Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees

Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health, as evidenced by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) and Ebola virus. Simian foamy viruses (SFVs) are ancient retroviruses that infect Old and New World monkeys and apes. Although not known to cause disease, these viruses are of public health interest because they have the potential to infect humans and thus provide a more general indication of zoonotic exposure risks. Surprisingly, no information exists concerning the prevalence, geographic distribution, and genetic diversity of SFVs in wild-living monkeys and apes. Here, we report the first comprehensive survey of SFVcpz infection in free-ranging chimpanzees (Pan troglodytes) using newly developed, fecal-based assays. Chimpanzee fecal samples (n = 724) were collected at 25 field sites throughout equatorial Africa and tested for SFVcpz-specific antibodies (n = 706) or viral nucleic acids (n = 392). SFVcpz infection was documented at all field sites, with prevalence rates ranging from 44% to 100%. In two habituated communities, adult chimpanzees had significantly higher SFVcpz infection rates than infants and juveniles, indicating predominantly horizontal rather than vertical transmission routes. Some chimpanzees were co-infected with simian immunodeficiency virus (SIVcpz); however, there was no evidence that SFVcpz and SIVcpz were epidemiologically linked. SFVcpz nucleic acids were recovered from 177 fecal samples, all of which contained SFVcpz RNA and not DNA. Phylogenetic analysis of partial gag (616 bp), pol-RT (717 bp), and pol-IN (425 bp) sequences identified a diverse group of viruses, which could be subdivided into four distinct SFVcpz lineages according to their chimpanzee subspecies of origin. Within these lineages, there was evidence of frequent superinfection and viral recombination. One chimpanzee was infected by a foamy virus from a Cercopithecus monkey species, indicating cross-species transmission of SFVs in the wild. These data indicate that SFVcpz (i) is widely distributed among all chimpanzee subspecies; (ii) is shed in fecal samples as viral RNA; (iii) is transmitted predominantly by horizontal routes; (iv) is prone to superinfection and recombination; (v) has co-evolved with its natural host; and (vi) represents a sensitive marker of population structure that may be useful for chimpanzee taxonomy and conservation strategies.
On the Tensor SVD and the Optimal Low Rank Orthogonal Approximation of Tensors

It is known that a higher order tensor does not necessarily have an optimal low rank approximation, and that a tensor might not be orthogonally decomposable (i.e., admit a tensor SVD). We provide several sufficient conditions which lead to the failure of the tensor SVD, and characterize the existence of the tensor SVD with respect to the higher order SVD (HOSVD). In the face of these difficulties to generalize standard results known in the matrix case to tensors, we consider the low rank orthogonal approximation of tensors. The existence of an optimal approximation is theoretically guaranteed under certain conditions, and this optimal approximation yields a tensor decomposition where the diagonal of the core is maximized. We present an algorithm to compute this approximation and analyze its convergence behavior. Numerical experiments indicate a linear convergence rate for this algorithm.
EVAcon: a protein contact prediction evaluation service

Here we introduce EVAcon, an automated web service that evaluates the performance of contact prediction servers. Currently, EVAcon is monitoring nine servers, four of which are specialized in contact prediction and five are general structure prediction servers. Results are compared for all newly determined experimental structures deposited into PDB (∼5–50 per week). EVAcon allows for a precise comparison of the results based on a system of common protein subsets and the commonly accepted evaluation criteria that are also used in the corresponding category of the CASP assessment. EVAcon is a new service added to the functionality of the EVA system for the continuous evaluation of protein structure prediction servers. The new service is accesible from any of the three EVA mirrors: PDG (CNB-CSIC, Madrid) (); CUBIC (Columbia University, NYC) (); and Sali Lab (UCSF, San Francisco) ().
Modeling extended contacts for nanotube and graphene devices

Carrier injection into carbon nanotubes and graphene nanoribbons, contacted by a metal coating over an arbitrary length, is studied by various means: Minimal models allow for exact analytic solutions which can be transferred to the original system with high precision. Microscopic ab initio calculations of the electronic structure at the carbon-metal interface allow us to extract -- for Ti and Pd as contacting materials -- realistic parameters, which are then used in large scale tight-binding models for transport calculations. The results are shown to be robust against non-epitaxially grown electrodes and disorder at the interface in general, as well as various refinements of the model.
Examining the Effectiveness of Testing Coverage Tools : An Empirical Study

Code coverage is one of the most important aspects of software testing, which helps software engineers to understand which portion of code has been executed using a given test suite throughout the software testing process. Automatic testing tools are widely utilized to provide testing coverage metrics in order to gauge the quality of software, but these tools may have some shortcomings such as the difference among the values of code coverage metric of a given program using different code coverage tools. Therefore, we designed and performed a controlled experiment to investigate whether these tools have a significant difference among the measured values of coverage metric or not. We collected the coverage data that consist of branch, line, statement, and method coverage metrics. Statistically, our findings show that there is a significant difference of code coverage results among the code coverage tools in terms of branch and method coverage metrics.
Factorized Orthogonal Latent Spaces

Existing approaches to multi-view learning are particularly effective when the views are either independent (i.e, multi-kernel approaches) or fully dependent (i.e., shared latent spaces). However, in real scenarios, these assumptions are almost never truly satisfied. Recently, two methods have attempted to tackle this problem by factorizing the information and learn separate latent spaces for modeling the shared (i.e., correlated) and private (i.e., independent) parts of the data. However, these approaches are very sensitive to parameters setting or initialization. In this paper we propose a robust approach to factorizing the latent space into shared and private spaces by introducing orthogonality constraints, which penalize redundant latent representations. Furthermore, unlike previous approaches, we simultaneously learn the structure and dimensionality of the latent spaces by relying on a regularizer that encourages the latent space of each data stream to be low dimensional. To demonstrate the benefits of our approach, we apply it to two existing shared latent space models that assume full dependence of the views, the sGPLVM and the sKIE, and show that our constraints improve the performance of these models on the task of pose estimation from monocular images.
Mobile Robot Navigation Using Omnidirectional Vision

The topic of this paper is the design and the implementation of a robot, which is capable of autonomous navigation within a homogeneous, weaklytextured environment. The architectural components of the robot are an RC model car, a remote controller extended with some custom electronics, a wireless camera with panoramic annular lens, and a standard PC for controlling the robot.
An algorithm for generating t-wise covering arrays from large feature models

A scalable approach for software product line testing is required due to the size and complexity of industrial product lines. In this paper, we present a specialized algorithm (called ICPL) for generating covering arrays from feature models. ICPL makes it possible to apply combinatorial interaction testing to software product lines of the size and complexity found in industry. For example, ICPL allows pair-wise testing to be readily applied to projects of about 7,000 features and 200,000 constraints, the Linux Kernel, one of the largest product lines where the feature model is available. ICPL is compared to three of the leading algorithms for t-wise covering array generation. Based on a corpus of 19 feature models, data was collected for each algorithm and feature model when the algorithm could finish 100 runs within three days. These data are used for comparing the four algorithms. In addition to supporting large feature models, ICPL is quick, produces small covering arrays and, even though it is non-deterministic, produces a covering array of a similar size within approximately the same time each time it is run with the same feature model.
Limited Memory Bundle Method for Large Bound Constrained Nonsmooth Optimization

1. Abstract Practical optimization problems often involve nonsmooth functions of hundreds or thousands of variables. As a rule, the variables in such large problems are restricted to certain meaningful intervals. In the report [Haarala, Makela, 2006] we have described an efficient adaptive limited memory bundle method for large-scale nonsmooth, possibly nonconvex, bound constrained optimization. Although it works very well in numerical experiments it suffers from one theoretical drawback. Namely, it is not necessarily globally convergent. In this paper, a globally convergent variant of this method is proposed. In addition, some results from numerical experiments are given. 2.
Nonnegative Multivariate Ar(1) Processes

Conditions for nonnegativity of a p-dimensional AR(1) process X (= UX (_i + e (are investigated in the paper. If all the elements of the matrix U are nonnegative, a new method for estimating U is proposed. It is proved that the estimators are strongly consistent. Small-sample properties of the estimators are illustrated in a simulation study.
Dense sampling and fast encoding for 3D model retrieval using bag-of-visual features

Our previous shape-based 3D model retrieval algorithm compares 3D shapes by using thousands of local visual features per model. A 3D model is rendered into a set of depth images, and from each image, local visual features are extracted by using the Scale Invariant Feature Transform (SIFT) algorithm by Lowe. To efficiently compare among large sets of local features, the algorithm employs bag-of-features approach to integrate the local features into a feature vector per model. The algorithm outperformed other methods for a dataset containing highly articulated yet geometrically simple 3D models. For a dataset containing diverse and detailed models, the method did only as well as other methods. This paper proposes an improved algorithm that performs equal or better than our previous method for both articulated and rigid but geometrically detailed models. The proposed algorithm extracts much larger number of local visual features by sampling each depth image densely and randomly. To contain computational cost, the method utilizes GPU for SIFT feature extraction and an efficient randomized decision tree for encoding SIFT features into visual words. Empirical evaluation showed that the proposed method is very fast, yet significantly outperforms our previous method for rigid and geometrically detailed models. For the simple yet articulated models, the performance was virtually unchanged.
A Method for Constructing LDPC Codes with Low Error Floor

This paper describes a novel progressive edge growth (PEG) algorithm for constructing LDPC codes with minimized block error probability over the binary erasure channel (BEC). The constructed codes provide superior performance and lower error floor compared to codes generated by previously known algorithms. Furthermore, an upper bound on the expected block error probability in the error floor region of the generated code is derived
A Detailed Study of Hardware Techniques That Dynamically Exploit Frequent Operands to Reduce Power Consumption in Integer Function Units ∗

The use of multiple pipelines in superscalar processors and increasing hardware support for intelligent compilers have resulted in processors becoming computationally intensive. There has been an increase in the number of function units, which are wider and operate at higher speeds. A high percentage of integer instructions executed in standard benchmarks reveal a high usage of integer function units. In this paper, we analyze three different techniques, namely, memoing (caching results that can be reused), narrow-width operand exploitation (limiting computation to low order bytes), and byte encoding (computation performed over significant bytes), that dynamically exploit operands to lower power consumption in integer function units. Each technique proposes avoiding redundant computation in a function unit and providing the output or a part of the output via alternate means. We analyze and compare these techniques in terms of power savings, area and delay overheads, and their effectiveness when applied to different integer function units. Previously, estimates of power savings based on switching activity were reported. Our implementation of integer function units (CLA, array multiplier, comparator, etc.) at the VLSI layout level and analysis using standard integer benchmarks from the SPEC CPU2000 suite provide realistic power savings, area, and delay overheads.
The study on the ultrasonic testing and contour measurement of scroll-type Profile

In this paper, the model of ultrasonic testing robot kinematics for the scroll-type profile is established, and the pose error compensation technology of detection robot is studied deeply. By the experimental verification, it is validated that the method can detect the internal defects of Scroll profile effectively. In addition, the non-contact scanning measurement of scroll-type Profile can be achieved based on inspection robot. Once this method is applied successfully in practice, not only the product quality and reliability of scroll compressor is improved, but also the theoretical and practical support for full inspection of the product is provided.
Recommended cultural and business practices for project based software organization of Pakistan for supporting restructuring of functional organization for implementing agile based development framework in software projects

The recent trend of software industry in Pakistan is a shift to adopt agile methodologies for software development. Keeping in view the challenges of methodology migration the current research provides a comprehensive analysis of structural requirements for project based organization to become agile with recommended cultural and business practices which can help organization to re-structure from functional to agile based projectized.
Structural Models Involving Highly Dimensional Fixed Point Problems: An Asymptotically Efficient Two-Stage Estimator

In this paper we consider a class of structural econometric models in which the distribution of the endogenous variables can be defined as the solution of a fixed-point problem. We propose a two-stage estimator which avoids repeated solution of the fixed point problem. The idea behind our estimator builds on previous work by Hotz and Miller (1993), Manski (1993) and Aguirregabiria and Mira (1999) in the context of dynamic discrete choice models. The first stage involves non-parametric estimation of the distribution of endogenous variables. In the second stage a pseudo-likelihood function is maximized. Given parameter values, the pseudo-likelihood function is computed by a single iteration on the fixed point operator, using the first stage non-parametric estimates as starting values. Our two-stage estimator is the value of the structural parameters that maximizes this pseudo-likelihood function. We state regularity conditions for consistency of this estimator and provide additional sufficient conditions under which the two-stage estimator can be used instead of a maximum likelihood estimator with no loss of asymptotic efficiency. We also show that these sufficient conditions will be satisfied if a Newton operator is used to solve the fixed point problem. Finally, we study the performance of this estimator in finite samples for several specific examples: a dynamic programming discrete choice model, a model of oligopolistic competition in a differentiated product market and a model of irreversible investment.
Order Optimal Coded Delivery and Caching: Multiple Groupcast Index Coding

The capacity of caching networks has received considerable attention in the past few years. A particularly studied setting is the case of a single server (e.g., a base station) and multiple users, each of which caches segments of files in a finite library. Each user requests one (whole) file in the library and the server sends a common coded multicast message to satisfy all users at once. The problem consists of finding the smallest possible codeword length to satisfy such requests. In this paper we consider the generalization to the case where each user places L ≥ 1 requests. The obvious naive scheme consists of applying L times the order-optimal scheme for a single request, obtaining a linear in L scaling of the multicast codeword length. We propose a new achievable scheme based on multiple groupcast index coding that achieves a significant gain over the naive scheme. Furthermore, through an information theoretic converse we find that the proposed scheme is approximately optimal within a constant factor of (at most) 18.
Adaptive control based on retrospective cost optimization

A discrete-time adaptive control law for stabilization, com- mand following, and disturbance rejection that is effective for systems that are unstable, MIMO, and/or nonminimum phase. The adaptive control algorithm includes guidelines concerning the modeling information needed for implementation. This information includes the relative degree, the first nonzero Markov parameter, and the nonminimum-phase zeros. Except when the plant has nonminimum-phase zeros whose absolute value is less than the plant's spectral radius, the required zero information can be approximated by a sufficient number of Markov parameters. No additional infor- mation about the poles or zeros need be known. Numerical examples are presented to illustrate the algorithm's effective- ness in handling systems with errors in the required modeling data, unknown latency, sensor noise, and saturation.
The Effect of Group Supervision on the Psychological Counseling Self-Efficacy Levels of Psychological Counseling Candidates

Psikolojik danisma becerileri, rehberlik ve psikolojik danismanlik mesleginin en onemli ogesidir. Psikolojik danisman adaylari lisans egitimlerinde, bireyle psikolojik danisma uygulamasi dersi kapsaminda onceden teorik olarak ogrendikleri bu mesleki becerileri uygulama firsati bulurlar ve bu uygulamalara yonelik supervizyon destegi alirlar. Bu calisma, grup supervizyonunun psikolojik danisman adaylarinin psikolojik danisma ozyeterligine etkisinin incelendigi karma desen bir arastirmadir. Nicel veriler, Psikolojik Danisma Ozyeterlik Olcegi; nitel veriler ise Psikolojik danisman adaylarinin degerlendirme raporlarindan elde edilmistir. Nicel bulgular, grup supervizyonunun psikolojik danisma ozyeterliginin tum alt boyutlarinda (kesif, icgoru, eylem, iliskide catismalar, danisan problemleri) etkili oldugunu gostermistir. Bu bulguyu destekleyen nitel bulgular ise katilimcilarin yanitlarinin duygular, mesleki gelisim, destekleyiciler ve guclukler olmak uzere dort temada ayristigini ortaya koymustur. Sonuc olarak bu arastirmadan elde edilen bulgular, bireyle psikolojik danisma uygulamasi dersi kapsaminda yurutulen grup supervizyonunun adaylarin psikolojik danisma ozyeterlik algilarini olumlu yonde etkiledigini gostermistir. Buna bagli olarak psikolojik danisman egitiminde mesleki becerilerin kazandirilmasinin yani sira adaylarin psikolojik danisma ozyeterligini de artirmanin dikkate alinmasi onerilmistir.
and wildfires frequency-area statistics of earthquakes , landslides An inverse cascade explanation for the power-law

Frequency-magnitude statistics for natural hazards can greatly help in probabilistic hazard assessments. An example is the case of earthquakes, where the generality of a power-law (fractal) frequency-rupture area correlation is a major feature in seismic risk mapping. Other examples of this power-law frequency-size behaviour are landslides and wildfires. In previous studies, authors have made the potential association of the hazard statistics with a simple cellular-automata model that also has robust power-law statistics: earthquakes with slider-block models, landslides with sandpile models, and wildfires with forest-fire models. A potential explanation for the robust power-law behaviour of both the models and natural hazards can be made in terms of an inverse-cascade of metastable regions. A metastable region is the region over which an 'avalanche' spreads once triggered. Clusters grow primarily by coalescence. Growth dominates over losses except for the very largest clusters. The cascade of cluster growth is self-similar and the frequency of cluster areas exhibits power-law scaling. We show how the power-law exponent of the frequency-area distribution of clusters is related to the fractal dimension of cluster shapes. The f requencysize statistics of a number of natural hazards appear to satisfy power-law (fractal) scaling to a good approximation under a wide variety of conditions (for a review, see Malamud 2004). These include earthquakes (Aki 1981; Turcotte & Malamud 2002), volcanic eruptions (Pyle 2000), wildfires (Malamud et al. 1998, 2005; Ricotta et al. 1999), landslides (Guzzetti et al. 2002; Malamud et al. 2004), asteroid impacts (Chapman & Morrison 1994; Chapman 2004) and potentially floods (Turcotte & Greene 1993; Turcotte 1994; Malamud et al. 1996; Malamud & Turcotte 2006). In this paper, we will consider the f requency-area statistics of three of these natural hazards: earthquakes, landslides, and wildfires. In each case the 'noncumulative' number of events N with area A satisfies the power-law relation
Development of fludarabine formulations in the treatment of chronic lymphocytic leukemia

Fludarabine is an antineoplastic agent used in the treatment of hematological malignancies, particularly chronic lymphocytic leukemia (CLL) and indolent B-cell lymphoma. Because of its immunosuppressive effects, fludarabine has been added to reduced intensity conditioning regimens. The oral formulation of fludarabine has become widely available. Pharmacokinetic studies have shown that an oral dose of 40 mg/m(2)/d would provide systemic drug exposure similar to the standard intravenous (IV) dose of 25 mg/m(2)/d. The oral dose can be taken once daily without any dietary restrictions. Dose adjustments are mandatory in patients with renal impairment to avoid increased toxicity. Several noncomparative trials in previously untreated and treated patients with CLL have shown that treatment with the oral formulation demonstrates similar efficacy compared to historical control groups treated with the IV formulation. The tolerability profile of oral fludarabine seems similar to that of the IV formulation. Myelosuppression and infectious complications are the most frequently reported adverse events. Gastrointestinal toxicity is more frequent with the oral formulation, but is usually of mild or moderate severity. Although oral fludarabine makes treatment more convenient, health care workers must be aware of the compliance behavior of each patient.