Miracle-dz/UniFAR-FTUs huggingface dataset:
A Period-Extender Gene, pex, That Extends the Period of the Circadian Clock in the Cyanobacterium Synechococcus sp. Strain PCC 7942

ABSTRACT We cloned the pS1K1 plasmid in the process of apparently “complementing” a circadian clock mutant of cyanobacteriumSynechococcus sp. strain PCC 7942, SP22, which has a 22-h period (T. Kondo, N. F. Tsinoremas, S. S. Golden, C. H. Johnson, S. Kutsuna, and M. Ishiura, Science 266:1233–1236, 1994). Sequence analysis revealed that SP22 did not have a mutation in the genomic DNA segment carried on pS1K1, and thesp22 mutation was later found in a recently cloned new clock gene, kaiC. Therefore, the period-extender genepex that was carried on pS1K1 was a suppressor gene for thesp22 mutation. The pex gene encoded a protein of 148 amino acid residues. No meaningful homologs were found in DNA or protein databases including the Synechocystis genome database. The pex gene was transcribed from 129 and 164 bp upstream of the translation initiation codon as 0.6-kb transcripts. The Pex protein was detected as a fusion protein with a molecular mass of 15 kDa by the epitope tag fusion method using a c-Myc epitope tag. Disruption of the pex gene in wild-type cells shortened the period of the rhythms by 1 h, although it did not affect other properties of the rhythms, whereas its overexpression extended the period by 3 h with a concomitant reduction in the amplitude of the rhythms. In various clock mutants examined, overexpression caused arrhythmicity. Thus, Pex is likely to function as a modifier of the circadian clock in Synechococcus.
A decision-theoretic approach in the design of an adaptive upper-limb stroke rehabilitation robot

This paper presents an automated system for a rehabilitation robotic device that guides stroke patients through an upper-limb reaching task. The system uses a partially observable Markov decision process (POMDP) as its primary engine for decision-making. The POMDP allows the system to automatically modify exercise parameters to account for the specific needs and abilities of different individuals, and to use these parameters to take appropriate decisions about stroke rehabilitation exercises. The performance of the system was evaluated through various simulations and by comparing the decisions made by the system with those of a human therapist for a single patient. In general, the simulations showed promising results and the therapist thought the system decisions were believable.
Personality and life satisfaction over 12 years: Contrasting mid- and late life.

Abstract. Both theoretical reasoning and empirical data suggest that personality and well-being have substantial interrelationships. However, more longitudinal evidence is required, and the relationship lacks research attention from a lifespan perspective. We examined the mid-term and long-term interrelations of Neuroticism and Extraversion with life satisfaction in two cohorts from middle and late adulthood, using data from the “Interdisciplinary Longitudinal Study of Adult Development (ILSE). ” Multigroup, cross-lagged models reveal personality to be more predictive of life satisfaction than vice versa. Furthermore, an aging effect occurs regarding the relationships between life satisfaction and personality, with life satisfaction being predictive of personality only in the old cohort. Controlling for health weakens the interrelationship. Results add to the understanding of lifespan dynamics among personality and life satisfaction.
A gene deletion that up-regulates viral gene expression yields an attenuated RSV vaccine with improved antibody responses in children

A live attenuated vaccine candidate for RSV may decrease viral replication while enhancing immunogenicity in children. Outflanking RSV Respiratory syncytial virus (RSV) infection may lead to severe respiratory illness in young children. Researchers are working to develop a live attenuated vaccine, which would mimic the natural course of infection; however, inhibiting viral replication also limits the immune response. Now, Karron et al. report that a version of RSV lacking the M2-2 protein can induce immunity despite decreased vaccine virus shedding in young children. The lack of M2-2 resulted in decreased viral RNA replication needed for virus production while allowing gene transcription and antigen synthesis required for stimulating the immune response. Children who received the vaccine produced anti-RSV antibodies without medically attended illness in the subsequent RSV season, suggesting that this approach may provide protective immunity to RSV. Respiratory syncytial virus (RSV) is the leading viral cause of severe pediatric respiratory illness, and a safe and effective vaccine for use in infancy and early childhood is needed. We previously showed that deletion of the coding sequence for the viral M2-2 protein (ΔM2-2) down-regulated viral RNA replication and up-regulated gene transcription and antigen synthesis, raising the possibility of development of an attenuated vaccine with enhanced immunogenicity. RSV MEDI ΔM2-2 was therefore evaluated as a live intranasal vaccine in adults, RSV-seropositive children, and RSV-seronegative children. When results in RSV-seronegative children were compared to those achieved with the previous leading live attenuated RSV candidate vaccine, vaccine virus shedding was significantly more restricted, yet the postvaccination RSV-neutralizing serum antibody achieved [geometric mean titer (GMT) = 1:97] was significantly greater. Surveillance during the subsequent RSV season showed that several seronegative RSV MEDI ΔM2-2 recipients had substantial antibody rises without reported illness, suggesting that the vaccine was protective yet primed for anamnestic responses to RSV. Rational design appears to have yielded a candidate RSV vaccine that is intrinsically superior at eliciting protective antibody in RSV-naïve children and highlights an approach for the development of live attenuated RSV vaccines.
Spatial Cluster Analysis Based on Evolutionary DNA Computing Technique

Spatial clustering is an important area in cluster analysis. Up to now, most computing models are implemented mostly by traditional von Neumann’s architecture. The purpose of this paper is to propose a simulated evolutionary DNA computing model and integrate DNA computing with cluster analysis. The proposed technique will apply for large scale, high parallel clustering problems potentially. KeywordsDNA computing, cluster analysis, spatial clustering, evolutionary computing.
A Review of Pulsed Electromagnetic Field (PEMF) Mechanisms at a Cellular Level: A Rationale for Clinical Use

Delivery of health care demands evidence-based practice. Evidence-based practice helps to ensure that all facets of health care delivery are subject to a higher level of accountability. This helps to assure that the patient is receiving treatment that has some proof of efficacy. In recent years, physiotherapy practice has been influenced by a swell of research which, in many cases, supports current practice and, in some cases, influences change of practice. Despite the fact that there is a significant increase in the numbers of clinical trials and reviews in Physiotherapy, including research in electromagnetic modalities and mechanical modalities, it is not uncommon for a practitioner to feel at a loss to answer, “Exactly how does this treatment work? ” This paper will review the mechanisms of action of the most common electromagnetic modalities and provide a rationale as to why “pulsed” fields seem to produce more significant effects compared with continuous applications. It will be shown that significant tissue healing effects, particularly with the modality PEMF, are likely the result of increased activity in non-excitable cells. The reputation of electromagnetic modalities has suffered in recent years, likely due to a lack of understanding of mechanisms for action. In the literature, the understanding in this area has made considerable progress over the past ten years. This review will explain the science at a cellular level and suggest the potential mechanisms for action for the modalities with specific focus on PEMF.
DAE time integration for real‐time applications in multi‐body dynamics

The equations of motion of multi‐body systems with kinematically closed loops are given by differential‐algebraic equations (DAE). Real‐time applications like hardware‐in‐the‐loop testbeds or driving simulators require appropriate integration methods that can solve the non‐linear constraints without exceeding an a priori fixed number of calculation steps. Partitioned linear‐implicit Euler methods can be extended by appropriate stabilization techniques to keep the error in the constraints bounded for arbitrary time intervals. These methods need a fixed low number of operations for each time step. One simplified Newton step for the projection onto the constraint manifold can prevent the drift‐off for arbitrary time intervals if the stepsize is sufficiently small. Selected methods were successfully implemented in the commercial vehicle simulation package veDYNA to improve substantially the simulation capabilities for vehicle‐trailer coupling.
Parental feeding practices in Turkish children with autism spectrum disorder: Factorial validation of the Feeding Strategies Questionnaire

ABSTRACT The Feeding Strategies Questionnaire (FSQ) has not previously been validated either in a Turkish sample or on children with autism spectrum disorder (ASD). In the present study, the factorial validity and reliability of the Turkish version of the FSQ were examined in order to use the assessment of the parental feeding practices on children with ASD. Further, the parental feeding strategies and their possible associations with various child demographic variables (i.e., children’s age groups, gender, severity, comorbidity, and body mass index [BMI]) were investigated. The present study suggests that the FSQ shows a good internal consistency, adequate split-half reliability, and acceptable factorial validity, which confirms that the FSQ can be used to assess the feeding strategies of parents and their children with ASD in a Turkish sample. The FSQ and factors scores were calculated as a moderate level. There were no significant differences in regard to FSQ by age group, gender, severity of disability, or comorbidity. BMI scores indicate the risk of overweight for a sample of Turkish children with ASD. There was a just significant and negative correlation between the coercive interactions factor of FSQ and BMI average score, which may be interpreted that when BMI score reduces, parents tend to be in coercive feeding style.
Air Quality, Biomarker Levels, and Health Effects on Staff in Korean Restaurants and Pubs Before and After a Smoking Ban.

INTRODUCTION The Korean government implemented a smoking ban at square floor area of ≥150 m(2), rather than <150 m(2), restaurants and pubs from July 2013. This study examined the effects of the smoking regulations in restaurants and pubs in terms of the air quality, biomarker levels and health effects on staff. METHODS Particulate matter smaller than 2.5 µm (PM2.5) was measured in 146 facilities before and 1 month after the ban. The urinary cotinine and 4-(methylnitrosamino)-1-(3-pyridyl)-1- butanol (NNAL) levels were measured in 101 staff members at 77 facilities before and 1 month after the ban. We also measured self-reported respiratory and sensory symptoms on both phases. RESULTS Of the 146 facilities, 121 facilities were included in the PM2.5 analysis. In ≥150 m(2) pubs, the indoor PM2.5 concentration was significantly reduced after the ban (p < .05). While the urinary cotinine concentrations of the staff in all facilities were not changed after the ban, the total NNAL concentrations of the staff in ≥150 m(2) pubs were significantly reduced after the ban (p < .05). The health effects on staff show that only sensory symptoms significantly improved in ≥150 m(2) facilities after the ban (p < .05). CONCLUSIONS The smoking ban significantly reduced the levels of PM2.5 and total NNAL concentrations in ≥150 m(2) pubs and improved sensory health among staff in ≥150 m(2) facilities. The results of this study can be useful in supporting an expansion of the smoking ban in all indoor places, including <150 m(2) restaurants and pubs.
Fault detection and diagnosis based on KPCA-CDBNs model

In order to improve the accuracy and stability of industrial fault detection and diagnosis, this paper introduces the deep learning theory and proposes an improved Deep Belief Networks (DBNs). In the first, this paper introduces the “centering trick” in the pre-training process of network. This method is done by subtracting offset values from visible and hidden variables. Then, in the process of network fine-tuning, the weights of network are added the White Gaussian Noise. This improved Deep Belief Networks combines with Kernel Principal Component Analysis (KPCA) into KPCA-CDBNs model. This paper applies this model into fault detection research of Tennessee Eastman (TE) and shows that the method of this paper has higher prediction and stability of fault detection and diagnosis.
A Probabilistic Constraint-based Approach to Protein Structure Predication

Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is believed that the dynamical folding of a protein to its native conformation is determined by the amino acid sequence of the protein. Given the usefulness of known protein structures in such valuable tasks as rational drug design, protein structure prediction is a highly active field of research in bioinformatics [2, 8]. During recent decades various methods have been developed along the following two main lines [2]. The first line of methods, called homology modeling, rely on assembling structures of proteins using structural fragments of similar sequences available in sources such as PDB [3]. The second line of methods, called ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. The folding of any particular protein is an extremely complex process; and simulation of the folding of even a small protein remains an insurmountable challenge to state-of-the-art computers. Many ab initio methods adopt reduced models [16] such as lattice models which alleviate the complexity of the process because of the reduced number of degrees of freedom. Reduced models cannot be expected to consistently generate predications with high accuracy. Nevertheless, the low resolution results obtained can be used to narrow the possible conformations from an exponentially large number to a number small enough that more computationally expensive methods can be applied.
Protein Stability and Domain Topology Determine the Transcriptional Activity of the Mammalian Glial Cells Missing Homolog, GCMb*

The glial cells missing (GCM) family of transcription factors consists of Drosophila GCM and the mammalian proteins GCMa and GCMb. They are expressed in a highly restricted manner during development and are known or assumed to be important regulators of developmental fate decisions. As the biochemical properties of GCMb have not been studied so far, we have undertaken a detailed structure-function analysis of the mouse GCMb (mGCMb) protein. DNA-binding specificity was very similar to that of other GCM proteins. Nevertheless, mGCMb was only a weak transcriptional activator in a number of different tissue culture systems. Interestingly, this was not due to an intrinsic absence of transactivation potential. In effect, we were able to identify two separate transactivation domains within mGCMb, one carboxyl-terminally adjacent to the DNA-binding domain and the second within the extreme carboxyl terminus. Activity of both transactivation domains was, however, modulated by an inhibitory region unique to mGCMb and located between the two transactivation domains. Furthermore, pulse-chase experiments proved that the mGCMb protein has a half-life approximately four times shorter than mGCMa. Introduction of the above mentioned inhibitory domain of mGCMb into mGCMa shortened the half-life of mGCMa to a value typical of mGCMb with a concomitant reduction in transactivation potential. Given the strong correlation between protein stability and transactivation potential, functional differences between the two mammalian GCM homologs are likely due to differences in stability with a single inhibitory region in mGCMb being involved in the reduction of both.
Physiological Adjustments and Circulating MicroRNA Reprogramming Are Involved in Early Acclimatization to High Altitude in Chinese Han Males

Background: Altitude acclimatization is a physiological process that restores oxygen delivery to the tissues and promotes oxygen use under high altitude hypoxia. High altitude sickness occurs in individuals without acclimatization. Unraveling the molecular underpinnings of altitude acclimatization could help understand the beneficial body responses to high altitude hypoxia as well as the altered biological events in un-acclimatized individuals. This study assessed physiological adjustments and circulating microRNA (cmiRNA) profiles in individuals exposed to high altitude, aiming to explore altitude acclimatization in humans. Methods: Ninety volunteers were enrolled in this study. Among them, 22 individuals provided samples for microRNA arrays; 68 additional individuals constituted the validation set. Un-acclimatized individuals were identified by the Lake Louise Scoring System. Thirty-three phenotypes were recorded pre- and post-exposure to high altitude, including stress hormones, lipid profiles, hematological indices, myocardial enzyme spectrum, and liver and kidney function related enzymes. CmiRNA expression profiles were assessed using miRCURYTM LNA Array (v.18.0) screening, with data validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Then, associations of plasma microRNA expression with physiological adjustments were evaluated. The biological relevance of the main differentially expressed cmiRNAs was explored by bioinformatics prediction. Results: Nineteen of the 33 phenotypes were significantly altered during early altitude acclimatization, including hematological indices, lipid profiles, and stress hormones; meanwhile, 86 cmiRNAs (79 up-regulated and 7 down-regulated) showed differential expression with statistical significance. Among them, 32 and 25 microRNAs were strongly correlated with low-density lipoprotein-cholesterol and total cholesterol elevations, respectively. In addition, 22 microRNAs were closely correlated with cortisol increase. In un-acclimatized individuals, 55 cmiRNAs were up-regulated and 36 down-regulated, compared with acclimatized individuals. The HIF signaling pathway was suppressed in un-acclimatized individuals. Conclusion: Physiological adjustments, including the hematological system, stress hormones, and lipid molecules contributed to early altitude acclimatization, and showed strong correlations with cmiRNA reprogramming. Moreover, acclimatized and un-acclimatized individuals showed different cmiRNA profile. Suppression of the HIF-1 signaling pathway by microRNA regulation may play a key role in the pathogenesis of un-acclimatization with high altitude hypoxia.
DanHong injection targets endothelin receptor type B and angiotensin II receptor type 1 in protection against cardiac hypertrophy

Cardiac hypertrophy (CH) is an independent risk factor for cardiovascular diseases (CVDs). Mitigating or preventing CH is the most effective strategy for the treatment of CVDs. DanHong injection (DH) is a Chinese herbal medicine preparation (CHMP) widely used in clinical treatment of several CVDs in China. However, the direct targets and cellular mechanisms for these protective effects remain unclear. This study was designed to illustrate the direct targets of DH in protecting against CH and investigate CH molecular pathogenesis. A hypertrophic cell model was induced by endothelin-1 (ET-1) on human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs). Real time cellular analysis (RTCA) cardio system and high content analysis (HCA) were used to detect the changes in contractile function, morphology and protein level of hypertrophic hiPS-CMs. Agonist and antagonist assay on receptors were performed using calcium mobilization high-throughput screening (HTS). DH significantly attenuated CH by modulating myocardial contractility, suppressing cell area enlargement and down-regulating ET-1-induced brain natriuretic peptide (BNP), actinin alpha 2 (ACTN2) and cardiac muscle troponin T (TNNT2) protein expression (P < 0.05). Endothelin receptor type B (ETBR) and angiotensin II receptor type 1 (AT1R) were DH direct targets, with IC50 value of 25.67 μL/mL and 1.10 μL/mL, respectively. Proteomics analysis showed that proteins involved in cell cycle inhibition, RNA processing, mitochondrial translation and cytoskeleton are significant regulated by DH treatment. These data revealed that ETBR and AT1R are DH direct targets on protecting against CH, providing a strategy to explore direct targets of CHMPs.
Development of a Procedural Guide to Implement Response to Intervention (RtI) With High-Ability Learners

In recent years, a focus on individual student needs has set the stage for tailoring educational interventions to address issues of students who are not working up to educational proficiency standards outlined in the No Child Left Behind (NCLB) legislation. This new pedagogical model may provide a unique opportunity to meet the needs of high-ability students who are not working to their potential in the classroom. Research indicates that gifted students allowed to work on material beyond the common core curriculum instead of merely maintaining the pace of the rest of the class actually perform better on end-of-the-year testing in math and science than gifted controls who did not pursue additional work. Bright students, like all students, demonstrate increased motivation and classroom performance when provided with academic material that appropriately challenges them. Response to intervention (RtI) establishes differentiated curriculum as the standard in America’s schools. It holds promise for all students, not only students who are lagging behind. RtI addresses student underperformance, whether due to a lack of motivation, boredom, or any number of potential factors moderating the learning of high-ability students as well as the average learner. This article reports on a study that developed and field tested a procedural guide for implementation of the RtI model with gifted students.
Polymorphism in Serotonin Receptor 3B Is Associated with Pain Catastrophizing

Pain catastrophizing, a coping style characterized by excessively negative thoughts and emotions in relation to pain, is one of the psychological factors that most markedly predicts variability in the perception of pain; however, only little is known about the underlying neurobiology. The aim of this study was to test for associations between psychological variables, such as pain catastrophizing, anxiety and depression, and selected polymorphisms in genes related to monoaminergic neurotransmission, in particular serotonin pathway genes. Three hundred seventy-nine healthy participants completed a set of psychological questionnaires: the Pain Catastrophizing Scale (PCS), the State-Trait Anxiety Inventory and Beck’s Depression Inventory, and were genotyped for 15 single nucleotide polymorphisms (SNPs) in nine genes. The SNP rs1176744 located in the serotonin receptor 3B gene (5-HTR3B) was found to be associated with pain catastrophizing scores: both the global score and the subscales of magnification and helplessness. This is the first study to show an association between 5-HTR3B and PCS scores, thus suggesting a role of the serotonin pathway in pain catastrophizing. Since 5-HTR3B has previously been associated with descending pain modulation pathways, future studies will be of great interest to elucidate the molecular pathways involved in the relation between serotonin, its receptors and pain catastrophizing.