bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Liquid Biopsy Based Purely Quantitative Digital Droplet PCR Assay for Detection of MLH1 Promoter Methylation in Colorectal Cancer Patients
Authors: Wang Danyi , O’Rourke Dennis , Garcia Jorge Sanchez , Cai Ti , Scheuenpflug Juergen , Feng Zheng 
Published: March 2021

Abstract
Background MutL Homolog 1 (MLH1) promotor methylation is associated with microsatellite instability high colorectal cancer (CRC). The strong correlation between methylation status and cancer development and progression has led to a growing interest in the use of methylation markers in circulating tumor DNA (ctDNA) for early cancer detection and longitudinal monitoring. As cancer-specific DNA methylation changes in body fluids are limited, it is particularly challenging to develop clinically applicable liquid biopsy methodologies with high sensitivity and specificity. The purpose of this study was to develop a fit-for-purpose methylation sensitive restriction enzyme (MSRE) based digital droplet PCR (ddPCR) assay to examine MLH1 promoter methylation in ctDNA in advanced CRC. Methods Primers and probes were designed to amplify CpG sites of the MLH1 promoter. Methylated and unmethylated control genomic DNA were sheared to mimic ctDNA and subjected to MSRE HpaII digestion. Plasma samples from 20 healthy donors and 28 CRC patients were analyzed with the optimized MSRE procedure using ddPCR. Results Using methylated and unmethylated controls, we optimized the conditions for HpaII enzyme digestion to ensure complete digestion and avoid false positives. Based on the results from the ddPCR assay using 1ng circulating cell-free DNA (cfDNA) input from healthy donors or CRC samples, ROC curves were generated with an area under the curve (AUC) value of 0.965. The optimal assay sensitivity and specificity was achieved when 8 positive droplets were used as acceptance criteria (78% sensitivity and 100% specificity). A tiered-based cutoff (20%, 50%, 80% percentile based) was applied to distinguish CRC samples with different methylation level.Conclusions Our study demonstrated that the liquid biopsy assay for MLH1 promoter methylation detection using purely quantitative ddPCR is a simple and ultrasensitive procedure that provides reliable methylation detection in ctDNA. The MSRE ddPCR approach can also be applied to other genes of interest where methylation patterns could reveal clinically relevant information for future clinical biomarker and/or companion diagnostic development.
Frontend Innovation And Top Income Inequality: Evidence From Emerging Markets
Authors: Eyisi Nwakego , Kanwal Asma 
Published: March 2021

Abstract
This paper contributes to the literature on income inequality, by extending existing models to examine the effect of front-end innovation (FEI) on top income inequality. We use a fixed effect panel regression, on annual country level data for twenty four emerging markets, over a twenty four (1995–2018) year period, and find an insignificant correlation between income inequality, and FEI. The instrumental variable estimates however, shows a significant association between measures of FEI and top income shares. Further, we confirm that FEI is weakly related with broad measures of income inequality. Our instrumentation strategy, and robustness checks, suggests that this correlation partly reflects a causality, from FEI to top income inequality. Finally, we show that FEI is necessary for the survival of new ventures, in the crucial early years. Overall, our findings confirm that FEI, is a significant determinant of increases, in entrepreneurial income share.
A Copper Alloy Light Cannon From Grodno – An Example of Early Firearms From Eastern Europe
Authors: Żabiński Grzegorz , Strzyż Piotr , Goryczka Tomasz , Aniołek Krzysztof , Miśta-Jakubowska Ewelina 
Published: March 2021

Abstract
The paper discusses a recent find of a copper alloy light cannon discovered at the Old Castle in Grodno, Belarus. First, the archaeological and historical contexts of the discovery are dealt with. Then, the morphology and typochronology of the cannon are discussed and relevant analogies are proposed. Next, the technology of manufacture of the cannon is dealt with on the basis of metallographic examinations and EDS analyses of the metal’s elemental composition. It was found out that the artefact had been made of leaded copper. The cannon can be dated to the late 14th c., as implied both by the find context, the morphology and the chemical composition of the artefact. Its deposition can possibly related to fights over the Old Castle in Grodno in this period, waged by Teutonic, Polish and Lithuanian forces. It can tentatively be assumed that the cannon was manufactured in a Teutonic Order’s workshop, but further research is necessary to verify this supposition.
Pathological Alterations in the Gastrointestinal Tract of a Porcine Model of DMD
Authors: Zhou Xiaodong , Ouyang Hongsheng , Pang Daxin , Han Renzhi , Tang Xiaochun 
Published: March 2021

Abstract
Patients with Duchenne muscular dystrophy (DMD) develop severe skeletal and cardiac muscle pathologies, which result in premature death. Therefore, the current therapeutic efforts are mainly targeted to correct dystrophin expression in skeletal muscle and heart. However, it was reported that DMD patients may also exhibit gastrointestinal and nutritional problems. How the pathological alterations in gastrointestinal tissues may contribute to the disease are not fully explored. Here we employed the CRISPR/Cas9 system combined with somatic nuclear transfer technology (SCNT) to establish a porcine model of DMD and explored their pathological alterations. We found that genetic disruption of dystrophin expression led1 to morphological gastrointestinal tract alterations, weakened the gastrointestinal tract digestion and absorption capacity, and eventually led to malnutrition and gastric dysfunction in the DMD pigs. This work provides important insights into the pathogenesis of DMD and highlights the need to consider the gastrointestinal dysfunction as an additional therapeutic target for DMD patients.
Robust Dynamic Optimization of a Dual-rotor System Based on Polynomial Chaos Expansion
Authors: xu bensheng , zang chaoping , Wang Xiaowei , Zhang Genbei 
Published: March 2021

Abstract
A novel methodology of robust dynamic optimization of a dual-rotor system based on polynomial chaos expansion (PCE) is developed in this paper. The dual-rotor system model was built by the Timoshenko theory and the finite element method. Instead of the direct Monte Carlo simulation (MCS), the PCE of the present dual-rotor system under support stiffness uncertainty is generated to facilitate a rapid analysis of stochastic responses and yield desirable results in significantly less number of functional evaluations. The PCE is explored as a basis for robust optimization, focusing on the problem of minimizing the unbalance response at operating conditions while minimizing its sensitivity to uncertainty in the support stiffness. This strategy avoids the use of MCS in order to effectively increase the efficiency of the optimization and significantly reduce the computing cost and time spending. The robust dynamic optimization attempts to both optimize the mean performance and minimizes the variance of the performance simultaneously. The multi-objective optimization results show that vibration response can be decreased and is significantly less sensitive to the variation of design parameters compared with initial design case by matching of unbalance amplitude and phase angle differences. Implementation of the proposed robust dynamic optimization in the present dual-rotor system illustrates its potential for further complicated applications.
Enhanced Extraction of Skin Interstitial Fluid Using a Tilted Microneedle Device Fabricated by 3D&nbsp;Printing
Authors: Kim Sanha , Lee Min Suk , Yang Hee Seok , Jung Jae Hwan 
Published: March 2021

Abstract
Interstitial fluid (ISF) is a body fluid that fills, surrounds cells and contains various biomarkers, but it has been challenging to extract ISF in a reliable and sufficient amount with high speed. To address the issues, we developed the tilted microneedle ISF collecting system (TMICS) fabricated by 3D printing. In this system, the microneedle (MN) was inserted at 66° to the skin by TMICS so that the MN length could be extended within a safe range of skin penetration. Moreover, TMICS incorporating three MN patches created reliable ISF collecting conditions by penetrating the skin at consistent angle and force, 4.9 N. Due to the MN length increase and the patch number expansion, the surface area of the penetrated tissue was increased, thereby confirming that ISF extraction efficiency was improved. Skin ISF was collected into the paper reservoir on the patch, and the absorbed area was converted into a volume. ISF extraction from the rat skin in vivo by TMICS was well tolerated, and the 2.9 μL of ISF was obtained within 30 sec. Therefore, TMICS is promising to apply in the diagnosis of multiple biomarkers in ISF with high speed and stability.
Identification of Novel Mutation Sites in DNAH1 of Multiple Morphological Anomalies of the Flagella Patients
Authors: Wang Xiong , Sha Yan-Wei , Zhu Xing-shen , Zhang Xiao-ya , Cui Yuan-qing , Chen Jie , Lian Hua-yu , Yan Wei , Yuan He-jia , Qin Wei-bing , Tang Yunge , Zhang Xin-zhong , Zhou Huiliang , Lu Zhongxian 
Published: March 2021

Abstract
BackgroundMultiple morphological anomalies of the sperm flagella (MMAF) is a term used to describe abnormalities in sperm morphology, which lead to primary infertility in males. Intracytoplasmic sperm injection (ICSI) is an effective treatment for MMAF. However, ICSI failure rates remain high in MMAF patients. Our purpose was to investigate novel gene mutations in a cohort of nineteen patients with MMAF and assess the impact of these mutations on assisted reproductive therapy.MethodsWe recruited nineteen infertile patients with MMAF and twenty healthy men with proven fertility at the Affiliated Yantai Yuhuangding Hospital of Qingdao University. The morphology of the spermatozoa was observed using Papanicolaou staining and the ultrastructure of the spermatozoa was inspected using transmission electron microscopy. Gene mutations were evaluated using whole-exome sequencing and novel mutations were further validated in patients and their parents using Sanger sequencing. The effect of these novel mutation sites on the expression of DNAH1 was analysed using immunofluorescence, and the effect of these novel mutations on pregnancy outcome was analysed using intracytoplasmic sperm injection (ICSI). ResultsSpermatozoa from 19 patients presented with a typical MMAF phenotype including severe ultrastructural defects. We identified ten novel mutation sites in the DNAH1 locus from six of these patients, none of which were identified in DNAH1 or the other MMAF-related genes from the twenty men with proven fertility. In the sperm from these patients, DNAH1 was absent. Three patients with DNAH1 mutation who underwent intracytoplasmic sperm injection (ICSI) had a good outcome. ConclusionHere, we describe several novel compound heterozygous mutations and a novel homozygous mutation in DNAH1 from six independent MMAF patients. This study adds to the body of knowledge surrounding the genetic landscape of MMAF and DNAH1 improving our ability to diagnose and treat MMAF efficiently.
Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
Authors: Xu Yong-Chao , Zhang Jie , Zhang Dong-Yan , Nan Ying-Hui , Ge Song , Guo Ya-Long 
Published: March 2021

Abstract
Background

Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown.
Results

Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare.
Conclusion

We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.
Modeling the COVID-19 Dynamics and Explaining the Portuguese CaseA Contribution for Fiting Differential Equation Solutions to Epidemiological Data
Authors: Beira Maria Jardim , Sebastião Pedro José 
Published: March 2021

Abstract
Compartmental epidemiological models are, by far, the most popular in the study of dynamics related with infectious diseases. It is, therefore, not surprising that they are frequently used to study the current COVID-19 pandemic. Taking advantage of the real-time availability of COVID-19 related data, we perform a compartmental model fitting analysis of the portuguese case, using an online open-access platform with the integrated capability of solving systems of differential equations. This analysis enabled the data-driven validation of the used model and was the basis for robust projections of different future scenarios, namely, increasing the detected infected population, reopening schools at different moments, allowing Easter celebrations to take place and population vaccination. The method presented in this work can easily be used to perform the non-trivial task of simultaneously fitting differential equation solutions to different epidemiological data sets, regardless of the model or country that might be considered in the analysis.
Fabrication of Porous TiVAlC Ceramics with Low-Temperature Reactive Synthesis Method
Authors: Zou Haoran , Li Xide , Zhang Chuo , Wen Yi , Fan Yiquan , Liu Yuzuo , Xiong Lieqiang , Zheng Xiao , Yang Junsheng 
Published: March 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Association Between Tumor Budding Grade and T Stage in Predicting Recurrence in High-risk Stage Ii Colorectal Cancer
Authors: Kodama Hiroyuki , Yamaguchi Toshifumi , Ishizuka Yasunobu , Aoki Masahiko , Miyamoto Takahiro , Terazawa Tetsuji , Shimamoto Fukutaro , Goto Masahiro , Hamamoto Hiroki , Osumi Wataru , Yamamoto Masashi , Tanaka Keitaro , Okuda Junji , Uchiyama Kazuhisa , Higuchi Kazuhide , Yukami Hiroki 
Published: March 2021

Abstract
In pathological stage (pStage) II colon cancer, factors such as T stage (T) are high-risk features (HRF) for recurrence. The SACURA trial showed that tumor budding (BD) grade was also associated with recurrence: the 5-year recurrence-free survival (RFS) rate was lower in patients in the BD3 group compared with that of other groups. Interestingly, the BD3 group had a higher proportion of patients with T4. We investigated the prognostic association between T4 and BD3 for recurrence in pStage II colorectal cancer (pII-CRC) with HRF. We analyzed pII-CRC patients with HRF between 2013–2018 at our hospital, Japan. Inclusion criteria were as follows: ≥1 HRF [<12 lymph nodes examined (<12LN), lymph/vascular-invasion, perineural-invasion, T, BD, and histologic-type]. We primarily analyzed the relationship between each factor and RFS. Among 2,920 pII-CRC patients, 448 had HRF. Of these, 43 (9.6%) had T4 and 236 (52.7%) had BD3. On initial analysis, <12LN (P=0.0412), tumor location (P=0.0023), T4 (P=0.0023), and BD3 (P=0.0396) were independent prognostic factors for RFS. Among 257 patients with BD3 and/or T4, the 5-year RFS rates were 81.3%, 74.6%, and 66.2% for patients with BD3 (214 patients), T4 (22 patients), and BD3 plus T4 (21 patients), respectively (hazard ratio 3.08, P=0.0079). pII-CRC patients with BD3 plus T4 had poorer prognosis than those with other factors.
Preparation of green synthesized copper oxide nanoparticles for efficient removal of lead from wastewaters
Authors: Zarrabi Amir , Ghasemi-Fasaei Reza 
Published: March 2021

Abstract
Green synthesis is a clean and eco-friendly process in which metal nanoparticles can be produced via reaction between a metal salt solution and plant organ extract. In present study, three copper oxide nanoparticles were synthesized using green synthesis processes from the leaf extracts of selected plants as abundant plant cover in the study area including astragalus (Astragalus membranaceus), rosemary (Salvia rosmarinus) and mallow (Malva sylvestris). The effectiveness of three green synthesized nanoparticles in the adsorption of lead ions from a polluted water was studied under laboratory conditions. According to the results, the removal efficiencies of the copper oxide nanoparticles synthesized from astragalus (A-CuO-NPs), rosemary (R-CuO-NPs) and mallow leaf extract (M-CuO-NPs) especially at the highest initial concentration of Pb (1.5 mM) were 88.4 %, 84.9 % and 69.6 %, respectively. Most probably due the smooth morphology and more uniform configuration of the M-CuO-NPs, the changes between equilibrium adsorption (qe) and equilibrium concentration (Ce) were more regular than those of the A-CuO-NPs and R-CuO-NPs. Accordingly the best fitted data to Langmuir and Freundlich isotherms were observed in the adsorption of Pb onto the M-CuO-NPs. Despite the lowest removal efficiency of the M-CuO-NPs, with the equal volumes of each leaf extract and CuSO4.5H2O solution (20 mM), the most produced dry weight was observed for these nanoparticles (4.3 g per 100 mL of leaf extract). According to the results reported herein, the copper oxide nanoparticles synthesized from different plant covers are efficient adsorption agents for Pb from wastewaters.
Maintaining face-to-face contact during the COVID-19 pandemic: a longitudinal qualitative investigation in UK primary care
Authors: Turner Andrew , Scott Anne , Horwood Jeremy , Salisbury Chris , Denholm Rachel , Scott Lauren , Iyer Geeta , Macleod John , Murphy Mairead 
Published: March 2021

Abstract
BackgroundIn March 2020 the COVID-19 pandemic required a rapid reconfiguration of UK general practice to minimise face-to-face contact with patients to reduce infection risk. However, some face-to-face contact remained necessary and practices needed to ensure such contact could continue safely.AimTo examine how practices determined when face-to-face contact was necessary and how face-to-face consultations were reconfigured to reduce COVID-19 infection risk. Design and SettingQualitative interview study in general practices in Bristol, North Somerset and South Gloucestershire.MethodLongitudinal semi-structured interviews with clinical and managerial practice staff at four timepoints between May and July 2020.ResultsPractices worked flexibly within general national guidance to determine when face-to-face contact with patients was necessary, influenced by knowledge of the patient, experience, and practice resilience. For example, practices prioritised patients according to clinical need using face-to-face contact to resolve clinician uncertainty or provide adequate reassurance to patients. To make face-to-face contact as safe as possible and keep patients separated, practices introduced a heterogeneous range of measures that exploited features of their indoor and outdoor spaces and altered their appointment processes. As national restrictions eased in June and July, the number and proportion of patients seen face-to-face generally increased. However, the reconfiguration of buildings and processes reduced the available capacity and put increased pressure on practices.ConclusionPractices responded rapidly and creatively to the initial lockdown restrictions. The variety of ways practices organised face-to-face contact to minimise infection highlights the need for flexibility in guidance.
Effects of Media Violence on Mental Health of Viewers
Authors: Kamal Madiha , Zahid Gulrukh 
Published: March 2021

Abstract
It has been evident that violence showing through media is creating numerous issues in youth as well as in younger children. In this study we have scrutinize the effect of violence exhibiting through the media, on the mental health of a viewer and as well as its effects on economics. By using a primary data methodology, a total of 100 respondents submitted their response to the database for this study. Majority of the participants in the survey were females aged between 18–24 years. The results have shown that by picturing violent content on media has an impact on mental health, both long term and short-term impacts depends on the content and its severity.