bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling multivariate associations with parental loneliness via perceived closeness and support
Authors: Hall Helen K. , Millear Prudence M. , Summers Mathew J. 
Published: June 2020

Objectives: Recent research findings suggest the prevalence of loneliness is increasing in middle-aged adults parenting children, challenging the notion this demographic is typically at low risk of loneliness. Method: The current study applied the cognitive discrepancy model as theoretical foundation to investigate the variance of individual and situational variables contributing to perceived closeness and support and consequently loneliness. Structural equation modeling was employed to identify multivariate contributors associated with parental loneliness in 323 parents with an average age of 37.69 ( SD = 5.96) years. Results: Results support the theoretical proposition that individual factors, rather than situational, contribute to a greater variance of a perceived gap in relationship closeness and support. It was found that emotional competence, ability to forgive, emotional stability, extraversion, and lower mood levels are significant contributors to a small cognitive gap in perceived relationship closeness and protective against parental loneliness. Relationship status contributed a weak direct effect over perceived relationship closeness and support. Situational factors, including number of children and household income, were non-significant risks for loneliness. Overall, the model accounted for 65% of perceived relationship closeness and support and 85% of loneliness. The limitation of small number of male participants is discussed with regard to the existing research gap investigating male loneliness. Conclusion: A Pathway to Loneliness Risk Model is proposed, demonstrating that through increasing an individual’s intrapersonal and interpersonal resources and challenging negative cognitive biases and maladaptive schemas regarding an individual’s perception of their relationships, may lead to a reduction in the individual’s risk for loneliness.
The Association of Body Mass Index and Adverse Clinico-Pathological Characteristics of Non-Metastatic Breast Cancer Among Patients from Saudi Arabia
Authors: Alghamdi Bashayer , Alghamdi Reema , Khallaf Raghad , faisal Konooz , Bishnaq Raghad , Abusanad Atlal 
Published: June 2020

Background: Obesity is a global health problem, especially in the Arab region, the prevalence of obesity is increasing. High body mass index (BMI) is a risk factor for many diseases, including cancer. Noticeably, breast cancer (BC) cases in Saudi Arabia occur at a younger age than western countries and different life style behaviours such as maintaining healthy body weight and physical activity may play a role in this. In this study, we aimed to investigate the association between BMI and BC clinicopathological features. Methods: This retrospective study was conducted by reviewing the records of females diagnosed with non-metastatic BC over four years. The association between BMI and patients’ demographics, BC histological type, receptor status, differentiation grade, tumor size, involvement of axillary lymph node, and performed procedures was analysed. Result: We studied 315 patients with non-metastatic BC. The mean age at the time of diagnosis was 52.43 years ±11.63. The mean BMI was 30.21±5.77. The mean tumor size was 3.19 cm ± 3.52. We found that the mean age of diagnosis is significantly greater in obese women than other BMI groups with a P-value = 0.025. A significant relationship was observed between BMI classification and tumor size in obese female patients aged ⩾ 40 years with P-value=0.022 Conclusion: The relationship between BMI and BC is still not clear, in this study we found an association with age at diagnosis and tumor size in older patients, characteristics as histological types, receptor status, lymph node involvement, and grade were not statistically significant.
Breast Fibromatosis, A Rare Benign Tumor Mimicking Breast Carcinoma: A Case Report
Authors: Samaka R. M. , Abu-Zeid A. Y. 
Published: June 2020

Objectives: Fibromatosis is a rare breast lesion that is considered locally aggressive tumor without metastasis. It doesn't need more than surgical excision with clean margins as a treatment but the recurrence is very common. Breast fibromatosis clinically mimics other lesions as fibromatosis like metaplastic tumor of breast. Therefore, recognition of breast fibromatosis is important for surgeons and histopathologists, in order to set a proper plan for management and avoid unnecessary extensive surgery. Comprehensive search revealed only 33 case reports as it's compromising less than 0.2% of all primary breast tumor. Case summary Methods and Materials: A 35 years old female patient complained of palpable left breast mass for four months. Her imaging belonged to BI-RAD (4) assessment category. The pathological examination of the core biopsy showed B3; spindle cell lesion. The patient underwent surgical excision of the mass and the histopathologic assessment revealed an infiltrative uncapsulated lesion composed of proliferated spindle shaped cells (mixed fibroblasts and myofibroblast like cells) arranged in sweeping fascicles with occasional extravasated RBCs. There was no mitosis, necrosis or atypia. There was no associated hyperplasia, atypical hyperplasia, insitu or invasive components. Results: Immunohistochemical studies showed positivity for SMA and B- Catenine and negativity for Pan CK and P63 that confirm our diagnosis. Conclusion: The conclusion of this case report is to stress upon keeping breast fibromatosis in mind as a potential differential diagnosis for fibromatosis like metaplastic carcinoma and other mimics of spindle cell lesions in breast.
Nusap1, Melk and L1cam Expression in Cervical Cancer Tissues; Prognostic and Clinicopathological Implications
Authors: Harb Ola A. , Elfeky Mariem A. , Elshafaay Basant Sh , Obaya Ahmed A. , Awd Amr A. , Alkilany Mohamed M. , Gertallah Loay M. 
Published: June 2020

Background: It is important to identify of novel therapeutic targets for cervical carcinoma. Nucleolar and spindle associated protein 1 (NUSAP1) could be able to bind microtubules, and has important role in spindle formation and mitotic progression. Maternal embryonic leucine zipper kinase (MELK) is a cell cycle related conserved protein kinase that is involved in control and regulation of the cell cycle, apoptosis, and carcinogenesis. The L1 cell adhesion molecule (L1-CAM) was discovered as a protein which has an essential role in cell migration and axon guidance in the nervous system. The Aim of This Study Is to investigate the tissue protein expression of NUSAP1, MELK and L1CAM in tissues of cervical carcinoma and to detect their prognostic roles. Methods: Expression of NUSAP1, MELK and L1CAM was evaluated in sections from 62 cases of cervical carcinoma using immunohistochemistry we followed our patients for 3 years correlate their expression with clinicopathological parameters and patients outcome. Results: High levels of NUSAP1, MELK and L1CAM expression was positively related to older age of the patients, high grade of the tumor, lympho-vascular invasion, advanced FIGO stage, poor survival rates and higher recurrence rate after successful therapy (p<0.001). L.N metastases (p=0.002), distant metastases (p=0.003). There are statistically significant positive association between NUSAP1, MELK and L1CAM Phi correlation coefficient= + 0.87 and + 0.721 respectively (p<0.001). Conclusion: NUSAP1, MELK and L1CAM are considered markers of poor prognosis in cervical carcinoma cells.
The Effect of Undergraduate Major Choices on the Earnings of Sub-Saharan African Immigrant and Native-Born College Graduates
Authors: Seeborg Michael , Ikpebe Ene 
Published: June 2020

A very high percentage of sub-Saharan African college-graduate immigrants in the United States have college degrees in science, technology, engineering, and mathematics (STEM) disciplines compared with native-born college graduates. This study uses a pooled cross-section (2013–2018) from the American Community Survey to compare the distribution of undergraduate majors of sub-Saharan African immigrants and native-born college graduates. We estimate ordinary least square (OLS) earnings functions that include detailed college major variables. We find that undergraduate major area of study is a significant predictor of earnings and that there is an overrepresentation of sub-Saharan African immigrants with high-paying undergraduate majors. However, after controlling for human capital differences, college-educated African immigrants have not achieved pay equity with their native-born counterparts. JEL Classifications: J61, J15, J26, I21
Respiratory Variation in Carotid Artery Peak Systolic Velocity Is Unable to Predict Fluid Responsiveness in Spontaneously Breathing Critically Ill Patients When Assessed by Novice Physician Sonologists
Authors: Abbasi Adeel , Nayeemuddin Mohammed , Azab Nader , Schick Alexandra , Lopardo Thomas , Phillips Gary S. , Merchant Roland C. , Levy Mitchell M. , Blaivas Michael , Corl Keith A. 
Published: June 2020

Background: Respiratory variation in carotid artery peak systolic velocity (ΔVpeak) assessed by point-of-care ultrasound (POCUS) has been proposed as a noninvasive means to predict fluid responsiveness. We aimed to evaluate the ability of carotid ΔVpeak as assessed by novice physician sonologists to predict fluid responsiveness. Methods: This study was conducted in 2 intensive care units. Spontaneously breathing, nonintubated patients with signs of volume depletion were included. Patients with atrial fibrillation/flutter, cardiogenic, obstructive or neurogenic shock, or those for whom further intravenous (IV) fluid administration would be harmful were excluded. Three novice physician sonologists were trained in POCUS assessment of carotid ΔVpeak. They assessed the carotid ΔVpeak in study participants prior to the administration of a 500 mL IV fluid bolus. Fluid responsiveness was defined as a ≥10% increase in cardiac index as measured using bioreactance. Results: Eighty-six participants were enrolled, 50 (58.1%) were fluid responders. Carotid ΔVpeak performed poorly at predicting fluid responsiveness. Test characteristics for the optimum carotid ΔVpeak of 8.0% were: area under the receiver operating curve = 0.61 (95% CI: 0.48-0.73), sensitivity = 72.0% (95% CI: 58.3-82.56), specificity = 50.0% (95% CI: 34.5-65.5). Conclusions: Novice physician sonologists using POCUS are unable to predict fluid responsiveness using carotid ΔVpeak. Until further research identifies key limiting factors, clinicians should use caution directing IV fluid resuscitation using carotid ΔVpeak.
Annual changes in the prevalence of asthma may be related to air pollution in Fukuoka: 29 years of observation
Authors: Odajima Hiroshi , Kawano Toshiaki , Wakatsuki Masatoshi , Akaminea Yuko , Okabe Koki , Oki Tuyoshi , Matsuzaki Hiroshi , Murakami Yoko , Iwata Mihoko , Taba Naohiko , Motomura Chikako , Honjo Satoshi , Ninomiya Takahito 
Published: June 2020

The relationship between the annual changes of the prevalence of bronchial asthma (BA) and that of concentrations of air pollutants has not been reported.We studied the annual prevalence of BA, remission of BA, and wheeze in children at the same five elementary schools in Fukuoka city, Japan, in October to November from 1988 to 2016 by the same methods using the same questionnaire.Annual changes in the prevalence of asthma among boys were related to changes in the air concentrations of NO (r=0.708), NO2(r=0.665) suspended particulate matter (SPM) (r=0.803), and smoking rate (r=0.741), but there were no such relationships among girls. Annual changes in the prevalence of wheeze were related to changes of NO, NO2, SPM, and smoking rate among boys and girls (NO: r=0.650, 0.660; NO2: r=0.556, 0.490; SPM: r=0.582, 0.518; smoking rate: r=0.656, 0.593, respectively) (all of the above are significant with p<0.05). There was no relationship between remission of BA and any of the pollutants.Annual changes in the prevalence of boys' BA and boys' and girls' wheeze among first-grade children (age 6 or 7 years) in Fukuoka were correlated with changes in the concentration of air pollutants (SPM, NO, NO2or smoking rate).Recent decrease of asthma prevalence in this area might be related to the decreasing tendency of air pollutant concentration. The causal relationship between the two will need to be verified in the future
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Authors: Yousif Ayman , Drou Nizar , Rowe Jillian , Khalfan Mohammed , Gunsalus Kristin C. 
Published: June 2020

Abstract
Background
As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).

Results
NASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.

Conclusions
NASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data
Authors: Chen Xiaoying , Zhang Bo , Wang Ting , Bonni Azad , Zhao Guoyan 
Published: June 2020

Abstract
Background
High throughput RNA sequencing is a powerful approach to study gene expression. Due to the complex multiple-steps protocols in data acquisition, extreme deviation of a sample from samples of the same treatment group may occur due to technical variation or true biological differences. The high-dimensionality of the data with few biological replicates make it challenging to accurately detect those samples, and this issue is not well studied in the literature currently. Robust statistics is a family of theories and techniques aim to detect the outliers by first fitting the majority of the data and then flagging data points that deviate from it. Robust statistics have been widely used in multivariate data analysis for outlier detection in chemometrics and engineering. Here we apply robust statistics on RNA-seq data analysis.

Results
We report the use of two robust principal component analysis (rPCA) methods, PcaHubert and PcaGrid, to detect outlier samples in multiple simulated and real biological RNA-seq data sets with positive control outlier samples. PcaGrid achieved 100% sensitivity and 100% specificity in all the tests using positive control outliers with varying degrees of divergence. We applied rPCA methods and classical principal component analysis (cPCA) on an RNA-Seq data set profiling gene expression of the external granule layer in the cerebellum of control and conditional SnoN knockout mice. Both rPCA methods detected the same two outlier samples but cPCA failed to detect any. We performed differentially expressed gene detection before and after outlier removal as well as with and without batch effect modeling. We validated gene expression changes using quantitative reverse transcription PCR and used the result as reference to compare the performance of eight different data analysis strategies. Removing outliers without batch effect modeling performed the best in term of detecting biologically relevant differentially expressed genes.

Conclusions
rPCA implemented in the PcaGrid function is an accurate and objective method to detect outlier samples. It is well suited for high-dimensional data with small sample sizes like RNA-seq data. Outlier removal can significantly improve the performance of differential gene detection and downstream functional analysis.
Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)
Authors: Xiao Huilin , Wang Chaoping , Khan Nadeem , Chen Mengxia , Fu Weihong , Guan Le , Leng Xiangpeng 
Published: June 2020

Abstract
Background
The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

Results
We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

Conclusions
In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.
Xylitol and erythritol inhibit real-time biofilm formation of Streptococcus mutans
Authors: Loimaranta Vuokko , Mazurel Danuta , Deng Dongmei , Söderling Eva 
Published: June 2020

Abstract
Background
Regular consumption of xylitol decreases the number of cariogenic streptococci in dental plaque. In vitro biofilm models to study the mechanism of xylitol action have been set-up, but the obtained results are contradictory. Biofilm growth is a dynamic process with time-specific characteristics that may remain undetected in conventional end-point biofilm tests. In this study we used an impedance spectroscopy instrument, xCELLigence Real Time Cell Analyzer (RTCA), that allows label-free, non-invasive real-time monitoring of biofilm formation, to explore effects of xylitol on biofilm formation by Streptococcus mutans. Based on the obtained information of biofilm dynamics, we assessed the number of viable bacteria, the polysaccharide content, and the expression levels of selected genes involved in glucan-mediated biofilm formation in different biofilm stages. Xylitol inhibition was compared with that of erythritol; another polyol suggested to have a positive impact on oral health.

Results
Our results showed that real-time monitoring provided new information of polyol-induced changes in S. mutans biofilm formation dynamics. The inhibitory effect of polyols was more pronounced in the early stages of biofilm formation but affected also the measured total amount of formed biofilm. Effects seen in the real-time biofilm assay were only partially explained by changes in CFU values and polysaccharide amounts in the biofilms. Both xylitol and erythritol inhibited real-time biofilm formation by all the nine tested S. mutans strains. Sensitivity of the strains to inhibition varied: some were more sensitive to xylitol and some to erythritol. Xylitol also modified the expression levels of gbpB, gtfB, gtfC and gtfD genes that are important in polysaccharide-mediated adherence of S. mutans.

Conclusion
The erythritol- and xylitol- induced inhibition of biofilm formation was only partly explained by decrease in the number of viable S. mutans cells or the amount of polysaccharides in the biofilm matrix, suggesting that in addition to reduced proliferation also the matrix composition and thereby the surface attachment quality of biofilm matrix may be altered by the polyols.
Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)
Authors: Li Mengdi , Cao Aqin , Wang Ruihua , Li Zeyu , Li Shaoqing , Wang Jianbo 
Published: June 2020

Abstract
Background
Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported.

Results
Here, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC2F12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies.

Conclusions
Taken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.