bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibroblast growth factor 21 is associated with increased serum total antioxidant capacity and oxidized lipoproteins in humans with different stages of chronic kidney disease
Authors: Gómez-Sámano Miguel Ángel , Vargas-Abonce Valerie Paola , Martínez-Sánchez Froylan David , Palacios-Báez Lucía , Vera-Zertuche Juan Mauricio , Navarro-Flores María Fernanda , Morales-García Mariana Guadalupe , Fonseca-Correa Jorge Ignacio , Zuarth-Vázquez Julia María , Vega-Vega Olynka , Correa-Rotter Ricardo , Rincón-Pedrero Rodolfo , Morales-Buenrostro Luis E. , Alberú-Gómez Josefina , Ramírez-González Julia Berenice , Pacheco-Domínguez Reyna Lizette , López-Cervantes Malaquías , Mendoza-de-la-Garza María de los Ángeles , Baeza-Arias Yolanda Victoria , Espinosa-Cuevas Ángeles , López-Carrasco Guadalupe , López-Estrada Angelina , Guillén-Pineda Luz Elizabeth , Gómez-Pérez Francisco Javier , Cuevas-Ramos Daniel 
Published: March 2021

Background and aims: Oxidative stress (OS) induces the production of fibroblast growth factor 21 (FGF21). Previous data have revealed that FGF21 protects cells from OS injury and death, making it a potential therapeutic option for many diseases with increased OS. However, the association of this growth factor with OS markers in humans with chronic kidney disease (CKD) remains unknown. This study aims to evaluate the association of serum FGF21 with serum total antioxidant capacity (TAC) and oxidized low-density lipoproteins (OxLDL) in subjects in different stages of kidney disease. Methods: This is a cross-sectional study that included 382 subjects with different stages of CKD, irrespective of type 2 diabetes (T2D) diagnosis. Associations of serum FGF21 with OxLDL, TAC, sex, age, body mass index (BMI), fasting plasma glucose, estimated glomerular filtration rate (eGFR), T2D, and smoking, were evaluated through bivariate and partial correlation analyses. Independent associations of these variables with serum FGF21 were evaluated using multiple linear regression analysis. Results: Serum FGF21 was significantly and positively correlated with age ( r = 0.236), TAC (lnTAC) ( r = 0.217), and negatively correlated with eGFR ( r = −0.429) and male sex ( r = −0.102). After controlling by age, sex, BMI, T2D, smoking, and eGFR; both TAC and OxLDL were positively correlated with FGF21 ( r = 0.117 and 0.158 respectively, p < 0.05). Using multiple linear regression analysis, eGFR, male sex, T2D, OxLDL, and TAC were independently associated with serum FGF21 (STDβ = −0.475, 0.162, −0.153, 0.142 and 0.136 respectively; p < 0.05 for all) adjusted for age, BMI, smoking, and fasting plasma glucose. Conclusion: A positive association between serum FGF21 and OS has been found independently of renal function in humans. Results from the present study provide novel information for deeper understanding of the role of FGF21 in OS in humans with CKD and T2D; mechanistic studies to explain the association of serum FGF21 with oxidative stress in CKD are needed.
Posterior tibial slope is a modifiable predictor of relatively large extension gaps in total knee arthroplasty for degenerative osteoarthritis
Authors: Shin Kyun-Ho , Kim Sang-Bum , Jang Ki-Mo , Lee Chul-Soo , Han Seung-Beom 
Published: March 2021

Background: During total knee arthroplasty (TKA) for osteoarthritis, the sagittal gap imbalance (SGI) with a relatively large extension gap is an important surgical challenge. We determined the predictors of SGI with a relatively large extension gap and evaluated the surgical outcomes of knees with SGI. Methods: 551 consecutive cases of primary TKA for osteoarthritis were retrospectively reviewed. The cohort was divided into two groups according to the SGI and statistically matched according to baseline characteristics via the inverse probability of treatment weighting method. Multiple linear and logistic regression analyses were performed to determine the predictors of sagittal gap difference (SGD) and SGI. Intergroup differences in clinical and radiological outcomes were analyzed. Results: Of all the knees included, 8.5% (n = 45) presented with SGI with a relatively large extension gap and required femoral sagittal balancing to manage SGI. The hyperextension angle (HA), preoperative joint line convergence angle (JLCA), and the change in posterior tibial slope (PTS) significantly correlated to SGD and predicted SGI with a relatively large extension gap. SGI group showed significant changes in femoral posterior condylar offset and joint line height compared to those without SGI (1.48 vs −0.45, 1.37 vs −0.51, respectively). Postoperative ROM and knee society knee scores were lower in SGI group. Conclusion: Knees requiring sagittal balancing to manage SGI with a relatively large extension gap is not uncommon in TKA for osteoarthritic knees. The change in PTS is an independent and modifiable predictor of SGI.
Short Term Stock Price Prediction in Indian Market: A Neural Network Perspective
Authors: Banerjee Soham , Mukherjee Diganta 
Published: March 2021

In recent times there has been an increasing level of debate whether patterns do exist in equity market movements and whether they can be predicted. In order to overcome the shortcomings of traditional time series models, we have focused our study on the application of non-parametric paradigms like stacked multi-layer perceptrons (MLP), long short term memory (LSTM), gated recurrent unit (GRU), bidirectional long short term memory (BLSTM) and gated bidirectional recurrent unit (BGRU) on three NSE listed banks to predict short term stock price, and compared their performance with a shallow neural network benchmark. We have predicted equity ‘Close Prices’ five minutes into the future, using a sliding window approach and have observed that average error in predictions of MLP, LSTM, GRU, BLSTM and BGRU models, varied between 0.09% and 0.1%, indicating their superior performance with regard to benchmark baseline of 0.88%. We have used the aforementioned predictions to determine price trends, which successfully outperformed the random walk baseline accuracy of 50%. JEL Classification: C45, C58, G11, G14
Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction
Authors: He Ming , Huang Chen , Liu Bo , Wang Yadong , Li Junyi 
Published: March 2021

AbstractBackgroundExploring the relationship between disease and gene is of great significance for understanding the pathogenesis of disease and developing corresponding therapeutic measures. The prediction of disease-gene association by computational methods accelerates the process.ResultsMany existing methods cannot fully utilize the multi-dimensional biological entity relationship to predict disease-gene association due to multi-source heterogeneous data. This paper proposes FactorHNE, a factor graph-aggregated heterogeneous network embedding method for disease-gene association prediction, which captures a variety of semantic relationships between the heterogeneous nodes by factorization. It produces different semantic factor graphs and effectively aggregates a variety of semantic relationships, by using end-to-end multi-perspectives loss function to optimize model. Then it produces good nodes embedding to prediction disease-gene association.ConclusionsExperimental verification and analysis show FactorHNE has better performance and scalability than the existing models. It also has good interpretability and can be extended to large-scale biomedical network data analysis.
Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)
Authors: Zhang Xiuming , Zhang Li , Ji Miaomiao , Wu Yifei , Zhang Songlin , Zhu Yanxun , Yao Jin , Li Zhi , Gao Hua , Wang Xiping 
Published: March 2021

Abstract
Background
B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryza sativa, little is known about the evolutionary history or expression patterns of BBX proteins in grapevine (Vitis vinifera L.).

Results
We identified a total of 25 VviBBX genes in the grapevine genome and named them according to the homology with Arabidopsis. These proteins were classified into five groups on the basis of their phylogenetic relationships, number of B-box domains, and presence or absence of a CCT domain or VP motif. BBX proteins within the same group showed similar exon-intron structures and were unevenly distributed in grapevine chromosomes. Synteny analyses suggested that only segmental duplication events contributed to the expansion of the VviBBX gene family in grapevine. The observed syntenic relationships between some BBX genes from grapevine and Arabidopsis suggest that they evolved from a common ancestor. Transcriptional analyses showed that the grapevine BBX genes were regulated distinctly in response to powdery mildew infection and various phytohormones. Moreover, the expression levels of a subset of BBX genes in ovules were much higher in seedless grapevine cultivars compared with seeded cultivars during ovule development, implying a potential role in seed abortion. Additionally, VviBBX8, VquBBX15a and VquBBX29b were all located in the nucleus and had transcriptional activity except for VquBBX29b.

Conclusions
The results of this study establish the genome-wide analysis of the grapevine BBX family and provide a framework for understanding the biological roles of BBX genes in grapevine.
Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
Authors: Bliznina Aleksandra , Masunaga Aki , Mansfield Michael J. , Tan Yongkai , Liu Andrew W. , West Charlotte , Rustagi Tanmay , Chien Hsiao-Chiao , Kumar Saurabh , Pichon Julien , Plessy Charles , Luscombe Nicholas M. 
Published: March 2021

AbstractBackgroundThe larvaceanOikopleura dioicais an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016)O. dioicalaboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved.ResultsHere, we present a chromosome-scale genome assembly (OKI2018_I69) of the OkinawanO. dioicaproduced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome.ConclusionsWe show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly ofO. dioica’s highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison betweenO. dioicapopulations, as well as of studies of chromosomal evolution in this lineage.
Genome-wide identification and functional characterization of the PheE2F/DP gene family in Moso bamboo
Authors: Li Long , Shi Qianqian , Li Zhouqi , Gao Jian 
Published: March 2021

Abstract
Background
E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of the Moso bamboo E2F/DP family has been limited.

Results
Here, we identified 23 E2F/DPs in the Moso bamboo genome, including nine E2F genes, six DP genes, eight DEL genes and one gene with a partial E2F domain. An estimation of the divergence time of the paralogous gene pairs suggested that the E2F/DP family expansion primarily occurred through a whole-genome duplication event. A regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. A yeast two-hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that the PheE2F-PheDP complex played important roles in winter Moso bamboo shoot growth. The qRT-PCR results showed that the PheE2F/DPs exhibited diverse expression patterns in response to drought and salt treatment and diurnal cycles.

Conclusion
Our findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.
Risk factors leading to trabeculectomy surgery of glaucoma patient using Japanese nationwide administrative claims data: a retrospective non-interventional cohort study
Authors: Shirai Chikako , Tsuda Satoru , Tarasawa Kunio , Fushimi Kiyohide , Fujimori Kenji , Nakazawa Toru 
Published: March 2021

Abstract
Background
Early recognition and management of baseline risk factors may play an important role in reducing glaucoma surgery burdens. However, no studies have investigated them using real-world data in Japan or other countries. This study aimed to clarify the risk factors leading to trabeculectomy surgery, which is the most common procedure of glaucoma surgery, of glaucoma patient using the Japanese nationwide administrative claims data associated with the diagnosis procedure combination (DPC) system.

Methods
It was a retrospective, non-interventional cohort study. Data were collected from patients who were admitted to DPC participating hospitals, nationwide acute care hospitals and were diagnosed with glaucoma between 2012 to 2018. The primary outcome was the risk factors associated with trabeculectomy surgery. The association between baseline characteristics and trabeculectomy surgery was identified using multivariable logistic regression analysis by comparing patients with and without trabeculectomy surgery. Meanwhile, the secondary outcomes included the rate of comorbidities, the rate of concomitant drug use and the treatment patterns of glaucoma eye drops at the index admission. Among patients with trabeculectomy surgery, the risk factors leading to cataract surgery were also evaluated as subgroup analysis.

Results
A total of 29,599 patients included in the analysis, 12,038 and 17,561 patients were in the glaucoma surgery and non-glaucoma surgery cohorts, respectively. The factors associated with the increase in trabeculectomy surgery were having allergies, taking concomitant drugs including cancer, depression, ischemic heart disease and peptic ulcer, being diagnosed with primary open-angle glaucoma and longer length of stay in hospital. In contrast, the factors associated with the decrease in trabeculectomy surgery were having hypertension, taking hypertension drug, age ≥ 80 and female.

Conclusions
Special focus on Japanese patients with glaucoma who have allergy-related comorbidities or take immune, nervous, circulatory or gastrointestinal system-related concomitant drugs seems to be desirable.
Axenfeld‐Rieger syndrome combined with a foveal anomaly in a three‐generation family: a case report
Authors: Gołaszewska Kinga , Dub Natalia , Saeed Emil , Mariak Zofia , Konopińska Joanna 
Published: March 2021

Abstract
Background
Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant eye disorder that can also affect other organs of the human body. The condition is primarily characterized by the anterior segmental abnormalities of the eye. Here, we present an observational case series of a three-generation family with ARS and unexpected foveal anomaly.

Case presentation
A 33-year-old woman was admitted to an Ophthalmology Clinic in Bialystok for left eye congenital cataract surgery. The patient (proband) was diagnosed with visual deterioration, multiple defects of iris, corectopia, displacement of the Schwalbe’s line, and phenotypic characteristics of ARS. A perimetric examination indicated peripheral visual field loss and signs typical for glaucoma. Based on the phenotypic symptoms and genetic test, the patient was diagnosed with Axenfeld Rieger Syndrome. However, the optical coherence tomography of the macula showed foveal anomaly (absence of the physiological pit), which is not typically associated with this genetic disorder. The patient’s family history revealed that her two daughters were undergoing treatment for congenital glaucoma, and one of the daughters also had foveal anomaly the same as her mother. Interestingly, an examination of the patient’s mother showed typical phenotypic features of ARS such as a defect of the iris, posterior embryotoxon, and coloboma, as well as foveal anomaly. A genetic test confirmed PITX2 mutation in both, proband’s two daughters and mother.

Conclusions
This study highlights the occurrence of ARS with unusual ophthalmic features such as foveal anomaly (absence of the physiological pit) in a three-generation family. Although ARS is known to represent the developmental defects of the anterior segment of the eye, it is very important to perform fundus evaluation to identify associated posterior segment anomalies that may affect visual acuity. The presence of ocular defects not typically associated with ARS suggests a wide spectrum of mutations within PITX2 gene which are required to identify in order to determine genotype- phenotype correlation in ARS affected individuals.
The national rate of intensive care units-acquired infections, one-year retrospective study in Iran
Authors: Izadi Neda , Eshrati Babak , Mehrabi Yadollah , Etemad Korosh , Hashemi-Nazari Seyed-Saeed 
Published: March 2021

Abstract
Background
Hospital-acquired infections (HAIs) in intensive care units (ICUs) are among the avoidable morbidity and mortality causes. This study aimed at investigating the rate of ICU-acquired infections (ICU-AIs) in Iran.

Methods
For the purpose of this multi-center study, the rate of ICU-AIs calculated based on the data collected through Iranian nosocomial infections surveillance system and hospital information system. The data expanded based on 12 months of the year (13,632 records in terms of “hospital-ward-month”), and then, the last observation carried forward method was used to replace the missing data.

Results
The mean (standard deviation) age of 52,276 patients with HAIs in the ICUs was 47.37 (30.78) years. The overall rate of ICU-AIs was 96.61 per 1000 patients and 16.82 per 1000 patient-days in Iran’s hospitals. The three main HAIs in the general ICUs were ventilator-associated events (VAE), urinary tract infection (UTI), and pneumonia events & lower respiratory tract infection (PNEU & LRI) infections. The three main HAIs in the internal and surgical ICUs were VAE, UTI, and bloodstream infections/surgical site infections (BSI/SSI). The most prevalent HAIs were BSI, PNEU & LRI and eye, ear, nose, throat, or mouth (EENT) infections in the neonatal ICU and PNEU & LRI, VAE, and BSI in the PICU. Device, catheter, and ventilator-associated infections accounted for 60.96, 18.56, and 39.83% of ICU-AIs, respectively. The ventilator-associated infection rate was 26.29 per 1000 ventilator-days. Based on the Pabon Lasso model, the lowest rates of ICU-AIs (66.95 per 1000 patients and 15.19 patient-days) observed in zone III, the efficient area.

Conclusions
HAIs are common in the internal ICU wards. In fact, VAE and ventilator-related infections are more prevalent in Iran. HAIs in the ICUs leads to an increased risk of ICU-related mortality. Therefore, to reduce ICU-AIs, the specific and trained personnel must be responsible for the use of the devices (catheter use and ventilators), avoid over use of catheterization when possible, and remove catheters earlier.
Health workers’ perspectives on informed consent for caesarean section in Southern Malawi
Authors: Bakker Wouter , Zethof Siem , Nansongole Felix , Kilowe Kelvin , van Roosmalen Jos , van den Akker Thomas 
Published: March 2021

AbstractObjectiveInformed consent is a prerequisite for caesarean section, the commonest surgical procedure in low- and middle-income settings, but not always acquired to an appropriate extent. Exploring perceptions of health care workers may aid in improving clinical practice around informed consent. We aim to explore health workers’ beliefs and experiences related to principles and practice of informed consent.MethodsQualitative study conducted between January and June 2018 in a rural 150-bed mission hospital in Southern Malawi. Clinical observations, semi-structured interviews and a focus group discussion were used to collect data. Participants were 22 clinical officers, nurse-midwives and midwifery students involved in maternity care. Data were analysed to identify themes and construct an analytical framework.ResultsDefinition and purpose of informed consent revolved around providing information, respecting women’s autonomy and achieving legal protection. Due to fear of blame and litigation, health workers preferred written consent. Written consent requires active participation by the consenting individual and was perceived to transfer liability to that person. A woman’s refusal to provide written informed consent may pose a dilemma for the health worker between doing good and respecting autonomy. To prevent such refusal, health workers said to only partially disclose surgical risks in order to minimize women's anxiety. Commonly perceived barriers to obtain a fully informed consent were labour pains, language barriers, women’s lack of education and their dependency on others to make decisions.ConclusionsHealth workers are familiar with the principles around informed consent and aware of its advantages, but fear of blame and litigation, partial disclosure of risks and barriers to communication hamper the process of obtaining informed consent. Findings can be used to develop interventions to improve the informed consent process.