Miracle-dz/UniFAR-FTUs huggingface dataset:
Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra.

The three-dimensional solution structure of a trisdecamer DNA duplex sequence, d(AGCTTGCCTTGAG). d(CTCAAGGCAAGCT), from a conserved region of HIV-1 genome's long terminal repeat, has been investigated using NMR spectroscopy and restrained molecular dynamics calculations. Interproton distances derived from two-dimensional nuclear Overhauser enhancement (2D NOE) experiments, using the iterative complete relaxation matrix algorithm MARDIGRAS, and torsion angles for sugar rings, estimated from stimulated fitting of double-quantum-filtered correlation (2QF-COSY) spectra, were obtained [Mujeeb, A. , Kerwin, S. M. , Egan, W. M. , Kenyon, G. L. , & James, T. L. (1992) Biochemistry 31, 9325-38]. These structural restraints have now been employed as the basis for structure refinement using restrained molecular dynamics (rMD) to search conformational space for structures consistent with the experimental restraints. Specifically, upper and lower bounds on the restraints were incorporated into the AMBER (version 4.0) total potential energy function of the system, the bounds being used to define the width of a flat-well penalty term in the AMBER force field. Confidence in the time-averaged structure obtained is engendered by convergence to essentially the same structure (root-mean-square deviation approximately 0.9 A) when two quite different DNA models, A-DNA and B-DNA (RMSD approximately 6.5 A), were employed as starting structures and when various initial trajectories were used for the rMD runs. The derived structure is further supported by the total energy calculated, the restraint violation energy, the restraint deviations, and the fit with experimental data. For the latter, the sixth-root residual index indicated a good fit of the determined structure with experimental 2D NOE spectral intensities (R1x < 0.07), and the RMS difference between vicinal proton coupling constants calculated for the derived structure and experimental coupling constants were also in reasonable agreement (JRMS = 0.9 Hz). While the structure of the trisdecamer is basically in the B-DNA family, some structural parameters manifest interesting local variations. The helix parameters indicate that, compared with classical B-DNA, the structure is longitudinally more compressed. Local structural variations at the two TG steps in particular together create bending into the major groove of the duplex. Comparison of the two-CTTG-tetrads in the duplex reveals that they have similar structures, with the TT moieties being almost identical; however, the -CTTG-pur sequence has a larger roll and slide for the -TG- step than for the -CTTG-pyr sequence, in accord with published X-ray crystallographic conclusions.
The HeartBeat model: A platform abstraction enabling fast prototyping of real-time applications on NoC-based MPSoC on FPGA

Future embedded systems will make use of many hundred, configurable or re-configurable, processing elements communicating through a network on chip (NoC), but there is lack of rapid automated design flows bridging the abstraction gap between the models of such systems and their implementation. Designing and programming NoC-based MPSoCs is a complex and error prone activity. However, capturing the design specification at a higher-level of abstraction using models based on models of computation (MoCs) offers a promising way of reducing design flaws at an early stage in the design flow. In this paper, we present the HeartBeat model, a concept for implementing applications based on the synchronous model of computation onto a NoC-based MPSoC platform on FPGA. Furthermore, we show that a platform complying to the constraints imposed by the HeartBeat model has real-time properties. The presented design flow significantly reduces the design time of a real-time embedded system implemented on a NoCbased MPSoC platform, enabling rapid design space exploration through fast prototyping of the solution.
Health Priorities and Health-Seeking Behaviors of Old Order Anabaptists in Southern Ontario With Emphasis on Cancer Screening

Background: Cancer-screening rates are low among Old Order Anabaptists; the burden of cancer is unknown. Purpose: To investigate cancer and health in the Old Order Anabaptist context. Specifically, to describe health priorities and health-seeking behaviors, crudely estimate cancer burden, and identify predictors of cancer screening. Method: A cross-sectional survey was distributed to households around Perth County, Ontario, in January 2014. Results: Response rate was 45%. Cancer burden was low. Cancer was a lower priority than general and mental health. After adjustment, family/friends motivated cancer screening for regular screeners (OR: 6.38, 95% CI [1.93, 21.07]) and symptoms was reported to motivate those underscreened/never screened (OR: 0.48, 95% CI [0.24, 0.96]). Conclusion: Cancer-screening participation may be low because the burden of cancer is low and there are other high-priority health concerns. Implications: Integrated cancer screening and holistic care may improve participation.
Accuracy of Perception of Body Size Among Overweight Latino Preadolescents After a 6-Month Physical Activity Skills Building Intervention

Background. Previous research has shown that overweight Latino children underestimate their body size. Erroneous perception of body size may have important health and behavioral implications and serve as a significant barrier to weight control. Objective. The aim of this study was to determine whether children’s perceptions of their body size became more accurate following a pediatric obesity intervention focused on increasing physical activity. Design/ methods. This analysis includes 61 overweight (body mass index ≥85%) Latino children (aged 8-11 years) parent—child dyads who completed a pilot randomized control trial. Results. After the intervention, 40.7% (11/27) of children in the intervention group rated their body size accurately compared with 21.2% (7/33) in the control group. The difference indicates a trend toward significance (P = .09). Conclusions. Participating in monthly physical activity skill building sessions may increase children’s accuracy in body size perception.This may be an important first step toward behavior modification.
An Empirical Investigation of Internet Banking in Taiwan

This paper investigates Internet banking adoption among Taiwanese bank customers. The paper examines the affect of involvement using TAM (technology acceptance model). From the PII (Personal Involvement Inventory) scales, the results indicate that involvement is significantly influenced by the characteristics of the person, stimulus and the situation. Two sets of regression analysis were conducted for the current study. The first analyze the direct influence of two factors, belief of perceived usefulness and perceived ease of use. The second set investigates the affect of involvement on perceived usefulness and perceived ease of use in determining behavioral intention. The study found perceived usefulness is strongly influenced by high involvement. Likewise, the study found that low involvement is strongly related to perceived ease of use. In determining behavioral intention, both high and low involvement significantly influence perceived usefulness and perceived ease of use, respectively.
Stock price prediction based on SVM : The impact of the stock market indices on the model performance

The challenge of stock forecasting is appealing because a small forecasting improvement can increase profit significantly. However, the volatile nature of the stock market makes it difficult to apply linear models, simple time-series or regression techniques. Consequently, support vector machine (SVM) has become a good alternative. It is a popular tool in time series forecasting for the capital investment industry. This machine learning technique which is based on a discriminative classifier algorithm, forecasts more accurately the financial data. By examining the stock price of 5 Moroccan banks, the experiment shows that the SVM can perform better when we add the global evolution of the market to the independent variables. To express the global evolution of the market, three indices of the Casablanca Stock Exchange are used : MASI, MADEX and Banks Sector Index.
Ranibizumab for subfoveal choroidal neovascularisation associated with Stargardt disease

Introduction To describe the clinical outcomes of intravitreal ranibizumab treatment for subfoveal choroidal neovascularisation (CNV) associated with Stargardt disease. Methods Prospective, interventional, case series. All patients underwent intravitreal ranibizumab injections following a pro re nata regimen with monthly examination, over a 24-month follow-up. Results Three eyes were included in the study. Best corrected visual acuity changed from 0.47±0.06 (mean±SD) at baseline to 0.90±0.17 LogMAR at the end of the 24-month follow-up. Overall, a mean number of 11 ranibizumab injections were administered in 24 months. Significant atrophic growth was detected in all cases, with the mean atrophy area increasing from 2.34±2.60 mm2 (mean±SD) at baseline to 4.23±3.31 mm2 at the end of the follow-up. Conclusions Ranibizumab treatment can stop the CNV progression, but cannot ensure a significant visual improvement. Macular atrophy tends to significantly enlarge under ranibizumab treatment over the follow-up.
Evaluation of genotoxic potential of neurotoxin anatoxin-a with the use of umuC test.

OBJECTIVE The aim of this study was to evaluate genotoxicity of anatoxin-a, cyanotoxin of neurotoxic activity. Additionally, other frequently detected cyanotoxin of previously described genotoxic potential, microcystin-LR, was used at the same concentrations, as well as the mixture of both toxins, anatoxin-a and microcystin-LR. DESIGN Genotoxicity of the toxins was determined with the use of the umuC assay, in which the induction and expression of the umuC - lacZ reporter gene was assessed. The test was conducted on Salmonella typhimurium TA 1535/pSK1002 strain, with and without metabolic transformation. The toxin concentrations were 0.25, 0.5, 1 and 2 µg/ml. The exposure time was 2 h. RESULTS The highest inefficient concentration of anatoxin-a without metabolic transformation was 0.25 µg/ml, of microcystin-LR was 0.5 µg/ml and in case of the toxin mixture all used concentrations induced the umuC gene. When S9 fraction was added to the samples, no effects were detected. CONCLUSION To our knowledge, this is the first report on genotoxic effects of anatoxin-a. Although the study is preliminary and needs further research, however, indicates the new potential activity of the toxin, as well as the possible increase of genotoxicity of other cyanotoxins, more stable in the environment, e.g. microcystin-LR.
Baby type robot "YOTARO"

Everyone had experienced meet a baby in the train or elevator and unconsciously smiles, waves hands or tries to outstare him. The kindness feeling to babies is inherent in human's natural emotion. When we interact with a baby, while they still not have capacity to do things by themselves, we will need to do anything and everything to them. The human's baby is the most conspicuous example about human's instincts where everybody takes care and be tender to him.
Are false negative direct immnufluorescence assays caused by varicella zoster virus gE mutant strains?

Strains of Varicella zoster virus (VZV) have been described recently in which a single base mutation in the gE epitope abrogates binding of the 3B3 monoclonal antibody, which is widely used for virus detection in diagnostic laboratories. These strains, named VZV‐MSP, are associated with a distinct phenotype in both in vitro culture and in SCID‐hu mice. We investigated the possibility that negative direct immunofluorescence results, using the 3B3 antibody, where the presence of virus was confirmed by polymerase chain reaction (PCR) or tissue culture are due in some cases to the MSP strain of VZV. A total of 249 vesicle fluid specimens from people with suspected shingles were examined using direct immunofluorescence, tissue culture and a nested multiplex PCR for VZV, herpes simplex virus type 1 (HSV‐1) and 2 (HSV‐2). VZV was detected in 218 of 249 (87.6%) cases. Forty‐five confirmed VZV specimens, but with negative (30) or indeterminate (15) immunofluorescence results, were analysed further. PCR was used to amplify a fragment in ORF 68 that encodes the VZV gE ectodmain recognised by 3B3 antibody. The fragments were sequenced and analysed for the single base change G448A (D150N), which is present in VZV‐MSP as compared with the reference Dumas strain. No VZV gE mutant (MSP/MSP‐like) was detected. Overall, PCR was found to be the most sensitive method of confirming VZV infection. False negative VZV immunofluorescence results are unlikely to be due to virus variants. J. Med. Virol. 73:631–635, 2004. © 2004 Wiley‐Liss, Inc.
Temporal Sequence Learning in Healthy Aging and Amnestic Mild Cognitive Impairment

Background/Study Context: Temporal sequence learning is a critical aspect of episodic memory that may be dependent on the temporal and frontal lobes. Because amnestic mild cognitive impairment (aMCI) and normal aging may result in changes within the temporal and frontal lobes, the present study investigated temporal sequence learning in patients with aMCI, cognitively normal older adults, and young adults. Methods: On each trial of a temporal sequence task, circles appeared one at a time at the end of each arm of a computerized radial eight-arm maze. Participants were asked to reproduce the temporal sequence by placing numbered circles (1 to 8) on the arms of the eight-arm maze. Participants were presented with the same fixed sequence on each trial until the sequence was replicated without any errors, or until 15 trials were presented. Results: Individuals with aMCI required significantly more trials to learn the temporal sequence compared with older adults (p < .05). Older adults required significantly more trials to learn the sequence than young adults (p < .05). Older adults and individuals with aMCI committed significantly more Trial 1 errors (p < .05) than young adults; however, there were no significant differences between the aMCI and older adult groups on Trial 1. Conclusion: The results suggest that temporal sequence learning deficits are detectable in aMCI. These deficits may disrupt a number of cognitive processes, such as episodic memory, that are important for the execution of daily activities. The results suggest that although temporal sequence learning declines with normal aging, this decline is greater in individuals who have a diagnosis of aMCI and are at higher risk for developing Alzheimer's disease.
Extinction and optical depth of contrails

One factor limiting the understanding of the climate impact from contrails and aircraft induced cloud modifications is the accurate determination of their optical depth. To this end, 14 contrails were sampled for 2756 s with instruments onboard the research aircraft Falcon during the CONCERT (CONtrail and Cirrus ExpeRimenT) campaign in November 2008. The young (<10 min old) contrails were produced by 9 commercial aircraft with weights of 47 to 508 t, among them the largest operating passenger aircraft, the Airbus A380. The contrails were observed at temperatures between 214 and 224 K and altitudes between 8.8 and 11.1 km. The measured mean in‐contrail relative humidity with respect to ice was 89 ± 12%. Six contrails were observed in cloud free air, the others were embedded in thin cirrus clouds. The observed contrails exhibited a mean ice water content of 2 mg m−3 and had a mean number concentration of 117 cm−3 and effective radius of 2.9 μm assuming asphericle particles with an aspect ratio of 0.5. Probability density functions of the extinction, with a mean (median) of 1.2 (0.7) km−1, and of the optical depth τ, with a mean (median) of 0.27 (0.13), are derived from the in situ measurements and are likely representative for young contrails from the present‐day commercial aircraft fleet at observation conditions. Radiative transfer estimates using the in‐situ measured contrail optical depth lead to a year‐2005 estimate of line‐shaped contrail radiative forcing of 15.9 mWm−2 with an uncertainty range of 11.1–47.7 mWm−2.
Digital Assisted Communication

The communication with the deaf community can prove to be very challenging without the use of sign language. There is a considerable difference between sign and written language as they differ in both syntax and semantics. The work described in this paper addresses the development of a bidirectional translator between several sign languages and their respective text, as well as the evaluation methods and results of those tools. A multiplayer game is using the translator is also described on this paper. The translator from sign language to text employs two devices, namely the Microsoft Kinect and 5DT Sensor Gloves in order to gather data about the motion and shape of the hands. This translator is being adapted to allow the communication with the blind as well. The Quantitative Evaluation Framework (QEF) and the ten-fold cross-validation methods were used to evaluate the project and show promising results. Also, the product goes through a validation process by sign language experts and deaf users who provide their feedback answering a questionnaire. The translator exhibits a precision higher than 90% and the projects overall quality rates are close to 90% based on the QEF.
Isolation and characterization of a nuclear depressive syndrome

Synopsis We investigated the nosology of endogenous depression by numerical taxonomy. Five hundred and sixty-nine patients diagnosed as having unipolar major depressive disorder in the NIMH Clinical Research Branch Program on the Psychobiology of Depression – Clnical were studied. Thirty-six symptoms which might distinguish endogenous from non-endogenous depressions were chosen from the literature. Patients' symptom profiles assessed by structured interview were grouped by two methods: a K-means improvement of Ward's method of cluster analysis, and a latent class algorithm. The methods produced very similar groups and several internal validity criteria suggested that the groups were not spurious. Cluster 1, ‘nuclear depression,’ included a nucleus of patients common to multiple definitions of endogenous depression. The non-nuclear group scored as less neurotic than the nuclear group on personality tests administered during the index episode. The groups do not differ in frequency, number or severity of reported life events prior to onset of the index episode. The nuclear group shows a poor prognosis on two-year prospective follow-up, greater disturbance on personality inventories, and increased heritability of depression in siblings.
Crystal structure of the carbohydrate recognition domain of the H1 subunit of the asialoglycoprotein receptor.

The human asialoglycoprotein receptor (ASGPR), also called hepatic lectin, is an integral membrane protein and is responsible for the clearance of desialylated, galactose-terminal glycoproteins from the circulation by receptor-mediated endocytosis. It can be subdivided into four functional domains: the cytosolic domain, the transmembrane domain, the stalk and the carbohydrate recognition domain (CRD). The galactose-binding domains belong to the superfamily of C-type (calcium-dependent) lectins, in particular to the long-form subfamily with three conserved intramolecular disulphide bonds. It is able to bind terminal non-reducing galactose residues and N-acetyl-galactosamine residues of desialated tri or tetra-antennary N-linked glycans. The ASGPR is a potential liver-specific receptor for hepatitis B virus and Marburg virus and has been used to target exogenous molecules specifically to hepatocytes for diagnostic and therapeutic purposes.Here, we present the X-ray crystal structure of the carbohydrate recognition domain of the major subunit H1 at 2.3 A resolution. While the overall fold of this and other known C-type lectin structures are well conserved, the positions of the bound calcium ions are not, indicating that the fold is stabilised by alternative mechanisms in different branches of the C-type lectin family. It is the first CRD structure where three calcium ions form an intergral part of the structure. In addition, the structure provides direct confirmation for the conversion of the ligand-binding site of the mannose-binding protein to an asialoglycoprotein receptor-like specificity suggested by Drickamer and colleagues. In agreement with the prediction that the coiled-coil domain of the ASGPR is separated from the CRD and its N-terminal disulphide bridge by several residues, these residues are indeed not alpha-helical, while in tetranectin they form an alpha-helical coiled-coil.
Corrected Identity of Isolates of Helicobacter Pylori Reference Strain NCTC11637

The reference strains NCTC11637 and NCTC11638 were among the very first Helicobacters ever cultured and have been distributed through national reference culture collections to researchers throughout the world. Because H. pylori is an extremely diverse species, such reference strains are invaluable as universal standards, provided that they are identified correctly.
Synergistic and antagonistic interaction between different branches of the immune system is related to melanin‐based coloration in nestling tawny owls

When exposed to parasites, hosts often mount energetically expensive immune responses, and this may alter resource allocation between competing life history traits including other components of the immune system. Here, we investigated whether a humoral immune challenge towards a vaccine reduces or enhances the cutaneous immune responses towards an injection of lipopolysaccharid (LPS, innate immunity) and phytohaemagglutinin (PHA, T‐cell immunity) in nestling tawny owls in interaction with the degree of plumage melanin‐based coloration. The humoral immune challenge enhanced the response to LPS similarly in differently coloured nestlings. In contrast, the same humoral immune challenge enhanced immune response to PHA in dark reddish melanic nestlings while reducing it in pale reddish melanic nestlings. Our results highlight that both antagonistic and synergistic interactions can take place among branches of immune system, and that the sign and magnitude of these interactions can vary with immune responses involved and the degree of melanin‐based coloration.