Miracle-dz/UniFAR-FTUs huggingface dataset:
A frame-based representation of genomic sequences for removing errors and rare variant detection in NGS data

We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions, traditionally used in signal processing for noise removal. We define a frame for genomes and sequenced reads to consist of discrete spatial signals of every k-mer of a given size. We show that each k-mer in the sequenced data can be projected onto multiple frames and these projections are maximized for spatial signals corresponding to the k-mer's substrings. Our proposed classifier, MultiRes, is trained on the projections of k-mers as features used for marking k-mers as erroneous or true variations in the genome. We evaluate MultiRes on simulated and real viral population datasets and compare it to other error correction methods known in the literature. MultiRes has 4 to 500 times less false positives k-mer predictions compared to other methods, essential for accurate estimation of viral population diversity and their de-novo assembly. It has high recall of the true k-mers, comparable to other error correction methods. MultiRes also has greater than 95% recall for detecting single nucleotide polymorphisms (SNPs), fewer false positive SNPs, while detecting higher number of rare variants compared to other variant calling methods for viral populations. The software is freely available from the GitHub link (this https URL).
Concept Discoveryin Image Databases using Orthogonal Polynomial Transformation

The objective of this paper is to propose a new algorithm for classifying the concept present in the image. The training images are segmented with fixed size blocks and featnres are extracted from it. The features are extracted by using the Orthogonal Polynomials based Transformation. From the feature set vectors, a codebook is generated for each concept class. Then significant class representative vectors are calculated which is used for classifying the concepts. The proposed method gives a better representation of training images. The approach definitely guarantees that the resnlts produced are promising.
Translating a detailed linguistic semantic representation into Horn clause logic

From the semantic representation produced by TANKA, a domain-independent, knowledge-scant, and interactive natural language analyzer, we construct Horn clauses which represent the facts or rules found in technical texts, specifically legal texts. This article describes the conversion process and the way it takes into account the detailed structure returned by the analyzer, a precise syntacticsemantic description of the sentence, and in particular at the three levels of noun phrase semantics, case structures and inter-clausal relations.
Ieee Transactions on Instrumentation and Measurement 1 Binder Identification by Means of Phantom Measurements

—This paper presents a technique to identify if two twisted pairs (TPs) share the same binder or not, based on single-ended line measurements. If the TPs share the binder only over a certain distance, this length is determined. We first show the challenges of achieving binder identification under normal differential operation. Next, we propose an alternative by measuring two TPs simultaneously in phantom mode. The proposed approach is validated by laboratory measurements.
Query rewriting for lightweight information integration

Light-weight information integration has to be able to effectively deal with settings where only partial mappings between the information sources to be integrated are defined. In our query rewriting approach, such partial mappings are used as the basis for defining several strategies to substitute elements in the query, and for introducing wildcards for relaxing the query when mappings are missing. The approach also supports the extension and refinement of the existing mappings based on the achieved query results and optional feedback of the user. This paper presents the proposed rewriting strategies, focusing on strategies exploiting ontological knowledge, and a comparison and evaluation of the strategies for real-world datasets.
The Spitzer Survey of the Small Magellanic Cloud: Discovery of Embedded Protostars in the H II Region NGC 346

We use Spitzer Space Telescope observations from the Spitzer Survey of the Small Magellanic Cloud (S3MC) to study the young stellar content of N66, the largest and brightest H II region in the SMC. In addition to large numbers of normal stars, we detect a significant population of bright, red infrared sources that we identify as likely to be young stellar objects (YSOs). We use spectral energy distribution (SED) fits to classify objects as ordinary (main-sequence or red giant) stars, asymptotic giant branch stars, background galaxies, and YSOs. This represents the first large-scale attempt at blind source classification based on Spitzer SEDs in another galaxy. We firmly identify at least 61 YSOs, with another 50 probable YSOs; only one embedded protostar in the SMC was reported in the literature prior to the S3MC. We present color selection criteria that can be used to identify a relatively clean sample of YSOs with IRAC photometry. Our fitted SEDs indicate that the infrared-bright YSOs in N66 have stellar masses ranging from 2 to 17 M☉, and that approximately half of the objects are stage II protostars, with the remaining YSOs roughly evenly divided between stage I and stage III sources. We find evidence for primordial mass segregation in the H II region, with the most massive YSOs being preferentially closer to the center than lower mass objects. Despite the low metallicity and dust content of the SMC, the observable properties of the YSOs appear consistent with those in the Milky Way. Although the YSOs are heavily concentrated within the optically bright central region of N66, there is ongoing star formation throughout the complex, and we place a lower limit on the star formation rate of 3.2 × 10-3 M☉ yr-1 over the last ~1 Myr.
Preoperative ultrasonographic examination of the radial artery and the cephalic vein and risks of dialysis arterio-venous fistula dysfunction

Summary Background: Hemodialysis used as renal replacement therapy requires a well-functioning vascular access. Arterio-venous fistula (AVF) created on the forearm is the best vascular access, but it also reveals numerous complications such as: lack of fistula maturation and hemodynamically significant stenoses. Many risk factors of fistula dysfunction are still not identified. Material/Methods: Radial artery and cephalic vein diameter and patency were ultrasonographically examined before forearm AVF creation. Intima-media complex width, blood flow and peak systolic velocity in distal part of radial artery were measured. Presence of thrombosis and post-inflammatory changes in cephalic vein were also checked. Forearm AVF was created in 66 patients. Fistula US examination was performed 3 and 12 months after operation with measurement of vessel diameter and blood flow. Fistula patency was observed in 24 months after creation. Comparison of pre- and postoperative US examinations between groups with well functioning and thrombosed fistulas was performed. Results: Primary patency of forearm AVF after 12 and 24 months was 65.2% and 53.0%, respectively. Patients with well functioning forearm AVF have significantly bigger cephalic vein diameter and peak systolic velocity in radial artery. We did not observe significant influence of radial artery intima-media complex width and radial artery diameter on AVF function. In postoperative examination, fistula diameter and flow significantly influenced the risk of AVF thrombosis. Conclusions: US examination of radial artery and cephalic vein performed before forearm AVF creation enables identification of patients with greater risk of fistula dysfunction. Cephalic vein diameter and peak systolic velocity are prognostic factors of fistula function. Control postoperative US examination of forearm fistula enables detection of AVF at risk of thrombosis.
Foxp3 Interacts with c-Rel to Mediate NF-κB Repression

Expression of the lineage-specific DNA-binding factor Foxp3 controls the development and function of naturally occurring regulatory T cells. Foxp3 has been shown to interact with a multitude of transcriptional regulators including NFAT, NF-κB (p65), Runx1 and RORγt, as well as the histone modification enzymes TIP60, HDAC7 and HDAC9. The sum of these interactions is believed to cause the change in the transcriptional program of regulatory T cells. Here we show that Foxp3 directly or as part of a multimeric complex engages with the NF-κB component c-Rel. We demonstrate that the N-terminal region of Foxp3 is required for the binding of c-Rel, but not NFAT. Conversely, deletion of the forkhead domain causes a loss of interaction with NFAT, but not c-Rel. Our findings are of particular interest, as c-Rel is crucial for the induction of Foxp3 in regulatory T cells during thymic development, but has to be repressed in mature regulatory T cells to maintain their suppressive phenotype.
Improving SVM Classification by Feature Weight Learning

This paper presents a new feature weighting method to improve the performance of support vector machine (SVM). The basic idea of this method is to translate the feature weight learning into the problem of choosing a kernel suitable for SVM classification. In more detail, this method tunes the width parameters of Gaussian ARD (Automatic Relevance Determination) kernel via optimizing a kernel evaluation criterion, i.e., kernel polarization. By using gradient ascent technique, each learned parameter indicates the relative importance of the corresponding feature. The proposed method is demonstrated with some UCI machine learning benchmark examples.
Combining the Forecasts in the ECB Survey of Professional Forecasters: Can Anything Beat the Simple Average?

In this paper, we explore the potential gains from alternative combinations of the surveyed forecasts in the ECB Survey of Professional Forecasters. Our analysis encompasses a variety of methods including statistical combinations based on principal components analysis and trimmed means, performance-based weighting, least squares estimates of optimal weights as well as Bayesian shrinkage. We provide a pseudo real-time out-of-sample performance evaluation of these alternative combinations and check the sensitivity of the results to possible data-snooping bias. The latter robustness check is also informed using a novel real time meta selection procedure which is not subject to the data-snooping critique. For GDP growth and the unemployment rate, only few of the forecast combination schemes are able to outperform the simple equal-weighted average forecast. Conversely, for the inflation rate there is stronger evidence that more refined combinations can lead to improvement over this benchmark. In particular, for this variable, the relative improvement appears significant even controlling for data snooping bias. JEL Classification: C22, C53
On Adaptive Measurement Inclusion Rate In Real-Time Moving-Horizon Observers

Abstract This paper investigates a self adaptation mechanism regarding the rate with which new measurements have to be incorporated in Moving-Horizon state estimation algorithms. This investigation can be viewed as the dual of the one proposed by the author in the context of real-time model predictive control. An illustrative example is provided in order to assess the relevance of the proposed updating rule.
Linear precoders for multiuser MIMO for finite constellations and a simplified receiver structure under controlled interference

This paper is an extension to the earlier proposed idea of exploiting the discrete constellation alphabets in linear precoding for the downlink of multiuser (MU) MIMO. In the earlier work, it was shown that the transmission of controlled interference to the users bears the potential of exploiting the interference structure in improving the error resilience. In this paper we propose a linear precoding strategy for the downlink of multiuser MIMO on the idea of controlled interference. However under the controlled interference, intuitive optimal receiver is Maximum Likelihood (ML) detector which would require an exhaustive search of the controlled interferers. It would have exponential search complexity in the number of users and their constellation sizes. We further propose in this paper a simplified receiver structure which exploits the interference structure by ML detection but its complexity is equivalent to that of a receiver that confronts no interference (in two user case). Monte Carlo simulations show the improved performance of the proposed linear precoding strategy relative to the existing linear precoding schemes.
Deduplication Potential of HPC Applications’ Checkpoints

HPC systems contain an increasing number of components, decreasing the mean time between failures. Checkpoint mechanisms help to overcome such failures for long-running applications. A viable solution to remove the resulting pressure from the I/O backends is to deduplicate the checkpoints. However, there is little knowledge about the potential to save I/Os for HPC applications by using deduplication within the checkpointing process. In this paper, we perform a broad study about the deduplication behavior of HPC application checkpointing and its impact on system design.
Ethical, Legal, and Professional Issues in Counseling

SECTION I: FOUNDATIONS 1. Introduction 2. Professional Identity of Counselors 3. Professional Practice in a Multicultural Society SECTION II: ISSUES 4. Client Rights and Counselor Responsibilities 5. Confidentiality and Privileged Communication 6. Records and Subpoenas, and Technology 7. Competence and Malpractice 8. Boundary Issues 9. Counseling Children and Vulnerable Adults 10. Counseling Families and Groups 11. Evaluation, Testing, and Diagnosis 12. Professional Relationships, Private Practice, and Healthcare Plans 13. Issues in Counselor Education 14. Supervision and Consultation 15. Research and Publications 16. Resolving Legal and Ethical Issues
Studying Memory Encoding to Promote Reliable Engagement of the Medial Temporal Lobe at the Single-Subject Level

The medial temporal lobe (MTL)—comprising hippocampus and the surrounding neocortical regions—is a targeted brain area sensitive to several neurological diseases. Although functional magnetic resonance imaging (fMRI) has been widely used to assess brain functional abnormalities, detecting MTL activation has been technically challenging. The aim of our study was to provide an fMRI paradigm that reliably activates MTL regions at the individual level, thus providing a useful tool for future research in clinical memory-related studies. Twenty young healthy adults underwent an event-related fMRI study consisting of three encoding conditions: word-pairs, face-name associations and complex visual scenes. A region-of-interest analysis at the individual level comparing novel and repeated stimuli independently for each task was performed. The results of this analysis yielded activations in the hippocampal and parahippocampal regions in most of the participants. Specifically, 95% and 100% of participants showed significant activations in the left hippocampus during the face-name encoding and in the right parahippocampus, respectively, during scene encoding. Additionally, a whole brain analysis, also comparing novel versus repeated stimuli at the group level, showed mainly left frontal activation during the word task. In this group analysis, the face-name association engaged the HP and fusiform gyri bilaterally, along with the left inferior frontal gyrus, and the complex visual scenes activated mainly the parahippocampus and hippocampus bilaterally. In sum, our task design represents a rapid and reliable manner to study and explore MTL activity at the individual level, thus providing a useful tool for future research in clinical memory-related fMRI studies.
Black holes and Abelian symmetry breaking

Black hole configurations offer insights on the nonlinear aspects of gravitational theories, and can suggest testable predictions for modifications of General Relativity. In this work, we examine exact black hole configurations in vector–tensor theories, originally proposed to explain dark energy by breaking the Abelian symmetry with a non-minimal coupling of the vector to gravity. We are able to evade the no-go theorems by Bekenstein on the existence of regular black holes in vector–tensor theories with Proca mass terms, and exhibit regular black hole solutions with a profile for the longitudinal vector polarisation, characterised by an additional charge. We analytically find the most general static, spherically symmetric black hole solutions with and without a cosmological constant, and study in some detail their features, such as how the geometry depends on the vector charges. We also include angular momentum, and find solutions describing slowly-rotating black holes. Finally, we extend some of these solutions to higher dimensions.
Routing Scalability in Multicore-Based Ad Hoc Networks

The integration of multicore processors into wireless mobile devices is creating new opportunities to enhance the speed and scalability of message routing in ad hoc networks. In this paper we study the impact of multicore technology on routing speed and node efficiency, and draw conclusions regarding the measures that should be taken to conserve energy and prolong the lifetime of a network. We formally define three metrics and use them for performance evaluation: Time-to-Destination (T2D), Average Routing Speedup (ARS), and Average-Node-Efficiency (ANE). The T2D metric is the time a message takes to travel to its destination in a loaded traffic network. ARS measures the average routing speed gained by a multicore-based network over a single-core based network, and ANE measures the average efficiency of a node, or the number of active cores. These benchmarks show that routing speedup in networks with multicore nodes increases linearly with the number of cores and significantly decrease traffic bottlenecks, while allowing more routings to be executed simultaneously. The average node efficiency, however, decreases linearly with the number of cores per node. Power-aware protocols and energy management techniques should therefore be developed to turn off the unused cores. Povzetek: Narejena je analiza povezljivosti vozlov omreuja.
Refractive changes after descemet stripping endothelial keratoplasty: a simplified mathematical model.

PURPOSE To develop a mathematical model that can predict refractive changes after Descemet stripping endothelial keratoplasty (DSEK). METHODS A mathematical formula based on the Gullstrand eye model was generated to estimate the change in refractive power of the eye after DSEK. This model was applied to four DSEK cases retrospectively, to compare measured and predicted refractive changes after DSEK. RESULTS The refractive change after DSEK is determined by calculating the difference in the power of the eye before and after DSEK surgery. The power of the eye post-DSEK surgery can be calculated with modified Gullstrand eye model equations that incorporate the change in the posterior radius of curvature and change in the distance between the principal planes of the cornea and lens after DSEK. Analysis of this model suggests that the ratio of central to peripheral graft thickness (CP ratio) and central thickness can have significant effect on refractive change where smaller CP ratios and larger graft thicknesses result in larger hyperopic shifts. This model was applied to four patients, and the average predicted hyperopic shift in the overall power of the eye was calculated to be 0.83 D. This change reflected in a mean of 93% (range, 75%-110%) of patients' measured refractive shifts. CONCLUSIONS This simplified DSEK mathematical model can be used as a first step for estimating the hyperopic shift after DSEK. Further studies are necessary to refine the validity of this model.
Russian artel revisited through the lens of the New Institutional Economics

Artels, a kind of semi-formal associations for co-operative labor, were widely spread in Russia right up to the early twentieth century. The most popular explanation of this phenomenon is specific Russian mentality, the so-called â€œartelnostâ€ , i.e. the internal commitment to collective work. The paper checks this statement and reveals that artels, as an organizational form of production in specific spheres which is characterized by the team use of inputs, existed mainly due to rather effective solving of adverse selection and moral hazard problems.
Buffer Capacity-Constrained Epidemic Routing Model in Mobile Ad-Hoc Networks

In order to understand the message propagation performance in Mobile ad-hoc Networks (MANETs), various methods and models have been proposed in the literature by applying a common pair wise meeting rate between mobile nodes. In this paper, based on this classical meeting rate, we develop an Ordinary Differential Equations (ODEs) based analytical frame-work aiming at depicting the propagation process of a target message while using a controlled epidemic routing protocol. Each relay node is assigned a threshold value of its buffer can be occupied by the target message copies in such the controlled epidemic routing. Further, we also investigate the effect of the threshold to the total buffer occupancy ratio over all the relay nodes using our proposed theoretical framework. The correctness of our analysis is validated by extensive simulations.
The efficiency of expenditure-related redistributive policies in the European countries

For the sample of European Union countries, the efficiency of social protection public expenditures in providing income support and diminishing income inequality is assessed using a two-step Data Envelopment Analysis. This paper adds to the literature in three ways. First, for each country, efficiency scores are derived using an input-oriented variable returns to scale model. As expected, the least efficient redistributive policies were found for countries with generous welfare systems. Second, the efficiency scores are calculated for two periods, before and after the recent economic crisis. The results obtained in this stage of the analysis highlighted the negative impact of the crisis on social protection public expenditure efficiency. Third, other non-discretionary determinants of social protection public expenditures were highlighted as well, using a censored normal Tobit estimation and an additional OLS estimation. The results were robust to the method of estimation and pointed out that higher efficiency scores are associated with higher employment rates and lower dependency ratios.
Computational model of partially irradiated nanodots for field-coupled computing devices

Co/Pt multilayers were proposed as a new promising media for Nanomagnet Logic computing. Modeling of irradiated Co/Pt films is challenging as Focused Ion Beam (FIB) irradiation locally changes the magnetic properties of the Co/Pt film. We implemented a computational model of partially irradiated nanodots and explained how to exploit asymmetric coupling for designing nanowires and logic gates.
Software development for the Space Station Freedom Program in the year 2000

This paper presents an overview of the Space Station Freedom Program (SSFP) Software Support Environment (SSE). The SSE is described in terms of a software architecture reference model which is a long-term goal architecture for the SSE. The existing SSE System is described followed by a description of the evolutionary approach taken by the project. Each of these topics is discussed in the context of how the SSE supports Ada software development.