DNA regulatory motif selection based on support vector machine (SVM) and its application in microarray experiment of Kashin-Beck disease

Conserved DNA sequences are essential to investigate the regulation and expression of nearby genes. The conserved regions can interact with certain proteins and can potentially determine the transcription speed and amount of the corresponding mRNA in gene replication process. In this paper, motifs of coexpressed genes of microarray experiments were explored with discovery algorithms. Then a selection algorithm based on support vector machine (SVM) was applied to identify those motifs which mostly influenced gene expression. This method combined the advantages from both matrix based motif finding and functional motif selection. When applied to Kashin-Beck disease (KBD), this method identified 9 motifs, and revealed that some motifs may be related to the immune reactions. In addition, we suggested that the methods used could be applied to other microarray experiments to explore the underlying relationships between motif types and gene functions.Key words: Support vector machine (SVM), microarray, motif discovery, gene regulation, Kashin-Beck disease

Optimizing the feeding operation of recombinant Escherichia coli during fed-batch cultivation based on Pontryagin's minimum principle

Recombinant Escherichia coli BL21 was used to produce human-like collagen in fed-batch culture. After building and analyzing the kinetic models of fed-batch cultures, the maximum specific growth rate, Yx/s and Yp/s were 0.411 h-1 , 0.428 g·g-1 and 0.0716 g/g, respectively. The square error of cell growth models, glucose consumption model and human-like collagen formation were almost all around 94%, which indicated that the kinetic model could describe the actual change well. According to the target, that is, to gain the highest productivity of human-like collagen, the feeding rate (F) was worked out on the basis of Pontryagin's minimum principle. In the verification experiments, the specific growth rate was controlled at 0.15 and 0.04 h-1 at the fed-batch and induction phase, respectively. The result showed that the concentrations of cell and human-like collagen could reach 87.6 and 6.11 g·L-1, and they were raised by 17.9 and 18.6%, respectively.Key words: Fed-batch culture, human-like collagen, maximum specific growth rate, Pontryagin's minimum principle, recombinant Escherichia coli

The TOC-Based Algorithm for Solving Multiple Constraint Resources: a Re-examination

published_or_final_versio

Control of Emi2 activity and stability through Mos-mediated recruitment of PP2A.

Before fertilization, vertebrate eggs are arrested in meiosis II by cytostatic factor (CSF), which holds the anaphase-promoting complex (APC) in an inactive state. It was recently reported that Mos, an integral component of CSF, acts in part by promoting the Rsk-mediated phosphorylation of the APC inhibitor Emi2/Erp1. We report here that Rsk phosphorylation of Emi2 promotes its interaction with the protein phosphatase PP2A. Emi2 residues adjacent to the Rsk phosphorylation site were important for PP2A binding. An Emi2 mutant that retained Rsk phosphorylation but lacked PP2A binding could not be modulated by Mos. PP2A bound to Emi2 acted on two distinct clusters of sites phosphorylated by Cdc2, one responsible for modulating its stability during CSF arrest and one that controls binding to the APC. These findings provide a molecular mechanism for Mos action in promoting CSF arrest and also define an unusual mechanism, whereby protein phosphorylation recruits a phosphatase for dephosphorylation of distinct sites phosphorylated by another kinase

Reinforcement Learning Tutor Better Supported Lower Performers in a Math Task

Resource limitations make it hard to provide all students with one of the most effective educational interventions: personalized instruction. Reinforcement learning could be a key tool to reduce the development cost and improve the effectiveness of, intelligent tutoring software that aims to provide the right support, at the right time, to a student. Here we illustrate that deep reinforcement learning can be used to provide adaptive pedagogical support to students learning about the concept of volume in a narrative storyline software. Using explainable artificial intelligence tools, we also extracted interpretable insights about the pedagogical policy learned, and we demonstrate that the resulting policy had similar performance in a different student population. Most importantly, in both studies the reinforcement-learning narrative system had the largest benefit for those students with the lowest initial pretest scores, suggesting the opportunity for AI to adapt and provide support for those most in need.Comment: 23 pages. Under revie

The reactivity ratios of group transfer copolymerization of acrylonitrile with methacrylates

Random copolymerization have been performed for three binary systems using 1-methoxy-2-methyl-1-trimethylsilyloxy propene(initiator) and tetrabutylammonium bibenzoate(catalyst) in tetrahydrofuran solution. The copolymer compositions were determined by elementary analysis for nitrogen and the results evaluated by the Kelen-Tudos method, The monomer pairs concerned are (1) acrylonitrile(AN) and methyl methacrylate(MMA), (2) AN and ethyl methacrylate(EMA), (3) AN and butyl methacrylate(BMA), The reactivity ratios determined in this study are: (1) r(AN)=10.22, r(MMA)=0.07; (2)r(AN)= 5.68, r(EMA)=0.16; (3) r(AN)=8.59, r(BMA)=0.09

Electrical stimulation of hindlimb skeletal muscle has beneficial effects on sublesional bone in a rat model of spinal cord injury

Spinal cord injury (SCI) results in marked atrophy of sublesional skeletal muscle and substantial loss of bone. In this study, the effects of prolonged electrical stimulation (ES) and/or testosterone enanthate (TE) on muscle mass and bone formation in a rat model of SCI were tested. Compared to sham-transected animals, a significant reduction of the mass of soleus, plantaris and extensor digitorum longus (EDL) muscles was observed in animals 6 weeks post-SCI. Notably, ES or ES + TE resulted in the increased mass of the EDL muscles. ES or ES + TE significantly decreased mRNA levels of muscle atrophy markers (e.g., MAFbx and MurF1) in the EDL. Significant decreases in bone mineral density (BMD) (−27%) and trabecular bone volume (−49.3%) at the distal femur were observed in animals 6 weeks post injury. TE, ES and ES + TE treatment significantly increased BMD by +6.4%, +5.4%, +8.5% and bone volume by +22.2%, and +56.2% and+ 60.2%, respectively. Notably, ES alone or ES + TE resulted in almost complete restoration of cortical stiffness estimated by finite element analysis in SCI animals. Osteoblastogenesis was evaluated by colony-forming unit-fibroblastic (CFU-F) staining using bone marrow mesenchymal stem cells obtained from the femur. SCI decreased the CFU-F+ cells by −56.8% compared to sham animals. TE or ES + TE treatment after SCI increased osteoblastogenesis by +74.6% and +67.2%, respectively. An osteoclastogenesis assay revealed significantly increased TRAP+ multinucleated cells (+34.8%) in SCI animals compared to sham animals. TE, ES and TE + ES treatment following SCI markedly decreased TRAP+ cells by −51.3%, −40.3% and −46.9%, respectively. Each intervention greatly reduced the ratio of RANKL to OPG mRNA of sublesional long bone. Collectively, our findings demonstrate that after neurologically complete paralysis, dynamic muscle resistance exercise by ES reduced muscle atrophy, downregulated genes involved in muscle wasting, and restored mechanical loading to sublesional bone to a degree that allowed for the preservation of bone by inhibition of bone resorption and/or by facilitating bone formation

Psychological Indicators and Perceptions of Adolescents in Residential Care

Abstract The institutionalization of adolescents has been mentioned in the literature with positive and negative aspects. This study investigated 61 adolescents in residential care aiming to evaluate psychological problems and perceptions related to the care, using interviews and the YSR. Data was evaluated using quantitative and qualitative analysis, using gender, age and length of institutionalization as variables. Results indicated clinical scores for psychological problems, except for externalizing problems, in younger girls recently taken into care and older boys institutionalized for longer periods. The perceptions about the care were negative or indifferent; elements of positivity were expressed by adolescents institutionalized for longer periods. Instability in the permanence in the care service and the reasons for having been taken into care were manifested with psychological distress. There were few contacts with the family of origin; the adolescents mentioned the importance of their families and the desire to leave the institution. Members of the institutional teams were indicated as sources of care and protection. This study reflects the challenges for the positive development of this population

The novel adipokine progranulin counteracts IL-1 and TLR4-driven inflammatory response in human and murine chondrocytes via TNFR1

Progranulin (PGRN) is a recently identified adipokine that is supposed to have anti-inflammatory actions. The proinflammatory cytokine interleukin-1? (IL1?) stimulates several mediators of cartilage degradation. Toll like receptor-4 (TLR4) can bind to various damage-associated molecular patterns, leading to inflammatory condition. So far, no data exist of PGRN effects in inflammatory conditions induced by IL1? or lipopolysaccharide (LPS). Here, we investigated the anti-inflammatory potential of PGRN in IL1?- or LPS-induced inflammatory responses of chondrocytes. Human osteoarthritic chondrocytes and ATDC-5 cells were treated with PGRN in presence or not of IL1? or LPS. First, we showed that recombinant PGRN had no effects on cell viability. We present evidence that PGRN expression was increased during the differentiation of ATDC-5 cell line. Moreover, PGRN mRNA and protein expression is increased in cartilage, synovial and infrapatellar fat pad tissue samples from OA patients. PGRN mRNA levels are upregulated under TNF? and IL1? stimulation. Our data showed that PGRN is able to significantly counteract the IL1?-induced expression of NOS2, COX2, MMP13 and VCAM-1. LPS-induced expression of NOS2 is also decreased by PGRN. These effects are mediated, at least in part, through TNFR1. Taken together, our results suggest that PGRN has a clear antiinflammatory function