bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA polymerase II and PARP1 shape enhancer-promoter contacts
Authors: Danko Charles , Barshad Gilad , Lewis James , Chivu Alexandra , Abuhashem Abderhman , Krietenstein Nils , Rice Edward , Rando Oliver J. , Hadjantonakis Anna-Katerina 
Published: July 2022

Abstract
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we studied enhancer-promoter contact architecture and communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription, and perturbations to transcription-associated proteins and thousands of candidate enhancers. Contact frequency between functionally validated enhancer-promoter pairs was most enriched near the +1 and +2 nucleosomes at enhancers and target promoters, indicating that functional enhancer-promoter pairs spend time in close physical proximity. Blocking RNA polymerase II (Pol II) caused major disruptions to enhancer-promoter contacts. Paused Pol II occupancy and the enzymatic activity of poly (ADP-ribose) polymerase 1 (PARP1) stabilized enhancer-promoter contacts. Based on our findings, we propose an updated model that couples transcriptional dynamics and enhancer-promoter communication.
Comparing Avian Species Richness Estimates from Structured and Semi-Structured Citizen- Science Data
Authors: Shen Fang-Yu , Ding Tzung-Su , Tsai Jo-Szu 
Published: July 2022

Abstract
Citizen science, including structured and semi-structured forms, has become a powerful tool to collect biodiversity data. However, semi-structured citizen science data have been criticized for higher variability in quality, including less information to adjust for imperfect detection. Species richness estimators may quantify bias in estimates. Here, we test the effectiveness of Chao1 estimator in eBird (semi-structured) by comparing it to averaged species richness in Breeding Bird Survey Taiwan, BBS (structured) and quantifying bias. We then fit a power function to compare bias while controlling for differences in count duration. The Chao1 estimator increased the species richness estimates from eBird data from 56% to 75% of the BBS. When singleton species predominated in eBird data, Chao1 overestimated richness by 7.45 times. Effects of short duration samples and variability in detectability skills of observers can lead to the biased estimates. Using the Chao1 estimator improved estimates of species richness from semi-structured data, but the strong effect of singleton species on bias, especially in short duration counts, should be evaluated in advance to reduce the uncertainty of estimation processes.
2L polyethylene glycol combined with castor oil versus 4L polyethylene glycol for bowel preparation before colonoscopy among inpatients
Authors: Xiong Zhe , Fang Ying , Feng Fangfang , Cheng Yiming , Zhang Huahui , Huo Chunyan , Huang Jin 
Published: July 2022

Abstract
Objectives: The study aimed to compare the cleansing effect, compliance and adverse of polyethylene glycol 2L with castor oil and polyethylene glycol 4L on bowel preparation prior to colonoscopy in inpatients.Methods: Our study retrospectively analyzed the medical records and colonoscopy reports of inpatients (n=673) who underwent colonoscopy at the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, and the inpatients were divided into two groups according to different bowel preparation protocols. BBPS is used to assess the degree of bowel cleanliness before colonoscopy. We statistically analyzed and compared the degree of bowel cleansing between 2L-PEG-CaO and 4L-PEG group, as well as the compliance and adverse effects of the medication in both groups.Results: Among 673 patients undergoing colonoscopy, 330 were prescribed 4L-PEG and 343 2L-PEG-CAO. Both groups of inpatients were matched for baseline characteristics. In the 4L-PEG and 2L-PEG-CaO groups, adequate bowel preparation rate was 72.4% and 77.3% (P=0.148), BBPS scores was 6.79±1.51 and 7.03±1.71 (P=0.056), and adverse event rate was 68.2% and 30.0% (P<0.001), respectively.Conclusion: The 2L-PEG combined with castor oil is an effective and safe cleansing regimen for bowel preparation and is relatively inexpensive and suitable for wider use.
The rural-urban divide of the relationship between polygynous marriage structures, multiple marriage unions, and self-rated happiness among currently married Ghanaian women
Authors: Ansah Kenneth Owusu , Dziwornu Emmanuel , Frimpong-Manso Kwabena , Dey Nutifafa Eugene Yaw , Duodu Precious Adade , Agbadi Pascal 
Published: July 2022

Abstract
Polygyny and multiple marital unions are generally associated with overall happiness deficits, yet the rural-urban differentials of these associations are not thoroughly interrogated. This study uses a nationally representative dataset of 7785 married and in-union Ghanaian women aged 15–49 years to investigate the rural-urban differences in the relationship between polygyny, multiple marital unions, and happiness. Findings show that rural married and in-union women in polygynous relationships [APOR = 0.760, 95% CI:0.60, 0.96] and were married more than once [APOR = 0.79, 95% CI:0.66, 0.94] were less likely to be happy. Age, education, household wealth, and region of residence were significantly associated with happiness only among rural married women. Both rural and urban married and in-union women in the Upper West and Upper East Regions were more likely to be happy than married women in the Greater Accra Region. Policies should enable rural women in polygyny and those in their second or more marital unions with happiness-enabling resources.
Modularity in design and production relationships: a field study in two automakers
Authors: Kubota Flavio Issao , Cauchick-Miguel Paulo Augusto , Hsuan Juliana , Lacerda Daniel Pacheco 
Published: July 2022

Abstract
Modularity-in-design (MID) and modularity-in-production (MIP) relationship has been gaining the attention of scholars and practitioners along the years. However, the literature does not specify how this connection occurs and its implications. This paper analyzes the relationship between MID and MIP within the automotive scenario and investigates its main technical and organizational implications. Through an abductive, matched-pair case study carried out in two large automakers, the study gathered data from interviews, on-site observations, and field notes from all interactions within the plants. The paper indicates that (i) both automakers prioritize modular design before modular production, characterizing a product-related approach, and (ii) the investigated automotive companies have different approaches when developing MID. One automaker focuses on product functionalities to develop the modules; the other company dedicates efforts towards a MID-MIP relationship through the industrial condominium concept. Results indicate significant propositions to be tested regarding MID-MIP connection, with original insights from two make-to-order (MTO) automotive companies.
Signal processing with MATLAB and Python for real-life structural health monitoring: A comparative implementation for post-processing
Authors: Patel Chandrabhan , Garg Naman , Panigrahi SK , Kumar Vikesh 
Published: July 2022

Abstract
Signal and data processing are necessary for analyzing the experimental data. Techniques of signal processing are well defined and handy for real-life application but applying those techniques to experimental data is challenging for the researcher. In structural health monitoring, post-processing helps remove noise and residuals from the data recorded through sensors. Various software and programming can help achieve the best signal processing algorithms. Each package has its solver to solve the signal processing algorithms. Due to the countless options available for signal processing, it is foremost to choose the best and most reliable package to solve the problem. Nowadays, MATLAB and Python are two packages that are reliable, popular, and accurate for multiple applications. This article compares MATLAB and Python for signal processing for structural health monitoring applications. File handling, simulating the signals, filter realization, filter response, and adding and removing noise from the signal are discussed and implemented for structural health monitoring. The real-life demonstration has been done using a simply supported beam, instrumented with Fiber Bragg Grating strain sensors. A comparative study of signal processing is done keeping structural health monitoring as the focus area.
Costunolide Protects Myocardial from Ischemia Reperfusion Injury through Nrf2 Activation
Authors: Li Weixin , Luo Yue , Huang Zhuqi , Shen Siyuan , Dai Chengyi , Shen Sirui , Liang Guang , Luo Wu 
Published: July 2022

Abstract
Purpose
Costunolide (Cos) is a naturally occurring sesquiterpene lactone that exhibits anti-oxidative properties. In this study, we demonstrated the protective mechanism of Cos against ischemia/reperfusion (I/R)-induced heart injury.
Methods
C57BL/6 mice were pretreated with Cos (10 mg/kg/day) or 1% CMC-Na for 1 week. The left anterior descending coronary artery (LAD) was ligated for 30 minutes for ischemia, and followed by ligation release for 4 hours for reperfusion. H9c2 cells challenged with tert-butyl hydroperoxide (TBHP) were used for in vitro studies.
Results
Pretreatment of Cos significantly reduced myocardial infarct size, serum CK-MB and LDH level in I/R injured heart. Cos administration significantly attenuated the amount of reactive oxygen species (ROS) and ameliorated the apoptosis both in in vitro and in vivo studies. Further investigation revealed that Cos significantly increased the expression of heme oxygenase 1 (HO-1) and NAD(P)H [quinone] dehydrogenase 1 (NQO-1). Meanwhile Cos increased B-cell lymphoma-2(Bcl-2) and decreased the BCL2-Associated X Protein (Bax) protein level. Silence of nuclear factor erythroid 2-related factor (Nrf2) significantly reverses the protective effect of Cos in TBHP-challenged H9C2 cells.
Conclusion
Our data clearly showed that Cos reduced TBHP challenged H9c2 cells and attenuated myocardial I/R injury through Nrf2 activation. These results indicate that Cos might be benefit in the therapy of myocardial I/R injury.
Clinical significance and potential application of cuproptosis-related genes in gastric cancer
Authors: Yan Jianing , Lin Yifan , Ye Guoliang , Shao Yongfu 
Published: July 2022

Abstract
Worldwide, gastric cancer (GC) is a common lethal solid malignancy with a poor prognosis. Cuproptosis is a novel kind of cell death mediated by protein lipoylation and the relationship between cuprotosis and GC prognosis. We estimated the expression level and prognostic values of pyroptosis-related genes (CRGs) in GC samples and related mechanisms using public databases and bioinformatics. Our results revealed that FDX1, LIAS, and MTF1 were differentially expressed in GC samples and exhibited important prognostic significance in the TCGA cohort. We constructed a nomogram model for overall survival and disease-specific survival prediction and validated it via calibration plots. Mechanistically, immune cell infiltration prominently affected the survival time of GC patients. Moreover, protein‒protein interaction network, KEGG pathway and gene ontology enrichment analyses demonstrated that FDX1, LIAS, MTF1 and related proteins played key roles in the tricarboxylic acid cycle and cuprotosis. GEO database validation showed that the expression levels of FDX1, LIAS, and MTF1 were consistent with those in the TCGA cohort. In conclusion, FDX1, LIAS, and MTF1 could serve as potential prognostic biomarkers for GC patients and provide novel targets for immunotarget therapy.
Progressive resolution optimizer (PRO) predominates over photon optimizer (PO) in sparing of spinal cord for spine SABR VMAT plans
Authors: Son Sangjun , Park So-Yeon 
Published: July 2022

Abstract
Background: we assessed the performance of the optimization algorithms by comparing volumetric modulated arc therapy generated by a progressive resolution optimized (VMATPRO) and photon optimizer (VMATPO) in terms of plan quality, MU reduction, sparing of the spinal cord (or cauda equina), and plan complexity.Methods: Fifty-seven patients who received spine stereotactic ablative radiotherapy (SABR) with tumors located in the cervical, thoracic, and lumbar spine were retrospectively selected. For each patient, VMATPRO and VMATPO with two full arcs were generated with using the PRO and PO algorithms. For dosimetric evaluation, the dose-volumetric (DV) parameters of the planning target volume (PTV), organs at risk (OARs), the corresponding planning organs at risk (PRV), and 1.5-cm ring structure surrounding the PTV (Ring1.5 cm) were calculate for all VMAT plans. The total number of monitor units (MUs) and the modulation complexity score for the VMAT (MCSv) were compared. To investigate the correlations of OAR sparing to plan complexity, Pearson’s and Spearman’s correlation tests were conducted between the two algorithms (PO – PRO, denoted as Δ) in the DV parameters for normal tissues, total MUs, and MCSv.Results: For the PTVs, Target conformity and dose homogeneity in the PTVs of VMATPRO were better than those of VMATPO with statistical significance. For the spinal cords (or cauda equine) and corresponding PRVs, all of the DV parameters for VMATPRO were markedly lower than those for VMATPO, with statistical significance (all p < 0.0001). Among them, the difference in the maximum dose to the spinal cord between VMATPRO and VMATPO was remarkable (9.04 Gy vs 11.08 Gy with p < 0.0001). For Ring1.5 cm, no significant difference in V115% for VMATPRO and VMATPO was observed.Conclusions: The use of VMATPRO resulted in coverage and uniformity of dose to the PTV, as well as OARs sparing, compared with that of VMATPO for cervical, thoracic, and lumbar spine SABR. Better dosimetric plan quality generated by the PRO algorithm was observed to result in higher total MUs and plan complexity. Therefore, careful evaluation of its deliverability should be performed with caution during the routine use of the PRO algorithm.
An edge detection algorithm for neutrosophic set based on adaptive threshold
Authors: Hu Zhaohui , Yang Liping , Du Zhanpeng , Na Yiming , Su Yulong 
Published: July 2022

Abstract
In image processing, edge detection is extremely important especially in feature detection. An edge detection algorithm for neutrosophic set based on adaptive threshold is proposed to effectively filter out the large amount of noise in the image and improve the detection speed and accuracy. The algorithm uses side window filtering algorithm to filter out noise based on neutrosophic set; Furthermore, it modifies the subset segmentation algorithm to split the image into three subsets of T, F, I; Then, an adaptive threshold extraction algorithm is proposed to segment the subset information; Finally, the segmentation information is merged to obtain edge features. In order to verify the effectiveness of the algorithm, an experiment is compared with the neutrosophic set edge detection algorithm based on maximum entropy (NMNE) under different noise conditions. An experimental comparison between Canny and Sober is also carried out additionally. Experimental results show that the algorithm has good anti-noise performance and improves the detection speed and accuracy of the neutrosophic set edge detection algorithm based on maximum entropy (NMNE). The algorithm proposed in this paper can provide an effective reference for mid- and high-level vision tasks.
A copper foam based surface enhanced Raman scattering substrate for glucose detection
Authors: Peng Wang , Xu Zhihan , Jia Xiangting , Liao Qingxi 
Published: July 2022

Abstract
Raman spectroscopy as a powerful characterization method for analyzing and testing the molecular structure of substances, which can quickly achieve non-destructive, qualitative and quantitative detection and analysis. Herein, a facile and low-cost method for preparation of highly sensitivity SERS substrates was implemented through the displacement reaction of copper foam immersed in AgNO3 ethanol solution. Due to the 3D structure of copper film and homogenous displacement, the Ag-Cu substrate showed high performance SERS enhancement (1.25 × 107), and the lowest detection concentration for R6G reached 10− 10 Mol/L. For glucose detection, mixed decanethiol (DT) / mercaptohexanol (MH) interlayer was used to enable glucose attach to the substrate surface, and the limit of detection reached to 1uM/L. The copper foam based SERS substrate makes the Ag-Cu SERS substrate promising for biological applications such diabetes testing.
Common genes regulating multiple abiotic stress response in rice: An analysis using supervised and unsupervised machine learning models
Authors: Sarkar Suman , Chidambaranathan Parameswaran , Jeughale Kishor , Sahoo Bandita , Sahoo Raj Kishore , Ray Hirakjyoti , Mohanty Lopamudra , Balasubramaniasai Cayalvizhi , Selvaraj Sabarinathan , Annamalai Anandan , Rathinam Prabhukarthikeyan Seenichamy , Behera Biswaranjan , Kumar Awadhesh , Katara Jawahar Lal , N Devanna Basanvantraya , Behera Lambodar , Samantaray Sanghamitra , Patra Bhaskar Chandra 
Published: July 2022

Abstract
Rice response to abiotic stresses is generally understood through comparison of gene expression and gene mapping between contrasting tolerant and susceptible genotypes. Machine learning uses large datasets and trains the data through building efficient models for pattern identification and feature importance (gene) prediction. This work explores the potential of using machine learning tools in identifying gene expression models common to different abiotic stress response in rice. For this, 146 rice microarray gene expression samples comprised of drought (57), salinity (35), cold (33) and heat (20) were categorized into two classes namely control, stress and analyzed using supervised (Random forest) and unsupervised (Cluster) machine learning algorithms. The best random forest trained model showed an accuracy of ~ 79% in the classification analysis with an ROC curve area of 0.7963. Besides, genes involved in ABA pathway, flowering, and secondary metabolites (Two PP2Cs, three expressed proteins, Flowering Promoter Factor-like, Terpene Synthase, Gamete EXpressed) were identified as common set of genes for multiple abiotic stress response in rice. Moreover, validation of these eight genes through q-PCR under vegetative stage drought stress identified intrinsic drought tolerance mechanism and drought responsiveness in drought tolerant and rainfed upland, aerobic, and irrigated rice varieties.
Establishment and validation of a nomogram model for predicting distant metastasis in medullary thyroid carcinoma: an analysis of the SEER database based on the AJCC 8th TNM staging system
Authors: Chen Zhufeng , Mao Yaqian , You Tingting , Chen Gang 
Published: July 2022

Abstract
Purpose: Medullary thyroid carcinoma (MTC) patients with distant metastasis frequently present a relatively poor survival prognosis. Our main purpose was developing anomogram model to predict distant metastasis in MTC patients.Methods: This was a retrospective study based on the Surveillance, Epidemiology, and End Results (SEER) database. Data of 852 MTC patientsdiagnosed from 2004 to 2015who undergone total thyroidectomy and neck lymph nodes dissection was included in our study. The log‐rank test was used to compare the differences of Kaplan-Meier curves of cancer-specific survival (CSS) in different groups. Independent risk factors were screened byunivariate and multivariate logistic regression analysissuccessively, which were used to develop a nomogram model predicting for distant metastasis risk.Results: CSS differed by different M stage, lymph node ratio (LNR) and age groups. Five clinical parametersincluding age>55 years, N1 stage, tumor size>40 mm, gross extra-thyroidal extension (ETE) and LNR>0.3were significantfor distant metastasis in MTC patients, which wereselectedto develop a nomogram. This model had satisfied discrimination with the AUC and C-index of 0.874, and C-index was confirmed to be 0.861 through bootstrapping validation. A decision curve analysis was subsequently made to evaluate the feasibility of this nomogram for predicting distant metastasis.Conclusions: Age, N stage, tumor size, gross ETE and LNR were extracted to develop a nomogram model for predicting the risk of distant metastasis in MTC. The model is of great significance for clinicians to timely identify patients with high risk of distant metastasis and make further clinical decisions.
Secondary metabolites with antibacterial activity produced by Quambalaria cyanescens isolated from unripened grapes
Authors: Mateo José Juan 
Published: July 2022

Abstract
Quambalaria cyanescens was identified on the surface of unripened grapes from the D. O. Manchuela (Spain); its behavour against some bacteria has been analyzed. Active compounds of each selected fungal strain were isolated, and their antibacterial activity assayed against various bacteria; the presence of inhibition zones and, therefore, the presence of secondary metabolites that inhibit bacterial growth were determined. This capacity was different according to the culture medium in which fungal strains were cultivated, and diverse inhibition zones were observed among bacteria used. Q. cyanescens produces metabolites with antibacterial activity so that microbiota on grapes surface represents a new ecological niche to be explored in the task of finding new antibiotics.
Comparison of the Effectiveness of Emotion Regulation Method based on Gross Model and Benson Muscle RelaxationTechnique on Resilience and Anger in Patients with Coronary Artery Disease
Authors: Ramazani Rahmat , mahale fatemeh mohammadi shir , Ranjbaripour Tahreh , Ahamdi Vahid , Peymani Javid 
Published: July 2022

Abstract
Background
Coronary heart disease which imposes a heavy burden on the health care system worldwide. Psychological factors are effective in the occurrence and persistence of this disease. The aim of this study was to compare the effectiveness of emotion regulation method based on Gross model and muscle relaxation technique on resilience and anger in patients with coronary heart disease.
Methods
The research method is quasi-experimental and pre-test-post-test and follow-up with the control group. The statistical population includes all patients with coronary heart disease (CHD) between 30 and 50 years old referred to medical centers and private clinics of cardiologists in Ilam in 2021, of which 60 people were available by random sampling and random distribution to three groups. Were divided. The data collection tool is the use of standard resilience and anger scales.
Results
The results of repeated measures analysis of variance showed the effectiveness of Gross model-based emotional regulation training in patient resilience, so that Benson muscle relaxation exercises compared to Gross model-based emotional regulation training increased patients' resilience and effect. It was better. Also, Benson muscle relaxation exercises were effective in reducing patients' anger. However, the results showed the ineffectiveness of Gross model-based emotion regulation training on anger.
Conclusions
By using Gross model emotion regulation training and Benson muscle relaxation exercises, we can take steps to provide services to patients with or with a history of heart disease and reduce the severity of the disease.