Miracle-dz/UniFAR-FTUs huggingface dataset:
The Protein Model Portal—a comprehensive resource for protein structure and model information

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal. org
Simulation Modeling of Large-Scale Ad-hoc Sensor Networks

In the scenario of a natural catastrophe or a terrorist attack, a large number of self-organizing, low-cost sensor devices can be deployed over the affected area. Each device equipped with its own power source, sensor, processing unit and low-power radio, can be imbued with the intelligence to seek out its neighbours and join in a wireless network spanning the geographic domain. The sensed quantities can then be forwarded to collections points, where the information is aggregated and presented to emergency response teams. We are developing a high-performance framework for the large-scale simulation of wireless ad-hoc networks (SWAN). Our framework is comprised of inter-operating sub-models for terrain, dispersion of hazardous substance, radio propagation, and the actual source code of ad-hoc networking protocols. In this paper, we describe the architecture of this framework and present experiments that confirm its usefulness in the study of routing algorithms.
Left ventricular diastolic abnormalities and the impact of hepatitis C virus infection in multitransfused Egyptian children

Introduction The aim of the study was to evaluate left ventricular cardiac systolic and diastolic functions by echocardiography in multitransfused children and the possible risk of hepatitis C virus infection as an additional factor impairing cardiac functions in these patients. Material and methods Echocardiographic studies of left ventricular function in 80 multitransfused patients aged 3 to 15 years with no clinical evidence of heart failure were included in our study. Anti-hepatitis C virus antibody was present in the sera of 25 of them. Twenty age and sex matched normal subjects were studied as a control. Results Results showed left ventricular systolic abnormalities in 15 cases (18%). Nine cases were HCV seropositive. Dilatation of left ventricle and impaired systolic function guided by FS (fractional shortening) was significantly reduced compared to normal subjects' mean FS (p<0.01). Systolic dysfunction is significantly observed in hepatitis C virus seropositive cases (mean FS 29±7.9 vs seronegative cases 31.4±10 (p<0.035). Restrictive left ventricular diastolic abnormalities were detected in 45 patients (56.25%). Diastolic dysfunction was represented in prolonged isovolumic relaxation time in comparison to the control group (p<0.03) and higher E wave (p<0.001) also increased the ratio of early to late diastolic velocity (E/A ratio, 2.03±0.59 vs 1.6±0.27, p<0.05). No significant difference in diastolic functions was found between HCV seropositive and seronegative groups. There is a weak negative correlation between left ventricular FS and serum ferritin level (r=0.77, p<0.001). Conclusions Multitransfused children are more liable to left ventricular diastolic dysfunction suggested by impaired relaxation probably due to iron overload and anaemia. Hepatitis C virus infection is an additional factor which might share in impairing left ventricular systolic function. Left ventricular performance is better preserved when chelation treatment is adjusted to maintain serum ferritin at <1000 ng/ml.
A road to classification in high dimensional space: the regularized optimal affine discriminant

Summary. For high dimensional classification, it is well known that naively performing the Fisher discriminant rule leads to poor results due to diverging spectra and accumulation of noise. Therefore, researchers proposed independence rules to circumvent the diverging spectra, and sparse independence rules to mitigate the issue of accumulation of noise. However, in biological applications, often a group of correlated genes are responsible for clinical outcomes, and the use of the covariance information can significantly reduce misclassification rates. In theory the extent of such error rate reductions is unveiled by comparing the misclassification rates of the Fisher discriminant rule and the independence rule. To materialize the gain on the basis of finite samples, a regularized optimal affine discriminant (ROAD) is proposed. The ROAD selects an increasing number of features as the regularization relaxes. Further benefits can be achieved when a screening method is employed to narrow the feature pool before applying the ROAD method. An efficient constrained co‐ordinate descent algorithm is also developed to solve the associated optimization problems. Sampling properties of oracle type are established. Simulation studies and real data analysis support our theoretical results and demonstrate the advantages of the new classification procedure under a variety of correlation structures. A delicate result on continuous piecewise linear solution paths for the ROAD optimization problem at the population level justifies the linear interpolation of the constrained co‐ordinate descent algorithm.
Methodological quality and reporting of ethical requirements in clinical trials

Objectives—To assess the relationship between the approval of trials by a research ethics committee (REC) and the fact that informed consent from participants (ICP) was obtained, with the quality of study design and methods. Design—Systematic review using a standardised checklist. Main measures—Methodological and ethical issues of all trials published between 1993 and 1995 in the New England Journal of Medicine, the Lancet, the Journal of the American Medical Association and the British Medical Journal were studied. In addition, clinical trials conducted in Spain and published by at least one Spanish author during the same period in any other journal were also included. Results—We studied the published articles of 767 trials and found the following indicators of lower methodological quality to be independent predictors for failure to disclose REC approval or ICP: absence of concealment of allocation, lack of justification for unblinded trials, not using a treatment for the patients in the control group, absent information on statistical methods, not including sample size estimation, not establishing the rules to stop the trial, and omitting the presentation of a baseline comparison of groups Conclusion—Trials of higher methodological and scientific quality were more likely to provide information about their ethical aspects.
Time-Dependent Rate Phenomenon in Viruses

ABSTRACT Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
Resource summary for pay-as-you-go dataspace systems

Dataspace systems are typically pay-as-you-go systems compared with traditional integration systems. Integration semantics and relationships among resources can be gradually enhanced over time. A system should support graceful transition between keyword query and structured query. A resource summary can be of great help in this situation, which provides an approximate overview of the entire structure of the dataspace. It can be refined over time when more and more semantics are obtained. We formally define a resource summary in this paper, and develop algorithms that allow us to automatically generate resource summaries and to refine them with the system running. Resource summaries are obviously important for advanced users and could be used in query optimization for pay-as-you-go dataspace systems.
An equilibrium model of the business cycle with household production and fiscal policy

We estimate a dynamic general equilibrium model of the U.S. economy that includes an explicit household production sector and stochastic fiscal variables. We use our estimates to investigate two issues. First, we analyze how well the model accounts for aggregate fluctuations. We find that household production has a significant impact and reject a nested specification in which changes in the home production technology do not matter for market variables. Second, we study the effects of some simple fiscal policy experiments and show that the model generates different predictions for the effects of tax changes than similar models without home production.
The Impact of Demand Correlation on Replenishment Policies for Multi-Product Stochastic Inventory Systems with Joint-Replenishment Costs

This paper analyzes optimal replenishment policies that minimize expected discounted cost of multi-product stochastic inventory systems. The distinguishing feature of the multi-product inventory system that we analyze is the existence of correlated demand and joint-replenishment costs across multiple products. While prior literature on multi-product stochastic inventory systems has focused on computation of heuristic policies that decouple the N product problem to N single product problems, our focus is on computing and finding the structure of the optimal policies for multi-product inventory systems, particularly when demand is correlated across products. The problem is formulated as a Markov Decision Process (MDP). A method to compute the optimal policy that uses a moving boundary based policy improvement scheme is proposed. Numerical examples show that the (s, c, d, S) policy closely approximates the optimal policy, and can significantly outperform the (s, c, S), P (s, S) and Q(s, S) policies analyzed in prior literature which assume independent demand.
MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions

Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.
Gender Differences in German Upward Income Mobility

We examine the upward labor income mobility of men and women in Germany using the GSOEP Cross National Equivalent File. Women have greater overall income mobility. However, utilizing a measure of upward income mobility and calculating the posterior probability that men’s upward income mobility is greater than women’s, we find that men have overall greater upward income mobility. Women have greater upward mobility in the lower initial income classes, in the upper initial income brackets men’s mobility is higher than women’s.
Wavelet denoising of the electrocardiogram signal based on the corrupted noise estimation

We present in this paper an algorithm of filtering the noisy real ECG signal. The classical wavelet denoising process, based on the Donoho et al. algorithm, at the 4th level, appears clearly the P and T waves whereas the R waves undergo considerable distortion. This is due to the interference of the WGN and the free noise ECG detail sequences at level 4. To overcome this drawback, our key idea is to estimate the corrupted WGN and consequently remove the noise interfering R waves at the 4th level detail sequence. Our denoising algorithm was applied to a set of the MIT-BIH arrhythmia database ECG records corrupted with a 0 dB WGN which provided an output SNR of around 6 dB and an MSE value of around 0.0011. A comparative analysis using the low pass Butterworth filter and the 4th level classical wavelet denoising provides the output SNR values of around 3 dB and MSE value of around 0.0018; which demonstrates the superior performance of our proposed denoising algorithm
Human detection base on Pc-SVM

PC-SVM is a new developed support vector machine classifier with probabilistic constrains which presence of samples probability in each class is determined based on a distribution function. The presence of noise causes incorrect calculation of support vectors thereupon margin can not be maximized. In the Pc-SVM, constraints boundaries and constraints occurrence have probability density functions which it helps for achieving maximum margin. The main target of this paper is introducing a robust visual object recognition based on PC- SVM. Human detection is used as benchmark problem for the proposed algorithm. Experimental results show superiority of the probabilistic constraints support vector machine (PC-SVM) relative to standard SVM in human detection.
Surface Base Selection in Pengo

My aim in this work is to defend what I’m calling the “Single Surface Base hypothesis. ” This is the hypothesis that underlying representations (URs) are restricted to a surface form from among the output forms in the paradigm, and to the surface form from the same morphological context for all lexical items. In 1977, Kentowicz and Kisseberth published Topics in Phonological Theory, with a chapter entitled “The Problem of Underlying Representations. ” In this chapter, they considered a number of hypotheses about the nature of URs, including a single surface base, which they called Hypothesis B’’. While this hypothesis has the advantage of being restrictive and concrete, Kenstowicz & Kisseberth argued against it on the grounds that phonological systems such as that of Pengo were inaccessible to such an analysis, because it appears that the same surface form in Pengo is not suitable as a base for all the lexical items of a particular class. Ultimately, they argued that the scope of variation in phonological systems made it necessary to postulate abstract URs for phonological paradigms. I have a new analysis of the Pengo data that shows that, far from representing this sort of counterexample, Pengo is actually a prime example of how surface base selection works, and has an explanatory capacity beyond a model using abstract URs.
The firm as a communication network

This paper analyzes how organizations can minimize costs of processing and communicating information. Communication is costly because it takes time for an agent to absorb new information sent by others. Agents can reduce this time by specializing in the processing of particular types of information. When these returns to specialization outweigh costs of communication, it is efficient for several agents to collaborate within a firm. It is shown that efficient networks involve centralization, that individuals delegate tasks to subordinates only if they are overloaded, and that the number of transits to the top tends to be equalized across individual information items. © 1994 by the President and Fellows of Harvard College and the Massachusetts Institute of Technology.
Multi-objective performance optimization of H.264 AVC encoder

We propose a multi-objective optimization framework based on genetic algorithms to enhance the performance of a video codec. The framework is designed to jointly minimize the complexity, memory usage in the encoder, bit rate and maximize the quality of the compressed video stream. In particular, the optimization framework is designed to determine the optimum coding parameters for the H.264 AVC video codec in a memory and bandwidth constrained environments. This was demonstrated through extensive experiments and mathematical formulation that resulted in the optimum solution for the optimization problem as the final outcome.
The Caudate Signals Bad Reputation during Trust Decisions

The ability to initiate and sustain trust is critical to health and well-being. Willingness to trust is in part determined by the reputation of the putative trustee, gained via direct interactions or indirectly through word of mouth. Few studies have examined how the reputation of others is instantiated in the brain during trust decisions. Here we use an event-related functional MRI (fMRI) design to examine what neural signals correspond to experimentally manipulated reputations acquired in direct interactions during trust decisions. We hypothesized that the caudate (dorsal striatum) and putamen (ventral striatum) and amygdala would signal differential reputations during decision-making. Twenty-nine healthy adults underwent fMRI scanning while completing an iterated Trust Game as trusters with three fictive trustee partners who had different tendencies to reciprocate (i.e., likelihood of rewarding the truster), which were learned over multiple exchanges with real-time feedback. We show that the caudate (both left and right) signals reputation during trust decisions, such that caudate is more active to partners with two types of “bad” reputations, either indifferent partners (who reciprocate 50% of the time) or unfair partners (who reciprocate 25% of the time), than to those with “good” reputations (who reciprocate 75% of the time). Further, individual differences in caudate activity related to biases in trusting behavior in the most uncertain situation, i.e. when facing an indifferent partner. We also report on other areas that were activated by reputation at p < 0.05 whole brain corrected. Our findings suggest that the caudate is involved in signaling and integrating reputations gained through experience into trust decisions, demonstrating a neural basis for this key social process.
Analogous Synaptic Plasticity Profiles Emerge from Disparate Channel Combinations

An open question within the Bienenstock-Cooper-Munro theory for synaptic modification concerns the specific mechanism that is responsible for regulating the sliding modification threshold (SMT). In this conductance-based modeling study on hippocampal pyramidal neurons, we quantitatively assessed the impact of seven ion channels (R- and T-type calcium, fast sodium, delayed rectifier, A-type, and small-conductance calcium-activated (SK) potassium and HCN) and two receptors (AMPAR and NMDAR) on a calcium-dependent Bienenstock-Cooper-Munro-like plasticity rule. Our analysis with R- and T-type calcium channels revealed that differences in their activation-inactivation profiles resulted in differential impacts on how they altered the SMT. Further, we found that the impact of SK channels on the SMT critically depended on the voltage dependence and kinetics of the calcium sources with which they interacted. Next, we considered interactions among all the seven channels and the two receptors through global sensitivity analysis on 11 model parameters. We constructed 20,000 models through uniform randomization of these parameters and found 360 valid models based on experimental constraints on their plasticity profiles. Analyzing these 360 models, we found that similar plasticity profiles could emerge with several nonunique parametric combinations and that parameters exhibited weak pairwise correlations. Finally, we used seven sets of virtual knock-outs on these 360 models and found that the impact of different channels on the SMT was variable and differential. These results suggest that there are several nonunique routes to regulate the SMT, and call for a systematic analysis of the variability and state dependence of the mechanisms underlying metaplasticity during behavior and pathology.