bluuebunny/crossref_metadata_2025_split huggingface dataset:
EDLMFC: An Ensemble Deep Learning Framework with Multi-scale Features Combination for ncRNA-protein Interaction Prediction
Authors: Wang Jingjing , Zhao Yanpeng , Gong Weikang , Liu Yang , Wang Mei , Huang Xiaoqian , Tan Jianjun 
Published: January 2021

Abstract
Background: Non-coding RNA (ncRNA) and protein interactions play essential roles in various physiological and pathological processes. The experimental methods used for predicting ncRNA-protein interactions are time-consuming and labor-intensive. Therefore, there is an increasing demand for computational methods to accurately and efficiently predict ncRNA-protein interactions.Results: In this work, we presented an ensemble deep learning-based method, EDLMFC, to predict ncRNA-protein interactions using the combination of multi-scale features, including primary sequence features, secondary structure sequence features, and tertiary structure features. Conjoint k-mer was used to extract protein/ncRNA sequence features, integrating tertiary structure features, then fed into an ensemble deep learning model, which combined convolutional neural network (CNN) to learn dominating biological information with bi-directional long short-term memory network (BLSTM) to capture long-range dependencies among the features identified by the CNN. Compared with other state-of-the-art methods under 5-fold cross-validation, EDLMFC shows the best performance with accuracy of 94.3% and 90.0% on RPI1807 and NPInter v2.0 datasets, respectively. The results of the independent test demonstrated that EDLMFC can effectively predict potential ncRNA-protein interactions from different organisms. Furtherly, EDLMFC is also shown to predict hub ncRNAs and proteins presented in ncRNA-protein networks of Mus musculus successfully.Conclusions: In general, our proposed method EDLMFC improved the accuracy of ncRNA-protein interaction predictions and anticipated providing some helpful guidance on ncRNA functions research.The source code of EDLMFC and the datasets used in this work are available at https://github.com/JingjingWang-87/EDLMFC.
Clostridioides Difficile Toxin B (tcdB) Peptide Mimotope Antibody-capture Enzyme Immunoassay in the Detection of Colorectal Cancer
Authors: Magat Edrienne Myenna , Balanag Gregg Austine , Cariño Ana Maria , Fellizar Allan , Sy-Ortin Teresa , Albano Pia Marie , Gueva Leonardo Jr Acosta 
Published: January 2021

Abstract
BACKGROUND: The role of certain gut microbes in the development of colorectal cancer has recently been understood. In our previous work, we have reported the reactivity of serum collected from CRC patients to peptide mimotopes of bacterial antigens associated with the development of CRC, hence, their potential in its detection. Here, we evaluate the diagnostic parameters of an anti- Clostridioides difficile toxin B (tcdB) peptide mimotope IgG and IgA antibody-capture enzyme-linked immunosorbent assay (ELISA) in the detection of CRC.METHODS: Prediction of the immunogenic epitopes of tcdB was made using the in silico B-cell epitope mapping tools available at the Immune Epitope Database and Analysis Resources (IEDB). Synthetic peptide analogs of the predicted epitopes which were used in the immunoassays were synthesized and purchased from Genscript (New Jersey, USA). Presence of anti-peptide IgG and IgA from serum collected from patients diagnosed with colorectal cancer were detected by a peptide antibody-capture indirect ELISA protocol developed in this study. Diagnostic parameters were computed. RESULTS: The amino acid position 1465 to 1474 of the reported sequence of tcdB (PDB Accession No. AGG91641.1) was predicted to be immunogenic. The peptide antibody-capture ELISA developed in this study gave diagnostic specificities of 94.9% and 97.4%, positive predictive values (PPV) of 86.6% and 93.3%, and likelihood ratios of 6.5 and 14.0 for IgG and IgA, respectively. Our results show the potential of the immunoassay designed in ruling in possibility of CRC during diagnosis.
Identification of the Bcl-2 and Bax Homologs From the Tick Rhipicephalus Haemaphysaloides and Their Function in the Degeneration of Tick Salivary Glands
Authors: Hu Shanming , Wang Yanan , Xu Zhengmao , Zhou Yongzhi , Cao Jie , Zhang Houshuang , Zhou Jinlin 
Published: January 2021

Abstract
BackgroundThe salivary gland of female ticks degenerates rapidly by apoptosis and autophagy after feeding. Bcl-2 family proteins play an important role in the apoptosis pathways but the functions of these proteins in ticks are unclear. We studied Bcl-2 and Bax homologs from the tick Rhipicephalus haemaphysaloides and determined their functions in the degeneration of the salivary glands.MethodsThe full-length cDNA of the RhBcl-2 and RhBax genes were obtained by transcriptome analysis and RhBcl-2 and RhBax were expressed in E. coli. Two molecules containing conserved BH (Bcl-2 family homology) domains were identified and named RhBcl-2 and RhBax. After protein purification and mouse immunizations, specific polyclonal antibodies (PcAb) were created in response to the recombinant protein. Reverse transcription quantitative PCR (RT-qPCR) and western blot were used to detect the existence of RhBcl-2 and RhBax in ticks. TUNEL assays were used to determine the apoptosis level in the salivary glands at different feeding times after gene silencing. The interactions between RhBcl-2 and RhBax were identified by co-transfection and GST pull-down assays. The RT-qPCR assay demonstrated that the transcription of RhBax genes increased significantly during the engorged periods of the tick developmental stages (engorged larval, nymph, and adult female ticks). ResultsTranscriptional levels of RhBcl-2 and RhBax in the salivary glands increased more significantly than other tissues post engorgement. RhBcl-2 treatment significantly restrained tick feeding. In contrast, RhBax interference had no effect on tick feeding. TUNEL staining showed that apoptosis levels were significantly reduced after interfering with RhBcl-2 expression. Co-transfection and GST pull-down assays showed that RhBcl-2 and RhBax could combine with each other, but failed to combine without the BH3 domain. Conclusions﻿This study identified the roles of RhBcl-2 and RhBax in tick salivary gland degeneration and clarifies their interactions.
Prevalence of High HDL-cholesterol and Its Associated Factors Among Childbearing Age Tunisian Women: a Cross-sectional Study
Authors: Cherifa Fatma Ben , Ati Jalila El , Doggui Radhouene , Ati-Hellal Myriam El 
Published: January 2021

Abstract

Background: The protective role of high HDL-C against cardiovascular risk has been questioned recently. Due to the increasing trend of CVD in Tunisia, this study aimed to determine the prevalence of high HDL-C and its associated factors in childbearing age Tunisian women. Methods: A cross-sectional survey was conducted among a subsample of 1689 women, aged 20 to 49 y in the Great Tunis region. Data on socio-demographic and lifestyle factors were collected by a questionnaire. Overall adiposity was assessed by BMI. All biological variables were assayed in blood samples coated with EDTA by enzymatic methods. Stata software (2015) was used for data management and statistical analysis. Results: High HDL-C values were recorded in 26.6% of selected women. After adjustment for all socio-demographic and lifestyle factors, age, hypertension and smoking were negatively associated with high HDL-C levels while family history of cancer was positively associated with high HDL-C in women. Conclusions: Additional investigation on the relationship between high HDL-C and cancer risk should be performed due to controversial results.
Fibrolipomatous Hamartoma of the Median Nerve of the Hand: A Case Report and Literature Review
Authors: Yu Yang , Yang Yazhu , Ge Jinghua , Wang Chen , Wang Tao , Fan Zhaoxiang , Xue Wenyu , Xu Hao , Shi Qi 
Published: January 2021

Abstract
Introduction: Fibrolipomatous Hamartoma (FLH) is a rare tumor-like disease, mainly occurs in benign tumors of the peripheral nerves of the upper limbs, which characterized by the overgrowth of neuronal fat and fibrous tissue.Case presentation: A patient had numbness of fingers in the left hand for more than 5 years. Three years ago, the superficial sensation at the metacarpophalangeal joint of the hypothenar of the left hand was weakened. Two years later, the distal ulnar side of the index finger and the distal radial side of the middle finger were secondary to weakened superficial sensation and megalodactyly symptoms of the middle finger and index finger of the left hand were developed. Physical examination showed a mass on the left palm side. MRI showed an abnormal subcutaneous fusiform signal at the palmar side of the left wrist: T1W1 isointensity, T2W1 inhomogeneous slightly hyperintense signal. The clinical features, radiologic presentations, treatment choice, and pathologic characteristic were illustrated. During the operation, the appearance of the nerve was hypertrophic and variant, without obvious masses, the proliferated fibrous tissues were showed a fusiform change, and the nerve fibers were degenerated and atrophied. Immunohistochemical results showed S-100 (+), NSE (focus +), EMA (portion +), GFAP (-), ERG (blood vessel +), SMA (blood vessel +), Ki-67 (1%+), NF (small region +). The patient's finger numbness symptom improved obviously and the condition was stable when paying a return visit 3 months after the operation. Conclusions：The clinical symptoms of FLH of median nerve mainly include gradually enlarged painless mass, macrodactyly, pain, numbness, paresthesia and carpal tunnel syndrome. The diagnosis mainly depends on ultrasonic examination and MRI. The pathological sections of FLH sometimes show perineurioma-like changes, which need to be identified by clinical and MRI features. The treatment methods include prophylactic carpal tunnel release (CTR) and nerve transplantation after the whole nerve resection. CTR, has been proven to be helpful for many patients suffering from carpal tunnel symptoms and can relieve most of the symptoms, is the main method. However, the pathogeny needs to be further explored.
Downlink multiple access interference cancellation for NOMA based on single-channel blind separation under imperfect CSI
Authors: Li Jiong , Fan Menlan 
Published: January 2021

Abstract
Successive interference cancellation (SIC) is one of the most common multiple access interference cancellation techniques in the downlink of the non-orthogonal multiple access (NOMA) system. However, this interference cancellation method has two disadvantages. One is that interference cancellation performance depends on perfect channel state information (CSI). Due to the influence of factors such as channel estimation errors, time-varying channel transmission, and feedback channel transmission delay, it is difficult for the receiver to obtain accurate channel state information. Second, when the power allocated by the base station to different users is close, the multiple access interference cancellation performance is poor. Based on the blind signal separation theory, this paper proposes a multiple access interference cancellation method based on single-channel signal separation, which solves the above two problems in the downlink signal reception of the NOMA system. The simulation results show the effectiveness of the algorithm proposed in this paper.
Longitudinal changes in the inferior cerebellar peduncle and lower limb motor recovery following subcortical infarction
Authors: Liu Gang , Guo Yaomin , Dang Chao , Peng Kangqiang , Tan Shuangquan , Xie Chuanmiao , Xing Shihui , Zeng Jinsheng 
Published: January 2021

Abstract
BackgroundThe cerebellum receives afferent signals from spinocerebellar pathways regulating lower limb movements. However, the longitudinal changes in the spinocerebellar pathway in the early stage of unilateral supratentorial stroke and their potential clinical significance have received little attention. MethodsDiffusion tensor imaging and Fugl-Meyer assessment of lower limb were performed 1, 4, and 12 weeks after onset in 33 patients with acute subcortical infarction involving the supratentorial areas, and in 33 normal subjects. We evaluated group differences in diffusion metrics in the bilateral inferior cerebellar peduncle (ICP) and analyzed the correlation between ICP diffusion metrics and changes to the Fugl-Meyer scores of the affected lower limb within 12 weeks after stroke. ResultsSignificantly decreased fractional anisotropy and increased mean diffusivity were found in the contralesional ICP at week 12 post stroke relative to controls (all P < 0.01) and those at week 1 (all P < 0.05). There were significant fractional anisotropy decreases in the ipsilesional ICP at week 4 (P = 0.008) and week 12 (P = 0.004) relative to controls. Both fractional anisotropy (rs = 0.374, P = 0.038) and mean diffusivity (rs = -0.499, P = 0.004) changes in the contralesional ICP correlated with changes in Fugl-Meyer scores of the affected lower limbs in all patients.ConclusionBilateral ICP degeneration occur in the early phase of supratentorial stroke and contralesional ICP degeneration may hinder recovery of the affected lower limb. ICP could serve as a potential therapeutic target for improving lower limb function after supratentorial stroke.
Improvement of cardiomyopathy after ketogenic diet in a patient with Leigh syndrome caused by MTND5 mutation
Authors: Wesół-Kucharska Dorota , Greczan Milena , Witulska Katarzyna , Piekutowska-Abramczuk Dorota , Ciara Elżbieta , Kowalski Paweł , Rokicki Dariusz 
Published: January 2021

Abstract
BackgroundMitochondrial diseases (MDs) are heterogeneous group of disorders caused by inborn defects in the mitochondrial respiratory chain (MRC) and malfunctions of cellular oxidative phosphorylation (OXPHOS). MDs are caused by mutations both in mitochondrial and nuclear DNA. Leigh syndrome (LS) is a neurodegenerative MD with specific clinical and neuroradiological features. There is a broad clinical spectrum of MDs, including organ-specific and multiorgan presentations with symptoms occurring at any age. High energy requiring organs are most frequently involved and cardiac involvement is common. At present there is no specific treatment for MD. Ketogenic diet (KD) has been proposed as a treatment option for patients with MD with seizures or myopathy. It is suggested that KD itself may trigger cardiological complications after long-term therapy, but according to an animal model study, KD could be considered as a therapeutic option for some mitochondrial cardiomyopathies.MethodHere we present a retrospective case report on a male infant diagnosed with LS (m.12706T > C in MTND5) with severe progressive hypertrophic cardiomyopathy, with significant cardiological improvement after KD implementation .ResultsThe ketogenic diet was introduced in a male infant with clinical, biochemical and radiological features of Leigh syndrome, confirmed by next-generation sequencing (NGS) (known pathogenic variant in mtDNA), suffering from severe progressive hypertrophic cardiomyopathy and heart failure with no significant improvement on cardiological treatment, mitochondrial cocktail therapy and mechanical ventilation. The follow-up after KD initiation have shown significant clinical improvement in cardiovascular efficiency and echocardiographic parameters with no adverse effect observed so far.ConclusionScreening for cardiomyopathy is a standard of care (SoC) in the management of patients with mitochondrial disease. Although there are reports suggesting the efficacy and safety of KD in patients with mitochondrial disease, more studies are needed to understand the pathophysiology of mitochondrial diseases and to determine which patients are likely to benefit from this therapy.
25-hydroxyvitamin D upregulates L6 muscle cell differentiation induced by mononuclear cells via the Notch signaling pathway
Authors: Domingues-Faria Carla , Rougé Stéphanie , Patrac Véronique , Salles Jérôme , Walrand Stéphane , Vasson Marie-Paule , Goncalves-Mendes Nicolas 
Published: January 2021

Abstract
During muscle regeneration, myoblasts engage in cross-talk with immune cells to achieve optimal proliferation and differentiation. In this process, cytokines secreted by immune cells are described to modulate the kinetic of muscle differentiation. Taking into account that immune and muscle cells are both targets of vitamin D, we investigated in vitro the impact of 25-hydroxyvitamin D (25(OH)D) on the transcriptional response of muscle cells in presence of mononuclear cells. To address this objective, an in vitro model of co-culture using L6 myogenic cell line and peripheral blood mononuclear cell (PBMC) isolated from rat was used and compared to L6 cultured alone. Cells were treated with 25(OH)D (125 nM) during the 6 days of differentiation. Gene expression of 25(OH)D metabolism actors, muscle differentiation and metabolism markers, and of Notch signaling pathway effectors were studied in L6 cells by qPCR. In mono-cultured L6 cells, a 25(OH)D treatment induced a 3-fold increase (p < 0.05) in VDR mRNA expression at 24 h while no change in mRNA expression of the muscle differentiation markers i.e. Myog, Myh2 and Des was observed. In the presence of PBMCs, the mRNA expression of these markers was enhanced (27.5 times for myogenin, p < 0.05) resulting in an overexpression of the Notch pathway effectors (Dll: 6.8-fold and Hes1: x3.8-fold, p < 0.05). The 25(OH)D counteracted these effects of the PBMCs on L6 gene expression with the exception of the interleukin 6 transcript and protein. In the present study, our in vitro approach demonstrates the importance of immune cells in stimulating muscle cell differentiation. Taken as a whole, the data show that 25(OH)D attenuates in vitro the Notch pathway-dependent effects of immune cells on muscle cell differentiation and energy metabolism.
Methane hydrates achieve both thick oceans and thick lithospheres in Enceladus and Mimas
Authors: Nishitani Ryusuke , Kimura Jun , Tani Atsushi , Sasaki Sho 
Published: January 2021

Abstract
The difference between the inactive surface of Mimas and the active surface of Enceladus is puzzling. We investigate the conditions under which both have a thick subsurface ocean and the thermal lithosphere of Mimas is thicker than that of Enceladus by using a one-dimensional simulation of thermal evolution. We adopt the initial core temperature, initial methane concentration, and tidal heating rate as free parameters in the calculation. The initial methane concentration and tidal heating rate greatly affect the current ocean thickness, although the initial core temperature does not affect the thickness. Methane hydrate forms at the base of the icy shell if the initial methane concentration is not 0. The methane hydrate layer plays an insulative role in an icy shell. When the initial methane concentration is 1000 , ∼2 GW is needed to achieve more than 50 km of the subsurface ocean on Mimas and ∼7.5 GW is needed to achieve more than 25 km of the subsurface ocean on Enceladus. These values are smaller than those needed when the initial methane concentration is 0 . The existence of the methane hydrate layer promotes the survival of the subsurface ocean because it insulates internal heat. In addition, it is found that the surface heat flux is depressed if the methane hydrate layer exists, which is consistent with the unrelaxed craters in Mimas. Methane hydrate may explain the thick oceans in Mimas and Enceladus and the inactive shell of Mimas.
TITLE: Utility of self-rated adherence for monitoring dietary and physical activity compliance and assessment of participant feedback of the Healthy Diet and Lifestyle Study pilot.
Authors: O’Reilly Holly , Panizza Chloe , Lim Unhee , Yonemori Kim M , Wilkens Lynne R , Shvetsov Yurii B , Harvie Michelle N , Shepherd John , Zhu Fengqing Maggie , Marchand Loïc Le , Boushey Carol J , Cassel Kevin D 
Published: January 2021

Abstract
Background: We examined the utility of self-rated adherence to dietary and physical activity (PA) prescriptions as a method to monitor intervention compliance and facilitate goal setting during the Healthy Diet and Lifestyle Study (HDLS). In addition, we assessed participants’ feedback of HDLS. HDLS, is a randomized pilot intervention that compared the effect of intermittent energy restriction combined with a Mediterranean diet (IER+MED) to a Dietary Approaches to Stop Hypertension (DASH) diet, with matching PA regimens, for reducing visceral adipose tissue area (VAT).Methods: Analyses included the 59 (98%) participants who completed at least one week of HDLS. Dietary and PA adherence scores were collected 8 times across 12-weeks, using a 0-10 scale (0=Not at all, 4=Somewhat, and 10=Following the plan very well). Adherence scores for each participant were averaged and assigned to high and low adherence categories using the group median (7.3 for diet, 7.1 for PA). Mean changes in VAT and weight from baseline to 12 weeks are reported by adherence level, overall and by randomization arm. Participants’ feedback at completion and 6 months post intervention were examined.Results: Mean ± SE, dietary adherence was 6.0 ± 0.2 and 8.2 ± 0.1, for the low and high adherence groups, respectively. For PA adherence, mean scores were 5.9 ± 0.2 and 8.5 ± 0.2, respectively. Compared to participants with low dietary adherence, those with high adherence lost significantly more VAT (22.9 ± 3.7 cm2 vs. 11.7 ± 3.9 cm2 [95% CI, -22.1 to -0.3]) and weight at Week 12 (5.4 ± 0.8 kg vs. 3.5 ± 0.6 kg [95% CI, -3.8 to -0.0]). For PA, compared to participants with low adherence, those with high adherence lost significantly more VAT (22.3 ± 3.7 cm2 vs. 11.6 ± 3.6 cm2 [95% CI, -20.7 to -0.8]). Participants’ qualitative feedback of HDLS was positive and the most common response, on how to improve the study, was to provide cooking classes.Conclusions: Results support the use of self-rated adherence as an effective method to monitor dietary and PA compliance and facilitate participant goal setting. Study strategies were found to be effective with promoting compliance to intervention prescriptions. Trial registration: ClinicalTrials.gov Identifier: NCT03639350. Registered 21st August 2018- Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03639350
A new method for the conservation of ancient colored paintings on ramie textiles
Authors: Liu Jiaojiao , Li Yuhu , Hu Daodao , Xing Huiping , Cao Xiaolian , Cao Jing , Jia Zhihui 
Published: January 2021

Abstract
Textiles are valuable cultural heritage items that are susceptible to several degradation processes due to their sensitive nature, such as the case of ancient ma colored-paintings. Therefore, it is important to take measures to protect the precious ma artifacts. Generally, ″ma″ includes ramie, hemp, flax, oil flax, kenaf, jute, and so on. In this paper, an examination and analysis of a painted ma textile were the first step in proposing an appropriate conservation treatment. Standard fiber and light microscopy were used to identify the fiber type of the painted ma textile. Moreover, custom-made reinforcement materials and technology were introduced with the principles of compatibility, durability and reversibility. The properties of tensile strength, aging resistance and color alteration of the new material to be added were studied before and after dry heat aging, wet heat aging and UV light aging. After systematic examination and evaluation of the painted ma textile and reinforcement materials, the optimal conservation treatment was established, and exhibition method was established. Our work presents a new method for the conservation of ancient Chinese painted ramie textiles that would promote the protection of these valuable artifacts.