Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical study of avian reticuloendotheliosis virus dimeric RNA generated in vivo and in vitro

The retroviral genome consists of two identical RNA molecules associated at their 5' ends by a stable structure called the dimer linkage structure. The dimer linkage structure, while maintaining the dimer state of the retroviral genome, might also be involved in packaging and reverse transcription, as well as recombination during proviral DNA synthesis. To study the dimer structure of the retroviral genome and the mechanism of dimerization, we analyzed features of the dimeric genome of reticuloendotheliosis virus (REV) type A and identified elements required for its dimerization. Here we report that the REV dimeric genome extracted from virions and infected cells, as well as that synthesized in vitro, is more resistant to heat denaturation than avian sarcoma and leukemia virus, murine leukemia virus, or human immunodeficiency virus type 1 dimeric RNA. The minimal domain required to form a stable REV RNA dimer in vitro was found to map between positions 268 and 452 (KpnI and SalI sites), thus corresponding to the E encapsidation sequence (J. E. Embretson and H. M. Temin, J. Virol. 61:2675-2683, 1987). In addition, both the 5' and 3' halves of E are necessary in cis for RNA dimerization and the extent of RNA dimerization is influenced by viral sequences flanking E. Rapid and efficient dimerization of REV RNA containing gag sequences in addition to the E sequences and annealing of replication primer tRNA(Pro) to the primer-binding site necessitate the nucleocapsid protein.
A Robust Method To Solve Mass Balances in Reversible Column Sections

Reversible composition profiles in azeotropic and reactive distillation were used as pieces of new methods for the prediction of product composition regions and minimum reflux in singleand multiple-feed columns. A simple and robust algorithm to solve the nonlinear equation system corresponding to mass and energy balances in a reversible distillation column section for highly nonideal mixtures is proposed. If a distillate (bottom) is specified, one additional variable has to be set to calculate a cross section in the rectifying (stripping) part. We initially use the concentration of the component to be eliminated in the section as the variable to be fixed. A former direct successive substitution (DSS) procedure used in a previous paper is here analyzed, and the conditions for convergence are discussed. A damped Newton-Raphson method (DNR) is an alternative also presented. The new algorithm involves an improved direct successive substitution (IDSS) outer loop and a bubble point temperature (BUTE) loop included. By assuming the liquid phase composition at the reversible section, solving BUTE, and using geometric considerations, a related “hypothetical” product composition can be calculated. The difference between the real and the “hypothetical” product composition is used to recompute the liquid phase. This method can be considered robust in view that it does not uses derivative calculations that cause numerical drawbacks in cases that maxima, minima, or turning points are reached. The initialization variables are the liquid mole fractions instead of temperatures and component flow rates, resulting in a more general case-independent method. The geometrical characteristics allow that the algorithm can be initialized in any arbitrary region of the concentration simplex. For constant relative volatility (CRV) mixtures, a small number of iterations are needed despite the start point selected. The convergence was found always satisfactory independently of the start point, even when inversions in volatility order of some components take place. Finally, a variant (secant) of imbedding homotopy continuation is proposed to efficiently trace the complete path of the reversible profile, using the IDSS algorithm as the corrector. This combination becomes necessary when multiple disjoint branches of a product pinch point curve must be computed in highly nonideal mixtures. Other approaches to the problem are mentioned and their results compared.
Can You Hear What I See? Nonverbal Communication and the Changing Face of TML

Business training and education are changing. Organizations have experienced dramatic changes in their structure, competitive environment, and the demographics and demands of their employees. As a result, organizations are seeking new and innovative ways to train employees. At the same time the evolution of technology mediated learning tools (TML) has resulted in flexible, interactive, engaging, learning technology tools that promote experiential learning, analytical thinking and problem solving. Simulation based technology mediated learning (SimTML) tools are gaining popularity in practice. SimTML facilitates lifelike environments that utilize animated pedagogical agents (APAs) which employ nonverbal communication traits in their interaction with the user. The effect is a lifelike, face-to-face interaction, between the user and the APA. The result is a flexible, interactive, engaging, TML tool that promotes experiential learning, analytical thinking and problem solving. This paper explores current SimTML technology, how we interact with learning technology, and provides selection and evaluation principles for organizations to use when evaluating SimTML tools for their own training programs.
Functional Studies of the Human Brain Using High‐speed Magnetic Resonance Imaging

Dramatic technical advances in magnetic resonance imaging (MRI or NMR) scanning speed and recent governmental approval for the routine use of NMR contrast agents have yielded techniques for quantitative imaging of cerebral hemodynamics. The technical basis of ultrafast imaging, the methodology of dynamic imaging with contrast agents, and results in normal subjects and patients are presented.
Prevalence of respiratory symptoms, features of asthma, and characteristics associated with respiratory disease, in 6-11 year olds in Manchester.

AIMS This paper describes the prevalence of respiratory symptoms, features of asthma, and characteristics associated with respiratory disease in 6-11 year old children in an historical cohort study. METHODS The study included 5086 children, all born in the same maternity unit in the north west of England over a four-year period. The prevalence of respiratory symptoms, features of asthma, and characteristics associated with respiratory disease were determined by the use of parent-completed questionnaires. Skin prick tests were used to ascertain atopic status. RESULTS The response was 47.5%. The prevalence of wheeze, asthma medication use and atopic sensitisation were 20.3%, 16.2% and 37.1% respectively. Wheeze and atopy were significantly more prevalent in boys (22.4% versus 17.9% and 43.0% versus 29.3%, respectively). CONCLUSIONS This study identified a high prevalence of respiratory disease in this population and provides a baseline for monitoring trends in respiratory disease in 6-11 year old children.
Parametric vs. Non-Parametric Methods for Estimating Option Implied Risk-Neutral Densities: The Case of the Exchange Rate Mexican Peso-US Dollar and Mexican Interest Rates

This research paper presents statistical comparisons between two methods that are commonly used to estimate option implied Risk-Neutral Densities (RND). These are: 1) mixture of lognormals (MXL); and, 2) volatility function technique (VFT). The former is a parametric method whilst the latter is a non-parametric approach. The RNDs are extracted from over-the-counter options on the Mexican Peso - US Dollar exchange rate and Mexican interest rates. According to the results the parametric method provided superior in-sample goodness-of-fit for interest rates, which is measured in terms of mean squared errors. For exchange rates both methods were statistically equal. The non-parametric method was the superior one in the out-of-sample evaluations for both financial assets. The implied mean, median and mode were, in general, statistically different between the competing approaches. It is recommended to apply the VFT instead of the MXL given that the former has superior accuracy and it can be estimated when there is a relatively short cross-section of option exercise price range. The results have implications for financial investors and policy makers, especially Central Banks, given that they could use the information content in options to analyze market's perceptions about the future expected variability of the financial assets under study.
Impaired processing of precursor polypeptides of temperature-sensitive mutants of Rauscher murine leukemia virus

The synthesis and processing of virus-specific precursor polypeptides in NIH/3T3 cells infected at the permissive temperature (31 degrees C) with temperature-sensitive (ts) mutants of Rauscher murine leukemia virus was studied in pulse-chase experiments at the permissive and nonpermissive (39 degrees C) temperatures. The newly synthesized virus-specific polypeptides were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis after immunoprecipitation with polyvalent and monospecific antisera against Rauscher murine leukemia virus proteins. In cells infected with ts mutants defective in early replication steps (the early mutants ts17 and ts29), and ts mutants defective in postintegration steps (the late mutants ts25 and ts26), the processing of the primary gag gene product was impaired at the nonpermissive temperature. gag-pr75 of all four mutants was converted into gag-pr65; however, gag-pr65 accumulated at the nonpermissive temperature, and the main internal virion polypeptide p30 was not formed. Therefore, the proteolytic cleavage is blocked beyond gag-pr65. Concomitantly, the formation of the env gene-related polypeptide p12(E) of all four mutants was blocked at the restrictive temperature. In contrast, cells infected with the late mutant ts28, which produced noninfectious virions at 39 degrees C, showed a normal turnover of the gag and env precursor polypeptides.
Cost prediction models for the comparison of two groups.

For trial-based economic evaluation where patient-specific cost data are not routinely available, cost prediction models are commonly used to estimate total cost for each patient. Typically, multiple regression techniques are used on data from diagnosis-matched, non-trial patients (where patient-level cost data are available) to model cost as a function of covariates that are observed on the trial subjects (e.g. length of hospital stay, procedures, etc.). The estimated beta coefficients provide a means of estimating the total cost for each patient in the trial. However, the variability of the beta coefficients due the measurement and sampling error is seldom included in the overall variance expression for mean costs by treatment group. In this paper we provide a method for estimating this variance and provide an example application
Active Learning and Confidence-rated Prediction

Author(s): Zhang, Chicheng | Advisor(s): Chaudhuri, Kamalika | Abstract: This thesis studies active learning and confidence-rated prediction, and the interplay between these two notions.Active learning is a machine learning paradigm that allows a learner to perform label queries over the examples interactively. The goal of active learning is to get an accurate classifier using only a few label queries. In this thesis, we take a step further in the study of active learning, with a focus on active learning with complex queries. Specifically:1. We study the problem of active learning with weak and strong labelers. We present a statistically consistent algorithm that has a lower cost complexity compared to learning with the strong labeler alone, under certain conditions.2. We consider active learning with a novel type of queries, namely search queries. We show that in the setting of model selection, using the search queries can substantially reduce the labeling efforts for active learning.Confidence-rated prediction considers the learning setting where the learned classifier is allowed to abstain, i.e. to predict ``I Don't know''. In this setting, abstaining rather than making a thoughtless classification decision may sometimes be preferable. In this thesis, we study confidence-rated prediction in batch and online settings, and advance the state of the art results. Specifically:1. In the batch setting, we propose a linear program based algorithm that has some optimality properties, and has superior performance over previous approaches.2. In the online setting, we propose an algorithm that achieves minimax optimal tradeoffs between its performance measures, and establish a novel combinatorial measure called Extended Littlestone's Dimension that characterizes the tradeoff.Furthermore, we propose confidence-based active learning, establishing a connection between active learning and confidence-rated prediction. We show that our confidence-based active learning algorithm achieves statistical consistency, works for general hypothesis classes and data distribution, and has a lower label complexity compared to the state of the art active learning algorithms.
From theory to therapy: Implications from an in vitro model of ramified microglia

Microglia are the principal immune cells in the central nervous system (CNS), characterized by a highly specific morphology and unusual antigenic phenotype. An increasing number of studies have focused on the role of microglia in the pathogenesis of neurodegenerative diseases. To elucidate the function of microglial cells under several neuropathological conditions, we have studied and established a cell culture model that allows us to cultivate microglial cells in their inactive, resting (ramified) phenotype. In the first part of this work, we describe the interaction of microglia cells with their epithelial (astrocytic) microenvironment. The second part reviews experiments with microglia cell cultures to elucidate underlying signalling pathways and summarizes recent advances of our knowledge in microglial molecular pathways that may ultimately lead to neurodegeneration. Microsc. Res. Tech. 54:18–25, 2001. © 2001 Wiley‐Liss, Inc.
Chemical Induction of mGluR 5-and Protein Synthesis – Dependent Long-Term Depression in Hippocampal Area CA 1

Huber, Kimberly M. , John C. Roder, and Mark F. Bear. Chemical induction of mGluR5and protein synthesis–dependent long-term depression in hippocampal area CA1. J Neurophysiol86: 321–325, 2001. Recent work has demonstrated that specific patterns of synaptic stimulation can induce long-term depression (LTD) in area CA1 that depends on activation of metabotropic glutamate receptors (mGluRs) and rapid protein synthesis. Here we show that the same form of synaptic modification can be induced by brief application of the selective mGluR agonist (RS)-3,5-dihydroxyphenylglycine (DHPG). DHPG-LTD 1) is a saturable form of synaptic plasticity, 2) requires mGluR5, 3) is mechanistically distinct fromN-methyl-D-aspartate receptor (NMDAR)–dependent LTD, and 4) shares a common expression mechanism with protein synthesis–dependent LTD evoked using synaptic stimulation. DHPG-LTD should be useful for biochemical analysis of mGluR5and protein synthesis–dependent synaptic modification.
Optimal filtering and quality control of the signal-averaged ECG. High-fidelity 1-minute recordings.

BACKGROUND The clinical performance of the signal-averaged ECG (SAECG) for prediction of ventricular tachycardia (VT) depends on its quality, or final noise level. However, signal averaging is a statistical estimation procedure that is time-consuming and vulnerable to noise-induced error. The optimally filtered SAECG is proposed as a simple, quality-assured procedure requiring only 1 minute of data. METHODS AND RESULTS The optimally filtered SAECG is based on measures of signal variance and time-frequency representations. Forty subjects were studied to compare a 0.3-microV root-mean-square (RMS) noise endpoint SAECG with an optimally filtered 64-beat ensemble. Eight SAECGs were computed with noise endpoints of 1.0-through 0.3-microV RMS. Noise measurements were also made directly from the filtered SAECG. From these and previously published data, sensitivity was predicted as a function of noise endpoint. Measured QRS parameters and final noise were highly similar between the optimally filtered SAECG and the 0.3-microV RMS noise endpoint SAECG. CONCLUSIONS The optimally filtered 64-beat SAECG achieves a performance (equivalent noise reduction, signal definition, and mathematically predicted sensitivity for VT) similar to a 0.3-microV RMS noise endpoint average. Testing in a large clinical database is required to validate the method for routine clinical use. SAECGs terminated by use of different noise measurement techniques are not directly comparable because of measurement technique dependence. However, a formula is presented for comparison of statistics between studies that have used the most popular noise measurement techniques.
Senescent Changes of the Normal Visual Field: an Age-Old Problem

Purpose. To examine the effect of normal aging on visual field sensitivity and identify the best-fitting function for normal populations. Methods. Full Threshold standard automated perimetry data (program 24-2, Humphrey Field Analyzer) was collated retrospectively from clinically normal subjects who had previously been recruited for studies of normal visual function. One eye of each subject was randomly selected for analysis. Linear, bilinear, and simple nonlinear candidate functions of mean sensitivity vs. age (independent variable) were applied to these cross-sectional population data. Differences in the aging effect by eccentricity and hemifield were also considered. Results. Data from 562 normal eyes were available for analysis. A significant negative relationship existed between age and mean visual field sensitivity within the cross-sectional population data. Coefficients of determination for the linear, bilinear, and nonlinear functions were 0.21, 0.20, and 0.26, respectively, indicating that the nonlinear function provided best characterization of the effect of age on mean sensitivity. A small but significant increase in the aging effect was present both peripherally (p < 0.001) and superiorly (p < 0.001). Discussion. The nonlinear function that provided the best fit to cross-sectional population data indicates that age exerts an increasing effect on perimetric sensitivity with age, which has implications for clinical devices that use linear age coefficients to correct for normal aging effects. A linear age correction will overestimate aging changes for younger subjects and, therefore, may miss early pathologic changes in visual sensitivity. Conversely, linear age correction will also underestimate aging changes for older subjects and, thus, may overcall pathological sensitivity loss in this group. The effect of age within subjects requires further investigation to provide reliable estimates of the effect of age on sensitivity.
Noninsulin‐dependent diabetes mellitus: effects on sperm morphological and functional characteristics, nuclear DNA integrity and outcome of assisted reproductive technique

The aim of the study was to compare the semen characteristics and nuclear DNA fragmentation in spermatozoa of diabetic and nondiabetic men undergoing assisted reproduction and correlate them with pregnancy outcome. Semen characteristics and nuclear DNA fragmentation were analysed using computer‐aided semen analysis system and sperm chromatin dispersion assay (SCD), respectively. Spermatozoa from diabetic patients showed significantly lower progressive (Type A) motility (14.64 ± 9.60 versus 17.99 ± 11.51, P < 0.02) and increased nuclear DNA fragmentation (37.05 ± 12.68 versus 21.03 ± 10.13, P < 0.001). Furthermore, a positive correlation was observed in diabetic patients in terms of blastocyst formation rate (38.13% versus 55.46%, P < 0.001), pregnancy rate (28.57% versus 46.34%, P < 0.001) and miscarriage rate (50.0% versus 24.56%, P < 0.001). The higher percentage of sperm DNA damage because of oxidative stress seen in diabetic patients may be responsible for the poor embryonic development and pregnancy outcome in these individuals.
A Method Study of Financial Distress Prediction

This paper simply introduces the main problems in financial forecast that we are facing in our country. Based on this, some general forecasting methods and techniques of financial distress are listed and analyzed. The main issues that should be considered in the process of predicting the financial distress are presented. Finally, a prediction method of financial distress, named modified sample matching method, is proposed in this paper.
A Penetration Testing Method for E-Commerce Authentication System Security

E-Commerce systems are suffering more and more security issues. Vulnerabilities of authentication systems are revealed when various attacks and malicious abuses are developed and deployed to violate security of system and information. To improve the ability to defend authentication system against invasion and abuse, a novel penetration testing method for E-Commerce authentication system is proposed to scrutinize the vulnerabilities of e-Commerce authentication system and evaluate severity level of potential vulnerabilities. The penetration testing method is an active vulnerability analysis and verification method that can mimic active attacks and perform exploitations by constructing effective and concise penetration testing cases. Through analyzing dynamic taint propagation, the presented method can determine feasibility of the attacks and evaluate security of authentication system. The experiment demonstrates the proposed method can serve as a viable and effective candidate for security detection of authentication system.
Relative tolerance of mesostable and thermostable protein homologs to extensive mutation

Evolvability, designability, and plasticity of a protein are properties that are important to protein engineers, but difficult to quantify. Here, we directly compare homologous AroQ chorismate mutases from the thermophile Methanococcus jannaschii and the mesophile Escherichia coli with respect to their capacity to accommodate extensive mutation. The N‐terminal helix comprising about 40% of these proteins was randomized at the genetic level using a binary pattern of hydrophobic and hydrophilic residues based on the respective wild‐type sequences. Catalytically active library members were identified by a survival‐selection assay in a chorismate mutase‐deficient E. coli strain. Functional variants were found ∼∼10‐times more frequently with the thermostable protein compared to its mesostable counterpart. Moreover, detailed sequence analysis revealed that functional M. jannaschii enzyme variants contained a smaller number of conserved residues and tolerated greater variability at individual sequence positions. Our results thus highlight the greater robustness of the thermostable protein with respect to amino acid substitution, while identifying specific sites important for constructing active enzymes. Overall, they support the notion that redesign projects will benefit from using a thermostable starting structure, even at very high mutational loads. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Digital breast tomosynthesis imaging using total variation and non-local means

Digital breast tomosynthesis (DBT) generates 3D images of breast by using 2D projections taken from a limited view angle. Due to the ill-posed nature of the image reconstruction in DBT alternative image reconstruction methods have been introduced for better image quality. In this study, an efficient DBT image reconstruction algorithm has been introduced. The proposed method was formulated as combination of algebraic reconstruction technique (ART), total variation (TV) and non-local means (NLM). A real DBT data set and a commercially available 3D phantom were used for performance evaluations. Results of our study showed that ART+TV+NLM helped in obtaining better reconstructed images than those obtained by ART and ART+TV in terms of reduced background noise, out-of-plane artifacts while keeping the details well-preserved.