bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer DNA methylation signature quantification of lifestyle exposures and cancer prognosis
Authors: Tao Kangpei , Sutton Jaim , Flanagan James M. 
Published: February 2021

Abstract
Background: Alcohol consumption, body mass index (BMI) and cigarette smoking are among the most well-studied lifestyle cancer risk exposures which can also change the host’s epigenetic methylation patterns. Some of the changes associated with lifestyle exposure are specific and stable over time, thus, can be used to predict and quantify the exposure. Although the link between these lifestyle exposures and increased odds ratio (OR) of different cancer types is well known, their role in predicting cancer survival remains less clear. We hypothesized that by using predicted lifestyle exposures based on the methylation profiles in tumour DNA we could predict the overall survival probability in cancer patients associated with these exposures. Results: The Cancer Genome Atlas (TCGA) Pan-Cancer dataset was used to test the prognostic value of the predicted DNAmethylation (DNAm) alcohol, BMI and smoking exposures in 24 cancer types (n= 8,238 subjects). Multivariable Cox proportional hazards models with adjustment for age, cancer stage and other exposures were used to calculate the hazards ratio (HR) for overall survival associated with these predicted DNAm exposures. We observed specific cancer types with strong associations between poorer survival and higher alcohol consumption (bladder, brain, esophageal, and head and neck cancers), higher BMI (bladder, pancreatic and post-menopausal breast cancers), and smoking (B-cell lymphoma, stomach, bladder and lung cancers). Interestingly, we also observed associations between better survival from kidney cancer with higher alcohol consumption and smoking exposures. For alcohol consumption we found a positive association between HR and OR across all cancers, indicating that for cancers where alcohol is a significant risk factor, it is also associated with poorer survival (p = 0.022). This was not the case for the BMI (p = 0.548) or smoking exposures (p = 0.193). Conclusions: In conclusion, these DNAm exposure signatures may provide novel information on the relationship between these lifestyle factors and cancer outcomes.
Role of IL-1β Mutation in Peri-implantitis: Systematic Review and Meta-analysis
Authors: Mendoza Irene Lafuente-Ibáñez de , Setien-Olarra Amaia , Fuente Ana María García-de la , Aguirre-Urizar José Manuel , Marichalar-Mendia Xabier 
Published: February 2021

Abstract
Background: To perform a systematic review and meta-analysis on the presence of IL-1β polymorphisms in patients with peri-implantitis (PI). PI is the main complication associated to dental implant therapy. Although its main risk factors are history of periodontitis, poor plaque control and lack of regular maintenance, genetic susceptibility could also be a determinant factor for its appearance. Single nucleotide polymorphisms (SNP) are small mutations of the DNA, that alter the osseointegration of implants. Interleukin 1β (IL-1β) is an inflammatory protein that participates in both destruction of the extracellular matrix and reabsorption of the alveolar bone.Methods: A bibliographical research was made in PubMed, Scopus and Web of Science (keywords: "single nucleotide polymorphism", “polymorphism”, "periimplantitis", "SNP" and "implant failure"). Results: There is no significant relation between of IL-1β (+3953) SNP and PI, but there is a statistically significant association of peri-implant bone loss with the homozygotic model of IL-1β (-511) (I2=0%, p=0.555; OR: 2.255; IC: 1.040-4.889)Conclusions: Absence of a strong link between of IL-1β polymorphisms and PI must be taken with caution due to the heterogeneous methodological design, sample size and diagnostic criteria of the studies. Thus, more well-designed studies are needed, that analyse the relationship between IL-1β polymorphism and PI.
Characteristics and prognosis of colorectal signet ring cell carcinoma in patients aged ≥ 65 years
Authors: Zhou Di , Yang Yong-jing , Niu Chun-cao , Yu Yong-jiang , Diao Jian-dong 
Published: February 2021

Abstract
Objective: To evaluate the prognostic value of age on colorectal signet ring cell carcinoma (SRCC) and identify the prognosis factors of patients aged ≥ 65 years.Methods: Patients were recruited from the Surveillance, Epidemiology, and End Results (SEER) database. We ensured that all characteristics were well balanced through adopting the propensity score matching (PSM) method. In addition, the prognostic factors were evaluated by the Cox proportional hazardous model.Results: Altogether 3305 cases were enrolled, including 1564 in elderly group (aged ³65 years). As a result, more patients were female, unmarried, white, earlier AJCC stage, tumor size ≤5cm, grade III/IV and located in cecum–transverse colon in the elderly group; whereas significant fewer patients received chemotherapy and radiotherapy. After 1:1 PSM analysis, each group contained 1032 cases. As discovered by Kaplan-Meier analysis, the elderly group was associated with remarkably dismal survival compared with the younger group after PSM analysis (P=0.0091).Moreover, grade, primary site, AJCC stage, tumor size, surgery and chemotherapy were identified as the independent prognostic factors for the elderly patients.Conclusion: The prognosis of colorectal SRCC aged ≥ 65 years was worse than the younger patients. We may need strengthen the chemotherapy of the eldly colorectal SRCC.
Random World and Quantum Mechanics
Authors: Król Jerzy , Bielas Krzysztof , Asselmeyer-Maluga Torsten 
Published: February 2021

Abstract
Quantum mechanics (QM) predicts probabilities on the fundamental level which are, via Born probability law, connected to the formal randomness of infinite sequences of QM outcomes. Recently it has been shown that QM is algorithmic 1-random in the sense of Martin-Löf. We extend this result and demonstrate that QM is algorithmic ω-random and generic precisely as described by the ’miniaturisation’ of the Solovay forcing to arithmetic. This is extended further to the result that QM becomes Zermelo-Fraenkel Solovay random on infinite dimensional Hilbert spaces. Moreover it is more likely that there exists a standard transitive model of ZFC M where QM is expressed in reality than in the universe V of sets. Then every generic quantum measurement adds the infinite sequence, i.e. random real r ∈ 2ω, to M and the model undergoes random forcing extensions, M[r]. The entire process of forcing becomes the structural ingredient of QM and parallels similar constructions applied to spacetime in the quantum limit. This shows the structural resemblance of both in the limit. We discuss several questions regarding measurability and eventual practical applications of the extended Solovay randomness of QM. The method applied is the formalization based on models of ZFC, however, this is particularly well-suited technique to recognising randomness questions of QM. When one works in a constant model of ZFC or in axiomatic ZFC itself the issues considered here become mostly hidden.
Identification of Stable QTL for Time to Maturation in Virginia-Type Peanut (Arachis hypogaea L.)
Authors: Kunta Srinivas , Agmon Sara , Hedvat Ilan , Levy Yael , Chu Ye , Ozias-Akins Peggy , Hovav Ran 
Published: February 2021

Abstract
Background Time-to-maturation (TTM) is an important trait contributing to adaptability, yield and quality in peanut (Arachis hypogaea L). Virginia market-type peanut belongs to the late-maturing A. hypogaea subspecies with considerable variation in TTM within this market type. Consequently, planting and harvesting schedule of peanut cultivars including Virginia market-type need to be optimized to maximize yield and grade. Little is known regarding the genetic control of TTM in peanut due to the challenge of phenotyping and limited DNA polymorphism. Here, we investigated the genetic control of TTM within the Virginia market-type peanut using a SNP-based high-density genetic map. Methods A recombinant inbred line (RIL) population of 260 lines, derived from a cross between two Virginia-type cultivars with contrasting TTM, was phenotyped in the field for two years following a randomized complete block design. TTM was determined by maturity index (MI) using a hull-scrape method. Other agronomic traits potentially related to TTM such as pod yield (PY), harvest index (HI), branching habit (BH), 50 pod weight (50PW), 50 seed weight (50SW) and shelling percentage (SP) were recorded as well. Genotyping was performed with the Affymetrix Axiom_Arachis2 SNP array. Genetic map construction and QTL mapping were performed by the Joinmap and MapQTL software, respectively.Results A genetic map was constructed with 1833 SNP markers covering a total map distance of 1773.5 cM. Thirty QTL were identified for all measured traits. Among the four QTL regions for MI, two stable QTL regions were identified on chromosomes A04 and B03, which explained phenotypic variation of 9.3% and 11.9%, respectively. QTL for HI were found to share the same loci as MI on chromosomes B03, B05, and B06, demonstrating the possible pleiotropic effect of HI on TTM. Significant but smaller effects on MI were detected for branching habit, pod yield and shelling percentage.Conclusions This study identified consistent QTL regions conditioning TTM for Virginia market-type peanut. The information and materials generated here can be used to further develop molecular markers to select peanut idiotypes suitable for diverse growth environments.
Insights into the secondary structural ensembles of the full SARS-CoV-2 RNA genome in infected cells
Authors: Rouskin Silvi , Lan Tammy , Allan Matthew , Malsick Lauren , Khandwala Stuti , Nyeo Sherry , Sun Yu , Guo Junjie , Bathe Mark , Griffiths Anthony 
Published: February 2021

Abstract
SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on native RNA structures in SARS-CoV-2 and most putative regulatory sequences are functionally uncharacterized. Here we report secondary structure ensembles of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and the algorithm ‘detection of RNA folding ensembles using expectation–maximization’ clustering (DREEM). Our results reveal previously undescribed alternative RNA conformations across the genome, including structures of the frameshift stimulating element (FSE), a major drug target, that are drastically different from prevailing in vitro population average models. Importantly, we find that this structural ensemble promotes frameshifting rates (~40%) similar to in vivo ribosome profiling studies and much higher than the canonical minimal FSE (~20%). Overall, our result highlight the value of studying RNA folding in its native, dynamic and cellular context. The genomic structures detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics.
A High-Fat Diet Increases Activation of The Glucagon-Like Peptide-1-Producing Neurons in The Nucleus Tractus Solitarii; An Effect That is Partially Reversed By Drugs Normalizing Glycaemia
Authors: Lietzau Grazyna , Ntika Stelia , Pintana Hiranya , Tracy Linda , Klein Thomas , Nyström Thomas , Darsalia Vladimer , Patrone Cesare , Krizhanovskii camilla 
Published: February 2021

Abstract
Glucagon-like peptide-1 (GLP-1) is a peripheral incretin and centrally active peptide produced in the intestine and nucleus tractus solitarii (NTS), respectively. GLP-1 not only regulates metabolism but also improves cognition and is neuroprotective. While intestinal GLP-1-producing cells have been well characterized, less is known about GLP-1-producing neurons in NTS. We hypothesized that obesity-induced type 2 diabetes (T2D) impairs the function of NTS GLP-1-producing neurons and glycaemia normalization counteracts this effect. We used immunohistochemistry/quantitative microscopy to investigate the number, potential atrophy, and activation (c-Fos-expression based) of NTS GLP-1-producing neurons, in non-diabetic versus obese/T2D mice (after 12 months of high-fat diet). NTS neuroinflammation was also assessed. The same parameters were quantified in obese/T2D mice treated from month 9 to 12 with two unrelated anti-hyperglycemic drugs: the dipeptidyl peptidase-4 inhibitor linagliptin and the sulfonylurea glimepiride. We show no effect of T2D on the number and volume but increased activation of NTS GLP-1-producing neurons. This effect was partially normalized by both anti-diabetic treatments, concurrent with decreased neuroinflammation. Increased activation of NTS GLP-1-producing neurons could represent an aberrant metabolic demand in T2D/obesity, attenuated by glycaemia normalization. Whether this effect represents a pathophysiological process preceding GLP-1 signaling impairment in the CNS, remains to be investigated.
Rat Bone Marrow Derived Mesenchymal Stem Cells (rBMMSCs) Encapsulated in Collagen Type I Containing Platelet-Rich Plasma for Osteoarthritis Treatment in Rat model
Authors: Islam Md Shahidul , Ebrahimi-Barough Somayeh , Mahtab Mamun Al , Shirian Sadegh , Aghayan Hamid Reza , Arjmand Babak , Allahverdi Amir , Esmaeili Faezeh , Taghdiri Vajiheh , Sadegh Amin Bigham , Ai Jafar 
Published: February 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Relationship Between Masked Hypertension Measured by Ambulatory Blood Pressure Monitoring and Left Ventricular Global Longitudinal Strain
Authors: Fu Ming , Hu Xiangming , Yi Shixin , Sun Shuo , Zhang Ying , Feng Yingqing , Zhou Yingling , Geng Qingshan , Dong Haojian 
Published: February 2021

Abstract
Masked hypertension (MHT), as an independent clinical entity, its subclinical cardiac dysfunction can be early detected by left ventricular global longitudinal strain (GLS). Yet the relationship between MHT and GLS is still unclear. Therefore, we tried to conduct a community-based cross-sectional study to define this relationship. A total of 308 consecutively enrolled participants from Dongguan, China, were divided into non-hypertension (NHT) and MHT groups. Baseline characteristics were recorded, and 2-dimentional speckle-tracking echocardiography and 24-hour ambulatory blood pressure monitoring were performed. Univariate and multivariate linear regression analyses were used to assess the associations between MHT and GLS, and the dose–response curve was plotted to demonstrate their relationship. The mean age of the NHT and MHT groups was 57 and 59 years, respectively. Signs of left ventricular diastolic function, E/A (1.01 ± 0.26 vs 0.86 ± 0.23, P < 0.001) and E/e’ (8.58 ± 2.02 vs 11.70 ± 3.37, P < 0.001) were reduced in the MHT group while those of the NHT group were nearly normal. The MHT group also showed a significantly lower (‘worse’) GLS than NHT (-15.79% ± 2.81% vs -19.62% ± 1.67% vs , P < 0.001) while left ventricular ejection fraction (LVEF) did not differ between the groups. Worse GLS was independently and significantly associated with MHT both in univariate (odds ratio [OR]: 1.97, P < 0.001) and stepwise multivariate regression analysis (OR: 1.99, P < 0.001). Further analysis showed adjusted nonlinear correlation between MHT and GLS. Our study described the relationship between MHT and GLS and concluded that -14% of GLS as the cut-off value reflected MHT-associated myocardial injury before LVEF decreases.
New-born Thermal Care in Western Uttar Pradesh – Gap Analysis Between Knowledge and Practices
Authors: Srivast Anurag , Saxena Sumit , Srivast Payal , Mahmood Syed Esan , Pandey Ruchi , Saxena Anju 
Published: February 2021

Abstract
Background: The provision of health care services including maternal and new-born care is considered to be a dynamic system of entitlement and obligations among people, the communities, service providers, and the concerned governments. Thermal control remains poor in new-born owing to immaturity of the thermoregulatory center and new-born become vulnerable to hypothermia especially premature babies, intrauterine growth retardation and LBW babies and even normal babies. Methods: The study population comprised women of reproductive age (15 to 49 years) who have delivered a live baby within the past 12 weeks prior to the conduct of study. Out of 6 block, most populous villages were selected, one near the CHC and 2nd farthest from CHC and high priority was given to villages where ASHA and ANM are appointed.61 villages of 6 blocks were covered under the study. Results: The knowledge on thermal protection of baby, 60.9% of the respondents were well aware about how to keep baby warm after delivery,71.4% of respondents knew that baby should be dried soon after birth, 64.9% of the respondents had idea of time to dry the baby, 69.6% of the respondents had knowledge that baby should be wrapped soon after birth.Conclusion: The findings of the study provide an insight into the existing knowledge and necessitate a need for quantitative studies in the study area to access knowledge & practices related to thermal protection of new-born. The authors emphasize on a need for improving community awareness for promotion of neonatal care and improve health system to meet the demands of birthing mothers and needs of neonates.
Evaluation of Transfer of Lead (Pb) in Soil Plant Animal System Assessment of Consequences of its Toxicity
Authors: Chen Fu , Ma Jing , Khan Zafar Iqbal , Ahmad Kafeel , Ahmed Tasneem , Malik Ifra Saleem , Ashfaq Asma , Munir Mudasra , Nazar Sonaina , Munir Zunaira , Ejaz Abid , Nadeem Muhammad , Mustafa Abd El Zehar M.A. , Al-Ghamdi Abdullah Ahmed , Alshamasi Fatin K.I. , Elshikh Mohmed Soliman 
Published: February 2021

Abstract
The instant endeavor was undertaken for determination of lead (Pb) in water, soil, forage and cow’s blood domesticated in contaminated area of heavy automobiles’ exhaust in Sahiwal town of district Sargodha Pakistan. Water samples showed that the concentration of lead (Pb) ranged from 1.14 mg kg− 1 to 0.44 mg kg− 1 at all sites. It was maximum at site 5 and minimum at site 2. Soil samples showed the concentration of Pb at all sites ranged from 1.58 mg kg− 1 to 0.279 mg kg− 1. It was maximum in soil where Avena sativa was grown at site 5 and was found minimum in soil where Zea mays was grown at site 2. While among samples of forage, the concentration of Pb ranges from 0.048 mg kg− 1 to 2.002 mg kg− 1. The highest Pb amount was found in Brassica campestris at site 1 and the minimum was recorded in Trifolium alexandrinum at site 2. Finally, the blood samples of cow depicted that concentration of Pb ranged from 4.468 mg kg− 1 to 0.217 mg kg− 1. It was maximum at site 1 and minimum at site 3.
Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells
Authors: Luo Jinsong , Liu Hong , Li Daniel K. Jun , Song Bin , Zhang Yi 
Published: February 2021

Abstract
Background
Mitochondrial transcription factor A (TFAM) is associated with a number of neurodegenerative diseases and also with asthma. TFAM deficiency-induced mitochondrial DNA stress primes the antiviral innate immune response in mouse embryonic fibroblasts. However, the role of TFAM in asthma related inflammation remains obscure. The purpose of this study was to investigate the regulatory mechanism of TFAM in asthma.
Results
In this study, we overexpressed TFAM in human lung epithelial cells (A549), then obtained the TFAM-regulated transcriptome by Illumina sequencing technology. Transcriptome analysis revealed that TFAM overexpression down-regulated and up-regulated the expression of 642 and 169 genes (DEGs), respectively. The TFAM-repressed genes were strongly enriched in cytokine-mediated signaling pathway, type I interferon- and INF-γ-mediated signaling pathways, and viral response pathways. We also revealed that 2563 alternative splicing events in 1796 genes (ASG) were de-regulated upon TFAM overexpression. These TFAM-responding ASGs were enriched in DNA repair, nerve growth factor receptor signaling pathway, and also transcription regulation. Further analysis revealed that the promoters of TFAM-repressed DEGs were enriched by DNA binding motifs of transcription factors whose alternative splicing was regulated by TFAM.
Conclusions
These findings suggested that TFAM regulates not only immune response gene expression in human lung epithelial cells, but also pre-mRNA alternative splicing which may mediate transcriptional regulation; this TFAM-centered gene regulation network could be targeted in developing therapies against various diseases.
Effectiveness of Yijinjing on Cognitive Functions in Post-stroke Patients With Mild Cognitive Impairment: Study Protocol for a Randomized Controlled Trial
Authors: Xue Xin , Jin Xue-Xing , Luo Kai-Liang , Liu Xin-Hao , Zhang Li , Hu Jun 
Published: February 2021

Abstract
Background: Statistics show that every year, 5.4 million people in the world suffer a stroke. Post-stroke cognitive impairment (PSCI) is one of the most common complications after stroke with a rate of 75%, which leads to decreased functions for independent living and reduced quality of life (QOL). Exercise training has been reported to be useful to improve the cognitive functions of post-stroke patients. Yijinjing, a traditional Chinese Qigong exercise characterized by an integration of mind and body in moderate exercise intensity, can improve cognitive functions of PSCI patients. This study aims to explore the feasibility and effectiveness of the Yijinjing exercise in this regard.Methods: A single-blind, randomized controlled trial will be employed with evaluations at three and six months. 72 PSCI patients will be recruited and randomly assigned to the Yijinjing exercise intervention group or the control group (1:1). Participants in the control group will receive routine rehabilitation therapies, including occupational therapy, physical therapy, acupuncture therapy, and health education 5 times a week for 3 months. The intervention group will receive a 12-week routine rehabilitation therapy combined with the Yijinjing exercise intervention for 40 minutes each session and 3 sessions a week. The primary outcome of cognition will be measured by the Montreal Cognitive Assessment scale (MoCA). Secondary outcomes include executive function, memory function, visuospatial function, sleep quality, gait and motor function, activity of daily living (ADL), and quality of life (QOL).Discussion: Current evidence has reported the effectiveness of traditional Chinese exercise in improving the post-stroke population’s motor functions. This research is a randomized controlled trial that evaluates traditional Chinese exercise’s effectiveness for PSCI patients. It is expected to expand the traditional Chinese exercise scope and provide a new treatment approach for stroke populations with cognitive impairments.Trail registration: Chinese Clinical Trial Registry, ChiCTR1900026532. Registered on 13 October 2019.