bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of fetal trisomy and single gene disease by massively parallel sequencing of extracellular vesicle DNA in maternal plasma: a proof-of-concept validation
Authors: Zhang Weiting , Lu Sen , Pu Dandan , Zhang Haiping , Yang Lin , Zeng Peng , Su Fengxia , Chen Zhichao , Guo Mei , Gu Ying , Luo Yanmei , Hu Huamei , Lu Yanping , Chen Fang , Gao Ya 
Published: November 2019

Abstract

Background
During human pregnancy, placental trophectoderm cells release extracellular vesicles (EVs) into maternal circulation. Trophoblasts also give rise to cell-free DNA (cfDNA) in maternal blood, and has been used for noninvasive prenatal screening for chromosomal aneuploidy. We intended to prove the existence of DNA in the EVs (evDNA) of maternal blood, and compared evDNA with plasma cfDNA in terms of genome distribution, fragment length, and the possibility of detecting genetic diseases.

Methods
Maternal blood from 20 euploid pregnancies, 9 T21 pregnancies, 3 T18 pregnancies, 1 T13 pregnancy, and 2 pregnancies with FGFR3 mutations were obtained. EVs were separated from maternal plasma, and confirmed by transmission electronic microscopy (TEM), western blotting, and flow cytometry (FACS). evDNA was extracted and its fetal origin was confirmed by quantitative PCR (qPCR). Pair-end (PE) whole genome sequencing was performed to characterize evDNA, and the results were compared with that of cfDNA. The fetal risk of aneuploidy and monogenic diseases was analyzed using the evDNA sequencing data.

Results
EVs separated from maternal plasma were confirmed with morphology by TEM, and protein markers of CD9, CD63, CD81 as well as the placental specific protein placental alkaline phosphatase (PLAP) were confirmed by western blotting or flow cytometry. EvDNA could be successfully extracted for qPCR and sequencing from the plasma EVs. Sequencing data showed that evDNA span on all 23 pairs of chromosomes and mitochondria, sharing a similar distribution pattern and higher GC content comparing with cfDNA. EvDNA showed shorter fragments yet lower fetal fraction than cfDNA. EvDNA could be used to correctly determine fetal gender, trisomies, and de novo FGFR3 mutations.

Conclusions
We proved that fetal DNA could be detected in EVs separated from maternal plasma. EvDNA shared some similar features to plasma cfDNA, and could potentially be used to detect genetic diseases in fetus.
Variable DNA methylation of aging-related genes is associated with male COPD
Authors: Du Xizi , Yuan Lin , Wu Mengping , Men Meichao , He Ruoxi , Wang Leyuan , Wu Shuangyan , Xiang Yang , Qu Xiangping , Liu Huijun , Qin Xiaoqun , Hu Chengping , Qin Ling , Liu Chi 
Published: November 2019

Abstract

Background
Chronic obstructive pulmonary disease (COPD) is a chronic lung inflammatory disease which has a close relationship with aging. Genome-wide analysis reveals that DNA methylation markers vary obviously with age. DNA methylation variations in peripheral blood have the potential to be biomarkers for COPD. However, the specific DNA methylation of aging-related genes in the peripheral blood of COPD patients remains largely unknown.

Methods
Firstly, 9 aging-related differentially expressed genes (DEGs) in COPD patients were screened out from the 25 aging-related genes profile through a comprehensive screening strategy. Secondly, qPCR and multiple targeted bisulfite enrichment sequencing (MethTarget) were used to detect the mRNA level and DNA methylation level of the 9 differentially expressed genes in the peripheral blood of 60 control subjects and 45 COPD patients. The candidate functional CpG sites were selected on the basis of the regulation ability of the target gene expression. Thirdly, the correlation was evaluated between the DNA methylation level of the key CpG sites and the clinical parameters of COPD patients, including forced expiratory volume in one second (FEV1), forced expiratory volume in one second as percentage of predicted volume (FEV1%), forced expiratory volume/ forced vital capacity (FEV/FVC), modified British medical research council (mMRC) score, acute exacerbation frequency and the situation of frequent of acute aggravation (CAT) score. Lastly, differentially methylated CpG sites unrelated to smoking were also determined in COPD patients.

Results
Of the 9 differentially expressed aging-related genes, the mRNA expression of 8 genes were detected to be significantly down-regulated in COPD group, compared with control group. Meanwhile, the methylated level of all aging-related genes was changed in COPD group containing 219 COPD-related CpG sites in total. Notably, 27 CpG sites of FOXO3 gene showed a lower False Discovery Rate (FDR) and higher methylation difference values. Also, some variable DNA methylation is associated with the severity of COPD. Additionally, of the 219 COPD-related CpG sites, 147 CpG sites were not related to smoking.

Conclusion
These results identified that the mRNA expression and DNA methylation level of aging-related genes were changed in male COPD patients, which provides a molecular link between aging and COPD. The identified CpG markers are associated with the severity of COPD and provide new insights into the prediction and identification of COPD.
Hepatitis C virus nonstructural protein 5A perturbs lipid metabolism by modulating AMPK/SREBP-1c signaling
Authors: Meng Ziyu , Liu Qiang , Sun Fujun , Qiao Ling 
Published: November 2019

Abstract

Background
Steatosis is an important clinical manifestation associated with chronic hepatitis C virus (HCV) infection. AMP-activated protein kinase (AMPK), a major mediator of lipid metabolism, regulates HCV-associated hepatic steatosis, but the underlying mechanisms remain obscure. Here we investigated the mechanism of HCV nonstructural protein 5A (NS5A)-induced lipid accumulation by the AMPK/SREBP-1c pathway.

Methods
We generated model mice by injecting recombinant lentiviral particles expressing the NS5A protein (genotype 3a) via the tail vein. The serum levels of alanine aminotransferase (ALT), free fatty acids (FFAs) and triglycerides (TG) were examined. H&E and Oil Red O staining were used to examine lipid droplets. Immunohistochemistry staining, quantitative real-time PCR and Western blotting were used to determine the expression of lipogenic genes.

Results
Our results showed that the serum levels of ALT, FFAs and TG, as well as the accumulation of hepatic lipid droplets, were increased significantly in mice infected with NS5A-expressing lentiviral particles. NS5A inhibited AMPK phosphorylation and increased the expression levels of sterol regulatory element binding protein-1c (SREBP-1c), acetyl-coenzyme A carboxylase 1 (ACC1) and fatty acid synthase (FASN) in vivo and in vitro. Further investigation revealed that pharmacological activation or ectopic expression of AMPK neutralized the upregulation of SREBP-1c, ACC1 and FASN, and ameliorated hepatic lipid accumulation induced by NS5A. Ectopic expression of SREBP-1c enhanced NS5A-induced hepatic lipid accumulation, which was dramatically reversed by pharmacological activation of AMPK.

Conclusions
Collectively, we demonstrate that NS5A induces hepatic lipid accumulation via the AMPK/SREBP-1c pathway.
Omission of adjuvant radiotherapy following breast-conserving surgery for elderly women with early-stage pure mucinous breast carcinoma
Authors: Wu San-Gang , Li Feng-Yan , Wang Jun , Lian Chen-Lu , Zhou Juan , He Zhen-Yu 
Published: November 2019

AbstractBackgroundWe aimed to ascertain population-based practice patterns and survival outcomes of postoperative radiotherapy following breast conserving-surgery (BCS) in elderly women (aged ≥65 years) with early-stage pure mucinous breast carcinoma (PMBC).MethodsPatients aged ≥65 years diagnosed with T1–2N0 and hormone receptor-positive PMBC between 1990 and 2010 were identified from the Surveillance, Epidemiology, and End Results database. Binomial logistic regression, Kaplan-Meier method, Multivariate Cox proportional hazards models, and propensity score matching (PSM) were used for statistical analysis.ResultsWe enrolled 3416 patients, including 1225 (35.9%) and 2191 (64.1%) in the no-radiotherapy and radiotherapy cohorts, respectively. The percentage of patients receiving postoperative radiotherapy following BCS was significantly lower after 2004 (59.5% between 2004 and 2010), relative to that before 2004 (71.1% between 1990 and 2003;P < 0.001). Before PSM, the 10-year breast cancer-specific survival (BCSS) rates were 98.1 and 93.2% for patients with and without postoperative radiotherapy (log-rank test,P < 0.001), respectively. In the PSM cohort, receiving postoperative radiotherapy was associated with better BCSS rates, with 10-year BCSS rates of 97.6 and 94.5% in patients with and without postoperative radiotherapy, respectively (log-rank test,P = 0.001). Multivariate Cox proportional analysis indicated that receiving postoperative radiotherapy was an independent factor associated with better BCSS before (P < 0.001) and after PSM (P = 0.001), relative to those not receiving postoperative radiotherapy.ConclusionsThis study shows a decreasing utilization of postoperative radiotherapy following BCS of elderly PMBC patients over time. However, postoperative radiotherapy following BCS should be administered for elderly women with PMBC owing to independent association with better survival.
Evaluating the optimal re-irradiation dose for locally recurrent esophageal squamous cell carcinoma after definitive radiotherapy
Authors: Xu Xiujuan , Wang Zhongming , Jiang Shunian , Shang Yuping , Wu Yan 
Published: November 2019

Abstract

Background
Re-irradiation (re-RT) has the active effect of relieving clinical symptoms and prolonging the survival of patients with recurrent esophageal squamous cell carcinoma (ESCC). However, the optimal re-RT dose is still uncertain. Here, we analyzed the prognostic factors associated with survival and explored the optimal re-RT dose for patients with recurrent ESCC following definitive radiotherapy.

Patients and methods
The data of 47 patients with recurrent ESCC who were retreated between 2010 and 2014 were retrospectively analyzed. All patients received a radiation dose > 50 Gy during the primary treatment. The median time to recurrence after primary radiotherapy was 26 months (range 6–120 months). All patients had in-field recurrence in the esophagus. Recurrence within the local site was observed in 37 patients (78.7%), and recurrence in both the local site and regional nodes were observed in 10 patients (21.3%). All patients received 3D conformal re-RT with a median dose of 58 Gy (range 26–64 Gy). Chemotherapy was sequentially used in 27.7% of the patients. Survival curves were constructed according to the Kaplan-Meier method and were compared by log-rank tests. The factors predictive of survival were identified with univariate and multivariate analyses.

Results
Dysphagia relief after re-RT was achieved in 20 of the 35 symptomatic patients (57.1%). The median survival time (MST) of all patients was 17 months, and the 1-, 2-, 3- and 5-year overall survival (OS) rates were 72.3, 25.5, 17.0 and 2.1%, respectively. In the univariate analysis, an Eastern Cooperative Oncology Group Performance Status (ECOG-PS) of 0–1 (P = 0.014), recurrence at the local site (P = 0.048), time to recurrence ≥24 months (P = 0.006) and re-RT dose ≥50 Gy (P < 0.001) were associated with favorable OS. In the multivariate analysis, only re-RT dose was an independent factor for OS (P = 0.007). Severe complications were observed in 7 patients, two of whom received a re-RT dose > 60 Gy.

Conclusion
Our results demonstrated that patients with recurrent ESCC following definitive radiotherapy had unfavorable OS. Re-RT could be considered a feasible and effective treatment modality. A re-RT dose > 50 Gy could improve the survival outcomes, and a dose > 60 Gy should be administered with caution due to the risk of severe complications.
Total aortic arch replacement surgery with a Core temperature of 34 °C
Authors: Li Quan , Qu Hong , Liu Tianqi , Yu Jianmin , Lv Meng 
Published: November 2019

Abstract

Background
Traditional aortic arch replacement surgery must be performed under moderate or deep hypothermia (22–28 °C) and circulatory arrest. Hypothermia and hypoperfusion can cause damage to the nervous system; therefore, postoperative brain and spinal cord complications are common. Improvements in surgical techniques are necessary to solve this problem. Herein, we report a method of total aortic arch replacement that can be performed at a core temperature of 34 °C, similar to other simple cardiac operations.

Case presentation
Four patients underwent surgery with this technique (3 males and 1 female, aged 48 to 67 years). Computed tomography angiography performed at admission showed a total aortic dissection, resulting in a diagnosis of Stanford type A aortic dissection. The patients underwent emergency aortic sinus remodelling, ascending aortic replacement, modified aortic arch replacement, and elephant trunk stenting. No patients had neurological complications. During a follow-up of more than 1-month, no patients had aortic valve regurgitation or anastomotic leak.

Conclusions
This technique can increase the operating temperature by approximately 6 to 12 °C and reduce the circulatory arrest time by approximately 18 to 28 min. All of the patients recovered well without any neurological complications, demonstrating the feasibility and safety of this technique. We believe that this technique can serve as a good alternative strategy for managing aortic dissection and aneurysm, especially for young surgeons who are acquiring experience in arch replacement surgery.
An abnormal left ventricular-atrial perforation after radiofrequency catheter ablation: a case report
Authors: Tao Tingting , Zheng Junnan , Xu Hongfei , Ni Yiming 
Published: November 2019

Abstract

Background
Cardiac radiofrequency ablation is a popular treatment for arrhythmias. However, it does have some complications, some of which are severe, even fatally. And there were limited reports on cardiac internal perforation after radiofrequency catheter ablation (RFCA) that required a surgical repair.

Case presentation
A 47-year-old male was admitted to our hospital due to chest congestion for 4 months. He received a radiofrequency catheter ablation (RFCA) 9 months prior to admission. On admission, an echocardiogram showed an abnormal perforation between the left ventricle and the left atrium with moderate mitral valve regurgitation. We therefore performed a mitral valve replacement (MVR) and fixed the abnormal atrial-ventricular breakage via median sternotomy.

Conclusions
Cardiac perforation is a severe complication of cardiac RFCA, operators should be extremely cautious to minimize radiofrequency associated perforations. Such a challenging and complex procedure should be deliberately considered by doctors and patients before implementation.
Passive hallux adduction decreases lateral plantar artery blood flow: a preliminary study of the potential influence of narrow toe box shoes
Authors: Jacobs Julia L. , Ridge Sarah T. , Bruening Dustin A. , Brewerton K. Annie , Gifford Jayson R. , Hoopes Daniel M. , Johnson A. Wayne 
Published: November 2019

AbstractBackgroundBlood flow is essential in maintaining tissue health. Thus, compromised blood flow can prevent tissue healing. An adducted hallux, as seen inside a narrow shoe, may put passive tension on the abductor hallucis, compressing the lateral plantar artery into the calcaneus and restricting blood flow. The purposes of this study were to compare lateral plantar artery blood flow before and after passive hallux adduction and to compare blood flow with arch height.MethodsForty‐five healthy volunteers (20 female, 25 male; age = 24.8 ± 6.8 yr; height = 1.7 ± 0.1 m; weight = 73.4 ± 13.5 kg) participated in this cross‐over design study. Arch height index (AHI) was calculated, and blood flow measurements were obtained using ultrasound (L8‐18i transducer, GE Logiq S8). The lateral plantar artery was imaged deep to abductor hallucis for 120 s: 60 s at rest, then 60 s of passive hallux adduction. Maximal passive hallux adduction was performed by applying pressure to the medial side of the hallux. Blood flow was calculated in mL/min, and pre‐passive hallux adduction was compared to blood flow during passive hallux adduction.ResultsLog transformed data was used to run a paired t‐test between the preadduction and postadduction blood flow. The volume of blood flow was 22.2% lower after passive hallux adduction compared to before (− 0.250 ± 0.063, p < 0.001). As AHI decreased, there was a greater negative change in blood flow. As baseline blood flow increased, there was also a greater negative change in blood flow.ConclusionsOur preliminary findings of decreased blood flow through passive hallux adduction indicate conditions that elicit passive hallux adduction (e.g. wearing narrow‐toed shoes) may have important effects on foot blood flow. Individuals with lower AHI appear to have a greater risk of decreased blood flow with passive hallux adduction.
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect
Authors: Esposito Daniel , Weile Jochen , Shendure Jay , Starita Lea M. , Papenfuss Anthony T. , Roth Frederick P. , Fowler Douglas M. , Rubin Alan F. 
Published: November 2019

Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB (https://www.mavedb.org), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
Biochemical characteristics and synergistic effect of two novel alginate lyases from Photobacterium sp. FC615
Authors: Lu Danrong , Zhang Qingdong , Wang Shumin , Guan Jingwen , Jiao Runmiao , Han Naihan , Han Wenjun , Li Fuchuan 
Published: November 2019

AbstractBackgroundMacroalgae and microalgae, as feedstocks for third-generation biofuel, possess competitive strengths in terms of cost, technology and economics. The most important compound in brown macroalgae is alginate, and the synergistic effect of endolytic and exolytic alginate lyases plays a crucial role in the saccharification process of transforming alginate into biofuel. However, there are few studies on the synergistic effect of endolytic and exolytic alginate lyases, especially those from the same bacterial strain.ResultsIn this study, the endolytic alginate lyase AlyPB1 and exolytic alginate lyase AlyPB2 were identified from the marine bacteriumPhotobacteriumsp. FC615. These two enzymes showed quite different and novel enzymatic properties whereas behaved a strong synergistic effect on the saccharification of alginate. Compared to that when AlyPB2 was used alone, the conversion rate of alginate polysaccharides to unsaturated monosaccharides when AlyPB1 and AlyPB2 acted on alginate together was dramatically increased approximately sevenfold. Furthermore, we found that AlyPB1 and AlyPB2 acted the synergistic effect basing on the complementarity of their substrate degradation patterns, particularly due to their M-/G-preference and substrate-size dependence. In addition, a novel method for sequencing alginate oligosaccharides was developed for the first time by combining the1H NMR spectroscopy and the enzymatic digestion with the exo-lyase AlyPB2, and this method is much simpler than traditional methods based on one- and two-dimensional NMR spectroscopy. Using this strategy, the sequences of the final tetrasaccharide and pentasaccharide product fractions produced by AlyPB1 were easily determined: the tetrasaccharide fractions contained two structures, ΔGMM and ΔMMM, at a molar ratio of 1:3.2, and the pentasaccharide fractions contained four structures, ΔMMMM, ΔMGMM, ΔGMMM, and ΔGGMM, at a molar ratio of ~ 1:1.5:3.5:5.25.ConclusionsThe identification of these two novel alginate lyases provides not only excellent candidate tool-type enzymes for oligosaccharide preparation but also a good model for studying the synergistic digestion and saccharification of alginate in biofuel production. The novel method for oligosaccharide sequencing described in this study will offer a very useful approach for structural and functional studies on alginate.
Lytic cycle of Besnoitia besnoiti tachyzoites displays similar features in primary bovine endothelial cells and fibroblasts
Authors: Jiménez-Meléndez Alejandro , Fernández-Álvarez María , Calle Alexandra , Ramírez Miguel Ángel , Diezma-Díaz Carlos , Vázquez-Arbaizar Patricia , Ortega-Mora Luis Miguel , Álvarez-García Gema 
Published: November 2019

Abstract

Background
Bovine besnoitiosis, caused by the cyst-forming apicomplexan parasite Besnoitia besnoiti, is a chronic and debilitating cattle disease that continues to spread in Europe in the absence of control tools. In this scenario, in vitro culture systems are valuable tools to carry out drug screenings and to unravel host-parasite interactions. However, studies performed in bovine target cells are scarce.

Methods
The objective of the present study was to obtain primary bovine aortic endothelial cells (BAECs) and fibroblast cell cultures, target cells during the acute and the chronic stage of the disease, respectively, from healthy bovine donors. Afterwards, expression of surface (CD31, CD34 and CD44) and intracellular markers (vimentin and cytokeratin) was studied to characterize cell populations by flow cytometry. Next, the lytic cycle of B. besnoiti tachyzoites was studied in both target cells. Invasion rates (IRs) were determined by immunofluorescence at several time points post-infection, and proliferation kinetics were studied by quantitative PCR (qPCR). Finally, the influence of bovine viral diarrhea virus (BVDV) co-infection on the host cell machinery, and consequently on B. besnoiti invasion and proliferation, was investigated in BAECs.

Results
Morphology and cytometry results confirmed the endothelial and fibroblast origins. CD31 was the surface marker that best discriminated between BAECs and fibroblasts, since fibroblasts lacked CD31 labelling. Expression of CD34 was weak in low-passage BAECs and absent in high-passage BAECs and fibroblasts. Positive labelling for CD44, vimentin and cytokeratin was observed in both BAECs and fibroblasts. Regarding the lytic cycle of the parasite, although low invasion rates (approximately 3–4%) were found in both cell culture systems, more invasion was observed in BAECs at 24 and 72 hpi. The proliferation kinetics did not differ between BAECs and fibroblasts. BVDV infection favoured early Besnoitia invasion but there was no difference in tachyzoite yields observed in BVDV-BAECs compared to BAECs.

Conclusions
We have generated and characterized two novel standardized in vitro models for Besnoitia besnoiti infection based on bovine primary target BAECs and fibroblasts, and have shown the relevance of BVDV coinfections, which should be considered in further studies with other cattle pathogens.