bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of satellite DNAs in Poa L.
Authors: Wei Linna , Liu Bo , Zhang Chunping , Yu Yang , Yang Xiaoxia , Dou Quanwen , Dong Quanmin 
Published: November 2020

Abstract
Background
Poa L. is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited.

Results
Four satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326 bp (Poa-326) and 353 bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species.

Conclusion
Four identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.
The molecular and gene/miRNA expression profiles of radioiodine resistant papillary thyroid cancer
Authors: Colombo Carla , Minna Emanuela , Gargiuli Chiara , Muzza Marina , Dugo Matteo , De Cecco Loris , Pogliaghi Gabriele , Tosi Delfina , Bulfamante Gaetano , Greco Angela , Fugazzola Laura , Borrello Maria Grazia 
Published: November 2020

Abstract
Background
Papillary thyroid cancer (PTC) is the most frequent endocrine tumor. Radioiodine (RAI) treatment is highly effective in these tumors, but up to 60% of metastatic cases become RAI-refractory. Scanty data are available on either the molecular pattern of radioiodine refractory papillary thyroid cancers (PTC) or the mechanisms responsible for RAI resistance.

Methods
We analyzed the molecular profile and gene/miRNA expression in primary PTCs, synchronous and RAI-refractory lymph node metastases (LNMs) in correlation to RAI avidity or refractoriness.
We classified patients as RAI+/D+ (RAI uptake/disease persistence), RAI−/D+ (absent RAI uptake/disease persistence), and RAI+/D- (RAI uptake/disease remission), and analyzed the molecular and gene/miRNA profiles, and the expression of thyroid differentiation (TD) related genes.

Results
A different molecular profile according to the RAI class was observed: BRAFV600E cases were more frequent in RAI−/D+ (P = 0.032), and fusion genes in RAI+/D+ cases. RAI+/D- patients were less frequently pTERT mutations positive, and more frequently wild type for the tested mutations/fusions. Expression profiles clearly distinguished PTC from normal thyroid. On the other hand, in refractory cases (RAI+/D+ and RAI−/D+) no distinctive PTC expression patterns were associated with either tissue type, or RAI uptake, but with the driving lesion and BRAF−/RAS-like subtype. Primary tumors and RAI-refractory LNMs with BRAFV600E mutation display transcriptome similarity suggesting that RAI minimally affects the expression profiles of RAI-refractory metastases. Molecular profiles associated with the expression of TPO, SLC26A4 and TD genes, that were found more downregulated in BRAFV600E than in gene fusions tumors.

Conclusions
The present data indicate a different molecular profile in RAI-avid and RAI-refractory metastatic PTCs. Moreover, BRAFV600E tumors displayed reduced differentiation and intrinsic RAI refractoriness, while PTCs with fusion oncogenes are RAI-avid but persistent, suggesting different oncogene-driven mechanisms leading to RAI refractoriness.
Host-adaptation of the rare Enterocytozoon bieneusi genotype CHN4 in Myocastor coypus (Rodentia: Echimyidae) in China
Authors: Yu Fuchang , Cao Yangwenna , Wang Haiyan , Liu Qiang , Zhao Aiyun , Qi Meng , Zhang Longxian 
Published: November 2020

Abstract
Background
Enterocytozoon bieneusi is a zoonotic gastrointestinal pathogen and can infect both humans and animals. The coypu (Myocastor coypus) is a semi-aquatic rodent, in which few E. bieneusi infections have been reported and the distribution of genotypes and zoonotic potential remains unknown.

Methods
A total of 308 fresh fecal samples were collected from seven coypu farms in China to determine the infection rate and the distribution of genotypes of E. bieneusi from coypus using nested-PCR amplification of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene.

Results
Enterocytozoon bieneusi was detected with an infection rate of 41.2% (n = 127). Four genotypes were identified, including three known genotypes (CHN4 (n = 111), EbpC (n = 8) and EbpA (n = 7)) and a novel genotype named CNCP1 (n = 1).

Conclusions
The rare genotype CHN4 was the most common genotype in the present study, and the transmission dynamics of E. bieneusi in coypus were different from other rodents. To the best of our knowledge, this is the first report of E. bieneusi infections in coypus in China. Our study reveals that E. bieneusi in coypus may be a potential infection source to humans.
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial
Authors: Keller Maria , Yaskolka Meir Anat , Bernhart Stephan H. , Gepner Yftach , Shelef Ilan , Schwarzfuchs Dan , Tsaban Gal , Zelicha Hila , Hopp Lydia , Müller Luise , Rohde Kerstin , Böttcher Yvonne , Stadler Peter F. , Stumvoll Michael , Blüher Matthias , Kovacs Peter , Shai Iris 
Published: November 2020

Abstract
Background
One of the major challenges in obesity treatment is to explain the high variability in the individual’s response to specific dietary and physical activity interventions. With this study, we tested the hypothesis that specific DNA methylation changes reflect individual responsiveness to lifestyle intervention and may serve as epigenetic predictors for a successful weight-loss.

Methods
We conducted an explorative genome-wide DNA methylation analysis in blood samples from 120 subjects (90% men, mean ± SD age = 49 ± 9 years, body mass-index (BMI) = 30.2 ± 3.3 kg/m2) from the 18-month CENTRAL randomized controlled trial who underwent either Mediterranean/low-carbohydrate or low-fat diet with or without physical activity.

Results
Analyses comparing male subjects with the most prominent body weight-loss (responders, mean weight change − 16%) vs. non-responders (+ 2.4%) (N = 10 each) revealed significant variation in DNA methylation of several genes including LRRC27, CRISP2, and SLFN12 (all adj. P < 1 × 10−5). Gene ontology analysis indicated that biological processes such as cell adhesion and molecular functions such as calcium ion binding could have an important role in determining the success of interventional therapies in obesity. Epigenome-wide association for relative weight-loss (%) identified 15 CpGs being negatively correlated with weight change after intervention (all combined P < 1 × 10− 4) including new and also known obesity candidates such as NUDT3 and NCOR2. A baseline DNA methylation score better predicted successful weight-loss [area under the curve (AUC) receiver operating characteristic (ROC) = 0.95–1.0] than predictors such as age and BMI (AUC ROC = 0.56).

Conclusions
Body weight-loss following 18-month lifestyle intervention is associated with specific methylation signatures. Moreover, methylation differences in the identified genes could serve as prognostic biomarkers to predict a successful weight-loss therapy and thus contribute to advances in patient-tailored obesity treatment.
Emerging evidence on noncoding-RNA regulatory machinery in intervertebral disc degeneration: a narrative review
Authors: Guo Hao-Yu , Guo Ming-Ke , Wan Zhong-Yuan , Song Fang , Wang Hai-Qiang 
Published: November 2020

AbstractIntervertebral disc degeneration (IDD) is the most common cause of low-back pain. Accumulating evidence indicates that the expression profiling of noncoding RNAs (ncRNAs), including microRNAs (miRNAs), circular RNAs (circRNAs), and long noncoding RNAs (lncRNAs), are different between intervertebral disc tissues obtained from healthy individuals and patients with IDD. However, the roles of ncRNAs in IDD are still unclear until now. In this review, we summarize the studies concerning ncRNA interactions and regulatory functions in IDD. Apoptosis, aberrant proliferation, extracellular matrix degradation, and inflammatory abnormality are tetrad fundamental pathologic phenotypes in IDD. We demonstrated that ncRNAs are playing vital roles in apoptosis, proliferation, ECM degeneration, and inflammation process of IDD. The ncRNAs participate in underlying mechanisms of IDD in different ways. MiRNAs downregulate target genes’ expression by directly binding to the 3′-untranslated region of mRNAs. CircRNAs and lncRNAs act as sponges or competing endogenous RNAs by competitively binding to miRNAs and regulating the expression of mRNAs. The lncRNAs, circRNAs, miRNAs, and mRNAs widely crosstalk and form complex regulatory networks in the degenerative processes. The current review presents novel insights into the pathogenesis of IDD and potentially sheds light on the therapeutics in the future.
Enhanced differentiation of human pluripotent stem cells into pancreatic endocrine cells in 3D culture by inhibition of focal adhesion kinase
Authors: Liu Xiaofang , Qin Jinhua , Chang Mingyang , Wang Shuyong , Li Yali , Pei Xuetao , Wang Yunfang 
Published: November 2020

Abstract
Background
Generation of insulin-producing cells from human pluripotent stem cells (hPSCs) in vitro would be useful for drug discovery and cell therapy in diabetes. Three-dimensional (3D) culture is important for the acquisition of mature insulin-producing cells from hPSCs, but the mechanism by which it promotes β cell maturation is poorly understood.

Methods
We established a stepwise method to induce high-efficiency differentiation of human embryonic stem cells (hESCs) into mature monohormonal pancreatic endocrine cells (PECs), with the last maturation stage in 3D culture. To comprehensively compare two-dimensional (2D) and 3D cultures, we examined gene expression, pancreas-specific markers, and functional characteristics in 2D culture-induced PECs and 3D culture-induced PECs. The mechanisms were considered from the perspectives of cell–cell and cell–extracellular matrix interactions which are fundamentally different between 2D and 3D cultures.

Results
The expression of the pancreatic endocrine-specific transcription factors PDX1, NKX6.1, NGN3, ISL1, and PAX6 and the hormones INS, GCG, and SST was significantly increased in 3D culture-induced PECs. 3D culture yielded monohormonal endocrine cells, while 2D culture-induced PECs co-expressed INS and GCG or INS and SST or even expressed all three hormones. We found that focal adhesion kinase (FAK) phosphorylation was significantly downregulated in 3D culture-induced PECs, and treatment with the selective FAK inhibitor PF-228 improved the expression of β cell-specific transcription factors in 2D culture-induced PECs. We further demonstrated that 3D culture may promote endocrine commitment by limiting FAK-dependent activation of the SMAD2/3 pathway. Moreover, the expression of the gap junction protein Connexin 36 was much higher in 3D culture-induced PECs than in 2D culture-induced PECs, and inhibition of the FAK pathway in 2D culture increased Connexin 36 expression.

Conclusion
We developed a strategy to induce differentiation of monohormonal mature PECs from hPSCs and found limited FAK-dependent activation of the SMAD2/3 pathway and unregulated expression of Connexin 36 in 3D culture-induced PECs. This study has important implications for the generation of mature, functional β cells for drug discovery and cell transplantation therapy for diabetes and sheds new light on the signaling events that regulate endocrine specification.
Sex-dependent alterations in the physiology of entorhinal cortex neurons in old heterozygous 3xTg-AD mice
Authors: Arsenault Dany , Tremblay Cyntia , Emond Vincent , Calon Frédéric 
Published: November 2020

AbstractWhile the higher prevalence of Alzheimer’s disease (AD) in women is clear, studies suggest that biological sex may also influence AD pathogenesis. However, mechanisms behind these differences are not clear. To investigate physiological differences between sexes at the cellular level in the brain, we investigated the intrinsic and synaptic properties of entorhinal cortex neurons in heterozygous 3xTg-AD mice of both sexes at the age of 20 months. This brain region was selected because of its early association with AD symptoms. First, we found physiological differences between male and female non-transgenic mice, providing indirect evidence of axonal alterations in old females. Second, we observed a transgene-dependent elevation of the firing activity, post-burst afterhyperpolarization (AHP), and spontaneous excitatory postsynaptic current (EPSC) activity, without any effect of sex. Third, the passive properties and the hyperpolarization-activated current (Ih) were altered by transgene expression only in female mice, whereas the paired-pulse ratio (PPR) of evoked EPSC was changed only in males. Fourth, both sex and transgene expression were associated with changes in action potential properties. Consistent with previous work, higher levels of Aβ neuropathology were detected in 3xTg-AD females, whereas tau deposition was similar. In summary, our results support the idea that aging and AD neuropathology differentially alter the physiology of entorhinal cortex neurons in males and females.
Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies
Authors: Kersloot Martijn G. , van Putten Florentien J. P. , Abu-Hanna Ameen , Cornet Ronald , Arts Derk L. 
Published: November 2020

Abstract
Background
Free-text descriptions in electronic health records (EHRs) can be of interest for clinical research and care optimization. However, free text cannot be readily interpreted by a computer and, therefore, has limited value. Natural Language Processing (NLP) algorithms can make free text machine-interpretable by attaching ontology concepts to it. However, implementations of NLP algorithms are not evaluated consistently. Therefore, the objective of this study was to review the current methods used for developing and evaluating NLP algorithms that map clinical text fragments onto ontology concepts. To standardize the evaluation of algorithms and reduce heterogeneity between studies, we propose a list of recommendations.

Methods
Two reviewers examined publications indexed by Scopus, IEEE, MEDLINE, EMBASE, the ACM Digital Library, and the ACL Anthology. Publications reporting on NLP for mapping clinical text from EHRs to ontology concepts were included. Year, country, setting, objective, evaluation and validation methods, NLP algorithms, terminology systems, dataset size and language, performance measures, reference standard, generalizability, operational use, and source code availability were extracted. The studies’ objectives were categorized by way of induction. These results were used to define recommendations.

Results
Two thousand three hundred fifty five unique studies were identified. Two hundred fifty six studies reported on the development of NLP algorithms for mapping free text to ontology concepts. Seventy-seven described development and evaluation. Twenty-two studies did not perform a validation on unseen data and 68 studies did not perform external validation. Of 23 studies that claimed that their algorithm was generalizable, 5 tested this by external validation. A list of sixteen recommendations regarding the usage of NLP systems and algorithms, usage of data, evaluation and validation, presentation of results, and generalizability of results was developed.

Conclusion
We found many heterogeneous approaches to the reporting on the development and evaluation of NLP algorithms that map clinical text to ontology concepts. Over one-fourth of the identified publications did not perform an evaluation. In addition, over one-fourth of the included studies did not perform a validation, and 88% did not perform external validation. We believe that our recommendations, alongside an existing reporting standard, will increase the reproducibility and reusability of future studies and NLP algorithms in medicine.
ParEst: joint estimation of the OFDM channel state information in MIMO systems
Authors: Zhang Zhenghao 
Published: November 2020

AbstractOFDM channel state information (CSI) is needed for determining key parameters in MIMO transmissions. In this paper, a novel CSI estimation method, ParEst, is proposed, which estimates the CSI from multiple transmitting antennas simultaneously. ParEst is based on a recent discovery that the CSI can be approximated very well by the linear combination of complex-based sinusoids on constant frequencies. ParEst finds the CSI of all antennas jointly by solving an optimization problem and achieves higher accuracy than existing heuristic methods. As the base sinusoids are on constant frequencies, ParEst pre-computes most key steps and reduces the run-time computation complexity to just a modest number of vector dot products equivalent to a few FFT calculations. ParEst can be applied to MIMO links in networks such as LTE, 5G, or Wi-Fi.
Analysis and simulation of a mathematical model of tuberculosis transmission in Democratic Republic of the Congo
Authors: Kasereka Kabunga Selain , Doungmo Goufo Emile F. , Ho Tuong Vinh 
Published: November 2020

AbstractAccording to the World Health Organization reports, tuberculosis (TB) remains one of the top 10 deadly diseases of recent decades in the world. In this paper, we present the modeling, analysis and simulation of a mathematical model of TB transmission in a population incorporating several factors and study their impact on the disease dynamics. The spread of TB is modeled by eight compartments including different groups, which are too often not taken into account in the projections of tuberculosis incidence. The rigorous mathematical analysis of this model is provided, the basic reproduction number ($\mathcal{R}_{0}$R0) is obtained and used for TB dynamics control. The results obtained show that lost to follow-up and transferred individuals constitute a risk, but less than the cases carrying germs. Rapidly evolving latent/exposed cases are responsible for the incidence increasing in the short and medium term, while slower evolving latent/exposed cases will be responsible for the persistent long-term incidence and maintenance of TB and delay elimination in the population. The numerical simulations of the model show that, with certain parameters, TB will die out or sensibly reduce in the entire Democratic Republic of the Congo (DRC) population. The strategies on which the DRC’s health system is currently based to fight this disease show their weaknesses because the TB situation in the DRC remains endemic. But monitoring contact, detection of latent individuals and their treatment are actions to be taken to reduce the incidence of the disease and thus effectively control it in the population.
A radiomics nomogram for the prediction of overall survival in patients with hepatocellular carcinoma after hepatectomy
Authors: Liu Qinqin , Li Jing , Liu Fei , Yang Weilin , Ding Jingjing , Chen Weixia , Wei Yonggang , Li Bo , Zheng Lu 
Published: November 2020

Abstract
Background
Hepatocellular carcinoma (HCC) is associated with a dismal prognosis, and prediction of the prognosis of HCC can assist in therapeutic decision-makings. An increasing number of studies have shown that the texture parameters of images can reflect the heterogeneity of tumors, and may have the potential to predict the prognosis of patients with HCC after surgical resection. The aim of this study was to investigate the prognostic value of computed tomography (CT) texture parameters in patients with HCC after hepatectomy and to develop a radiomics nomogram by combining clinicopathological factors and the radiomics signature.

Methods
In all, 544 eligible patients were enrolled in this retrospective study and were randomly divided into the training cohort (n = 381) and the validation cohort (n = 163). The tumor regions of interest (ROIs) were delineated, and the corresponding texture parameters were extracted. The texture parameters were selected by using the least absolute shrinkage and selection operator (LASSO) Cox model in the training cohort, and a radiomics signature was established. Then, the radiomics signature was further validated as an independent risk factor for overall survival (OS). The radiomics nomogram was established based on the Cox regression model. The concordance index (C-index), calibration plot and decision curve analysis (DCA) were used to evaluate the performance of the radiomics nomogram.

Results
The radiomics signature was formulated based on 7 OS-related texture parameters, which were selected in the training cohort. In addition, the radiomics nomogram was developed based on the following five variables: α-fetoprotein (AFP), platelet-to-lymphocyte ratio (PLR), largest tumor size, microvascular invasion (MVI) and radiomics score (Rad-score). The nomogram displayed good accuracy in predicting OS (C-index = 0.747) in the training cohort and was confirmed in the validation cohort (C-index = 0.777). The calibration plots also showed excellent agreement between the actual and predicted survival probabilities. The DCA indicated that the radiomics nomogram showed better clinical utility than the clinicopathologic nomogram.

Conclusion
The radiomics signature is a potential prognostic biomarker of HCC after hepatectomy. The radiomics nomogram that integrated the radiomics signature can provide a more accurate estimation of OS than the clinicopathologic nomogram for HCC patients after hepatectomy.
Recurrence hernia in the broad ligament of the uterus: a case report
Authors: Hashimoto Yoshifumi , Kanda Tatsuo , Chida Tadasu , Suda Kazuyoshi 
Published: November 2020

Abstract
Background
Bowel herniation through a defect in the broad ligament of the uterus is a rare disease and few cases of recurrence have been reported. We report herein a recurrence case of a patient with broad ligament hernia (BLH), along with a review of the literature.

Case presentation
A 53-year-old woman complaining of abdominal pain was transported to our hospital. She had a history of laparotomy for small-bowel obstruction associated with hernia in the broad ligament of the uterus 10 years ago at a local hospital. Abdominal pelvic contrast-enhanced computed tomography revealed that the mesentery of the dilated bowels converged at a thick band in the pelvis, suggesting closed loop obstruction of the small bowel. The patient underwent urgent laparotomy and was diagnosed with bowel herniation through an opening in the broad ligament of the uterus on the right side, which was ipsilateral with the previous surgery. The hernia orifice was widened by incision and incarcerated bowel segments were released and preserved because ischemia was reversible. The membranous defect of BLH was closed by suture with braded silk strings.

Conclusions
Although BLH is a rare disease, patients face a significant risk of disease recurrence. Nonabsorbable suture may be advisable for closure of the hernia orifice in BLH.