bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting long non-coding RNA MALAT1 reverses cancerous phenotypes of breast cancer cells through microRNA-561-3p/TOP2A axis.
Authors: Hajibabaei Sara , Nafissi Nahid , Azimi Yasamin , Mahdian Reza , Rahimi-Jamnani Fatemeh , Valizadeh Vahideh , Rafiee Mohammad Hesam , Azizi Masoumeh 
Published: December 2022

Abstract

Non-coding RNAs, including Inc-RNA and miRNA, had been reported to regulate gene expression and were associated with cancer progression. MicroRNA-561-3p (miR-561-3p), as a tumor suppressor, has been reported to play a role in preventing cancer cell progression, and MALAT1 (Lnc-RNA) has also been demonstrated to promote malignancy in various cancer, such as breast cancer (BC). In this study, we aimed to determine the correlation between miR-561-3p and MALAT1 and their roles in breast cancer progression. The expression of MALAT1, mir-561- 3p, and topoisomerase alpha 2 (TOP2A) as a target of miR-561-3p was determined in BC clinical samples and cell lines via qRT-PCR. The binding site between MALAT1, miR-561-3p, and TOP2A was investigated by performing the dual luciferase reporter assay. MALAT1 was knocked down by siRNA, and cell proliferation, apoptotic assays, and cell cycle arrest were evaluated. MALAT1 and TOP2A were significantly upregulated, while mir-561-3p expression was downregulated in BC samples and cell lines. MALAT1 knockdown significantly increased miR 561 3p expression, meaningfully inverted by co-transfection with the miR 561 3p inhibitor. Furthermore, the knockdown of MALAT1 by siRNA inhibited proliferation, induced apoptosis, and arrested the cell cycle at the G1 phase in BC cells. Notably, the mechanistic investigation revealed that MALAT1 predominantly acted as a competing endogenous RNA in BC by regulating the miR-561-3p/TOP2A axis. Based on our results, MALAT1 upregulation in BC may function as a tumor promoter in BC via directly sponging miRNA 561-3p, and MALAT1 knockdown serves a vital antitumor role in BC cell progression through the miR-561- 3p/TOP2A axis.
Determination of Soil Quality Index in Areas with High Erosion Risk and Usability in Watershed Rehabilitation Applications
Authors: DEMİR Yasin , DEMİR Azize DOĞAN , MERAL Alperen , YÜKSEL Alaaddin 
Published: December 2022

Abstract
Erosion is an important environmental issue threatening natural resources and ecosystems, especially soil and water. Soil losses occur in many parts of the world due to erosion at different degrees, and various rehabilitation plans have been carried out to reduce these losses. However, soil protection applications are generally carried out by considering only the essential characteristics of the soil. This may decrease the chance of success of rehabilitation applications. The present study aimed to determine the soil quality index (SQI) by weighting the soil quality parameters according to the Analytical Hierarchy Process (AHP) in the Çapakçur microcatchment (Bingöl, Türkiye) where soil loss is high. Accordingly, 428 soil samples were taken from the study area and analyzed. The soil losses in the Çapakçur watershed were calculated employing the Revised Universal Soil Loss Equation (RUSLE). To determine the soil quality index, a total of 20 indicators were used, including (i) physical soil properties, (ii) chemical soil properties, and (iii) soil nutrient content. Soil quality index results are divided into classes between 1 and 5. As a result of the study, the annual total amount of soil lost from the microcatchment was calculated as 96 915.20 tons, and the yearly average amount of soil lost from the unit area was calculated as 10.14 tons.ha-1. According to SQI, the largest area in the micro-catchment was Class-2 (weak), with 39.49%, whereas the smallest area was 1.4% (the most suitable). However, it was determined that there was a significant negative relationship between SQI and soil erodibility. Considering the SQI distribution of the area in the planning of soil protection and erosion prevention practices in watershed rehabilitation studies may increase success.
Predictive factors for degenerative lumbar spinal stenosis: A model obtained from a machine learning algorithm technique
Authors: Abbas Janan , Yousef Malik , Peled Natan , Hershkovitz Israel , Hamoud Kamal 
Published: December 2022

Abstract
Background
Degenerative lumbar spinal stenosis (DLSS) is the most common spine disease in the elderly population. It is usually associated with lumbar spine joints/or ligaments degeneration. Machine learning technique is an exclusive method for handling big data analysis; however, the development of this method for spine pathology is rare. This study aims to detect the essential variables that predict the development of symptomatic degenerative lumbar spinal stenosis (DLSS) using the random forest of machine learning (ML) algorithms technique.
Methods
A retrospective study with two groups of individuals. The first included 165 with symptomatic DLSS (sex ratio 80 M/85F), and the second included 180 individuals from the general population (sex ratio: 90M/90F) without lumbar stenosis symptoms. Lumbar spine measurements such as vertebral/or spinal canal diameters from L1 to S1 were conducted on computerized tomography (CT) images (Brilliance 64, Philips Medical System, Cleveland, OH). Demographic and health data of all the participants (e.g., body mass index and diabetes mellitus) were also recorded.
Results
The decision tree model of ML demonstrate that the AP diameter of the bony canal at L5 (males) and L4 (females) levels have the greatest stimulus for symptomatic DLSS (scores of 1 and 0.938). In addition, combination of these variables with other lumbar spine features is mandatory for developing the DLSS.
Conclusions
Our results indicate that combination of lumbar spine characteristics such as bony canal and vertebral body dimensions rather than the presence of a sole variable is highly associated with symptomatic DLSS onset.
Molecular characterization of waterborne protozoa in surface water and sediment in Brazil: a taxonomic survey of ciliated protozoa and their correlation with Giardia duodenalis and Cryptosporidium spp.
Authors: Bonatti Taís Rondello , Siqueira-Castro Isabel Cristina Vidal , Leal Diego Averaldo Guiguet , Durigan Maurício , Dias Roberto Júnio Pedroso , Franco Regina Maura Bueno 
Published: December 2022

Abstract
The detection of Giardia duodenalis and Cryptosporidium spp. was performed, along with the identification of the ciliated protozoa biodiversity, to evaluate the correlation between these protozoa in freshwater quality monitoring. Water and sediment samples from two sites in the Atibaia River (Campinas, São Paulo, Brazil) were collected monthly for two years (n = 96). Pathogenic protozoa in water and sediment were detected by using immunomagnetic separation, followed by visualization by immunofluorescence assay (IFA). All positive aliquots in IFA were subjected to DNA extraction and subsequently nested PCR. Qualitative (in vivo observation and silver impregnation) and quantitative (in vivo enumeration) analyses were performed for the ciliated protozoa. Giardia cysts were detected in 62.5% of the surface water samples and Cryptosporidium spp. in 25.0%. In the sediment, cysts were detected in 35.4% samples and oocysts in 16.6%. A total of 57 samples positive for Giardia cysts were subjected to sequencing, 40 of which were harboring G. duodenalis (24 were characterized as sub assemblage AII). For ciliated protozoa, 73 taxa belonging to 53 genera were identified over the period of the study. These results revealed a high degree of contamination by waterborne protozoa in the main water source which supplies drinking water for more than one million people in Campinas (São Paulo), highlighting the need for continuous monitoring of this catchment site. In addition, the present study provides important data regarding the sources of the water body degradation, i.e., fecal contamination of human origin, in addition to the survey of the ciliated protozoa.
Elevated gonadotropin levels are associated with increased biomarker risk of Alzheimer’s disease in midlife women
Authors: Nerattini Matilde , Rubino Federica , Jett Steven , Andy Caroline , Yepez Camila Boneu , Zarate Camila , Carlton Caroline , Kodancha Vibha , Loeb-Zeitlin Susan , Havryliuk Yelena , Pahlajani Silky , Williams Schantel , Berti Valentina , Dyke Jonathan , Brinton Roberta Diaz , Mosconi Lisa 
Published: December 2022

Abstract
Menopause has been implicated in women’s greater life-time risk for Alzheimer’s disease (AD) due to its disruptive action on multiple neurobiological mechanisms resulting in amyloid-β deposition and synaptic dysfunction.While these effects are typically attributed to declines in estradiol, mechanistic analyses implicate pituitary gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), in AD pathology. In transgenic mouse models of AD, increasing FSH and LH accelerate amyloid-β deposition, while inhibiting these hormones prevents emergence of AD lesions and neurodegeneration. Herein, we take a translational approach to show that, among midlife women at risk for AD, FSH elevations over the menopause transition are associated with higher amyloid-β burden, and both FSH and LH increases are associated with lower gray matter volume in AD-vulnerable brain regions. Results were independent of age, hormone therapy usage, and plasma estradiol levels. These findings provide novel therapeutic targets for sex-based precision medicine strategies for AD prevention.
Factors affecting the need for silicon tube implantation in cases of congenital dacriostenosis: Time of delivery, mode of delivery and age of operation
Authors: Yavuz Sibel , İlhan Hatice Deniz , Ersoy Merve 
Published: December 2022

Abstract
Purpose
To evaluate the delivery time, mode of delivery, age at the time of operation, and surgical methods applied in cases of congenital nasolacrimal duct obstruction (CNLDO).
Methods
This study retrospectively included a total of 207 eyes of 160 patients who underwent surgery for CNLDO between February 2012 and April 2021. According to their age at the time of operation, the patients were divided into 0–12, 12–24, 24–36, 36–48 and > 48 months groups. The cases were evaluated as term/preterm according to the delivery time and cesarean section/vaginal delivery according to the mode of delivery. The surgical methods applied were examined as probing alone and probing plus silicone tube implantation.
Results
Of the cases, 190 (91.8%) were born at term and 17 (0.08%) were born preterm, and there was no statistically significant difference in the silicone tube implantation rates according to the time of delivery. The rate of tube implantation was statistically significantly higher in the vaginal delivery group than in the cesarean section group (p = 0.001; p < 0.01). The rate of silicone tube implantation was higher in those who were older than the age of the operation.
Conclusions
Although the rate of those who were born by cesarean section was higher in probing cases, those who required silicone intubation were more common in those who were born vaginally. This suggests that dacryostenosis in the vaginally born cases resulted from a persistent structural and anatomical obstruction despite the presence of a high intrauterine pressure increase and enzymatic lysis.
Real-time measurements of vascular permeability in the mouse eye using vitreous fluorophotometry
Authors: Colé Nadine , Thoele Janina , Ullmer Christoph , Foxton Richard 
Published: December 2022

Abstract
Breakdown of blood-retinal barrier integrity underpins pathological changes in numerous ocular diseases, including neovascular age-related macular degeneration (nAMD) and diabetic macular edema (DME). Whilst anti-vascular endothelial growth factor (VEGF) therapies have revolutionised disease treatment, novel therapies are still required to meet patients' unmet needs. To help develop new treatments, robust methods are needed to measure changes in vascular permeability in ocular tissues in animal models. We present here a method for detecting vascular permeability using fluorophotometry, which enables real-time measurements of fluorescent dye accumulation in different compartments of the mouse eye. We applied this method in several mouse models with different increased vascular leakage, including models of uveitis, diabetic retinopathy and choroidal neovascularization (CNV). Furthermore, in the JR5558 mouse model of CNV, we observed with anti-VEGF post-treatment a longitudinal reduction in permeability, in the same animal eyes. We conclude fluorophotometry is a useful method for measuring vascular permeability in the mouse eye, and can be used over multiple time points, without the need to sacrifice the animal. This method has the potential to be used in both basic research for studying the progression and factors underlying disease, but also for drug discovery and development of novel therapeutics.
Value of thyroid cancer history in the prognosis of pancreatic cancer: a SEER population-based study
Authors: He Jun , Wang Yu , Chen Xiangmei , Chen Wenxiang , Zhou Jianyin 
Published: December 2022

Abstract
Thyroid cancer patients have a good prognosis, and their long survival increases the likelihood of developing a second primary tumor. Meanwhile, pancreatic cancer (PC) has a poor prognosis and therapeutic efficacy. However, the association between prior thyroid cancer and the subsequent PC prognosis is unknown. Herein, we selected pathologically diagnosed PC patients older than 17 between 2010 and 2015 from the SEER database. We used propensity score matching (PSM) to reduce confounding factors between groups and matched each PC patient witha history of thyroid cancerwith 10 PC patients without a history of thyroid cancer. Finally, we selected 103 PC patients with prior thyroid cancer and 1030 PC patients without prior thyroid cancer. Then, we analyzed the factors influencing the overall survival (OS) and the cancer-specific survival (CSS) of PC patients. The median overall survival of PC patients with and without a history of thyroid cancer was 12 and 9 months, respectively. The history of thyroid cancer in PC patients reduced the PC-specific mortality (p < 0.05). Prior thyroid cancer might increase PC patients’ survival and reduce PC-specific death, especially in male patients.
Subject terms: Cancer
Integrating Development Inhomogeneity into Geohazards Risk Assessment Framework in Mountainous Areas – A Case Study in Lushan-Baoxing counties, Southwestern China
Authors: He Yufeng , DING Mingtao , Zheng Hao , Gao Zemin , Huang Tao , Duan Yu , Cui Xingjie , Luo Siyuan 
Published: December 2022

Abstract
The impact of geohazards on mountainous settlement have been focused in recent years. Despite the booming development in the modeling of hazards and vulnerability, the risk assessment in mountainous area still have difficulty in absence of refined data. Moreover, development imbalances widely exist in mountainous areas, which ignored in previous researches. In this study, the development imbalances were quantified and integrated into risk assessment framework, which be applied in Lushan and Baoxing mountainous areas. The refined distribution of soc-economic data is obtained by using spatialization from the census, which eases the situation of the lack of data. Then, a frequency ratio-random forest (FR-RF) model is conducted to evaluate the geohazards hazard. Meanwhile, vulnerability was evaluated using triangular fuzzy number‑based analytic hierarchy process (TFN-AHP). In vulnerability assessment, the inhomogeneity index is integrated to evaluate the imbalance between indicators, the use of which can reward a more realistic vulnerability result. Finally, risk map was produced by multiplying hazard and vulnerability. The risk assessment framework is successfully applied in Lushan and Baoxing counties of Southwestern China, which is a typical mountainous area with frequent earthquakes, uneven development, and a lack of high-precision data. The total area of high and extremely high hazard (868.82 km2), vulnerability (258.66 km2), and risk (113.49 km2) are estimated and mapped.
Immune Response Serves as a Bridge between Abnormal Lipid and Bone Metabolism: A Differential Expression Genes Profile Analysis Based on Clinical Data-mining
Authors: Zhang Fangqing , Wu Jiashuo , Xia Jing , Ruan Haonan , Wang Jingxun , Xue Haotian , Li Yuzhuo , Shi Yue 
Published: December 2022

Abstract
Accumulating evidence demonstrates that adipogenic metabolism is intricately connected with bone mass regulation in rodent models and humans. Energy metabolism dysfunction includes diseases such as obesity, insulin resistance, and diabetes. People with these diseases are often accompanied by bone loss and abnormal bone structure and function. Similarly, the incidences of obesity and lipid metabolism disorders are incredibly high after impaired bone formation and bone resorption. Existing studies have reported a deep connection between abnormal lipid and bone metabolism. However, little is known about the underlying molecular mechanisms leading to comorbidity. Herein, bioinformatics and systems biology approaches were utilized to compare clinical datasets of obese subjects to those with bone-related disorders including osteoporosis (OP), osteoarthritis (OA), osteosarcoma (OS), and low osteogenic potential (LOP) to investigate the potential genetic links. A significant number of overlapping differentially expressed genes (DEGs) were involved in regulating the inflammatory and immune processes. As per the biological enrichment analyses, these DEGs were distributed in the biological processes and signaling pathways related to inflammatory responses such as taxis, chemotaxis, leukocyte chemotaxis, regulation of immune response, and leukocyte activation. Protein-protein interaction and gene regulation networks were constructed to understand the potential interaction effects between common DEGs, microRNAs (miRNAs), transcription factors (TFs), and chemical compounds. Drug prediction was used to screen for potential pharmacological therapies against comorbidity between lipid and bone metabolic disorder (CLBD). Together, our findings provide insights into the potential association between abnormal lipid and bone metabolism. Further, it lays the foundation for developing novel therapeutic strategies that apply agents of immune-related diseases to treat CLBD clinically.
Spatial Pattern and Genetic Diversity of Marine Bacterial Communities of Coastal Seawater and Sediments from Qatar
Authors: El-Malah Shimaa S. , Rasool Kashif , Jabbar Khadeeja Abdul , Sohail Muhammad Umar , Baalousha Husam Musa , Mahmoud Khaled A. 
Published: December 2022

Abstract
Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized the indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa and 16S rRNA sequencing to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites of Qatar over different seasons. The concentration levels of indicator bacteria were affected by increasing temperature and pH and decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediments, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, respectively, while Clostridia (13.72%) was abundant in sediment only. Results suggest that the sediments can act as a reservoir for indicators of bacteria with higher diversity and lower abundance as compared to seawater. This study helps to understand the impact of environmental conditions on the diversity and structural behavior of microbial communities specific to the marine environment of the Arabian Gulf.
PCP-ACO: a deadline-constrained workflow scheduling algorithm for cloud environment
Authors: Shobeiri Peyman , Rastaghi Mehdi Akbarian , Abrishami Saeid , Shobiri Behnam 
Published: December 2022

Abstract
A cloud computing environment is the most popular choice for workflow execution, as it gives customers on-demand access to computing resources. However, in cloud workflow scheduling, cloud-native requirements regarding QoS requirements such as monetary cost and execution time should be taken into account. This paper proposes PCP-ACO, a list scheduling algorithm for minimizing the execution cost of a workflow, while meeting its user-defined deadline in cloud environments. In PCP-ACO, first a topological sort of the workflow tasks is computed to assign a priority to each task. Then, Ant Colony Optimization (ACO) meta-heuristic is used to assign a proper resource to each task of the workflow, in order of their priorities. The Partial Critical Path (PCP) concept is also used as a heuristic to guide ACO algorithm. Several experiments are conducted using real scientific workflows, and the cost saving is compared with PSO and IC-PCP algorithms. The experimental results show that the proposed algorithm outperforms other compared algorithms in terms of cost saving.
Functionalization of Jute and Jute-Cotton Fabrics through Flame- retardant Finish
Authors: Begum Most Setara , Kader Abdul , Milašius Rimvydas 
Published: December 2022

Abstract
The ligno-cellulosic Jute fiber, which holds the second largest volume among the natural cellulosic fibers after Cotton. This study focuses on the determination of the flame-retardance (FR) properties of pure Jute and Jute-Cotton fabrics treated with Pyrovatex CP New at concentrations of 90% (owf), M:L: 1:7. A significant improvement in flame-retardancy was determined on both fabrics. After the ignition period, the recorded flame spread time was zero second on both FR treated fabrics; on the other hand, it was measured 21 seconds and 28 seconds to burn the entire length (15cm) of untreated Jute and Jute-Cotton fabrics, respectively. Within these flame-spread times, the length of the char was 2.1 cm and 2.57 cm in the Jute and Jute-Cotton fabrics, respectively. The physio-mechanical properties dropped remarkably after the FR finish in both the warp and weft directions of both fabrics. The SEM images determined the deposition of flame-retardant finishes on the fabric surface. FTIR characterization showed that the inherent properties of the fibers were not affected by the flame-retardant chemical. The TGA analysis showed that the early decomposition occurred on both FR treated fabrics and hence formed more char than the untreated samples. A significant improvement in residual mass (more than 40%) was observed in both fabrics after FR treatment. The detected formaldehyde content on the FR treated samples was much higher; however, it was still in the limit of the allowed formaldehyde content present in textiles that are designed for outerwear and not worn next to the skin. The findings reported in this study show the potential application of Pyrovatex CP New to jute-based materials.