bluuebunny/crossref_metadata_2025_split huggingface dataset:
LinkedImm: a linked data graph database for integrating immunological data
Authors: Bukhari Syed Ahmad Chan , Pawar Shrikant , Mandell Jeff , Kleinstein Steven H. , Cheung Kei-Hoi 
Published: August 2021

AbstractBackgroundMany systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Query Language) databases are popular in the biomedical domain, NoSQL database technologies have been used as a more relationship-based, flexible and scalable method of data integration.ResultsWe have created a graph database integrating data from multiple sources. In addition to using a graph-based query language (Cypher) for data retrieval, we have developed a web-based dashboard that allows users to easily browse and plot data without the need to learn Cypher. We have also implemented a visual graph query interface for users to browse graph data. Finally, we have built a prototype to allow the user to query the graph database in natural language.ConclusionWe have demonstrated the feasibility and flexibility of using a graph database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to discover novel relationships among heterogeneous biological data and metadata.
Metabolome and transcriptome analysis of flavor components and flavonoid biosynthesis in fig female flower tissues (Ficus carica L.) after bagging
Authors: Wang Ziran , Song Miaoyu , Wang Zhe , Chen Shangwu , Ma Huiqin 
Published: August 2021

Abstract
Background
Bagging can improve the appearance of fruits and increase the food safety and commodification, it also has effects on intrinsic quality of the fruits, which was commonly reported negative changes. Fig can be regarded as a new model fruit with its relatively small genome size and long fruit season.

Results
In this study, widely targeted metabolomics based on HPLC MS/MS and RNA-seq of the fruit tissue of the ‘Zibao’ fig before and after bagging were analyzed to reveal the metabolites changes of the edible part of figs and the underneath gene expression network changes. A total of 771 metabolites were identified in the metabolome analysis using fig female flower tissue. Of these, 88 metabolites (including one carbohydrate, eight organic acids, seven amino acids, and two vitamins) showed significant differences in fruit tissue before and after bagging. Changes in 16 structural genes, 13 MYB transcription factors, and endogenous hormone (ABA, IAA, and GA) metabolism and signal transduction-related genes in the biosynthesis pathway of flavonoids after bagging were analyzed by transcriptome analysis. KEGG enrichment analysis also determined significant differences in flavonoid biosynthesis pathways in female flower tissue before and after bagging.

Conclusions
This work provided comprehensive information on the composition and abundance of metabolites in the female flower tissue of fig. The results showed that the differences in flavor components of the fruit before and after bagging could be explained by changes in the composition and abundance of carbohydrates, organic acids, amino acids, and phenolic compounds. This study provides new insights into the effects of bagging on changes in the intrinsic and appearance quality of fruits.
The global, regional, and national burden of acute pancreatitis in 204 countries and territories, 1990–2019
Authors: Li Chang-li , Jiang Meng , Pan Chun-qiu , Li Jian , Xu Li-gang 
Published: August 2021

Abstract
Background
Acute pancreatitis is a common and potentially lethal gastrointestinal disease, but literatures for the disease burden are scarce for many countries. Understanding the current burden of acute pancreatitis and the different trends across various countries is essential for formulating effective preventive intervenes. We aimed to report the incidence, mortality, and disability-adjusted life-years (DALYs) caused by acute pancreatitis in 204 countries and territories between 1990 and 2019.

Methods
Estimates from the Global Burden of Disease Study 2019 (GBD 2019) were used to analyze the epidemiology of acute pancreatitis at the global, regional, and national levels. We also reported the correlation between development status and acute pancreatitis’ age-standardized DALY rates, and calculated DALYs attributable to alcohol etiology that had evidence of causation with acute pancreatitis. All of the estimates were shown as counts and age-standardized rates per 100,000 person-years.

Results
There were 2,814,972.3 (95% UI 2,414,361.3–3,293,591.8) incident cases of acute pancreatitis occurred in 2019 globally; 1,273,955.2 (1,098,304.6–1,478,594.1) in women and 1,541,017.1 (1,307,264.4–1,814,454.3) in men. The global age-standardized incidence rate declined from 37.9/100,000 to 34.8/100,000 during 1990–2019, an annual decrease of 8.4% (5.9–10.4%). In 2019, there were 115,053.2 (104,304.4–128,173.4) deaths and 3,641,105.7 (3,282,952.5–4,026,948.1) DALYs due to acute pancreatitis. The global age-standardized mortality rate decreased by 17.2% (6.6–27.1%) annually from 1.7/100,000 in 1990 to 1.4/100,000 in 2019; over the same period, the age-standardized DALY rate declined by 17.6% (7.8–27.0%) annually. There were substantial differences in the incidence, mortality and DALYs across regions. Alcohol etiology attributed to a sizable fraction of acute pancreatitis-related deaths, especially in the high and high-middle SDI regions.

Conclusion
Substantial variation existed in the burden of acute pancreatitis worldwide, and the overall burden remains high with aging population. Geographically targeted considerations are needed to tailor future intervenes to relieve the burden of acute pancreatitis in specific countries, especially for Eastern Europe.
Mixed adenoneuroendocrine carcinomas of stomach and ampulla of vater after curative-intent resection: a single center cases series
Authors: Yang Sishu , Lu Jiong , Cai Yulong , Li Bei , Xiong Xianze 
Published: August 2021

Abstract
Background
Mixed adenoneuroendocrine carcinoma is a rare clinical manifestation, especially in the gastric and ampullary. The purpose of this study was to investigate the clinicopathological features and prognosis of mixed adenoneuroendocrine carcinoma in the gastric and ampullary and summarize related treatment suggestions.

Methods
In all, 32 cases of mixed adenoneuroendocrine carcinoma in the gastric and ampullary that were diagnosed from resected specimens were analyzed from 2009 to 2015. The corresponding demographic, clinicopathological and survival data were retrospectively reviewed.

Results
The 1-year, 3-year and 5-year survival rates were 78.1%, 28.1 and 9.4%, respectively, and the median overall survival was 28.0 months. In all, 75.0% (24/32) had lymph node metastasis at the time of initial diagnosis. A multivariate analysis revealed that TNM stage (HR 6.444 95%CI 1.477–28.121 P = 0.013), lymph nodes metastasis (HR10.617 95%CI 1.409–79.997 P = 0.022), vascular invasion (HR 5.855 95%CI 1.719–19.940 P = 0.005), grade of the adenocarcinoma component (HR 3.876 95%CI 1.451–10.357 P = 0.007) and CD56 positivity (HR 0.265 95%CI 0.100–0.705 P = 0.008) were independent predictors of overall survival.

Conclusions
Mixed adenoneuroendocrine carcinoma is an aggressive clinical entity with a poor prognosis. Taking both the neuroendocrine component and the adenocarcinoma component into consideration of optimal treatment is strongly recommended.
Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology
Authors: Zhao Huan , Yang Yichao , Lyu Jiangfeng , Ren Xuyi , Cheng Wei 
Published: August 2021

Abstract
Background
Respiratory tract infections are the most common infections that lead to morbidity and mortality worldwide. Early recognition and precise diagnosis of microbial etiology is important to treat LRTIs promptly, specifically and effectively.

Objectives
To establish a method based on multiplex reverse transcription (MRT)-PCR and MassARRAY technology for the simultaneous detection of 27 respiratory pathogens and explore its clinical application value.

Methods
Analytical sensitivity and specificity of the MRT-PCR-MassARRAY system were validated using inactivated bacterial and viral strains. Also we analyzed samples from 207 patients by MassARRAY methods and compared the results with consensus PCR/reverse transcription (RT)-PCR.

Results
The minimum detection limit of our MRT-PCR-MassARRAY method for pathogens was 10–100 copies/μl, with high specificity. Comparison test with consensus PCR/RT-PCR on 207 clinical samples, the positive, negative, and total correlation rates were 100, 98.68, and 99.03%, respectively. There was a high degree of agreement between the test results of the two methods (P < 0.01 by McNemar’s test).

Conclusion
Our detection system of 27 respiratory pathogens based on MassARRAY technology has high sensitivity and specificity, high throughput, and is simple to operate. It provides diagnostic value for the clinical diagnosis of respiratory pathogens and is of great significance in the screening of respiratory pathogens.
Low Seroprevalence of SARS-CoV-2 in Rhode Island blood donors during may 2020 as determined using multiple serological assay formats
Authors: Nesbitt Daniel J. , Jin Daniel P. , Hogan Joseph W. , Yang Jenny , Chen Haidee , Chan Philip A. , Simon Melissa J. , Vargas Matthew , King Ewa , Huard Richard C. , Bandy Utpala , Hillyer Christopher D. , Luchsinger Larry L. 
Published: August 2021

Abstract
Background
Epidemic projections and public health policies addressing Coronavirus disease (COVID)-19 have been implemented without data reporting on the seroconversion of the population since scalable antibody testing has only recently become available.

Methods
We measured the percentage of severe acute respiratory syndrome- Coronavirus-2 (SARS-CoV-2) seropositive individuals from 2008 blood donors drawn in the state of Rhode Island (RI). We utilized multiple antibody testing platforms, including lateral flow immunoassays (LFAs), enzyme-linked immunosorbent assays (ELISAs) and high throughput serological assays (HTSAs). To estimate seroprevalence, we utilized the Bayesian statistical method to adjust for sensitivity and specificity of the commercial tests used.

Results
We report than an estimated seropositive rate of RI blood donors of approximately 0.6% existed in April–May of 2020. Daily new case rates peaked in RI in late April 2020. We found HTSAs and LFAs were positively correlated with ELISA assays to detect antibodies specific to SARS-CoV-2 in blood donors.

Conclusions
These data imply that seroconversion, and thus infection, is likely not widespread within this population. We conclude that IgG LFAs and HTSAs are suitable to conduct seroprevalence assays in random populations. More studies will be needed using validated serological tests to improve the precision and report the kinetic progression of seroprevalence estimates.
Different resting-state network disruptions in newly diagnosed drug-naïve Parkinson’s disease patients with mild cognitive impairment
Authors: Hou Yanbing , Wei Qianqian , Ou Ruwei , Zhang Lingyu , Yuan Xiaoqin , Gong Qiyong , Shang Huifang 
Published: August 2021

Abstract
Background
Cognitive impairment is a common non-motor symptom in patients with Parkinson’s disease (PD). Mild cognitive impairment (MCI) is also prevalent in nondemented PD patients, even in newly diagnosed PD patients. The possible impacts of MCI on brain function activities for PD patients need more investigation, and the potential of emerging technologies for detecting underlying pathophysiology of cognitive signs in PD can be further improved.

Method
Forty-seven newly diagnosed drug-naïve PD patients (28 PD-MCI patients and 19 PD patients with cognitively unimpaired (PD-CU)) and 28 healthy controls (HCs) underwent resting-state functional MRI. The connectivity patterns of specific networks were investigated through the independent component analysis among PD-MCI, PD-CU and HCs groups.

Results
The independent component analysis revealed significantly decreased functional connectivity (FC) of the default mode network, visual network and sensorimotor network in the PD-MCI subgroup compared with the HC group. Furthermore, FC of the default mode network was positively correlated with memory scores from the brief visuospatial memory test-revised, and FC of the visual network was positively correlated with visuospatial scores from the clock copying test in the PD-MCI group. In all patients with PD, FC of the sensorimotor network negatively correlated with motor severity scores from the Unified PD Rating Scale (UPDRS) part III. On the other hand, the potential damage was more likely to occur in FC between the sensorimotor network and limbic network, and between the ventral attention network and visual network in all PD patients.

Conclusions
Newly diagnosed drug-naïve PD-MCI patients showed characteristic damage of FC within the default mode network, visual network and sensorimotor network, and all PD patients presented impaired FC between the sensorimotor network and limbic network, and FC between the ventral attention network and visual network. These network-wide functional aberrations may underline the pathophysiology of PD.
Barriers and facilitators in cervical cancer screening uptake in Abidjan, Côte d'Ivoire in 2018: a cross-sectional study
Authors: Boni Simon P. , Gnahatin Franck , Comoé Jean-Claude , Tchounga Boris , Ekouevi Didier , Horo Apollinaire , Adoubi Innocent , Jaquet Antoine 
Published: August 2021

Abstract
Backgrounds
Cervical cancer (CC) incidence remains unacceptably high in Côte d’Ivoire. In an effort to prevent this malignant condition, a national CC screening program has been scaled up in the country. This study aimed at assessing CC screening uptake and its associated factors in Abidjan in 2018.

Methods
A cross-sectional survey was conducted from July to September 2018 in the main healthcare facilities of three randomly selected out of the eight health districts of Abidjan. During the study period, a standardized questionnaire was administrated by research assistants to all women aged 25 to 55 years old, attending the three participating facilities. Demographics, knowledge on CC, personal history of CC screening and reasons for not attending CC screening were collected. A logistic regression model was computed to document factors associated with reported CC screening uptake.

Results
A total of 1158 women with a median age of 32 years (IQR [27–36]), including 364 (31.4%) with no formal education were included. Of those participants, 786 (67.9%) had ever heard about CC. CC screening uptake at least once was reported by 7.5% [95% CI: 6.0–9.0] participants. In multivariable analysis, being ≥45 years (aOR: 6.2 [2.3–17.2]), having a university level (aOR: 2.8 [1.2–6.6]) (versus non formal education) and access to mass campaign information (aOR: 18.2 [8.5–39.1]) were associated with a reported CC screening uptake. The main reported barriers to CC screening were unawareness towards CC screening (75.5%), negligence (20.5%), fear of CC detection (3.9%) and fear of additional costs (3.3%).

Conclusion
CC screening uptake remains low despite current initiatives to support awareness and prevention in Abidjan. Awareness campaigns need to be massively increased with the adjunction of tailored messages based on the level of women’s education to enhance the CC screening coverage and reach the WHO goal of CC elimination by 2030.
Effect of acute and chronic liver diseases on the thyroid function in children
Authors: Bebars Gihan M. , Sayed Madeha A. , Hamdy Lamia , Abdel Aziz Reem A. 
Published: August 2021

Abstract
Background
Thyroid hormones modulate hepatic function through regulation of basal metabolic rate in addition; the liver metabolizes the thyroid hormones and regulates their endocrine effects.

Objectives
To assess thyroid functions in children with acute and chronic liver diseases.

Methods
85 studied children were divided into 4 groups; group 1 (20 children) with acute hepatitis (AH), group 2 (20 children) chronic liver disease1 (CLD1; relatively preserved liver functions including Child-Pugh stage A), group 3 (20 children) chronic liver disease2 (CLD2; includes Child-Pugh stage B or C), group 4 (25 children) controls. All groups were subjected to detailed history, physical examination, Complete blood count, liver, renal function tests, viral markers, and thyroid functions (FT3, FT4, TSH).

Results
Free T3 levels were lower in children with AH, CLD1 and CLD2. There was significant increase in TSH serum levels in CLD2.In acute hepatitis a negative correlation between serum free T4 and AST (r = -0.991), positive correlation between serum TSH and AST, VLDL, and cholesterol levels (r= 0.503, 0.533 and 0.498). A positive correlation between free T3 levels and prothrombin concentration (r= 0.991). Negative correlations between free T3 levels and PT, serum bilirubin and LDL serum levels in children with CLD2 (r= -0.992) (r= -0.902) and (r= -0.946)

Conclusion
Acute and chronic liver diseases affect thyroid function in children and is correlated with the disease severity.
Ethnic group differences in obesity in Asian Americans in California, 2013–2014
Authors: Gong Shaoqing , Wang Kesheng , Li Ying , Zhou Zhongliang , Alamian Arsham 
Published: August 2021

AbstractBackgroundObesity has been generally understudied in Asian Americans. It is important to identify subgroups of Asian Americans at high risk of obesity to help develop targeted interventions for those subgroups. This study aimed to examine the disparities in obesity among Asians (i.e., Chinese, Filipino, Japanese, Korean, and Vietnamese) living in California.MethodsA sample of Adult Americans in California (n = 47,970) including Asian American adults (n = 3810) aged 18 years or older were obtained from the 2013–2014 California Health Interview Survey (the U.S. nation’s largest state cross-sectional health survey). Body mass index was calculated using self-reported height and weight. Weight status was determined using the WHO Asian BMI cut points in 4 categories: < 18.5 kg/m2(underweight), 18.5–22.9 kg/m2(normal weight), 23–27.5 kg/m2(overweight), and ≥ 27.5 kg/m2(obese). Multiple logistic regression analyses were used to estimate odds ratio (OR) and 95% confidence interval (CI) after adjustment for covariates.ResultsOverall, the prevalence of Asians was 23.3% for obesity and 40.0% for overweight. The obesity prevalence was higher in Asians who were males, aged 45–64 years old, had higher family income, were current smokers, never got married, had lower education level, had an insufficient level of physical activity, and had more frequent consumption of fast foods. After adjusting for other factors, compared to Whites, being Hispanics and Blacks were associated with higher odds of obesity (OR = 1.47, 95%CI = 1.31–1.65; OR = 2.04, 95%CI = 1.65–2.53, respectively); being Chinese, Korean, and Vietnamese were associated with lower odds of obesity (OR = 0.28, 95%CI = 0.18–0.45; OR = 0.14, 95%CI = 0.04–0.46; OR = 0.28, 95%CI = 0.14–0.58, respectively). Compared to Chinese, being Japanese and Filipino were associated with higher odds of obesity (OR = 2.75, 95%CI = 1.52–4.95; OR = 2.90, 95%CI = 1.87–4.49, respectively).ConclusionsThe prevalence of adult obesity was high among Asian Americans in California. Ethnic/racial disparities in obesity among Asian Americans in California were observed in 2013–2014. Compared to Whites, being Chinese, Korean, Vietnamese were associated with lower odds of obesity. Among Asians, compared to Chinese, being Japanese and being Filipino were associated with higher odds of obesity. These findings can help design better interventions to reduce racial and ethnic disparities in obesity, especially for Asian Americans.
FGF-2 promotes angiogenesis through a SRSF1/SRSF3/SRPK1-dependent axis that controls VEGFR1 splicing in endothelial cells
Authors: Jia Tao , Jacquet Thibault , Dalonneau Fabien , Coudert Pauline , Vaganay Elisabeth , Exbrayat-Héritier Chloé , Vollaire Julien , Josserand Véronique , Ruggiero Florence , Coll Jean-Luc , Eymin Béatrice 
Published: August 2021

Abstract
Background
Angiogenesis is the process by which new blood vessels arise from pre-existing ones. Fibroblast growth factor-2 (FGF-2), a leading member of the FGF family of heparin-binding growth factors, contributes to normal as well as pathological angiogenesis. Pre-mRNA alternative splicing plays a key role in the regulation of cellular and tissular homeostasis and is highly controlled by splicing factors, including SRSFs. SRSFs belong to the SR protein family and are regulated by serine/threonine kinases such as SRPK1. Up to now, the role of SR proteins and their regulators in the biology of endothelial cells remains elusive, in particular upstream signals that control their expression.

Results
By combining 2D endothelial cells cultures, 3D collagen sprouting assay, a model of angiogenesis in cellulose sponges in mice and a model of angiogenesis in zebrafish, we collectively show that FGF-2 promotes proliferation, survival, and sprouting of endothelial cells by activating a SRSF1/SRSF3/SRPK1-dependent axis. In vitro, we further demonstrate that this FGF-2-dependent signaling pathway controls VEGFR1 pre-mRNA splicing and leads to the generation of soluble VEGFR1 splice variants, in particular a sVEGFR1-ex12 which retains an alternative last exon, that contribute to FGF-2-mediated angiogenic functions. Finally, we show that sVEGFR1-ex12 mRNA level correlates with that of FGF-2/FGFR1 in squamous lung carcinoma patients and that sVEGFR1-ex12 is a poor prognosis marker in these patients.

Conclusions
We demonstrate that FGF-2 promotes angiogenesis by activating a SRSF1/SRSF3/SRPK1 network that regulates VEGFR1 alternative splicing in endothelial cells, a process that could also contribute to lung tumor progression.