomography
Authors: Rakha Shaimaa , Batouty Nihal M. , ElDerie Ahmad AbdelAleem , Hussein Amira 
Published: June 2024

Abstract
Background
Arterial switch operation (ASO) is the standard surgical choice for D-transposition of great arteries (D-TGA). However, the implications of ASO on pulmonaries, coronaries, and aorta have not been adequately investigated. The current study evaluates arterial morphologic changes post-ASO at intermediate-term surveillance.

Methods
From May 2021 to May 2022, patients with D-TGA who underwent ASO for more than six months were recruited. Preoperative and operative data were collected. Patients were assessed using echocardiography (ECHO) and multislice CT angiography (MSCT) to evaluate pulmonary, coronary, and aortic arterial anatomy.

Results
Twenty patients were included with median age of 11 (10-23.25) days at ASO and 14 (7.25–32.75) months on last follow-up. Neo-aortic regurgitation was detected in 12(60%) and neo-pulmonary regurgitation in 3 (15%). Using ECHO, complete evaluation of pulmonary arteries (PAs) was not achieved in 35% and incomplete coronaries assessment in 40% of cases. No stenosis was detected in coronaries using MSCT, although coronary anomalies were found in 9/20 (45%). Dilated Aortic annulus was detected in 16/20 (80%), dilated aortic root in 18/20 (90%), and dilated sinotubular junction in 70%. Right PA stenosis was diagnosed in 10/20 (50%) and left PA(LPA) stenosis in 7/20 (35%). Although Z-score of PAs did not correlate with aortic data, LPA bending angle was positively correlated to neo-aortic root diameter and Z-score (rho = 0.65,p = 0.016; rho = 0.69,p = 0.01), respectively.

Conclusion
Echocardiography alone is not a conclusive surveillance tool for detecting late post-ASO anatomic changes in D-TGA patients. Cardiac MSCT should be considered for comprehensive evaluation on the intermediate-term follow-up post-ASO to accurately track morphologic abnormalities in the aorta, pulmonary, and coronary arteries.
Is comorbidity alone responsible for changes in health-related quality of life among critical care survivors? A purpose-specific review
Authors: Orwelius Lotti , Wilhelms Susanne , Sjöberg Folke 
Published: June 2024

Abstract
Background
Health-related quality of life (HRQoL) is one of the most important outcome variables for assessing the effectiveness of intensive care, together with mortality and survival, where comorbidity is suggested to have high impact. However, studies are lacking that examine to what extent HRQoL is affected after a general ICU period, beyond that of the effects that may be claimed to be due to comorbidities.

Design
Purpose-specific literature review including literature searches in PubMed, Cinahl, Scopus, and Cochrane library between 2010 and 2021.

Measurements and results
This Purpose-specific, i.e., task focused review examines HRQoL (assessed by either SF-36 or EQ-5D, > 30 days after leaving the hospital) in adult patients (≥ 18 years) having an ICU length of stay > 24 h. Further, the HRQoL comparisons were adjusted for age or comorbidity. A total of 11 publications were found. A majority comprised observational, prospective cohort studies, except three that were either case–control, cross-sectional comparison, or retrospective cohort studies. A total of 18,566 critically ill patients were included, and the response rate ranged from 16 to 94%. In all studies, a recurrent relevant finding was that HRQoL after ICU care was affected by pre-ICU comorbidities. In three studies (n = 3), which included a comorbidity adjusted control group, there were no effect of the critical care period itself on the registered HRQoL after the critical care period.

Conclusion
Health-Related Quality of Life (HRQoL) in former ICU patients appears to be primarily influenced by comorbidity. A notable limitation in this field of research is the high heterogeneity observed in the studies reviewed, particularly in terms of the HRQoL measurement tool employed, the duration of follow-up, the methodology for comorbidity assessment, and the adjustments for age and sex. Despite these variations and the limited number of studies in the review, the findings suggest a minimal HRQoL impact beyond the effects of comorbidity. Given the significant dearth of comprehensive studies in this domain, there is an escalating call for more thorough and detailed research endeavours.

Graphical abstract
Immune evasion impacts the landscape of driver genes during cancer evolution
Authors: Gourmet Lucie , Sottoriva Andrea , Walker-Samuel Simon , Secrier Maria , Zapata Luis 
Published: June 2024

Abstract
Background
Carcinogenesis is driven by interactions between genetic mutations and the local tumor microenvironment. Recent research has identified hundreds of cancer driver genes; however, these studies often include a mixture of different molecular subtypes and ecological niches and ignore the impact of the immune system.

Results
In this study, we compare the landscape of driver genes in tumors that escaped the immune system (escape +) versus those that did not (escape −). We analyze 9896 primary tumors from The Cancer Genome Atlas using the ratio of non-synonymous to synonymous mutations (dN/dS) and find 85 driver genes, including 27 and 16 novel genes, in escape − and escape + tumors, respectively. The dN/dS of driver genes in immune escaped tumors is significantly lower and closer to neutrality than in non-escaped tumors, suggesting selection buffering in driver genes fueled by immune escape. Additionally, we find that immune evasion leads to more mutated sites, a diverse array of mutational signatures and is linked to tumor prognosis.

Conclusions
Our findings highlight the need for improved patient stratification to identify new therapeutic targets for cancer treatment.
Ecology and geography of Cache Valley virus assessed using ecological niche modeling
Authors: Muller John A. , López Krisangel , Escobar Luis E. , Auguste Albert J. 
Published: June 2024

Abstract
Background
Cache Valley virus (CVV) is an understudied Orthobunyavirus with a high spillover transmission potential due to its wide geographical distribution and large number of associated hosts and vectors. Although CVV is known to be widely distributed throughout North America, no studies have explored its geography or employed computational methods to explore the mammal and mosquito species likely participating in the CVV sylvatic cycle.

Methods
We used a literature review and online databases to compile locality data for CVV and its potential vectors and hosts. We linked location data points with climatic data via ecological niche modeling to estimate the geographical range of CVV and hotspots of transmission risk. We used background similarity tests to identify likely CVV mosquito vectors and mammal hosts to detect ecological signals from CVV sylvatic transmission.

Results
CVV distribution maps revealed a widespread potential viral occurrence throughout North America. Ecological niche models identified areas with climate, vectors, and hosts suitable to maintain CVV transmission. Our background similarity tests identified Aedes vexans, Culiseta inornata, and Culex tarsalis as the most likely vectors and Odocoileus virginianus (white-tailed deer) as the most likely host sustaining sylvatic transmission.

Conclusions
CVV has a continental-level, widespread transmission potential. Large areas of North America have suitable climate, vectors, and hosts for CVV emergence, establishment, and spread. We identified geographical hotspots that have no confirmed CVV reports to date and, in view of CVV misdiagnosis or underreporting, can guide future surveillance to specific localities and species.

Graphical Abstract
Identification of transposable element families from pangenome polymorphisms
Authors: Sierra Pío , Durbin Richard 
Published: June 2024

Abstract
Background
Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.

Results
We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.

Conclusions
Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.
A feasibility study of in vivo quantitative ultra-short echo time-MRI for detecting early cartilage degeneration
Authors: Su Xiaolian , Wang Yitong , Chen Jieying , Liang Zonghui , Wan Lidi , Tang Guangyu 
Published: June 2024

Abstract
Objectives
To explore the feasibility of Ultra-short echo time (UTE) – MRI quantitative imaging in detecting early cartilage degeneration in vivo and underlying pathological and biochemical basis.

Methods
Twenty volunteers with osteoarthritis (OA) planning for total knee arthroplasty (TKA) were prospectively recruited. UTE-MRI sequences and conventional sequences were performed preoperatively. Regions of interests (ROIs) were manually drawn on the tibial plateau and lateral femoral condyle images to calculate MRI values. Cartilage samples were collected during TKA according to the preset positions corresponding to MR images. Pathological and biochemical components of the corresponding ROI, including histological grading, glycosaminoglycan (GAG) content, collagen integrity, and water content were obtained.

Results
91 ROIs from volunteers of 7 males (age range: 68 to 78 years; 74 ± 3 years) and 13 females (age range: 57 to 79 years; 67 ± 6 years) were evaluated. UTE-MTR (r = −0.619, p < 0.001), UTE-AdiabT1ρ (r = 0.568, p < 0.001), and UTE-T2* values (r = −0.495, p < 0.001) showed higher correlation with Mankin scores than T2 (r = 0.287, p = 0.006) and T1ρ (r = 0.435, p < 0.001) values. Of them, UTE-MTR had the highest diagnostic performance (AUC = 0.824, p < 0.001). UTE-MTR, UTE-AdiabT1ρ and UTE-T2* value was mainly related to collagen structural integrity, PG content and water content, respectively (r = 0.536, −0.652, −0.518, p < 0.001, respectively).

Conclusion
UTE-MRI have shown greater in vivo diagnostic value for early cartilage degeneration compared to conventional T2 and T1ρ values. Of them, UTE-MTR has the highest diagnostic efficiency. UTE-MTR, UTE-AdiabT1ρ, and UTE-T2* value mainly reflect different aspects of cartilage degeneration--integrity of collagen structure, PG content, and water content, respectively.

Critical relevance statement
Ultra-short echo time (UTE)-MRI has the potential to be a novel image biomarkers for detecting early cartilage degeneration in vivo and was correlated with biochemical changes of early cartilage degeneration.

Key Points

Conventional MR may miss some early cartilage changes due to relatively long echo times.

Ultra-short echo time (UTE)-MRI showed the ability in identifying early cartilage degeneration in vivo.

UTE-MT, UTE-AdiabT1ρ, and UTE-T2* mapping mainly reflect different aspects of cartilage degeneration.

Graphical Abstract
Hepatitis A virus infection associated with bilateral pleural effusion, ascites, and acalculous cholecystitis in childhood: a case report
Authors: Breim Fatima , Roumi Jamal Bakri , Kanaa Lama , Bourghol Saleh , Jazmati Besher , Dadah Samia 
Published: June 2024

Abstract
Background
Acute hepatitis A infection is common among children in developing nations. The clinical presentation in children is usually asymptomatic and anicteric, and it is a self-limiting infection. Rarely, it can be associated with extrahepatic complications such as pleural effusion, acalculous cholecystitis, and ascites.

Case presentation
An 8-year-old middle eastern child presented with abdominal pain, jaundice in the sclera, yellowish color of urine, and poor appetite. In the last two days, abdominal distension developed. After conducting diagnostic investigations, the child was diagnosed with HAV hepatitis associated with bilateral pleural effusion, acalculous cholecystitis, and ascites. He was managed conservatively with vitamin K supplementation and supportive parenteral fluids. After 4 days, clinical improvement was observed.

Conclusion
Hepatitis A infections presented with extrahepatic manifestations like pleural effusion, acalculous cholecystitis, and ascites are very rare, especially in children. There have been some reports of these manifestations occurring in isolation, but for them to co-exist to our knowledge, this has only been reported in two cases in the literature, and this is the third case with all these three rare complications being presented simultaneously in a single child. Although HAV infection is an asymptomatic and self-limiting viral disease in childhood, it can manifest with rare extrahepatic complications, so pediatricians should be aware of this rare association to avoid unnecessary investigations.
A prospective clinical study of the influence of oral protein intake on [18F]FET-PET uptake and test–retest repeatability in glioma
Authors: Chehri Sarah , Henriksen Otto Mølby , Marner Lisbeth , Christensen Mette , Muhic Aida , Poulsen Hans Skovgaard , Law Ian 
Published: June 2024

Abstract
Background
O-(2-[18F]fluoroethyl)-l-tyrosine positron emission tomography ([18F]FET PET) scanning is used in routine clinical management and evaluation of gliomas with a recommended 4 h prior fasting. Knowledge of test–retest variation of [18F]FET PET imaging uptake metrics and the impact of accidental protein intake can be critical for interpretation. The aim of this study was to investigate the repeatability of [18F]FET-PET metrics and to assess the impact of protein-intake prior to [18F]FET PET scanning of gliomas.

Results
Test–retest variability in the non-protein group was good with absolute (and relative) upper and lower limits of agreement of + 0.15 and − 0.13 (+ 9.7% and − 9.0%) for mean tumour-to-background ratio (TBRmean), + 0.43 and − 0.28 (+ 19.6% and − 11.8%) for maximal tumour-to-background ratio (TBRmax), and + 2.14 cm3 and − 1.53 ml (+ 219.8% and − 57.3%) for biological tumour volume (BTV). Variation was lower for uptake ratios than for BTV. Protein intake was associated with a 27% increase in the total sum of plasma concentration of the l-type amino acid transporter 1 (LAT1) relevant amino acids and with decreased standardized uptake value (SUV) in both healthy appearing background brain tissue (mean SUV − 25%) and in tumour (maximal SUV − 14%). Oral intake of 24 g of protein 1 h prior to injection of tracer tended to increase variability, but the effects on derived tumour metrics TBRmean and TBRmax were only borderline significant, and changes generally within the variability observed in the group with no protein intake.

Conclusion
The test–retest repeatability was found to be good, and better for TBRmax and TBRmean than BTV, with the methodological limitation that tumour growth may have influenced results. Oral intake of 24 g of protein one hour before a [18F]FET PET scan decreases uptake of [18F]FET in both tumour and in healthy appearing brain, with no clinically significant difference on the most commonly used tumour metrics.
Diversity, composition, and structure of a 1-hectare tree plot in the cloud forest of the Sierra Nevada de Santa Marta, Colombia
Authors: Fortier Riley P. , Bernal-Escobar Manuel , Kullberg Alyssa T. , Osorio Ospina Juan Camilo , Herrera Medina Yeison , Aragón Lina , Palacios Hurtado Camilo , Contreras Maria Paula 
Published: June 2024

Abstract
Key Message
We present data from a new delimited 1-ha forest plot on the Sierra Nevada de Santa Marta in Colombia and describe its tree diversity, composition, and structure. This data can be used in regional analyses and help to refine remote sensing models. Future censuses will provide data on the demographics of rare, endangered, and endemic trees that can be used for their conservation. Dataset access is at https://doi.org/10.15472/ftwol2. Associated metadata are available at https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/a4a7855f-4cb2-459b-a1a2-287bd1e6d587.
The emerging and diverse roles of F-box proteins in spermatogenesis and male infertility
Authors: Zhuang Xuan , Ruan Jun , Zhou Canquan , Li Zhiming 
Published: June 2024

AbstractF-box proteins play essential roles in various cellular processes of spermatogenesis by means of ubiquitylation and subsequent target protein degradation. They are the substrate-recognition subunits of SKP1–cullin 1–F-box protein (SCF) E3 ligase complexes. Dysregulation of F‑box protein‑mediated proteolysis could lead to male infertility in humans and mice. The emerging studies revealed the physiological function, pathological evidence, and biochemical substrates of F-box proteins in the development of male germ cells, which urging us to review the current understanding of how F‑box proteins contribute to spermatogenesis. More functional and mechanistic study will be helpful to define the roles of F-box protein in spermatogenesis, which will pave the way for the logical design of F-box protein-targeted diagnosis and therapies for male infertility, as the spermatogenic role of many F-box proteins remains elusive.