Miracle-dz/UniFAR-FTUs huggingface dataset:
Kinetic analysis of Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase, wild type and mutants, reveals roles of active site amino acids.

Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase (YgbP or IspD) catalyzes the conversion of 2-C-methyl-D-erythritol 4-phosphate (MEP) and cytidine triphosphate (CTP) to 4-diphosphocytidyl-2-C-methylerythritol (CDPME). Pulse chase experiments established that the reaction involves an ordered sequential mechanism with mandatory initial binding of CTP. On the basis of analysis of the previously reported crystal structures of apo-YgbP as well as YgbP complexed with both CTP.Mg(2+) and CDPME.Mg(2+) [Richard, S. B. , Bowman, M. E. , Kwiatkowski, W. , Kang, I. , Chow, C. , Lillo, A. M. , Cane, D. E. , and Noel, J. P. (2001) Nat. Struct. Biol. 8, 641-648], a group of active site residues were selected for site-directed mutagenesis and steady-state kinetic analysis. Both Lys27 and Lys213 were shown to be essential to catalytic activity, consistent with their proposed role in stabilization of a pentacoordinate phosphate transition state resulting from in-line attack of the MEP phosphate on the alpha-phosphate of CTP. In addition, Thr140, Arg109, Asp106, and Thr165 were all shown to play critical roles in the binding and proper orientation of the MEP substrate.
Halo: High-Assurance Locate for Distributed Hash Tables

We study the problem of reliably searching for resources in untrusted peer-to-peer networks, where a significant portion of the participating network nodes may act maliciously to subvert the search process. We present a new method called Halo for performing redundant searches over a distributed hash table (DHT) structure to achieve high integrity and availability levels without affecting the storage and communication complexities of the underlying DHT. Other schemes for redundant searches have proposed new or modified DHTs with increased storage requirements at nodes, requiring modifications at all nodes in the network. In contrast, Halo aims to serve as a middleware component, making “black-box” calls of the underlying primitive search operation to eventually provide a new composite search operation of higher assurance. We apply this concept to the popular and well-studied DHT Chord, and demonstrate the efficiency and security of our approach though analytical modeling and simulation-based analysis. For example, we show that for 12% malicious nodes in the network, a regular Chord operation fails 50–60% of the time. In contrast, Halo reduces this failure rate to 1%. We show how our scheme lends itself to a recursive version that can tolerate 22% malicious nodes with the same level of success, while regular Chord fails 70–80% of the time.
Phorbol ester treatment increases the exocytic rate of the transferrin receptor recycling pathway independent of serine-24 phosphorylation

In Chinese hamster ovary (CHO) fibroblast cells the protein kinase C activating phorbol ester, phorbol myristate acetate (PMA), stimulates an increase in cell surface transferrin receptor (TR) expression by increasing the exocytic rate of the recycling pathway. The human TR expressed in CHO cells is similarly affected by PMA treatment. A mutant human TR in which the major protein kinase C phosphorylation site, serine 24, has been replaced with the non-phosphorylatable amino acid glycine has been constructed to investigate the role of receptor phosphorylation in the PMA induced up-regulation. The Gly-24- substituted receptor binds, internalizes, and recycles Tf. Furthermore, the altered receptor mediates cellular Fe accumulation from diferric- Tf, thereby fulfilling the receptor's major biological role. The Gly-24 TR behaves identically to the wild-type TR when cells are treated with PMA. Therefore, Ser-24 phosphorylation is not required for the PMA- induced redistribution of the human TR expressed in CHO cells. The increased TR expression on the cell surface after PMA treatment results from an increase in the rate of exocytosis of the recycling receptors. No change in the endocytic rate or the size of the recycling receptor pool was observed. These results indicate that the PMA effect on the TR surface expression may result from a more general perturbation of membrane trafficking rather than a specific modulation of the TR.
Enhancement of Satellite Earth Station in Sudan

— this paper deals with the satellite link budget in 3 different aspects which are: How to determine the coverage in to percentage form by using Pythagoras theorem in addition of some assumptions, second aspect is the required power toward and from the satellite, and last aspect is how to eliminate the earth station performance in percentage form by using Eb/No. The research takes 25 locations in the Sudan, gives for each location the specific code. The overall output the OBO ,IBO ,distance ,OFD,C/N,C/Tu ,C/Tco-ch ,C/Ty , Lu ,Ld all are required in order to achieve the 3 aspects. Also enhancing the performance to the optimum in regardless of coverage location is done by controlling in 3 main parameters, this means, the coverage is not a problem in reaching the optimum performance.
Feasibility study of uniaxial structures used for invisible cloak design

The purpose of this paper is to study realization feasibility of the cloak structures where the continuously-varying structure is realized as multilayer structure with the stepwise approximation of the constitutive parameters. In order to do that, the influence of the number of cloak layers is investigated, and it is shown that with only three layers it is possible to obtain a better cloak performance than the Schurig cloak (containing ten layers), and that with ten or more layers one can design a cloak that is practically invisible. These results are obtained by merging the program for analyzing uniaxial cylindrical structures with the global optimization program based on the particle swarm optimization algorithm.
Scalar quantization error analysis for image subband coding using QMFs

The authors analyze the coding errors due to quantization by explicitly incorporating a mathematical model for a Lloyd-Max quantizer into a quadrature mirror filter (QMF) splitting and reconstruction scheme (P. H. Westerink et al., 1988). This approach explicitly incorporates quantization errors into a QMF system by means of a quantizer model. This makes it possible to discriminate between different types of coding errors, such as the aliasing error. Other errors that can be distinguished are a QMF design error, a signal error, and a random error, which is uncorrelated with the original image. Both a mean-squared error calculation and a subjective judgment of the coding errors show that the aliasing errors can be neglected for filter lengths of 12 taps or more. The signal error determines the sharpness of the reconstructed image, while the random error is most visible in the flat areas. >
NeuroVR 1.5 - A Free Virtual Reality Platform for the Assessment and Treatment in Clinical Psychology and Neuroscience

At MMVR 2007 we presented NeuroVR (http://www.neurovr.org) a free virtual reality platform based on open-source software. The software allows non-expert users to adapt the content of 14 pre-designed virtual environments to the specific needs of the clinical or experimental setting. Following the feedbacks of the 700 users who downloaded the first version, we developed a new version - NeuroVR 1.5 - that improves the possibility for the therapist to enhance the patient's feeling of familiarity and intimacy with the virtual scene, by using external sounds, photos or videos. Specifically, the new version now includes full sound support and the ability of triggering external sounds and videos using the keyboard. The outcomes of different trials made using NeuroVR will be presented and discussed.
Dedicated autonomous scan-based testing (DAST) for embedded cores

The complexity of today's chips is such that relying solely upon external ATE resources is insufficient for scan test. In this work, we develop the concept of dedicated autonomous scan-based testing (DAST) by proposing a scheme that introduces hierarchy and separates the functionality of ATE resources into two distinctive classes: a) test data communication, and b) test data control and observation. To simplify the ATE for embedded digital core testing, we propose transferring ATE test data control/observation functions to one or more Embedded Autonomous Sequencers (EAS) dedicated to single or multiple embedded cores of an SoC We present implementation results of our DAST methodology when applied to a number of SoC benchmarks.
Scale-Invariant Amplitude Spectrum Modulation for Visual Saliency Detection

Saliency detection is one of the key issues in simulating visual attention selection. Most attention models adopt the competitive structure to simulate the human visual system. Although these models provide remarkable results and convincing biological plausibility, they are still confronted with many difficulties in practical applications because of their extreme time cost and parameter sensitivity. Recently, a new saliency detection approach based on Fourier transform, as represented by spectral residual (SR) and phase Fourier transform (PFT), has been attracting much attention for its excellent accuracy and computational speed. All these models can be unified into one framework called amplitude spectrum modulation (ASM). The aim of this paper is to explore the intrinsic mechanism of ASM and develop an advanced ASM model. After analyzing SR and PFT, we give a mathematical description for the fundamental idea and the inherent limitations of the existing ASM models. A new saliency detective model, based on the scale-invariant ASM, scene and context-based modulation, and competitive structure, is also proposed breaking through the limitations of the traditional ASM models. Simulation results suggest that the proposed model is more accurate in predicting human eye fixation and is more robust against different types of stimulus when compared with competing models.
Less is More: Financial Constraints and Innovative Efficiency

We show that financial constraints may benefit innovation by improving the efficiency of innovative activities. We measure firm-level innovative efficiency by patents (or patent citations) scaled by R&D (research and development) investment or the number of employees, and find that financial constraints are positively associated with innovative efficiency. Tests using the 1989 junk bond crisis as an exogenous shock to financial constraints suggest a causal interpretation for the link. Consistent with agency problems, the positive effect of financial constraints on innovative efficiency is stronger among firms with high excess cash holdings and low investment opportunities, and among firms in less competitive industries. Financial constraints appear to mitigate free cash flow problems that induce firms to make unproductive R&D investment in fields out of their direct expertise. Our findings point to a bright side of the role of financial constraints for corporate investment in intangible assets.
HAEMOGLOBIN (ERYTHROGEN™)-ENHANCED MICROCALLUS FORMATION FROM PROTOPLASTS OF INDICA RICE (ORYZA SATIVA L.)

The beneficial effects have been studied of supplementing culture medium with 1 : 100–1 : 500 (v:v) of a commercial haemoglobin solution (Erythrogen™) on the mitotic division of cell suspension- derived protoplasts of Indica rices (Oryza sativa L.). Protoplasts were cultured in liquid medium, at densities of 1.5 × 106 or 2.5 × 106ml−1, on nitrocellulose membranes overlaying a semi-solidified medium layer that was supplemented with both Erythrogen™ and nurse cells of Lolium multiflorum. The mean final plating efficiencies (FPEs) of rice cv. BR26 protoplasts cultured with 1:200 (v:v) Erythrogen™, at 1.5 × 106ml−1 (0.018 ± 0.003%; n = 8) and 2.5 × 106ml−1 (0.016 ± 0.002%; n = 8), were both significantly (P < 0.05) greater than controls lacking Erythrogen™ (0.0058 ± 0.002%; n = 8 and 0.0041 ± 0.001%; n = 8, respectively). Similarly, the mean FPEs of cv. Bini protoplasts cultured with 1:200 (v:v) Erythrogen™ at 1.5 × 106ml−1 (0.012 ± 0.003%; n = 6) and 2.5 × 106ml−1 (0.017 ± 0.001%; n = 6) were also significantly (P < 0.05) greater than their respective controls (0.003 ± 0.001%, n = 6 and 0.002 ± 0.001%, n = 6). In contrast, supplementation with 1:100 or 1:500 (v:v) Erythrogen™ did not lead to sustained mitotic division and microcallus formation in both rice cultivars.
The "vanishing embryo" phenomenon in an oocyte donation programme.

BACKGROUND We studied the incidence of vanishing embryos (VE) in pregnancies achieved by oocyte donation and evaluated the obstetric and perinatal complications. METHOD A retrospective study was carried out based on a chart review of 399 patients with multiple pregnancies from our oocyte donation programme. We defined vanishing phenomenon as the early resorption, in the first trimester, of one or more embryos in a multiple gestation, after confirming embryonic heart activity by transvaginal ultrasound. RESULTS Vanishing embryo was observed in 75 patients (18.8%). In 60 patients (80%) this phenomenon occurred before the ninth gestational week. A higher incidence of VE was observed in patients who initially showed a higher number of gestational sacs (P < 0.03). Vaginal bleeding in the first trimester was significantly higher in patients with VE (P < 0.005). Miscarriage rate was similar in pregnancies with and without VE (P = NS). The incidence of pregnancy induced hypertension was decreased in the group with VE (P < 0.03). Preterm spontaneous rupture of membranes occurred more frequently in pregnancies with VE (P < 0.05). However, gestational age at delivery was similar in the group with VE and the controls. CONCLUSIONS The high incidence of VE in pregnancies achieved by oocyte donation should be considered when counselling patients with high order multiple gestations.
Tune Your Brown Clustering, Please

Brown clustering, an unsupervised hierarchical clustering technique based on ngram mutual information, has proven useful in many NLP applications. However, most uses of Brown clustering employ the same default configuration; the appropriateness of this configuration has gone predominantly unexplored. Accordingly, we present information for practitioners on the behaviour of Brown clustering in order to assist hyper-parametre tuning, in the form of a theoretical model of Brown clustering utility. This model is then evaluated empirically in two sequence labelling tasks over two text types. We explore the dynamic between the input corpus size, chosen number of classes, and quality of the resulting clusters, which has an impact for any approach using Brown clustering. In every scenario that we examine, our results reveal that the values most commonly used for the clustering are sub-optimal.
WANTING ROBUSTNESS IN MACROECONOMICS LARS PETER HANSEN AND THOMAS J. SARGENT

1.1. Foundations. von Neumann and Morgenstern (1944) and Savage (1954) created mathematical foundations that applied economists have used to construct quantitative dynamic models for policy making and empirical analyses. The mathematical foundations give modern dynamic models internal coherence and sharp empirical predictions. However, those foundations should invite researchers to confront the unsettling fact that their models are approximations. That would expose logical problems that until recently have been swept under the rug, but that still call for repair. A model is a probability distribution over a sequence. Applied dynamic economists readily accept that their models are approximations because applied models must be tractable, that is, feasible to solve, estimate, and simulate. With tractability comes misspeci cation. Model misspeci cation is unavoidable in applied economic research. Admitting model misspeci cation raises especially interesting problems for rational expectations models because the rational expectations assumption excludes model misspeci cation. The rational expectations hypothesis imposes a communism of models: the people being modeled know the model. This makes the economic analyst, the policy maker, and the agents being modeled all share the same model, i.e., the same probability distribution over sequences of outcomes. Imposition of a common model removes economic agents' models as objects that require separate speci cation. The idea that models are approximations puts more models in play than the rational expectations equilibrium concept handles. To say that a model is an approximation is to say that it approximates another model. Viewing models as approximations requires reforming the common models requirement imposed by rational expectations. The consistency of models imposed by rational expectations has profound implications about the design and impact of macroeconomic policy-making, e.g. see Lucas (1976) and Sargent and Wallace (1975). There is little work studying how
Sharp mandibular bone irregularities after lower third molar extraction: Incidence, clinical features and risk factors

Objectives: The purpose of this study was to determine the incidence and clinical symptoms associated with sharp mandibular bone irregularities (SMBI) after lower third molar extraction and to identify possible risk factors for this complication. Study Design: A mixed study design was used. A retrospective cohort study of 1432 lower third molar extractions was done to determine the incidence of SMBI and a retrospective case-control study was done to determine potential demographic and etiologic factors by comparing those patients with postoperative SMBI with controls. Results: Twelve SMBI were found (0.84%). Age was the most important risk factor for this complication. The operated side and the presence of an associated radiolucent image were also significantly related to the development of mandibular bone irregularities. The depth of impaction of the tooth might also be an important factor since erupted or nearly erupted third molars were more frequent in the SMBI group. Conclusions: SMBI are a rare postoperative complication after lower third molar removal. Older patients having left side lower third molars removed are more likely to develop this problem. The treatment should be the removal of the irregularity when the patient is symptomatic. Key words:Third molar, postoperative complication, bone irregularities, age.
Learning a Sparse Representation from Multiple Still Images for On-Line Face Recognition in an Unconstrained Environment

In a real-world environment, a face detector can be applied to extract multiple face images from multiple video streams without constraints on pose and illumination. The extracted face images will have varying image quality and resolution. Moreover, also the detected faces will not be precisely aligned. This paper presents a new approach to on-line face identification from multiple still images obtained under such unconstrained conditions. Our method learns a sparse representation of the most discriminative descriptors of the detected face images according to their classification accuracies. On-line face recognition is supported using a single descriptor of a face image as a query. We apply our method to our newly introduced BHG descriptor, the SIFT descriptor, and the LBP descriptor, which obtain limited robustness against illumination, pose and alignment errors. Our experimental results using a video face database of pairs of unconstrained low resolution video clips of ten subjects, show that our method achieves a recognition rate of 94% with a sparse representation containing 10% of all available data, at a false acceptance rate of 4%
Proteomic and Genomic Analyses of Antimony Resistant Leishmania infantum Mutant

Background Antimonials remain the primary antileishmanial drugs in most developing countries. However, drug resistance to these compounds is increasing and our understanding of resistance mechanisms is partial. Methods/Principal Findings In the present study, quantitative proteomics using stable isotope labelling of amino acids in cell culture (SILAC) and genome next generation sequencing were used in order to better characterize in vitro generated Leishmania infantum antimony resistant mutant (Sb2000.1). Using the proteomic method, 58 proteins were found to be differentially regulated in Sb2000.1. The ABC transporter MRPA (ABCC3), a known marker of antimony resistance, was observed for the first time in a proteomic screen. Furthermore, transfection of its gene conferred antimony resistance in wild-type cells. Next generation sequencing revealed aneuploidy for 8 chromosomes in Sb2000.1. Moreover, specific amplified regions derived from chromosomes 17 and 23 were observed in Sb2000.1 and a single nucleotide polymorphism (SNP) was detected in a protein kinase (LinJ.33.1810-E629K). Conclusion/Significance Our results suggest that differentially expressed proteins, chromosome number variations (CNVs), specific gene amplification and SNPs are important features of antimony resistance in Leishmania.
High-dimensional gene expression profiling studies in high and low responders to primary smallpox vaccination.

BACKGROUND The mechanisms underlying smallpox vaccine-induced variations in immune responses are not well understood, but are of considerable interest to a deeper understanding of poxvirus immunity and correlates of protection. METHODS We assessed transcriptional messenger RNA expression changes in 197 recipients of primary smallpox vaccination representing the extremes of humoral and cellular immune responses. RESULTS The 20 most significant differentially expressed genes include a tumor necrosis factor-receptor superfamily member, an interferon (IFN) gene, a chemokine gene, zinc finger protein genes, nuclear factors, and histones (P ≤ 1.06E(-20), q ≤ 2.64E(-17)). A pathway analysis identified 4 enriched pathways with cytokine production by the T-helper 17 subset of CD4+ T cells being the most significant pathway (P = 3.42E(-05)). Two pathways (antiviral actions of IFNs, P = 8.95E(-05); and IFN-α/β signaling pathway, P = 2.92E(-04)), integral to innate immunity, were enriched when comparing high with low antibody responders (false discovery rate, < 0.05). Genes related to immune function and transcription (TLR8, P = .0002; DAPP1, P = .0003; LAMP3, P = 9.96E(-05); NR4A2, P ≤ . 0002; EGR3, P = 4.52E(-05)), and other genes with a possible impact on immunity (LNPEP, P = 3.72E(-05); CAPRIN1, P = . 0001; XRN1, P = . 0001), were found to be expressed differentially in high versus low antibody responders. CONCLUSION We identified novel and known immunity-related genes and pathways that may account for differences in immune response to smallpox vaccination.
The Effects of Maximal Intensity Exercise on Cognitive Performance in Children

Abstract High intensity physical exercise has previously been found to lead to a decline in cognitive performance of adults. The aim of this study was to determine the effects of maximal intensity exercise on cognitive performance of children. Using a repeated-measures design, 20 children and adolescents aged 8-17 years completed a battery of tests measuring memory and attention. Forward and Backward Digit Span tests, the Rey Auditory-Verbal Learning Test (RAVLT) and the Digit Symbol Substitution Test (DSST) were performed at baseline, immediately after, and one hour after a maximal cardiopulmonary exercise test. Forward and Backward Digit Span scores significantly improved post-recovery compared with baseline measurements. There was a significant decrease in RAVLT scores post-exercise, which returned to baseline values after recovery. The DSST test scores were mildly elevated from post-exercise to after recovery. Maximal intensity exercise in children and adolescents may result in both beneficial and detrimental cognitive effects, including transient impairment in verbal learning. Cognitive functions applying short term memory improve following a recovery period. Parents, educators and coaches should consider these changes in memory and attention following high-intensity exercise activities in children.