bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Cyamus Boopis from A Humpback Whale (Megaptera novaeangliae) in the Coastal East China Sea
Authors: Qiao Ying , Ma Xiaowan , Chen Bingyao , Zhong Shengping , Chen Xuyang 
Published: July 2020

Abstract
Background: Cyamus boopis is an amphipod crustacean that obligately parasitizes the body surface of the humpback whale, Megaptera novaeangliae. The life cycle of C. boopis does not include a swimming stage, and the crustacean spends its entire life on the body of M. novaeangliae. Methods: On November 15, 2017, a male humpback whale was found stranded on the coast of the cape of Yuan Tuo, Qidong, Nantong, JiangSu province, China. Parasites were collected from the carcass of this whale and identified by morphological techniques and molecular analysis. Results: A total of 15 C. boopis specimens were collected, and eight females and seven males were morphologically identified. A phylogenetic tree of cytochrome c oxidase subunit 1 revealed that the collected specimens clustered together with previously reported C. boopis sequences from the Northern Hemisphere. Conclusion: This is the first report of C. boopis in a humpback whale from the East China Sea and supplements data from humpback whales found off the coast of China. In addition, our data provide supplementary data on the migration paths of humpback whales.
Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma
Authors: Yin Wen , Tan Jun , Xin Zhaoqi , Zhou Quanwei , Cao Yudong , Wu Zhaoping , Lei Wang , Jiang Xingjun , Ren Caiping , Tang Guihua 
Published: July 2020

Abstract
Background
Gliomas account for the majority of fatal primary brain tumors, and there is much room for development in the underlying pathogenesis, the multistep progression of glioma, and how to improve survival. In our study, we aimed to identify potential biomarkers or therapeutic targets of glioma and study the mechanism underlying the tumor progression.
Methods
We downloaded the microarray datasets (GSE43378 and GSE7696) from the Gene Expression Omnibus (GEO) database. Then, we used weighted gene co-expression network analysis (WGCNA) to screen potential biomarkers or therapeutic targets in the tumor progression. ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) algorithm and TIMER (Tumor Immune Estimation Resource) database were used to analyze the correlation between the selected genes and tumor microenvironment. Real-time reverse transcriptione polymerase chain reaction was used to measure the selected gene. Transwell and wound healing assay were used to measure the cell migration and invasion capacity.
Results
We identified specific module genes which were positively correlated with WHO grade but negatively correlated with OS of glioma. Importantly, we identified that 6 hub genes (COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, and COL5A2) could regulate the immunosuppressive microenvironment of glioma. Moreover, we found that these collagen genes were significantly involved in the epithelial-mesenchymal transition (EMT) process of glioma. Finally, taking COL5A2 as a further research object, the results showed that knockdown of COL5A2 significantly inhibited the migration and invasion of SHG44 and A172 cells.
Conclusions
In summary, our study demonstrated that collagen genes play important role in regulating the immunosuppressive microenvironment and EMT process of glioma and could serve as potential therapeutic targets for glioma management.
The relationship between RECK Gene Polymorphisms and the prognosis of cholangiocarcinoma
Authors: Wang Ning , Li Yanni , Zheng Yanfang , Chen Huoming , Wen Xiaolong , Li Zhaoxia 
Published: July 2020

Abstract
Background

The study was designed to examine the reversion inducing cysteine rich protein with Kazal motifs (RECK) levels in patients with cholangiocarcinoma (CCA) and assess its role in CCA prognosis.
Methods

Quantitative real-time PCR (qRT-PCR) was used to determine the expression of RECK mRNA in 127 pairs of CCA samples and controls. Chi-square test was conducted to analyze the effects of clinical features on RECK expression. Kaplan-Meier curves were plotted to determine the overall survival rate of CCA patients with different RECK expression. The prognostic biomarkers for CCA patients were identified using the Cox regression analysis.
Results

Significantly down-regulated expression of RECK mRNA was determined in CCA tissues compared to noncancerous controls (P < 0.05). Chi-square test suggested reduced RECK expression was related with invasion depth (P = 0.026), differentiation (P = 0.025), lymphatic metastasis (P = 0.010) and TNM stage (P = 0.015). However, age, sex, tumor size and family history had no significant links with RECK expression (all, P > 0.05). The survival curves showed that patients with low RECK expression had a shorter overall survival rate than those with high RECK expression. Both the univariate analysis (P = 0.000, HR = 5.290, 95%CI = 3.195–8.758) and multivariate analysis (P = 0.000, HR = 5.376, 95%CI = 2.231–8.946) demonstrated that RECK was an independent biomarker for predicting the outcomes of CCA patients.
Conclusions

Taken together, the expression of RECK was down-regulated in CCA and it might be an efficient biomarker for CCA patients.
Associations between pre-pregnancy body mass index and gestational weight gain with pregnancy outcomes in women with polycystic ovary syndrome
Authors: Zhang Lirui , Zheng Wei , Liu Cheng , Liang Xin , Zhang Li , Tian Zhihong , Li Guanghui 
Published: July 2020

Abstract
BackgroundPolycystic ovary syndrome (PCOS), a reproductive endocrine disorder affecting females of childbearing age, is associated with poor pregnancy outcomes. Both inappropriate pre-pregnancy body mass index (BMI) and gestational weight gain (GWG) could affect the perinatal outcomes in general pregnant women, which raises the question whether various BMI or GWG has impact on pregnancy outcomes in PCOS women. Therefore, we conducted a retrospective study in 722 PCOS women to explore the associations between pre-pregnancy BMI and GWG with pregnancy outcomes among PCOS women with the view of generating vital information that can guide weight management in this group of individuals.MethodsA retrospective study was conducted targeting baseline characteristics, laboratory data and pregnancy outcomes in 722 singleton pregnant women. We performed multivariable logistic regression analysis to investigate the relationship between BMI and GWG with perinatal outcomes after controlling for appropriate confounding factors.ResultsOur results showed that being underweight were increased the risk of small for gestational age (SGA), but reduced the risk of large for gestational age (LGA). In addition, we found overweight but not obesity individuals were more susceptible to develop preeclampsia compared those with normal weights. For PCOS women with BMI＜25 kg/m2 before pregnancy, inadequate GWG was a protective factor for gestational hypertension and postpartum hemorrhage(PPH). However, excessive GWG increased the possibility of LGA birth in individuals with BMI＜25 kg/m2 . Excessive GWG also increased the chances of undergoing a cesarean section in individuals with BMI ≥ 25 kg/m2. Inadequate GWG didn’t reduce the risk of LGA for women with BMI ≥ 25 kg/m2, similarly, excessive GWG didn’t decrease the chance of delivering SGA infant for women with BMI＜25 kg/m2.ConclusionThe impacts of pre-pregnancy BMI, GWG on maternal and infant outcomes among PCOS women are similar to what has been reported in general pregnant women. However, some unique trends exist in PCOS women. Overall, these findings indicate that women with PCOS need to begin weight management before pregnancy.
Reducing Mechanical Wear of Elbows and Pipes Due to Solid Particles Flow by Using Nano Coating Technique
Authors: Kareem Laith Abd UL , AlIthari Ali Sadiq , AlZurfi Nabeel 
Published: July 2020

Abstract
The problem of failure for elbows and pipes due to the effects of solid particles flow with a high velocity, facing a lot of industrial foundations now days. This work investigated factors that cause failure by mechanical wear inside elbows and pipes of cement transportation which manufacturing from low carbon steel (St-52-3) and find out a method for reducing this mechanical wear. Coating with layers of nanoparticles of tungsten carbides (WC) using a thermal spray process with a high-velocity oxy-fuel technique (HVOF) is one of those methods. The coating process was done for samples from the same material of elbow and pipe material. Some tests were done for these samples with different coating thicknesses (30, 40, and 50 µm) by placing them inside the elbow as well as standard wear tests (pin on disc). The results showed a decrease in the mechanical wear for the sample coated with 50 µm of WC layer by 71% compared with that without coating, while the results of the pin on disc test showed a decrease in wear about 97% for the sample coated with 50 µm. The photographs of the scanning electron microscope (SEM) were used to determine the thickness of the coating layer on samples. The numerical simulation was also implemented to simulate the erosion profile inside the elbow by using the commercial code STAR CCM + based on the CFD technique; the predicted results showed a good agreement with the experimental data with accuracy reaches 94%.
Integrated metabolomics and transcriptomics analysis of monolayer and neurospheres from glioblastoma cells
Authors: Peixoto Joana , Janaki-Raman Sudha , Schlicker Lisa , Schmitz Werner , Walz Susanne , Herold-Mende Christel , Soares Paula , Schulze Almut , Lima Jorge 
Published: July 2020

Abstract
Background: Altered metabolism is a hallmark of cancer and metabolic reprogramming can regulate several malignant properties to drive tumourigenesis. Metabolic processes contribute to carcinogenesis by modulating proliferation, survival and differentiation. Here, we studied how metabolic pathways are deregulated in cancer stem-like cells, a specific pool of cells that is thought to be responsible for cancer growth and recurrence. Cancer stem-like cells are particularly relevant in glioblastoma (GBM), the most lethal form of primary brain tumours.Methods: We have analysed the transcriptome and metabolome of an established GBM cell line (U87) and a patient-derived GBM stem-like cell line (NCH644) exposed to neurosphere or monolayer culture conditions. By integrating transcriptome and metabolome data, we identified key metabolic pathways and gene signatures that are associated with stem-like and differentiated states in GBM cells.Results: By principal component analysis and hierarchical clustering, we demonstrated that neurospheres and monolayer cells differ substantially in their metabolism and gene regulation. Furthermore, by performing a joint pathway analysis of transcriptome and metabolome data, we found that neurosphere culture conditions induce a similar metabolic rewiring in the two cellular systems and significantly regulate the same metabolic pathways. Finally, arginine biosynthesis was identified as the most significantly regulated pathway in neurospheres from both cell lines, although individual nodes of this pathway were distinctly regulated in the two cellular systems.Conclusions: Neurosphere conditions, as opposed to monolayer conditions, cause a transcriptomic and metabolic rewiring that may be crucial for the regulation of stem-like features. Arginine biosynthesis may be a key metabolic pathway in stemness regulation, by supporting the specific needs of the different cell populations. Different GBM cell lines show distinct regulation of these metabolic pathways, which are crucial to direct metabolites towards nucleotide or arginine synthesis, respectively. Finally, as part of open science data, the data set generated is of great value as a resource for the scientific community.
Comparative Transcripto me Analysis Depicts Candidate Genes Involved in Skin Color Differentiation in Red Tilapia
Authors: He Jinzhao , Feng Pengfei , Qin Junqi , Teng Yun , Luo Xu , Chen Zigui , Ma Huawei , Zhou Dayan 
Published: July 2020

Abstract
Background

This study aimed to investigate the genetic molecular mechanism of body color differentiation and variation of red tilapia, selecting the main genes related to the variation and cultivating the pure and stable red tilapia variety.
Results

The effects of different temperature treatments on body color and survival of Guam red tilapia, pearl white red tilapia and Florida red tilapia were compared. Besides, comparative transcriptome analysis was used to screen the candidate genes linked to the skin color differentiation of pearl white red tilapia. Among them, the body color of Guam red tilapia changed when the water temperature dropped to 16 − 14 °C, and continued to drop to about 11 °C, it was discolored in a large area reaching above 90%. According to the differential analysis: Tyrosine Kinase STYK1, HSP70, HSP30 and Transcription factor Sp6 expressions were significantly increased in the low temperature group, while MC1R, Transcription factor (MafB, jun-D, AP-1, E2F5, ETV6, Sp9, Sp7, E2F1, Sp4) expressions were notably decreased.
Conclusions

In this study, the expressive quantity of tyrosine protein kinase in the low temperature group HLF7 was significantly higher than that in the normal temperature group HLF3, which indicated that the melanin synthesis ability was enhanced in the low temperature group HLF7. The result was consistent with the tendency of red tilapia to become darker as the temperature gradient decreased.
Improving the interpretability of random forest models of genetic association in the presence of non-additive interactions
Authors: Orlenko Alena , Moore Jason H 
Published: July 2020

Abstract
Background: Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex diseases such as Alzheimer’s, diabetes, and cardiovascular disease. Detecting interactions requires careful selection of analytical methods, and some machine learning algorithms are unable or underpowered to detect or model feature interactions that exhibit non-additivity. The Random Forest method is often employed in these efforts due to its ability to detect and model non-additive interactions. In addition, Random Forest has the built-in ability to estimate feature importance scores, a characteristic that allows the model to be interpreted with the order and effect size of the feature association with the outcome. This characteristic is very important for epidemiological and clinical studies where results of predictive modeling could be used to define the future direction of the research efforts. An alternative way to interpret the model is with a permutation feature importance metric which employs a permutation approach to calculate a feature contribution coefficient in units of the decrease in the model’s performance. Currently, it is unclear which Random Forest feature importance metric provides a superior estimation of the true informative contribution of features in genetic association analysis. Results: To address this issue, and to improve interpretability of Random Forest predictions, we compared different methods for feature importance estimation in real and simulated datasets with non-additive interactions. As a result, we detected a discrepancy between the metrics evaluations for the real-world datasets and further established that the permutation feature importance metric provides more precise feature importance rank estimation for the simulated datasets with non-additive interactions. Conclusions: By analyzing both real and simulated data, we established that the permutation feature importance metric provides more precise feature importance rank estimation in the presence of non-additive interactions.
Prevalence of smoking and smoking predictors among adolescents in Qassim, Saudi Arabia: Does the Healthy City Program make any Difference?
Authors: Alasqah Ibrahim , Mahmud Ilias , East Leah , Usher Kim 
Published: July 2020

Abstract
Aim: To compare the prevalence of smoking and smoking predictors among adolescents between cities running a healthy city program (HCP cities) and the cities that are not running such a program (NHCP cities) in the Qassim region, Saudi Arabia. Subject and Methods: A cross-sectional survey using a self-reported questionnaire on the prevalence of smoking and smoking predictors among adolescents in Qassim region, Saudi Arabia was undertaken between April and September 2017. Using multi-staged cluster sampling, probability proportionate to the size, we surveyed 364 adolescents from three HCP cites and 769 adolescents from three NHCP cities. Results: The overall prevalence of smoking among school-aged adolescents in Qassim is 5.2% (95% CI: 3.9-6.5). Smoking prevalence among adolescents in the HCP cities is 8.8% (95% CI: 5.9-11.7); while in the NHCP cities it is 3.5% (95% CI: 2.2-4.8). The prevalence of at least one smoker among close friends in HCP and NHCP cities is 67.3% (62.5-72.1) and 72.2% (69-75.3), respectively. The prevalence of at least one smoker in the family of the adolescents in HCP and NHCP cities is 58% (52.9-63.1) and 44.3% (40.8-47.9), respectively. Among the socio-demographic variables, smoking is significantly associated with gender (OR: .08) *, age (OR: 1.61) and academic performance (OR: .27). Prevalence of smoking among adolescents is significantly higher in HCP cities than in NHCP cities (OR: 3.03; 95% CI: 1.7-5.4). Conclusion: Prevalence of smoking and key smoking risk factors were found to be higher in cities implementing the healthy city program, despite exposure to an anti-smoking campaign being higher in these cities. Given these findings, we recommend further in-depth evaluation of the program.
Uncomplicated falciparum malaria among schoolchildren in Bajil district of Hodeidah governorate, west of Yemen: Association with anaemia and underweight
Authors: Alwajeeh Talal S , Abdul-Ghani Rashad , Allam Amal F. , Farag Hoda F. , Khalil Safia S.M. , Shehab Amel Y. , El-Sayad Mona H. , Alharbi R.A. , Al Shaia S.R. , Azazy Ahmed A. 
Published: July 2020

Abstract
Background
Malaria, malnutrition and anaemia are major public health problems in Yemen, with Hodeidah being the most malaria-afflicted governorate. To address the lack of relevant studies, this study was conducted to determine the prevalence of Plasmodium falciparum and its relation to nutritional status and haematological indices among schoolchildren in Bajil district of Hodeidah governorate, west of Yemen.
Methods
This cross-sectional study was conducted among 400 schoolchildren selected randomly from four schools in Bajil district. Data about demographic characteristics, risk factors and anthropometric measurements of age, height and weight were collected. Duplicate thick and thin blood films were prepared, stained with Giemsa and examined microscopically for malaria parasites. The density of P. falciparum asexual stages was estimated on thick films. EDTA-blood samples were examined for the haematological indices of haemoglobin (Hb) and blood cell counts.
Results
P. falciparum was prevalent among 8.0% (32/400) of schoolchildren with a mean parasite density of 244.3 \(\pm\)299.3/µl of blood and most infections showing low-level parasitaemia, whereas Plasmodium vivax was detected in one child (0.25%). Residing near water collections was a significant predictor of falciparum malaria (OR = 2.4, 95% CI = 1.14–5.05; p = 0.019) in schoolchildren. Mild anaemia was prevalent among more than half of P. falciparum-infected schoolchildren and significantly associated with falciparum malaria, with a mean Hb concentration of 10.7 \(\pm\)1.0 g/dL. Although the mean values of the total white blood cells, monocytes and platelets were significantly lower in infected than non-infected schoolchildren, they were within normal ranges. More than half of the children were malnourished, with stunting (39.3%) and underweight (36.0%) being the most prevalent forms of malnutrition; 6.3% of children were wasted. Underweight (OR = 3.3, 95% CI = 1.55–6.93; p = 0.001), but not stunting or wasting, was a significant predictor of falciparum malaria among schoolchildren.
Conclusion
Asymptomatic falciparum malaria is prevalent among schoolchildren in Bajil district of Hodeidah Governorate, with predominance of low parasitaemic infections and significant association with mild anaemia and underweight. Residence near water collection is a significant predictor of infection with falciparum malaria among schoolchildren. Further studies among children with severe malaria and those with high parasite densities are recommended.
Haptoglobin gene diversity and incidence of uncomplicated malaria among children in Iganga, Uganda
Authors: Lwanira Catherine Nassozi , Kironde Fred , Swedberg Göte 
Published: July 2020

Abstract
Background
Haptoglobin (Hp) is an acute phase protein that takes part in systemic regulation of heme during P.falciparum infections. Numerous genotypes of haptoglobin have been reported in malaria endemic populations. In this study, the relationship between haptoglobin genotypes and incidence of uncomplicated malaria in a cohort of children living in a malaria-endemic area of Uganda was determined.
Methods
This is an extension of a longitudinal study comprising of 423 children aged between six months and nine years, who were actively followed up for one year. Malaria episodes occurring in the cohort children were detected and the affected children treated with national policy drug regimen. Haptoglobin genotypes were determined by an allele-specific PCR method and their frequencies were calculated. A multivariate negative binomial regression model was used to estimate the impact of haptoglobin genotypes on incidence of uncomplicated malaria in the children’s cohort. In all statistical tests, a P – value of < 0.05 was considered as significant.
Results
The prevalences of the Hp1-1, Hp2-1 and Hp2-2 genotypes in the children’s cohort were 41%, 36.2% and 22.9% respectively. The overall frequency for the Hp1 allele was 59%, while Hp2 allele occurred at a frequency of 41%. After adjustment of incidence rates for age, insecticide treated bed net (ITN) use and malaria history, the incidence of uncomplicated malaria for children carrying the Hp 2–2 genotype and those with the Hp 2 − 1 genotype was statistically similar (P = 0.41). Also, no difference in the incidence of uncomplicated malaria was observed between children carrying the Hp 1–1 genotype and those having the Hp 2 − 1 genotype (P = 0.84) or between Hp 2–2 V s Hp 1–1 genotypes (P = 0.50).
Conclusions
This study showed that the Hp 1–1 and Hp 2 − 1 genotypes each occur in nearly 4 in 10 children and the Hp 2–2 genotype occurs in 2 of every 10 children. No association with incidence of uncomplicated malaria was found. Additional studies of influence of haptoglobin genotypes on P.falciparum malaria severity are needed to understand the role of these genotypes in malarial protection.