bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clip placement to prevent delayed bleeding after colonic endoscopic mucosal resection (CLIPPER): study protocol for a randomized controlled trial
Authors:   on behalf of the Dutch EMR Study Group, Turan Ayla S. , Moons Leon M. G. , Schreuder Ramon-Michel , Schoon Erik J. , Terhaar sive Droste Jochim S. , Schrauwen Ruud W. M. , Straathof Jan Willem , Bastiaansen Barbara A. J. , Schwartz Matthijs P. , Hazen Wouter L. , Alkhalaf Alaa , Allajar Daud , Hadithi Muhammed , van der Spek Bas W. , Heine Dimitri G. D. N. , Tan Adriaan C. I. T. L. , de Graaf Wilmar , Boonstra Jurjen J. , Voogd Fia J. , Roomer Robert , de Ridder Rogier J. J. , Kievit Wietske , Siersema Peter D. , Didden Paul , van Geenen Erwin J. M. 
Published: January 2021

Abstract
Background
Endoscopic mucosal resection (EMR) for large colorectal polyps is in most cases the preferred treatment to prevent progression to colorectal carcinoma. The most common complication after EMR is delayed bleeding, occurring in 7% overall and in approximately 10% of polyps ≥ 2 cm in the proximal colon. Previous research has suggested that prophylactic clipping of the mucosal defect after EMR may reduce the incidence of delayed bleeding in polyps with a high bleeding risk.

Methods
The CLIPPER trial is a multicenter, parallel-group, single blinded, randomized controlled superiority study. A total of 356 patients undergoing EMR for large (≥ 2 cm) non-pedunculated polyps in the proximal colon will be included and randomized to the clip group or the control group. Prophylactic clipping will be performed in the intervention group to close the resection defect after the EMR with a distance of < 1 cm between the clips. Primary outcome is delayed bleeding within 30 days after EMR. Secondary outcomes are recurrent or residual polyps and clip artifacts during surveillance colonoscopy after 6 months, as well as cost-effectiveness of prophylactic clipping and severity of delayed bleeding.

Discussion
The CLIPPER trial is a pragmatic study performed in the Netherlands and is powered to determine the real-time efficacy and cost-effectiveness of prophylactic clipping after EMR of proximal colon polyps ≥ 2 cm in the Netherlands. This study will also generate new data on the achievability of complete closure and the effects of clip placement on scar surveillance after EMR, in order to further promote the debate on the role of prophylactic clipping in everyday clinical practice.

Trial registration
ClinicalTrials.gov NCT03309683. Registered on 13 October 2017. Start recruitment: 05 March 2018. Planned completion of recruitment: 31 August 2021.
Managing clinical trials during COVID-19: experience from a clinical research facility
Authors: Shiely Frances , Foley Jean , Stone Amy , Cobbe Emma , Browne Shaunagh , Murphy Ellen , Kelsey Maeve , Walsh-Crowley Joanne , Eustace Joseph A. 
Published: January 2021

AbstractThere is a dearth of literature on best practices for managing clinical trials, and little is understood on the role of the clinical trial manager. The COVID-19 pandemic has brought this into focus, and the continuance of clinical trials worldwide has been catapulted into a state of uncertainty as countries enter lockdown to manage the spread of the virus. Participant retention is an ongoing issue in clinical trials, and the concern is that in the current pandemic environment, attrition will be an issue which could potentially jeopardise trial completion. The current situation has necessitated timely problem solving by the trial manager to ensure trials remain open, and most importantly, that participant safety, paramount in clinical trials, is monitored. The purpose of our study is to highlight key issues arising in the management of clinical trials during a pandemic from first-hand experience in a clinical research facility managing both academic and commercial clinical trials. We offer some practical guidance on solution implementation.
Cellular and humoral peritoneal immunity to Mesocestoides vogae metacestode infection in mice
Authors: Mačak Kubašková Terézia , Mudroňová Dagmar , Vargová Miroslava , Reiterová Katarína , Hrčková Gabriela 
Published: January 2021

AbstractBackgroundHere,Mesocestoides (M.) vogaeinfection in mice is proposed as a suitable experimental model for studying the immunity in the peritoneal cavity of mice.MethodsTo investigate the kinetics of immune parameters inM. vogae-infected mice, we detected, using flow cytometry, the expression of selected lymphoid and myeloid markers within the peritoneal cell population at day 0, 3, 6, 10, 14, 19, 25, 30 and 35 post-infection. Then, using ELISA, we analyzed the cytokine IFN-γ, TGF-β, IL-4 and IL-10 responses and the levels of anti-M. vogaeIgG and IgM antibodies in the peritoneal lavage fluid. Cells isolated from the peritoneal cavity were subjected to further molecular analysis. To assess cell activation, peritoneal cells were exposed to LPS, and culture supernatants were collected and assayed for the level of cytokines and production of nitrite. Ly6C+ and Ly6G+ cells were isolated using MACS from the peritoneal cells at day 35 post-infection. Both MACS-isolated subsets were co-cultured with preactivated T cells to measure their suppressive capacity. Next, the role of parasite excretory-secretory antigens in induction of CD11b+ myeloid cells with the suppressive phenotype and the production of IL-10 was examined.ResultsIn the peritoneal cavity an initial increase of CD11b+Gr-1+F4/80highMHC IIhighcells, NK, NKT cells and CD8+ cytotoxic T cells was observed in the first week of infection. At day 14 post-infection, an increase in the number of myeloid CD11b+Gr-1+ cells was detected, and most of this cell population expressed low levels of F4/80 and MHC II in later stages of infection, suggesting the impairment of antigen-presenting cell functions, probably through the excretory-secretory molecules. Moreover, we confirmed that peritoneal Gr1+ cells (Ly6C+ and Ly6G+ population) are phenotypically and functionally consistent with myeloid-derived suppressor cells. Metacestode infection elicited high levels of IL-10 and upregulated STAT-3 in peritoneal cells. A higher level of IgM suggests that this isotype may be predominant and is involved in the host protection.ConclusionsMesocestoides vogaetetrathyridia induced the recruitment of immunosuppressive cell subsets, which may play a key role in the downregulation of immune response in long-term parasitic diseases, and excretory-secretory antigens seem to be the main regulatory factor.Graphical Abstract
The Dfam community resource of transposable element families, sequence models, and genome annotations
Authors: Storer Jessica , Hubley Robert , Rosen Jeb , Wheeler Travis J. , Smit Arian F. 
Published: January 2021

AbstractDfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.
Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer
Authors: Suman Medha , Dugué Pierre-Antoine , Wong Ee Ming , Joo JiHoon Eric , Hopper John L. , Nguyen-Dumont Tu , Giles Graham G. , Milne Roger L. , McLean Catriona , Southey Melissa C. 
Published: January 2021

Abstract
Background
Tumour DNA methylation profiling has shown potential to refine disease subtyping and improve the diagnosis and prognosis prediction of breast cancer. However, limited data exist regarding invasive lobular breast cancer (ILBC). Here, we investigated the genome-wide variability of DNA methylation levels across ILBC tumours and assessed the association between methylation levels at the variably methylated regions and overall survival in women with ILBC.

Methods
Tumour-enriched DNA was prepared by macrodissecting formalin-fixed paraffin embedded (FFPE) tumour tissue from 130 ILBCs diagnosed in the participants of the Melbourne Collaborative Cohort Study (MCCS). Genome-wide tumour DNA methylation was measured using the HumanMethylation 450K (HM450K) BeadChip array. Variably methylated regions (VMRs) were identified using the DMRcate package in R. Cox proportional hazards regression models were used to assess the association between methylation levels at the ten most significant VMRs and overall survival. Gene set enrichment analyses were undertaken using the web-based tool Metaspace. Replication of the VMR and survival analysis findings was examined using data retrieved from The Cancer Genome Atlas (TCGA) for 168 ILBC cases. We also examined the correlation between methylation and gene expression for the ten VMRs of interest using TCGA data.

Results
We identified 2771 VMRs (P < 10−8) in ILBC tumours. The ten most variably methylated clusters were predominantly located in the promoter region of the genes: ISM1, APC, TMEM101, ASCL2, NKX6, HIST3H2A/HIST3H2BB, HCG4P3, HES5, CELF2 and EFCAB4B. Higher methylation level at several of these VMRs showed an association with reduced overall survival in the MCCS. In TCGA, all associations were in the same direction, however stronger than in the MCCS. The pooled analysis of the MCCS and TCGA data showed that methylation at four of the ten genes was associated with reduced overall survival, independently of age and tumour stage; APC: Hazard Ratio (95% Confidence interval) per one-unit M-value increase: 1.18 (1.02–1.36), TMEM101: 1.23 (1.02–1.48), HCG4P3: 1.37 (1.05–1.79) and CELF2: 1.21 (1.02–1.43). A negative correlation was observed between methylation and gene expression for CELF2 (R = − 0.25, P = 0.001), but not for TMEM101 and APC.

Conclusions
Our study identified regions showing greatest variability across the ILBC tumour genome and found methylation at several genes to potentially serve as a biomarker of survival for women with ILBC.
Gender score development in the Berlin Aging Study II: a retrospective approach
Authors: Nauman Ahmad Tauseef , Behlouli Hassan , Alexander Nicholas , Kendel Friederike , Drewelies Johanna , Mantantzis Konstantinos , Berger Nora , Wagner Gert G. , Gerstorf Denis , Demuth Ilja , Pilote Louise , Regitz-Zagrosek Vera 
Published: January 2021

AbstractIn addition to biological sex, gender, defined as the sociocultural dimension of being a woman or a man, plays a central role in health. However, there are so far few approaches to quantify gender in a retrospective manner in existing study datasets. We therefore aimed to develop a methodology that can be retrospectively applied to assess gender in existing cohorts. We used baseline data from the Berlin Aging Study II (BASE-II), obtained in 2009–2014 from 1869 participants aged 60 years and older. We identified 13 gender-related variables and used them to construct a gender score by using primary component and logistic regression analyses. Of these, nine variables contributed to a gender score: chronic stress, marital status, risk-taking behaviour, personality attributes: agreeableness, neuroticism, extraversion, loneliness, conscientiousness, and level of education. Females and males differed significantly in the distribution of the gender score, but a significant overlap was also found. Thus, we were able to develop a gender score in a retrospective manner from already collected data that characterized participants in addition to biological sex. This approach will allow researchers to introduce the notion of gender retrospectively into a large number of studies.
New evidence for a hydroxylation pathway for anaerobic alkane degradation supported by analyses of functional genes and signature metabolites in oil reservoirs
Authors: Shou Li-Bin , Liu Yi-Fan , Zhou Jing , Liu Zhong-Lin , Zhou Lei , Liu Jin-Feng , Yang Shi-Zhong , Gu Ji-Dong , Mu Bo-Zhong 
Published: January 2021

AbstractMicrobial degradation of recalcitrant alkanes under anaerobic conditions results in the accumulation of heavy oil fraction in oil reservoirs. Hydroxylation of alkanes is an important activation mechanism under anaerobic conditions, but the diversity and distribution of the responsible microorganisms in the subsurface environment are still unclear. The lack of functional gene polymerase chain reaction (PCR) primers and commercially available intermediate degradation chemical compounds are the major obstacles for this research. In this investigation, PCR primers for the ahyA gene (encoding alkane hydroxylase) were designed, evaluated, and improved based on the nucleotide sequences available. Using microbial genomic DNA extracted from oil-contaminated soil and production water samples of oil reservoirs, ahyA gene nucleotide sequences were amplified and retrieved successfully from production water sample Z3-25 of Shengli oilfield. Additionally, the signature biomarker of 2-acetylalkanoic acid was detected in both Shengli and Jiangsu oilfields. These results demonstrate that anaerobic hydroxylation is an active mechanism used by microorganisms to degrade alkanes in oxygen-depleted oil reservoirs. This finding expands the current knowledge of biochemical reactions about alkane degradation in subsurface ecosystems. In addition, the PCR primers designed and tested in this study serve as an effective molecular tool for detecting the microorganisms responsible for anaerobic hydroxylation of alkanes in this and other ecosystems.
Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa
Authors: Braynen Janeen , Yang Yan , Yuan Jiachen , Xie Zhengqing , Cao Gangqiang , Wei Xiaochun , Shi Gongyao , Zhang Xiaowei , Wei Fang , Tian Baoming 
Published: January 2021

Abstract
Background
Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa.

Results
The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin’s biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated.

Conclusion
Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.
Bias correction for direct spectral estimation from irregularly sampled data including sampling schemes with correlation
Authors: Damaschke Nils , Kühn Volker , Nobach Holger 
Published: January 2021

AbstractThe prediction and correction of systematic errors in direct spectral estimation from irregularly sampled data taken from a stochastic process is investigated. Different sampling schemes are investigated, which lead to such an irregular sampling of the observed process. Both kinds of sampling schemes are considered, stochastic sampling with non-equidistant sampling intervals from a continuous distribution and, on the other hand, nominally equidistant sampling with missing individual samples yielding a discrete distribution of sampling intervals. For both distributions of sampling intervals, continuous and discrete, different sampling rules are investigated. On the one hand, purely random and independent sampling times are considered. This is given only in those cases, where the occurrence of one sample at a certain time has no influence on other samples in the sequence. This excludes any preferred delay intervals or external selection processes, which introduce correlations between the sampling instances. On the other hand, sampling schemes with interdependency and thus correlation between the individual sampling instances are investigated. This is given whenever the occurrence of one sample in any way influences further sampling instances, e.g., any recovery times after one instance, any preferences of sampling intervals including, e.g., sampling jitter or any external source with correlation influencing the validity of samples. A bias-free estimation of the spectral content of the observed random process from such irregularly sampled data is the goal of this investigation.
Energy-efficient hierarchical routing in wireless sensor networks based on fog computing
Authors: Abidoye Ademola Philip , Kabaso Boniface 
Published: January 2021

AbstractWireless sensor networks (WSNs) have been recognized as one of the most essential technologies of the twenty-first century. The applications of WSNs are rapidly increasing in almost every sector because they can be deployed in areas where cable and power supply are difficult to use. In the literature, different methods have been proposed to minimize the energy consumption of sensor nodes to prolong WSNs utilization. In this article, we propose an efficient routing protocol for data transmission in WSNs; it is called energy-efficient hierarchical routing protocol for wireless sensor networks based on fog computing. Fog computing is integrated into the proposed scheme due to its capability to optimize the limited power source of WSNs and its ability to scale up to the requirements of the Internet of things applications. In addition, we propose an improved ant colony optimization algorithm that can be used to construct an optimal path for efficient data transmission for sensor nodes. The performance of the proposed scheme is evaluated in comparison with P-SEP, EDCF, and RABACO schemes. The results of the simulations show that the proposed approach can minimize sensor nodes’ energy consumption, data packet losses, and extends the network lifetime. We are aware that in WSNs, the certainty of the sensed data collected by a sensor node can vary due to many reasons such as environmental factors, drained energy, and hardware failures.
Rough fuzzy model based feature discretization in intelligent data preprocess
Authors: Chen Qiong , Huang Mengxing 
Published: January 2021

AbstractFeature discretization is an important preprocessing technology for massive data in industrial control. It improves the efficiency of edge-cloud computing by transforming continuous features into discrete ones, so as to meet the requirements of high-quality cloud services. Compared with other discretization methods, the discretization based on rough set has achieved good results in many applications because it can make full use of the known knowledge base without any prior information. However, the equivalence class of rough set is an ordinary set, which is difficult to describe the fuzzy components in the data, and the accuracy is low in some complex data types in big data environment. Therefore, we propose a rough fuzzy model based discretization algorithm (RFMD). Firstly, we use fuzzyc-means clustering to get the membership of each sample to each category. Then, we fuzzify the equivalence class of rough set by the obtained membership, and establish the fitness function of genetic algorithm based on rough fuzzy model to select the optimal discrete breakpoints on the continuous features. Finally, we compare the proposed method with the discretization algorithm based on rough set, the discretization algorithm based on information entropy, and the discretization algorithm based on chi-square test on remote sensing datasets. The experimental results verify the effectiveness of our method.
Contradictions in the promotion of publishing academic and scientific journal articles, and the inability to cope with the new coronavirus (COVID-19)
Authors: Jalali Rostam , Hosseinian-Far Amin , Mohammadi Masoud 
Published: January 2021

Abstract
Background
Translating research into practice is a central priority within the National Institutes of Health (NIH) Roadmap. The underlying aim of the NIH Roadmap is to accelerate the movement of scientific findings into practical health care provisions through translational research.

Main text
Despite the advances in health sciences, emerging infectious diseases have become more frequent in recent decades. Furthermore, emerging and reemerging pathogens have led to several global public health challenges. A question, and to an extent a concern, arises from this: Why our health care system is experiencing several challenges in encountering the coronavirus outbreak, despite the ever-growing advances in sciences, and the exponential rise in the number of published articles in the first quartile journals and even the ones among the top 1%?

Conclusion
Two responses could be potentially provided to the above question: First, there seems to be a significant gap between our theoretical knowledge and practice. And second that many scholars and scientists publish papers only to have a longer list of publications, and therefore publishing is viewed as a personal objective, rather than for improving communities’ public health.