bluuebunny/crossref_metadata_2025_split huggingface dataset:
CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas
Authors: Chen Yaxin , Wang Gang , Li Jingyi , Xia Lei , Zhu Lin , Li Wenxing , Luo Qiang , Liao Yinlu , Lin Yao , Bi Liyun , Chen Hubin , Chu Jiemei , Li Yueqi , Su Jinming , Ye Li , Jiang Jun-jun , Liang Hao , Li Weimin , An Sanqi 
Published: October 2022

Abstract
Background
As a key process in transcriptional regulatory mechanisms, alternative splicing (AS) plays a crucial role in maintaining the diversity of RNA and protein expression, and mediates the immune response in infectious diseases, especially for the COVID-19. Therefore, urgent data gathering and more research of AS profiles in microbe-infected human cells are needed to improve understanding of COVID-19 and related infectious diseases. Herein, we have created CASA, the COVID-19 Alternative Splicing Atlas to provide a convenient computing platform for studies of AS in COVID-19 and COVID-19-related infectious diseases.

Methods
In CASA, we reanalyzed thousands of RNA-seq datasets generated from 65 different tissues, organoids and cell lines to systematically obtain quantitative data on AS events under different conditions. A total of 262,994 AS events from various infectious diseases with differing severity were detected and visualized in this database. In order to explore the potential function of dynamics AS events, we performed analysis of functional annotations and drug-target interactions affected by AS in each dataset. RNA-binding proteins (RBPs), which may regulate these dynamic AS events are also provided for users in this database.

Results
CASA displays microbe-induced alterations of the host cell splicing landscape across different virus families and helps users identify condition-specific splicing patterns, as well as their potential regulators. CASA may greatly facilitate the exploration of AS profiles and novel mechanisms of host cell splicing by viral manipulation. CASA is freely available at http://www.splicedb.net/casa/.
Novel pathogenic variants in CUBN uncouple proteinuria from renal function
Authors: Gan Chun , Zhou Xindi , Chen Dan , Chi Huan , Qiu Jiawen , You Hui , Chen Yaxi , Wang Mo , Yang Haiping , Jiang Wei , Li Qiu 
Published: October 2022

Abstract
Background
Proteinuria is an unfavorable clinical condition highly associated with a risk of renal and cardiovascular disease in chronic kidney disease (CKD). However, whether all proteinuria forms are linked to renal impairment are still unclear. Cubilin is an endocytic receptor highly expressed in renal proximal tubules mediating uptake of albumin, transferrin and α1-microglobulin.

Methods
Exome sequencing method initially identified candidate genes. With the application of exome sequencing combined with Sanger sequencing, we further focused on CUBN through bioinformatics analysis. The pathogenic effects of the potentially causative variants were verified utilizing complementary analysis of clinical data and systematic characterization of the variants’ expression and function with clinical samples and in vitro experiments in HEK293T cell lines along with in vivo experiments in mice.

Results
In this study, we identified four novel variants locating after the vitamin B12 (vitB12)-binding domain of Cubilin (encoded by CUBN, NM_001081.3: c.4397G > A (p.C1466Y), c.6796C > T (p.R2266X), c.6821 + 3A > G and c.5153_5154delCT (p.S1718X)) in two families. Moreover, the variants severely affected the expression and function of Cubilin in renal proximal tubules and caused albuminuria, increasing levels in urine transferrin and α1-microglobulin, but without progressive glomerular filtration barrier (GFB) impairment, vitB12 deficiencies or abnormal blood levels of HDL and albumin. Further mechanistic insights showed that the variants after the vitB12-binding domain of CUBN merely disrupted the association with Amnionless (AMN) that exhibited aberrant localization in cell cytoplasm rather than membrane.

Conclusions
Here, our findings suggested that different mutation types after the vitB12-binding domain of CUBN uncouple proteinuria from glomerular filtration barrier, that may be an unexpectedly common benign condition in humans and may not require any proteinuria-lowering treatment or renal biopsy.
The influence of 10-year Nuss bar placement on bar removal: a case report
Authors: Gu Haihua , Xu Guanxin , Liu Tianshu , Zhang Sai 
Published: October 2022

Abstract
Background
The Nuss bar is commonly used for minimally invasive correction of pectus excavatum and is usually removed within 2–3 years. Here, we report a case of 10-year bar placement after the Nuss procedure accompanied by unique complications of thoracic malformation that have not been described before. The asymmetric pectus carinatum caused by bar displacement and significant rib periosteal hyperplasia is described for the first time.

Case presentation
A 23-year-old man was admitted to our hospital due to the main complaint of obvious chest discomfort when lifting heavy weights. The bar removal was seriously delayed due to his loss to follow-up. Chest asymmetry and distant heart sounds were found during a physical examination. A chest CT scan demonstrated that the right end of the lower bar originally fixed outside the ribs had shifted into the thoracic cavity, and the left costal cartilage was obviously protruding. Additionally, the displaced bars were separated from the sternum and tightly attached to the pericardium, resulting in abnormalities of the anterior mediastinum. These secondary thoracic deformities made the patient extremely prone to massive hemorrhage or multiple rib fractures when sliding the bars out. However, serious consequences were avoided due to reasonable adjustments to the usual bar removal procedures.

Conclusion
This case demonstrates a specific type of bar displacement caused by prolonged placement of the bars and highlights the importance of rigorous follow-up of patients after the Nuss procedure.
Development and clinical validation of CT-based regional modified Centiloid method for amyloid PET
Authors: Kim Soo-Jong , Ham Hongki , Park Yu Hyun , Choe Yeong Sim , Kim Young Ju , Jang Hyemin , Na Duk L. , Kim Hee Jin , Moon Seung Hwan , Seo Sang Won 
Published: October 2022

Abstract
Background
The standard Centiloid (CL) method was proposed to harmonize and quantify global 18F-labeled amyloid beta (Aβ) PET ligands using MRI as an anatomical reference. However, there is need for harmonizing and quantifying regional Aβ uptakes between ligands using CT as an anatomical reference. In the present study, we developed and validated a CT-based regional direct comparison of 18F-florbetaben (FBB) and 18F-flutemetamol (FMM) Centiloid (rdcCL).

Methods
For development of MRI-based or CT-based rdcCLs, the cohort consisted of 63 subjects (20 young controls (YC) and 18 old controls (OC), and 25 participants with Alzheimer’s disease dementia (ADD)). We performed a direct comparison of the FMM-FBB rdcCL method using MRI and CT images to define a common target region and the six regional VOIs of frontal, temporal, parietal, posterior cingulate, occipital, and striatal regions. Global and regional rdcCL scales were compared between MRI-based and CT-based methods. For clinical validation, the cohort consisted of 2245 subjects (627 CN, 933 MCI, and 685 ADD).

Results
Both MRI-based and CT-based rdcCL scales showed that FMM and FBB were highly correlated with each other, globally and regionally (R2 = 0.96~0.99). Both FMM and FBB showed that CT-based rdcCL scales were highly correlated with MRI-based rdcCL scales (R2 = 0.97~0.99). Regarding the absolute difference of rdcCLs between FMM and FBB, the CT-based method was not different from the MRI-based method, globally or regionally (p value = 0.07~0.95). In our clinical validation study, the global negative group showed that the regional positive subgroup had worse neuropsychological performance than the regional negative subgroup (p < 0.05). The global positive group also showed that the striatal positive subgroup had worse neuropsychological performance than the striatal negative subgroup (p < 0.05).

Conclusions
Our findings suggest that it is feasible to convert regional FMM or FBB rdcSUVR values into rdcCL scales without additional MRI scans. This allows a more easily accessible method for researchers that can be applicable to a variety of different conditions.
Liver resection in a patient with persistent positive PCR test for coronavirus disease 2019 (COVID-19): a case report
Authors: Sugita Akiho , Inagaki Fuyuki F. , Takemura Nobuyuki , Nakamura Mai , Ito Kyoji , Mihara Fuminori , Yamamoto Kei , Morioka Shinichiro , Kokudo Norihiro 
Published: October 2022

Abstract
Background
The perioperative mortality rate is high in patients with coronavirus disease 2019 (COVID-19), and infection control measures for medical care providers must be considered. Therefore, the timing for surgery in patients recovering from COVID-19 is difficult.

Case presentation
A 65-year-old man was admitted to a hospital with a diagnosis of moderate COVID-19. He was transferred to our hospital because of risk factors, including heavy smoking history, type 2 diabetes mellitus, and obesity (BMI 34). Vital signs on admission were a temperature of 36.1 °C, oxygen saturation > 95% at rest, and 94% on exertion with 3 L/min of oxygen. Chest computed tomography (CT) showed bilateral ground-glass opacities, predominantly in the lower lungs. Contrast-enhanced abdominal CT incidentally revealed a liver tumor with a diameter of 80 mm adjacent to the middle hepatic vein, which was diagnosed as hepatocellular carcinoma (HCC). After being administered baricitinib, remdesivir, dexamethasone, and heparin, the patient’s COVID-19 pneumonia improved, his oxygen demand resolved, and he was discharged on day 13. Furthermore, the patient was initially scheduled for hepatectomy 8 weeks after the onset of COVID-19 following a discussion with the infection control team. However, 8 weeks after the onset of illness, a polymerase chain reaction (PCR) test was performed on nasopharyngeal swab fluid, which was observed to be positive. The positive results persisted till 10 and 11 weeks after onset. Both Ct values were high (≥ 31) out of 45 cycles, with no subjective symptoms. Since we determined that he was no longer contagious, surgery was performed 12 weeks after the onset of COVID-19. Notably, medical staff wearing personal protective equipment performed extended anatomical resection of the liver segment 8 ventral area in a negative-pressure room. The patient had a good postoperative course, with no major complications, including respiratory complications, and was discharged on postoperative day 14. Finally, none of the staff members was infected with COVID-19.

Conclusions
We reported a case regarding the timing of surgery on a patient with persistently positive PCR test results after COVID-19, along with a literature review.
The Food and Nutrition Security for Manitoba Youth (FANS) study: rationale, methods, dietary intakes and body mass index
Authors: Slater Joyce , Pilli Bhanu , Hinds Aynslie , Katz Alan , Urquia Marcelo L. , Sanguins Julianne , Green Chris , Cidro Jaime , Chateau Dan , Nickel Nathan 
Published: October 2022

Abstract
Background
Good nutrition and access to healthy foods are essential for child growth and development. However, there are concerns that Canadian children do not have a healthy diet, which may be related to dietary choices as well as lack of access to healthy foods. The FANS (Food and Nutrition Security for Children and Youth) study examined the nutrition and food security status of youth in the province of Manitoba, Canada. This paper describes methods, dietary intakes, and body mass index for the FANS study.

Methods
This cross-sectional study included 1587 Manitoba grade nine students who completed a self-administered web-based survey. Data was collected on demographic characteristics, dietary intake (24-h recall), food behaviors, food security, and self-report health indicators. Dietary data was compared to national dietary guidelines (Dietary Reference Intakes and Canada’s Food Guide). Mean and median nutrient and food group intakes were calculated with corresponding measures of variability. Chi-square tests compared percentage of respondents not meeting key nutrients and food groups. Significant differences in percentage of total servings for each food group were determined by a Kruskal–Wallis test, and differences between different caloric groups were assessed using Dunn’s test for post-hoc comparisons.

Results
Half of study respondents were female (50.5%). Median energy intake was higher in males (2281 kcal) compared with females (1662 kcal), with macronutrient distribution of 52%, 16%, and 32% for carbohydrates, protein, and fats respectively. Most participants consumed inadequate fibre (94%), vitamin D (90%), and calcium (73%), while median sodium intakes exceeded recommendations for males but not females. A majority of participants did not meet Health Canada’s recommendations for food group servings: Vegetables and Fruit (93%), Milk and Alternatives (74%), Meat and Alternatives (57%) and Grain Products (43%). Other Foods, including sugar sweetened beverages and juice, were consumed by most participants. Higher energy consumers had a greater proportion of food servings coming from Other Foods. 72.1% of students were classified as having a healthy weight and 25% were classified as overweight or obese.

Conclusion
Poor dietary intakes and body mass index values indicate an urgent need for policy and program strategies to support healthy eating habits and food awareness in Manitoba youth.
How is the Topic of Intersex Athletes in Elite Sports Positioned in Academic Literature Between January 2000 and July 2022? A Systematic Review
Authors: Jensen Marisa , Schorer Jörg , Faber Irene R. 
Published: October 2022

AbstractBackgroundWithin the topic of intersex athletes in elite sports, science has become a decisive factor in decision- and policy-making. However, in the academic literature approaches to this topic vary. An overview of these approaches is proposed to provide better insight into relevant aspects and underlying values and may serve as a starting point on the path toward a solid solution of the question of categorization of intersex athletes in elite sporting competition.ObjectiveThis systematic review aims to discover how the topic of intersex elite athletes is positioned in the academic literature from January 2000 to July 2022 from a neutral perspective.MethodsA comprehensive search in eleven databases using the search terms [intersex* and sport*] yielded 87 articles. A qualitative content analysis was conducted to find all authors’ statements including perspectives on intersex athletes and proposals for solutions. Underlying values were extracted and connected to each other during axial coding.ResultsThe results provide an overview of the sometimes-contradictory perspectives toward intersex elite athletes and proposals for solutions. Three core values were distilled: social justice for intersex elite athletes, competition fairness, and evidence-based practice. The authors’ statements disclose an interaction/conflict between social justice and competition fairness.ConclusionsThe results raise an important discussion on the role of science within the topic of intersex elite athletes. A multidisciplinary approach including scientists and other experts is suggested to find an appropriate solution. Additionally, more awareness on intersex variations is needed for a better overall understanding and to ensure a respectful approach for everyone involved.
BCG downregulates PD1 and PD-L1 expression in bladder cancer cells co-cultivated with peripheral blood mononuclear cells
Authors: Leite Katia R. M. , Morais Denis Reis , Massoco Cristina , Reis Sabrina T. , Viana Nayara I. , Silva Iran A. , Guimaraes Vanessa , Pimenta Ruan , Arantes Gabriel , Srougi Miguel , Nahas Willian Carlos 
Published: October 2022

Abstract
Purpose
BCG is the standard of care to treat high risk non-muscle invasive bladder cancer (NMIBC), reducing recurrence. PD-L1 is a ligand of the co-inhibitory receptor PD1 that has been shown to be expressed by tumor cells of distinct origin related to unfavorable prognosis. The development of a new class of target drugs that inhibit PD-L1 and PD1 has opened a new perspective for urothelial cancer treatment. Although there are few studies searching for the role of BCG over PD1 and PD-L1, many clinical trials are in course using the immune checkpoint inhibitors together with BCG as a new regime to treat NMIBC.

Material and methods
We analyzed the expression of PD1 and PD-L1 using qRT-PCR in RT4 bladder cancer (BCa) epithelial cells co-cultivated with peripheral blood mononuclear cells (PBMC) after treatment with BCG.

Results
There was a significantly reduction in PD1 and PD-L1 expression by BCa epithelial cells after BCG treatment. In PBMC PD1 was significantly overexpressed.

Conclusion
Our results suggest that one of the mechanisms related to the success of BCG in reducing tumor recurrence in NMIBC may be related to the negative control of PD1 and PD-L1 in tumor cells.
A systems biology approach for investigating significantly expressed genes among COVID-19, hepatocellular carcinoma, and chronic hepatitis B
Authors: Sokouti Babak 
Published: October 2022

Abstract
Background
Worldwide, COVID-19’s death rate is about 2%, considering the incidence and mortality. However, the information on its complications in other organs, specifically the liver and its disorders, is limited in mild or severe cases. In this study, we aimed to computationally investigate the typical relationships between liver-related diseases [i.e., hepatocellular carcinoma (HCC), and chronic hepatitis B (CHB)] and COVID-19, considering the involved significant genes and their molecular mechanisms.

Methods
We investigated two GEO microarray datasets (GSE164805 and GSE58208) to identify differentially expressed genes (DEGs) among the generated four datasets for mild/severe COVID-19, HCC, and CHB. Then, the overlapping genes among them were identified for GO and KEGG enrichment analyses, protein–protein interaction network construction, hub genes determination, and their associations with immune cell infiltration.

Results
A total of 22 significant genes (i.e., ACTB, ATM, CDC42, DHX15, EPRS, GAPDH, HIF1A, HNRNPA1, HRAS, HSP90AB1, HSPA8, IL1B, JUN, POLR2B, PTPRC, RPS27A, SFRS1, SMARCA4, SRC, TNF, UBE2I, and VEGFA) were found to play essential roles among mild/severe COVID-19 associated with HCC and CHB. Moreover, the analysis of immune cell infiltration revealed that these genes are mostly positively correlated with tumor immune and inflammatory responses.

Conclusions
In summary, the current study demonstrated that 22 identified DEGs might play an essential role in understanding the associations between the mild/severe COVID-19 patients with HCC and CHB. So, the HCC and CHB patients involved in different types of COVID-19 can benefit from immune-based targets for therapeutic interventions.
Right ventricular function as a predictor of short-term mortality in patients with sepsis and septic shock: an observational study
Authors: Bendary Ahmed , Said Hany , Elemary Metwally , Mahrous Mohamed 
Published: October 2022

Abstract
Background
In recent years, attention has shifted to the role of right ventricular (RV) dysfunction in prediction of clinical outcome among patients with septic shock. However, very few studies have correlated RV dysfunction with survival early in the course of sepsis. In the period from September 2021 to July 2022, we included a total number of 248 patients within 24 h of their presentation with sepsis. All patients were subjected to a comprehensive echocardiographic study to evaluate different parameters of RV function and LV systolic and diastolic functions. We aimed primarily to study the predictive value of RV dysfunction on 30-day all-cause mortality rates and ventilator-free days.

Results
Almost half of study population (48.4%) showed evidence of RV dysfunction (in isolation or with LV dysfunction), with 25.4% showing evidence of isolated RV dysfunction. Patients with RV dysfunction had a significantly higher APACHE 2 (P < 0.001) score and 30-day all-cause mortality rates (P = 0.003) compared to those without RV dysfunction. A significant association was reported between 30-d mortality and dysfunction status (P = 0.025). Those with no dysfunction had lower mortality (14.1%) than in those with RV dysfunction only (33.3%), LV dysfunction only (20%), and RV + LV dysfunction (31.6%). No significant difference was observed in ventilator free days according to dysfunction status (P = 0.081). A multivariate logistic regression analysis showed that RV dysfunction was among the significant independent predictors for 30-day mortality (OR 2.01, 95% CI 1.07–3.81, P = 0.031), controlling for the effect of age and gender.

Conclusions
In a cohort of ICU patients with early sepsis, RV dysfunction is found to be common and predictive of 30-day mortality irrespective to the LV function.
Emerging biomarkers for the detection of cardiovascular diseases
Authors: Thupakula Sreenu , Nimmala Shiva Shankar Reddy , Ravula Haritha , Chekuri Sudhakar , Padiya Raju 
Published: October 2022

AbstractBackgroundThe prevalence of cardiovascular disease (CVD) has been continuously increasing, and this trend is projected to continue. CVD is rapidly becoming a significant public health issue. Every year there is a spike in hospital cases of CVD, a critical health concern in lower- and middle-income countries. Based on identification of novel biomarkers, it would be necessary to study and evaluate the diagnostic requirements or CVD to expedite early detection.Main bodyThe literature review was written using a wide range of sources, such as well-known medical journals, electronic databases, manuscripts, texts, and other writings from the university library. After that, we analysed the specific markers of CVD and compiled a systematic review. A growing body of clinical research aims to identify people who are at risk for cardiovascular disease by looking for biomolecules. A small number of biomarkers have been shown to be useful and reliable in medicine. Biomarkers can be used for a variety of clinical applications, such as predicting heart disease risk, diagnosing disease, or predicting outcomes. As a result of the ability for a single molecule to act as a biomarker, its usefulness in medicine is expected to increase significantly.ConclusionsBased on assessing the current trends in the application of CVD markers, we discussed and described the requirements for the application of CVD biomarkers in coronary heart disease, cerebrovascular disease, rheumatic heart disease, and other cardiovascular illnesses. Furthermore, the current review focuses on biomarkers for CVD and the procedures that should be considered to establish the comprehensive nature of the expression of biomarkers for cardiovascular illness.