Miracle-dz/UniFAR-FTUs huggingface dataset:
New prognostic biomarker CMTM3 in low grade glioma and its immune infiltration

Background The CKLF-like MARVEL transmembrane domain-containing 3 (CMTM3) is differentially expressed in a variety of tumors and closely related to tumor occurrence and progression. The expression of CMTM3 was significantly elevated in glioma compared with normal brain tissue, to explore the potential function of CMTM3 in the prognosis and immune infiltration of glioma has certain clinical significance. Methods The tumor data in this study were derived from the sequencing data of various tumors in The Cancer Genome Atlas (TCGA) database. Low-grade glioma (LGG) data in the TCGA database include sequencing and clinical data. Clinical data mainly include survival time, survival outcome, age, WHO classification and other information. Sequencing data for normal tissues were obtained from the Genotype Tissue Expression (GTEx) database. Statistical analyses were mainly performed using bioinformatics tools and the corresponding R software (version 3.6.3). The Mann-Whitney U test (Wilcoxon rank sum test) was used to compare the expression differences between the tumor group and the normal group. Survival analysis was conducted using log-rank test to compare whether the overall survival (OS) time was statistically different between the CMTM3 high and low expression groups. The Tumor Immunity Estimation Resource (TIMER) database was used for immune infiltration analysis. Results The results showed that the expression of CMTM3 in World Health Organization (WHO) II and WHO III gliomas was significantly higher than that of normal tissues (P<0.05). Glioma with high CMTM3 expression showed a lower overall survival (OS) (P<0.05). Gene enrichment analysis showed that CMTM3 was significantly enriched in 4 pathways (FDR <0.25, P<0.05). A high correlation was detected between CMTM3 and a variety of immune cells. CMTM3 is highly correlated with macrophages (r=0.536, P=1.31e-36), dendritic cells (r=0.546, P=2.85e-38), CD4+ T cells (r=0.517, P=6.17e-34). Conclusions The CMTM3 gene can be used as a potential prognostic marker for WHO grade II and WHO grade III glioma, is related to the immune infiltration in glioma microenvironment, and may became a new immunotherapy target.
Variants in the VDR Gene May Influence 25(OH)D Levels in Type 1 Diabetes Mellitus in a Brazilian Population

Vitamin D has been considered a strong contributing factor to type 1 diabetes mellitus (T1DM). Many studies have investigated polymorphisms in the VDR gene in association with T1DM in different populations, but there are still conflicting findings. This study aimed to evaluate the association of four variants in the VDR gene (rs7975232, rs1544410, rs731236, and rs2228570) with T1DM risk and vitamin D levels within a population from North Region, Brazil, as well as the influence of genomic ancestry on T1DM. A total of 65 T1DM patients and 83 non-T1DM patients were enrolled in this study. VDR gene polymorphisms were assessed using Sanger sequencing analysis. Genomic ancestry was analyzed using a set of 61 ancestry-informative markers. T1DM patients showed higher European genomic contribution and lower Native American genomic contribution when compared to non-T1DM patients. T1DM patients with AA genotype in rs1544410 or CC genotype in rs731236 had significantly lower 25(OH)D levels compared to the other two genotypes (p = 0.013 and p = 0.02, respectively), while T1DM with TT genotype in rs2228570 had higher 25(OH)D levels compared to CC + TC in the same polymorphism (p = 0.011). Our findings suggest that the association between 25(OH)D and T1DM may be modified by VDR variants, possibly influencing the development of this autoimmune disease.
Meanings and expressions of co-responsibility: A small qualitative study based on the reflections from Chilean social workers involved in public-private child welfare

The study critically explores the meanings and expressions of co-responsibility based on the experience of Chilean social workers involved in public-private child welfare. It draws upon critical institutionalism to frame thematic analysis of interviews with practitioners participating in these arrangements. Results show that meanings and expressions of co-responsibility are diverse and co-exist in intervention. Some meanings are that co-responsibility is the responsibility assumed by the State as the first guarantor of rights with a private that takes responsibility for clients. It also means collaboration in a neoliberal system. Regarding expressions, it takes the form of a programmatic execution that operationalizes the rights approach. Another one is that co-responsibility expresses in individualistic performance that neglects the other colleague. Implications for critical social work practice, policy, and scholarship are discussed, based on the diversity of meanings and expressions of co-responsibility identified.
Field programmable gate array–based servo control integrated chip for a six-axis articulated robot manipulator

The objective of this article is to build a field programmable gate array–based six-axis servo control integrated chip which can integrate the function of a motion trajectory planning and the function of six position/speed/current servo controllers into one integrated chip. In the work, first, a mathematical modeling of a robot manipulator with the actuator using permanent magnet synchronous motor is derived. Second, the proportional controller in the position loop, a proportional–integral controller in the speed loop and a vector controller in the current loop for each axis are applied. Third, a system on a programmable chip) technology which comprises an Altera field programmable gate array chip and an embedded soft-core Nios-II processor is considered to develop the proposed servo control integrated chip. However, in the servo control integrated chip, it has two modules. The first module is an embedded soft-core Nios-II processor which is used to generate the motion trajectory planning by software. The second module presents a six-axis servo controller intellectual property by hardware which is applied to execute six position/speed/current controllers. Therefore, the function of a motion trajectory command and the function of six position/speed/current servo controllers for a six-axis robot manipulator can be integrated into one field programmable gate array. Finally, to verify the effectiveness and correctness of the proposed field programmable gate array–based servo control integrated chip, a six-axis robot manipulator is applied and some experimental results are demonstrated.
Shape variation in the carapace of Chinese mitten crabs (Eriocheir sinensis H. Milne Edwards, 1853) in Yangcheng Lake during the year-long culture period

Abstract To evaluate whether ontogenetic development over the grow-out culture period can cause geographical plasticity of carapace shape in a certain region, geometric morphometric analysis was used, in this study, to determine the ontogenetic changes in the carapace morphology of Chinese mitten crabs (Eriocheir sinensis) originating from Yangcheng Lake, China, during a year of growth from coin-sized juveniles to market-sized adults. The morphological differences in the carapace throughout the year of culture were characterized using a 35-landmark point system. We used principal component analysis and linear discriminant analysis to determine morphological variation using thin-plate spline analysis and mesh deformation. During the growth process, the changes in the carapace were mainly concentrated in the third and fourth anterolateral teeth and on the M-shaped pattern. During the growth of male and female crabs throughout the year, the shape of the carapace changed considerably over the first six months. Afterwards, the shape of the carapace began to stabilize and could not be differentiated through discriminant analysis. This study is the first to use geometric morphometrics to analyze the ontogenetic changes in the carapace shape of E. sinensis crabs native to Yangcheng Lake. The results demonstrate that it takes a long time for the carapace morphology of native crabs to stabilize.
Map-Matching Algorithm for Applications in Multimodal Transportation Network Modeling

Generalized Transit Feed Specification (GTFS) files have gained wide acceptance by transit agencies, which now provide them for most major metropolitan areas. The public availability GTFSs combined with the convenience of presenting a standard data representation has promoted the development of numerous applications for their use. Whereas most of these tools are focused on the analysis and utilization of public transportation systems, GTFS data sets are also extremely relevant for the development of multimodal planning models. The use of GTFS data for integrated modeling requires creating a graph of the public transportation network that is consistent with the roadway network. The former is not trivial, given limitations of networks often used for regional planning models and the complexity of the roadway system. A proposed open-source algorithm matches GTFS geographic information to existing planning networks and is also relevant for real-time in-field applications. The methodology is based on maintaining a set of candidate paths connecting successive geographic points. Examples of implementations using traditional planning networks and a network built from crowdsourced OpenStreetMap data are presented. The versatility of the methodology is also demonstrated by using it for matching GPS points from a navigation system. Experimental results suggest that this approach is highly successful even when the underlying roadway network is not complete. The proposed methodology is a promising step toward using novel and inexpensive data sources to facilitate and eventually transform the way that transportation models are built and validated.
Gastrointestinal Endoscopy and Coronavirus Disease-2019 Pandemic

Coronavirus disease-2019 (COVID-19) is a disease caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2). It has become a pandemic since March 11, 2020. It carries a significant burden and hampers gastrointestinal endoscopy practice. Since SARS-CoV-2 receptors are found in the gastrointestinal tract, COVID-19 also manifests as gastrointestinal symptoms. The viable virus is also detected in stool, carrying a high risk of transmission. Therefore, gastrointestinal endoscopy practice needs to be changed to prevent spreading from patients and medical personnel. All patients should be screened for the possibility of infection. Triage is done to determine the urgency of cases. Elective cases are postponed while semi-urgent and urgent cases are treated accordingly. A level 2 personal protective equipment (PPE) should be used for negative/suspected COVID-19 and a level 3 PPE is used for the confirmed case. Endoscopy unit should have negative-pressure room or proper ventilation, separated unit between negative/suspected and confirmed cases, exclusive equipment for COVID-19 case, and proper disinfection of equipment and room. Medical personnel must be screened regularly and positive information regarding gastrointestinal endoscopy practice should be spread to patients.
Molecular Fingerprint of BMD Patients Lacking a Portion in the Rod Domain of Dystrophin

BMD is characterized by a marked heterogeneity of gene mutations resulting in many abnormal dystrophin proteins with different expression and residual functions. The smaller dystrophin molecules lacking a portion around exon 48 of the rod domain, named the D8 region, are related to milder phenotypes. The study aimed to determine which proteins might contribute to preserving muscle function in these patients. Patients were subdivided, based on the absence or presence of deletions in the D8 region, into two groups, BMD1 and BMD2. Muscle extracts were analyzed by 2-D DIGE, label-free LC-ESI-MS/MS, and Ingenuity pathway analysis (IPA). Increased levels of proteins typical of fast fibers and of proteins involved in the sarcomere reorganization characterize BMD2. IPA of proteomics datasets indicated in BMD2 prevalence of glycolysis and gluconeogenesis and a correct flux through the TCA cycle enabling them to maintain both metabolism and epithelial adherens junction. A 2-D DIGE analysis revealed an increase of acetylated proteoforms of moonlighting proteins aldolase, enolase, and glyceraldehyde-3-phosphate dehydrogenase that can target the nucleus promoting stem cell recruitment and muscle regeneration. In BMD2, immunoblotting indicated higher levels of myogenin and lower levels of PAX7 and SIRT1/2 associated with a set of proteins identified by proteomics as involved in muscle homeostasis maintenance.
Smith Chart-based Design of a Dual Band Real Impedance Matching Network

ABSTRACT This paper presents a Smith chart-based methodology for designing a dual band real impedance matching network. The focus is to depict the dual band behavior using Smith chart, giving a better insight into analytical equations thus derived. To validate the design methodology, a dual band 3dB Wilkinson power divider is designed at two frequencies i.e. 0.9 GHz and 2.45 GHz. Summary of the derived equations and a generic MATLAB code is appended, as a quick design tool.
Transient Destabilization of Declarative Memory—Opposing Impact of Physical Exercise or Rest after Encoding in Typically Developing Children and Children with Attention Deficit Hyperactivity Disorder but No Difference after Subsequent Sleep

Background: Children are especially sensitive to a broad range of influences and show a remarkable capacity for learning. One prominent example is declarative memory, which may be influenced by a variety of factors and is impaired in attention deficit hyperactivity disorder (ADHD). Exercise and sleep, or both combined, might foster declarative memory. Methods: Here, 12 typically developing children (TDC) and 12 age-matched children with ADHD participated in an exercise and rest condition before a night in the sleep laboratory. Declarative memory was encoded before exercise or rest and retrieved before and after a night of sleep. Results: Exercise in TDC but rest in ADHD lead to a transient destabilization of declarative memory, while there were no more differences after a night of sleep. Rapid eye movement (REM) sleep latency was prolonged after exercise in both groups. Conclusions: Exercise leads to opposing effects on immediate declarative memory formation. The factors or contexts that promote or hinder declarative memory formation in children ADHD and TDC differ, and further work is needed to determine the recommendations for declarative learning in children with ADHD.
Daily Prediction and Multi-Step Forward Forecasting of Reference Evapotranspiration Using LSTM and Bi-LSTM Models

Precise forecasting of reference evapotranspiration (ET0) is one of the critical initial steps in determining crop water requirements, which contributes to the reliable management and long-term planning of the world’s scarce water sources. This study provides daily prediction and multi-step forward forecasting of ET0 utilizing a long short-term memory network (LSTM) and a bi-directional LSTM (Bi-LSTM) model. For daily predictions, the LSTM model’s accuracy was compared to that of other artificial intelligence-based models commonly used in ET0 forecasting, including support vector regression (SVR), M5 model tree (M5Tree), multivariate adaptive regression spline (MARS), probabilistic linear regression (PLR), adaptive neuro-fuzzy inference system (ANFIS), and Gaussian process regression (GPR). The LSTM model outperformed the other models in a comparison based on Shannon’s entropy-based decision theory, while the M5 tree and PLR models proved to be the lowest performers. Prior to performing a multi-step-ahead forecasting, ANFIS, sequence-to-sequence regression LSTM network (SSR-LSTM), LSTM, and Bi-LSTM approaches were used for one-step-ahead forecasting utilizing the past values of the ET0 time series. The results showed that the Bi-LSTM model outperformed other models and that the sequence of models in ascending order in terms of accuracies was Bi-LSTM > SSR-LSTM > ANFIS > LSTM. The Bi-LSTM model provided multi-step (5 day)-ahead ET0 forecasting in the next step. According to the results, the Bi-LSTM provided reasonably accurate and acceptable forecasting of multi-step-forward ET0 with relatively lower levels of forecasting errors. In the final step, the generalization capability of the proposed best models (LSTM for daily predictions and Bi-LSTM for multi-step-ahead forecasting) was evaluated on new unseen data obtained from a test station, Ishurdi. The model’s performance was assessed on three distinct datasets (the entire dataset and the first and the second halves of the entire dataset) derived from the test dataset between 1 January 2015 and 31 December 2020. The results indicated that the deep learning techniques (LSTM and Bi-LSTM) achieved equally good performances as the training station dataset, for which the models were developed. The research outcomes demonstrated the ability of the developed deep learning models to generalize the prediction capabilities outside the training station.
Long Noncoding RNA LOC554202 Predicts a Poor Prognosis and Correlates with Immune Infiltration in Thyroid Cancer

Thyroid cancer (TC) is one of the widely diagnosed carcinomas in women before the age of 30. Nevertheless, there is currently a lack of specific biomarkers for predicting the prognosis of TC. Long noncoding RNAs (lncRNAs) were important regulators in human cancer progression as previously described. Unfortunately, there is little known on these lncRNAs' functions and molecular mechanisms in TC. In our literature, we found that LOC554202 (MIR31HG) was upregulated in TC samples and correlated with clinicopathological features, including M stage, N stage, and lymph nodes examined status in TC. In addition, we found that LOC554202 overexpression was evidently correlated with high immune infiltrate levels of CD8+ T cells, macrophage, neutrophil, myeloid dendritic cells, and B cells in TC. Knockdown of LOC554202 impeded TC cell proliferation and cycle progression. We found that LOC554202 had an association with metabolic pathways, vesicle-mediated transport, tricarboxylic acid cycle, Hedgehog signaling pathway, and Hippo signaling pathway in TC. Reducing LOC554202 hindered TC cell proliferation and cycle progression. Finally, we found that LOC554202 participated in modulating the expression of the regulators of Hippo signaling and TCA pathway, such as CCND2, CCND3, SDHC, SDHD, SUCLA2, and SUCLG1. We thought that this study would largely enhance our understanding of LOC554202's functional roles in human TC progression and immune response.
Cre/LoxP Genetic Recombination Sustains Cartilage Anabolic Factor Expression in Hyaluronan Encapsulated MSCs Alleviates Intervertebral Disc Degeneration

(1) Background: Inexplicable low back and neck pain frequently results from spinal disc degeneration with an imbalanced intervertebral disc (IVD) cell homeostasis. We hypothesize that introducing MSC expressing a sustained cartilage-anabolic factor in the IVD may stimulate the mucoid materials secreted from the IVD cells, promote the MSC’s chondrogenesis and maintain the hydration content providing mechanical strength to decelerate the disc degeneration progression; (2) Methods: This study expressed a cartilage-anabolic factor runx1 by a baculoviral vector (BV) transduced MSCs through a Cre/LoxP gene editing and recombination system for sustained recombinant runx1 transcription factor production. The Cre/LoxP BV modified MSCs were encapsulated by hyaluronan hydrogel, due to its’ vital composition in ECM of a healthy disc and transplanted to a punctured coccygeal disc in rats through micro-injection, followed by X-ray radiography and histological analysis at the 4- and 12-weeks post-transplantation; (3) Results: Data reveals the Cre/LoxP BV system-mediated long-termed runx1 gene expression, possessing good biosafety characteristics in the in vitro cell transduction and in vivo MSCs transplantation, and maintained superior hydration content in the disc than that of mock transduced MSCs; (4) Conclusions: This proof-of-concept study fulfills the need of implanting therapeutic cells accompanied with microinjection in the disc, such as a discography and paves a road to manufacture composite hyaluronan, such as peptide modified hyaluronan as an MSC carrier for IVD regeneration in the future study.
Fumonisin B2 Induces Mitochondrial Stress and Mitophagy in Human Embryonic Kidney (Hek293) Cells—A Preliminary Study

Ubiquitous soil fungi parasitise agricultural commodities and produce mycotoxins. Fumonisin B2 (FB2), the structural analogue of the commonly studied Fumonisin B1 (FB1), is a neglected mycotoxin produced by several Fusarium species. Mycotoxins are known for inducing toxicity via mitochondrial stress alluding to mitochondrial degradation (mitophagy). These processes involve inter-related pathways that are regulated by proteins related to SIRT3 and Nrf2. This study aimed to investigate mitochondrial stress responses in human kidney (Hek293) cells exposed to FB2 for 24 h. Cell viability was assessed via the methylthiazol tetrazolium (MTT) assay, and the half-maximal inhibitory concentration (IC50 = 317.4 µmol/L) was estimated using statistical software. Reactive oxygen species (ROS; H2DCFDA), mitochondrial membrane depolarisation (JC1-mitoscreen) and adenosine triphosphate (ATP; luminometry) levels were evaluated to assess mitochondrial integrity. The relative expression of mitochondrial stress response proteins (SIRT3, pNrf2, LONP1, PINK1, p62 and HSP60) was determined by Western blot. Transcript levels of SIRT3, PINK1 and miR-27b were assessed using quantitative PCR (qPCR). FB2 reduced ATP production (p = 0.0040), increased mitochondrial stress marker HSP60 (p = 0.0140) and suppressed upregulation of mitochondrial stress response proteins SIRT3 (p = 0.0026) and LONP1 (p = 0.5934). FB2 promoted mitophagy via upregulation of pNrf2 (p = 0.0008), PINK1 (p = 0.0014) and p62 (p < 0.0001) protein expression. FB2 also suppressed miR-27b expression (p < 0.0001), further promoting the occurrence of mitophagy. Overall, the findings suggest that FB2 increases mitochondrial stress and promotes mitophagy in Hek293 cells.
Design and Implementation of the Active Aided Knowledge for CAE Based on JSP

It is practically significant to establish an efficient man machine integration-the system of active aided knowledge with the continual increase of mental labor cost in products.The system was developed by JSP which is of dynamic web technology.The sytemcan detect user's knowledge structure,provide active support knowledge,reduce unnecessary burden on the knowledge of user.Taking Ansys finite element analysis of automotive ball stud as an example,the results show the utility of the system.