Miracle-dz/UniFAR-FTUs huggingface dataset:
Semisynthetic protein nanoreactor for single-molecule chemistry

Significance The modulation of ionic current flowing through an individual protein pore provides information at the single-molecule level about chemical reactions occurring within the pore. However, chemistry investigated in this way has been largely confined to the reactions of thiolates, presented by the side chains of cysteine residues. The introduction of unnatural amino acids would provide a large variety of reactive side chains with which additional single-molecule chemistry could be investigated. Here we have produced semisynthetic protein pores containing a terminal alkyne and used the pores as a nanoreactor to study Cu(I)-catalyzed azide-alkyne cycloaddition. A long-lived intermediate (4.5 s) in the reaction was directly observed. The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach.
A two-level simulator for spaceborne SAR

A novel two-level simulator for spaceborne Synthetic Aperture Radar (SAR) is presented in this paper, and this simulator consists of two different simulation levels: the raw signal level and the image level and the implementations are discussed in detail. For the raw signal level, a new model with higher computation efficiency based on Graphic Processor Unit (GPU) to generate the radar echoes is proposed. For the image level, an efficient approach to create single-look image is processed. Finally some experimental results by the novel simulator are presented. These results demonstrate not only the validity of the proposed simulator but also the conformability of the two simulation levels.
The education of students about ISO/IEC 29110 software engineering standards and their implementations in very small entities

Worldwide, a large majority of organizations developing software are entities having up to 25 people. Since most published software engineering standards had been developed by and for large organizations, most Very Small Entities (VSEs) did not have the expertise to adapt or tailor those software engineering standards to meet their needs. The ISO/IEC 29110 series of standards and guides was specifically developed for VSEs developing software. Many countries that had not participated to international standard development, decided to join the ISO working group mandated to develop the ISO/IEC 29110 series. Since the ISO/IEC 29110 engineering and management guides are easily understandable and freely available, it has greatly helped their adoption. More than 17 countries, such as Colombia, Brazil, Haiti, Jordan, Malaysia, Mexico, Peru and Thailand are teaching ISO/IEC 29110. ISO/IEC 29110 has been used by many students to develop their first products. Many countries have adopted ISO/IEC 29110 as a national standard. A few countries are helping their VSEs in the adoption, implementation and certification activities with government programs. Low cost independent certification and assessment schemes allow VSEs to demonstrate recognition of their competences to local and international customers and partners.
Motivational Interviewing Intervention 1 The Effectiveness of a Motivational Interviewing Primary-Care Based Intervention on Physical Activity and Predictors of Change in a Disadvantaged Community

Little research exists on the impact of behaviour change interventions in disadvantaged communities. We conducted a prospective study to explore the effectiveness of motivational interviewing (MI) on physical activity (PA) change within a deprived community and the psychosocial predictors of change in PA including stage of change (SOC), self-efficacy (SE), social support (SS), and variables from self-determination theory (SDT) and the theory of planned behaviour (TPB). Five MI counsellors recruited 207 patients and offered MI sessions to support PA behaviour change. At six-months there were significant improvements in PA, SOC, and SS. A dose-response relationship was evident; those who attended 2 or more MI consultations increased their total PA more than those who attended just one. High attendees also significantly improved SOC, family SS, and external regulation. Hierarchical regression analyses indicated that number of sessions, change in SOC, and identified regulation from SDT predicted 31.3% and 23.3% of the change in total PA and walking respectively (with the addition of friend SS for walking). Change in PBC and attitudes from TPB, friend SS, intrinsic motivation from SDT, and number of sessions predicted 21.7% of vigorous PA changes. Change in amotivation was borderline significant in the final step. MI is an effective approach for promoting PA amongst lower SES groups in the short term. The study demonstrates good translational efficacy, and contributes to a limited number of PA interventions targeting low income groups in the UK.
Guidelines for virtual simulator sickness experimentation

Recently, 3D is being popular. 3D environment causes virtual (or simulator) sickness. Therefore, many researches have been done in this field, but the method is not standardized. The standardization is strongly required in this research filed. In this paper, the standardization of the method of experiment for virtual sickness research is attempted. The guideline of the experiment is proposed based on survey of previous researches.
Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification

Three rice MAGIC populations were developed to better integrate QTL identification and breeding. MAGIC populations are valuable for QTL identification, 8‐way populations being more powerful. QTL (2 and 3) were identified for heading date and plant height, respectively. One novel QTL for PH was identified on chromosome 12 using the 8‐way population.
Shuffling Adaptive Clinical Trials

Clinical trials are interventional studies on human beings, designed to test the hypothesis for diagnostic techniques, treatments, and disease preventions. Any novel medical technology should be evaluated for its efficacy and safety by clinical trials. The costs associated with developing drugs have increased dramatically over the past decade, and fewer drugs are obtaining regulatory approval. Because of this, the pharmaceutical industry is continually exploring new ways of improving drug developments, and one area of focus is adaptive clinical trial designs. Adaptive designs, which allow for some types of prospectively planned mid-study changes, can improve the efficiency of a trial and maximize the chance of success without undermining validity and integrity of the trial. However it is felt that in adaptive trials; perhaps by using accrued data the actual patient population after the adaptations could deviate from the originally target patient population and so to overcome this drawback; special methods like Bayesian Statistics, predicted probability are used to deduce data-analysis. Here, in this study, mathematical model of a new adaptive design (shuffling adaptive trial) is suggested which uses real-time data, and because there is no gap between expected and observed data, statistical modifications are not needed. Results are obviously clinically relevant.
An intervention to promote physical activity in Mexican elementary school students: building public policy to prevent noncommunicable diseases

Physical activity is an important component of strategies for health promotion and prevention of noncommunicable diseases. It is also associated with decreased risk for cardiovascular disease in overweight and obese adults and children. This article addresses the initial description of a physical activity intervention for children attending public elementary schools in Mexico. The objective was to develop a replicable model based on a strategic public, private, academic, and social partnership that would have a short-term impact on the metabolic health of children and be useful for building effective public policy. Forty-nine schools (20 000 students) participated, and 5 schools were selected for evaluation. The intervention included a 30-minute supervised middle-effort interchangeable routine, 5 days a week for a complete school year, adapted for different school conditions and students of different ages. Evaluation included anthropometric measurements and biochemical markers. Actual prevalence of combined overweight and obesity in these children was 31.9%. The intervention was successfully implemented in all schools. No change in body mass index, waist circumference, or other anthropometric indicators was found. However, changes in biochemical markers showed a significant decrease in blood glucose, total cholesterol, and cholesterol-low-density lipoproteins, reflecting a positive effect on cardiovascular health indicators.
Mesenchymal stem cells overexpressing interleukin‐10 attenuate collagen‐induced arthritis in mice

Mesenchymal stem cells (MSCs) have the inherent ability to migrate to multiple organs and to exert immunosuppressive activity. The aim of this study was to investigate the anti‐arthritogenic effects of interleukin (IL)‐10‐transduced MSCs (IL‐10‐MSC) on the development of inflammatory arthritis. DBA/1 mice were immunized with type II collagen (CII) to induce inflammatory arthritis and then injected weekly three times with IL‐10‐MSCs 21 days after primary immunization. Control mice received vehicle or MSCs alone. Serum anti‐CII antibody and T cell response to CII were determined. The results showed that cultured IL‐10‐MSCs were able to secrete high amounts of IL‐10 in vitro. Injection of IL‐10‐MSCs decreased the severity of arthritis significantly. However, there was no difference in arthritis severity between mice treated with MSC and vehicle alone. Anti‐CII antibody titres in the sera and T cell proliferative response to CII in lymph node cells were decreased significantly in mice treated with IL‐10‐MSCs compared with vehicle‐treated mice. Serum IL‐6 level was also decreased by the administration of IL‐10‐MSCs. In contrast, spleen cells of IL‐10‐MSC‐treated mice produced higher amounts of IL‐4 than those of control mice. Interestingly, although not as potent as IL‐10‐MSCs, injection of naive MSCs alone decreased serum levels of IL‐6 and anti‐CII antibody, while increasing IL‐4 production from cultured splenic cells. Taken together, systemic administration of genetically modified MSCs overexpressing IL‐10 inhibits experimental arthritis not only by suppressing autoimmune response to CII but also by regulating cytokine production, and thus would be a new strategy for treating rheumatoid arthritis.
Ebselen Decreases Oxygen Free Radical Production and Iron Concentrations in the Hearts of Chronically Iron-Overloaded Mice

Chronic iron overload is a major cause of cardiac failure throughout the world, but its pathogenesis remains to be clarified. It is conjectured that the toxicity of iron is due to its ability to catalyze the formation of oxygen free radicals (OFR), which can damage cellular membranes, proteins, and DNA. The authors report on the cardioprotective effects of the glutathione peroxidase (GPx) mimic ebselen on iron concentrations in the heart and GPx activity, and on the production of the cytotoxic aldehydes hexanal, 4-hydroxyl-2-nonenal (HNE), and malondialdehyde (MDA). Fifteen B6D2F1 mice were randomized to 1 of 3 treatment groups for a total of 20 treatments: 1) control (0.1 mL normal saline i.p. per mouse, per day); 2) iron-only (10 mg iron dextran i.p. per mouse, per day); 3) iron plus ebselen (25 mg/kg p.o. per mouse, per day). In comparison to iron-only treated mice, the authors’ findings show that supplementation with ebselen can decrease both cytotoxic aldehyde and iron concentrations in heart tissue. Additionally, mice supplemented with ebselen had an increase in GPx activity level in comparison to iron-only treated mice. To the authors’knowledge, this is the first study to examine the cardioprotective effects of ebselen against OFR damage in a model of chronic iron overload. These findings suggest that ebselen may have significance in the management of disorders of iron overload.
Update on peptidylarginine deiminases and deimination in skin physiology and severe human diseases

Deimination (or citrullination) is a recently described post‐translational modification, but its consequences are not yet well understood. It is catalysed by peptidylarginine deiminases (PADs). These enzymes transform arginyl residues involved in a peptidyl link into citrullyl residues in a calcium‐dependent manner. Several PAD substrates have already been identified like filaggrin and keratins K1 and K10 in the epidermis, trichohyalin in hair follicles, but also ubiquitous proteins like histones. PADs act in a large panel of physiological functions as cellular differentiation or gene regulation. It has been suggested that deimination plays a role in many major diseases such as rheumatoid arthritis, multiple sclerosis, Alzheimer's disease and psoriasis. Five human genes (PADIs), encoding five highly conserved paralogous enzymes (PAD1‐4 and 6), have been characterized. These genes are clustered in a single locus, at 1p35‐36 in man. Only PAD1‐3 are expressed in human epidermis. PADs seem to be controlled at transcriptional, translational and activity levels and they present particular substrate specificities. In this review, we shall discuss these main biochemical, genetic and functional aspects of PADs together with their pathophysiological implications.
Diagnostic Tests for Alzheimer's Disease: Generating and Evaluating Evidence to Inform Insurance Coverage Policy

The Policy Development Group (PDG) is an independent group brought together by the Institute for Clinical and Economic Review (ICER) and composed of academic experts, patient advocates, clinicians, epidemiologists, ethicists, and medical policy representatives of stakeholder groups including health plans and manufacturers. PDG members and their affiliations are listed below; in addition, declared conflicts of interest and other potential influences on judgment are described in Appendix A to this document. Purpose In April, 2011, for the first time in 27 years, diagnostic criteria for Alzheimer's disease (AD) were revised by clinical and policy experts under the leadership of the National Institutes of Health and the Alzheimer's Association. These new guidelines were the first to include consideration of the findings of multiple forms of biomarker tests and highlighted the major changes that had occurred in how experts think about AD and design studies of potential treatments. This evolution in diagnostic criteria has come at a time when research on different diagnostic techniques is expanding rapidly, many new treatments intended to delay the progression of AD are undergoing evaluation, and public interest in obtaining access to promising tests and treatments is growing. Outside of their uses in drug development and clinical research trials, the current clinical value of performing any type of formal diagnostic or biomarker testing for AD is controversial. The possible benefits of testing have been posited to include: helping identify patients, possibly even individuals with no symptoms, for initiation of treatment; helping clinicians decide whether additional diagnostic evaluation is necessary to look for disorders other than AD that impair cognitive function; reassuring patients who receive a negative test; and allowing patients with a positive test to plan their future more effectively. But at a time when available treatments for AD are unable to improve long-term outcomes, there is no consensus regarding the clinical benefits of diagnostic testing, and most imaging and biomarker tests for AD are not covered by public or private insurers. As the search for more effective treatments for AD continues, many questions remain about how to design clinical trials so that it is possible to evaluate different tests for AD in a way that will generate " adequate " evidence not only for patients and clinicians, but for insurers as well. The goal of this project is to seize the opportunity to address this policy need in a collaborative and pro-active manner. It is collaborative because …
Segmentation of the Sylvian fissure in brain images

In this paper, we propose an automatic method to segment the Sylvian fissure (SF) from T1-weighted magnetic resonance (MR) images. The method consists of four steps. First, morphological methods are applied to remove non-brain tissues. Then, 2D region growing is used to segment the cerebral spinal fluid (CSF) and gray matter (GM) in the SF, in which spatial relationships are used to control the region growing. A modified fuzzy c-means (FCM) clustering algorithm is introduced as well, which is more accurate than the conventional FCM method. After that, we get the 3D volume of the SF through segmenting CSF and GM slice by slice. Finally, CSF in the SF is extracted incorporating the anatomical information on a constant cortex thickness. We have demonstrated our method through both phantom and patient data.
Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant.

A novel actinobacterial strain, designated CPCC 201356(T), was isolated from a rhizosphere soil sample of the medicinal plant Astragalus membranaceus and subjected to a polyphasic taxonomic analysis. Good growth occurred at 20-32 °C, at pH 7.0-7.5 and with 0-1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H(4)) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C(16 : 0), iso-C(15 : 0) and C(17 : 1)ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356(T) belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch with Geodermatophilus obscurus DSM 43160(T). The organism showed 16S rRNA gene sequence similarity of 97.7 % with G. obscurus DSM 43160(T). DNA-DNA hybridization between strain CPCC 201356(T) and G. obscurus DSM 43160(T) was 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species, Geodermatophilus ruber sp. nov., is proposed; the type strain is CPCC 201356(T) (=DSM 45317(T) =CCM 7619(T)).
Grey Relational Analysis Method for Interval-Valued Intuitionistic Fuzzy Multiple Attribute Decision Making

The aim of this paper is to investigate the multiple attribute decision making problems with interval-valued intuitionistic fuzzy information, in which the information about attribute weights is completely known, and the attribute values take the form of interval-valued intuitionistic fuzzy numbers. A modified grey relational analysis (GRA) method is proposed. Then, based on the traditional GRA method, calculation steps for solving interval-valued intuitionistic fuzzy multiple attribute decision-making problems with known weight information are given. The degree of grey relation between every alternative and positive ideal solution and negative ideal solution are calculated. Then, according to the concept of the GRA, a relative relational degree is defined to determine the ranking order of all alternatives by calculating the degree of grey relation to both the positive-ideal solution (PIS) and negative-ideal solution (NIS) simultaneously. Finally, an illustrative example is given to verify the developed approach and to demonstrate its practicality and effectiveness.
Joint performance optimization of primary networks and cognitive radio networks

In this paper, we study the resource allocation issues related to OFDM-based multiuser cognitive radio cellular networks, where both of primary network and secondary network are investigated to make an all-round evaluation of the network performance, including the Quality of Experience (QoE) of the primary users (PUs) and the minimal rate requirement of the secondary users (SUs). Since the general resource allocation optimization task we formulate leads to challenging mixed integer nonlinear programming problems, we first propose a heuristic subchannel allocation method to remove the awkward integer constraints. Then an efficient distribution algorithm, which yields nearly linear computational complexity, is developed to work out the optimal power allocation. Simulation results indicate that our proposed resource allocation scheme works better under different performance metrics as compared to others. Moreover, our proposed distribution algorithms converge stably and quickly.
Methicillin‐Resistant Staphylococcus aureus (MRSA) ST398 in Pig Farms and Multispecies Farms

During the last few years, methicillin‐resistant Staphylococcus aureus (MRSA) ST398 has been isolated frequently from livestock, especially from pigs and to a lesser extent from cattle and poultry. To gain insight into the distribution of this bacterium in pig farms versus multispecies farms, 30 Belgian farms (10 pig, 10 pig/poultry and 10 pig/cattle farms) were screened for the presence of MRSA. On each farm, 10 nasal swabs were taken from pigs. When present, cattle (n = 10) were sampled in the nares and poultry (n = 10) in the nares, earlobes and cloaca. A selection of the obtained isolates were further characterized using multilocus sequence typing (MLST), spa typing, SCCmec typing, pulsed field gel electrophoresis (PFGE), multiple‐locus variable‐number tandem repeat analysis (MLVA) and antimicrobial susceptibility testing. On 26 of 30 farms, MRSA was isolated from pigs. Furthermore, MRSA was also isolated from poultry and cattle on one pig/poultry and five pig/cattle farms, respectively. All tested MRSA isolates belonged to ST398. Eight spa types (t011, t034, t567, t571, t1451, t2974, t3423 and t5943) were detected, among which t011 predominated. SCCmec cassettes type IVa and V were present in 20% and 72% of the isolates, respectively. When combining the results of the two remaining typing methods, PFGE and MLVA, eighteen genotypes were obtained of which one genotype predominated (56% of the positive farms). All MRSA isolates were resistant to tetracycline. Resistance to trimethoprim, aminoglycosides, macrolides, lincosamides, fluoroquinolones and chloramphenicol was also observed. In conclusion, there was no effect of the farm type on the MRSA status of the pigs. A statistically significant difference was observed when comparing the pig/poultry or the pig/cattle MRSA status on the multispecies farms. Additionally, a wide variety of MRSA ST398 strains was found within certain farms when combining different typing methods.