Miracle-dz/UniFAR-FTUs huggingface dataset:
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes

The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their ‘Reviewed’ status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address: .
Handling Soft Constraints and Goals Preferences in SGPlan ∗

In this paper, we present the partition-and-resolve strategy in SGPlan (hereafter called SGPLan 5 ) for fully supporting all language features in PDDL3.0. Based on the architecture of SGPlan that supported PDDL2.2 (here-after called SGPLan 4 ), SGPLan 5 partitions a large planning problem into subproblems, each with its own sub-goal, and resolves those inconsistent solutions using our extended saddle-point condition. Subgoal partitioning is effective for solving large planning problems because each partitioned subproblem involves a substantially smaller search space than that of the original problem. In SGPLan 5 , we generalize subgoal partitioning so that the goal state of a subproblem is no longer one goal fact as in SGPLan 4 , but can be any fact with loosely coupled constraints with other subproblems. We have further developed methods for representing a planning problem in a multi-valued form and for carrying out partitioning in the transformed space. The multi-valued representation leads to more ef ﬁ cient heuristics for resolving trajectory and temporal constraints and goal preferences.
7 An Overview of SoC Buses

The electronics industry has entered the era of multimillion-gate chips, and there is no turning back. This technology promises new levels of integration on a single chip, called the system-on-a-chip (SoC) design, but also presents significant challenges to the chip designers. Processing cores on a single chipmay number well into the high tens within the next decade, given the current rate of advancements [1]. Interconnection networks in such an environment are, therefore, becoming more and more important [2]. Currently, on-chip interconnection networks are mostly implemented using buses. For SoC applications, design reuse becomes easier if standard internal connection buses are used for interconnecting components of the design. Design teams developing modules intended for future reuse can design interfaces for the standard bus around their particular modules. This allows future designers to slot the reuse module into their new design simply, which is also based around the same standard bus [3]. Shrinking process technologies and increasing design sizes have led to highly complex billiontransistor integrated circuits (ICs). As a consequence, manufacturers are integrating increasing numbers of components on a chip. A heterogeneous SoC might include one or more programmable components such as general-purpose processors cores, digital signal processor cores, or application-specific intellectual property (IP) cores, as well as an analog front end, on-chip memory, I=O devices, and other application-specific circuits. In other words, a SoC is an IC that implements most or all the functions of a complete electronic system [4]. On-chip bus organized communication architecture (CA) is among the top challenges in CMOS SoC technology due to rapidly increasing operation frequencies and growing chip size. In general, the performance of the SoCdesign heavily depends upon the efficiency of its bus structure. The balance of computation and communication in any application or task is, of course, known as a fundamental determinant of Vojin Oklobdzija/Digital Systems and Applications 6195_C007 Page Proof page 1 11.7. 2007 2:16am Compositor Name: JGanesan
How stem cells speak with host immune cells in inflammatory brain diseases

Advances in stem cell biology have raised great expectations that diseases and injuries of the central nervous system (CNS) may be ameliorated by the development of non‐hematopoietic stem cell medicines. Yet, the application of adult stem cells as CNS therapeutics is challenging and the interpretation of some of the outcomes ambiguous. In fact, the initial idea that stem cell transplants work only via structural cell replacement has been challenged by the observation of consistent cellular signaling between the graft and the host. Cellular signaling is the foundation of coordinated actions and flexible responses, and arises via networks of exchanging and interacting molecules that transmit patterns of information between cells. Sustained stem cell graft‐to‐host communication leads to remarkable trophic effects on endogenous brain cells and beneficial modulatory actions on innate and adaptive immune responses in vivo, ultimately promoting the healing of the injured CNS. Among a number of adult stem cell types, mesenchymal stem cells (MSCs) and neural stem/precursor cells (NPCs) are being extensively investigated for their ability to signal to the immune system upon transplantation in experimental CNS diseases. Here, we focus on the main cellular signaling pathways that grafted MSCs and NPCs use to establish a therapeutically relevant cross talk with host immune cells, while examining the role of inflammation in regulating some of the bidirectionality of these communications. We propose that the identification of the players involved in stem cell signaling might contribute to the development of innovative, high clinical impact therapeutics for inflammatory CNS diseases.
Bottlenecks in the transfer of software engineering technology: lessons learned from a consortium failure

From observations gathered during a study of large software development projects, it was concluded that the software engineering technology (SET) transfer process is plagued with problems involving learning, technical communication, and negotiation. The underlying causes of these problems are discussed. The observations presented here attempted to help facilitate the MCC Software Technology program technology transfer of advanced software development technology, which mostly failed. Technology transfer was a major goal and risk of the MCC Software Technology program. <<ETX>>
Sparse Fast Fourier Transform for Exactly and Generally K-Sparse Signals by Downsampling and Sparse Recovery

Fast Fourier Transform (FFT) is one of the most important tools in digital signal processing. FFT costs O(N \log N) for transforming a signal of length N. Recently, Sparse Fourier Transform (SFT) has emerged as a critical issue addressing how to compute a compressed Fourier transform of a signal with complexity being related to the sparsity of its spectrum. In this paper, a new SFT algorithm is proposed for both exactly K-sparse signals (with K non-zero frequencies) and generally K-sparse signals (with K significant frequencies), with the assumption that the distribution of the non-zero frequencies is uniform. The nuclear idea is to downsample the input signal at the beginning; then, subsequent processing operates under downsampled signals, where signal lengths are proportional to O(K). Downsampling, however, possibly leads to "aliasing. " By the shift property of DFT, we recast the aliasing problem as complex Bose-Chaudhuri-Hocquenghem (BCH) codes solved by syndrome decoding. The proposed SFT algorithm for exactly K-sparse signals recovers 1-\tau frequencies with computational complexity O(K \log K) and probability at least 1-O(\frac{c}{\tau})^{\tau K} under K=O(N), where c is a user-controlled parameter. For generally K-sparse signals, due to the fact that BCH codes are sensitive to noise, we combine a part of syndrome decoding with a compressive sensing-based solver for obtaining $K$ significant frequencies. The computational complexity of our algorithm is \max \left( O(K \log K), O(N) \right), where the Big-O constant of O(N) is very small and only a simple operation involves O(N). Our simulations reveal that O(N) does not dominate the computational cost of sFFT-DT.
In Vitro Properties of Orthodontic Adhesives with Fluoride or Amorphous Calcium Phosphate

This in vitro study evaluated the efficacy of orthodontic adhesives with fluoride or amorphous calcium phosphate (ACP) in reducing bacterial adhesion and enamel demineralization. Forty human premolars each sectioned buccolingually into three parts were bracketed with control resin (Transbond XT) or adhesives containing ACP (Aegis Ortho) or fluoride (QuickCure). Artificial lesions induced by pH cycling were examined by X-ray photoelectron spectrophotometry (XPS) and polarized light microscopy (PLM). After 28 days, Aegis Ortho demonstrated the lowest calcium and phosphorous content by XPS analysis. After 42 days, reductions in lesion depth areas were 23.6% for Quick Cure and 20.3% for Aegis Ortho (P < 0.05). In the presence of 1% sucrose, adhesion of Streptococcus mutans to Aegis Ortho and Quick Cure was reduced by 41.8% and 37.7% (P < 0.05) as compared to Transbond XT. Composites containing ACP or fluoride reduced bacterial adherence and lesion formation as compared to a composite without ACP or fluoride.
Towards nanomedicines: design protocols to assemble, visualize and test carbon nanotube probes for multi-modality biomedical imaging

Nanomedicine is an interdisciplinary field, still in its infancy, where an accurate scientific assessment of potential risks and benefits is urgently needed, as is the engagement of end users and the public in this facet of the nanotechnology debate. There is increasing interest in improving our understanding of the interactions between nanomaterials and living systems, with regard to both the underlying chemistry and the physics of effects on the nanoscale. Ultimately, such knowledge promises new vistas for designing the ‘smart’ medicines of the future, of which targeted personalized drugs are the holy grail. Imaging and therapeutic components, including metallic radioisotopes, semiconductor quantum dots and magnetic materials, may be used to construct ‘nanocarriers’ (by encapsulation or conjugation) by rapid and simple (covalent and supramolecular) chemistry. The biomedical functions of the resulting materials are as yet largely unexplored. Encapsulation in nanocarriers could achieve delivery of the reagents (imaging and therapeutic drugs) to the sites of action in the body, while minimizing systemic toxicity and enzymatic degradation. These functional systems have the potential to become a general solution in drug delivery. Here we review recent developments concerning the applications of nanoparticles, including carbon nanotubes, as synthetic scaffolds for designing nanomedicines. This article will also focus on how understanding and design at the molecular level could help interdisciplinary teams develop research towards new diagnostics and therapeutics both in the short and the long term.
On the Genetic Interpretation of Disease Data

Background The understanding of host genetic variation in disease resistance increasingly requires the use of field data to obtain sufficient numbers of phenotypes. We introduce concepts necessary for a genetic interpretation of field disease data, for diseases caused by microparasites such as bacteria or viruses. Our focus is on variance component estimation and we introduce epidemiological concepts to quantitative genetics. Methodology/Principal Findings We have derived simple deterministic formulae to predict the impacts of incomplete exposure to infection, or imperfect diagnostic test sensitivity and specificity on heritabilities for disease resistance. We show that these factors all reduce the estimable heritabilities. The impacts of incomplete exposure depend on disease prevalence but are relatively linear with the exposure probability. For prevalences less than 0.5, imperfect diagnostic test sensitivity results in a small underestimation of heritability, whereas imperfect specificity leads to a much greater underestimation, with the impact increasing as prevalence declines. These impacts are reversed for prevalences greater than 0.5. Incomplete data recording in which infected or diseased individuals are not observed, e.g. data recording for too short a period, has impacts analogous to imperfect sensitivity. Conclusions/Significance These results help to explain the often low disease resistance heritabilities observed under field conditions. They also demonstrate that incomplete exposure to infection, or suboptimal diagnoses, are not fatal flaws for demonstrating host genetic differences in resistance, they merely reduce the power of datasets. Lastly, they provide a tool for inferring the true extent of genetic variation in disease resistance given knowledge of the disease biology.
Social Comparison and Effect of Discrimination among Levels of Originality on Self-Assessed Originality

Ss high and low in originality as defined by the “picture construction” portion of the Torrance Tests of Creative Thinking, Form A (Torrance, 1968) judged the originality of drawings made by others and by themselves. 52 Ss low in originality discriminated among three independently defined levels of originality of drawings made by others more accurately than 52 Ss high in originality. Ss low in originality who were told they had made accurate judgments as to the originality of other's drawings increased the judgment of their own originality specimens, while high original Ss who were told their judgments of other's originality were not very accurate did not increase judgment of their originality specimens. The implications of these results for Festinger's (1954) social-comparison theory are discussed.
Rotation-, scaling-, and translation-robust image watermarking using Gabor kernels

In this paper, we propose a RST-robust watermarking algorithm which exploits the orientation feature of a host image by using 2D Gabor kernels. From the viewpoint of watermark detection, host images are usually regarded as noise. However, since geometric manipulations affect watermarks as well as the host images simultaneously, evaluating host image can be helpful to measure the nature of distortion. To make most use of this property, we first hierarchically find the orientation of the host image with 2D Gabor kernels and insert a modified reference pattern aligned to the estimated orientation in a selected transformed domain. Since the pattern is generated in a repetitive manner according to the orientation, in its detection step, we can simply project the signal in the direction of image orientation and average the projected value to obtain a 1-D average pattern. Finally, correlation of the 1-D projection average pattern with watermark identifies periodic peaks. Analyzed are experimental results against geometric attacks including aspect ratio changes and rotation.
Unsupervised Methods of Topical Text Segmentation for Polish

This paper describes a study on performance of existing unsupervised algorithms of text documents topical segmentation when applied to Polish plain text documents. For performance measurement five existing topical segmentation algorithms were selected, three different Polish test collections were created and seven approaches to text pre-processing were implemented. Based on quantitative results (Pk and WindowDiff metrics) use of specific algorithm was recommended and impact of pre-processing strategies was assessed. Thanks to use of standardized metrics and application of previously described methodology for test collection development, comparative results for Polish and English were also obtained.
A wideband VCO with constant tuning-gain and uniform sub-band interval for single-chip UHF RFID reader

A novel VCO with constant tuning-gain and uniform sub-band interval is presented in this paper for single-chip UHF RFID reader application. An optimized calculation method is proposed to attain the accurate capacitor ratio for digital-controlled capacitor array units. The resistor-biased switched-capacitor structure is used to achieve large frequency range and optimized phase noise performance. The circuit is realized in 0. 18μm CMOS process and the simulation results show that the VCO features a tuning-gain from 46.8 to 50.7MHz/V with ±4% variation and a sub-band interval from 47 to 49 MHz with ±2% variation for frequencies from 3.23 to 4.03GHz and phase noise of -128.5dBc/Hz at 1MHz offset from 3.6GHz carrier. The whole circuit consumes 5.9mA from a 3.3 V to 2.5 V LDO-biased power supply.
A new stability analysis and stabilization of uncertain switched linear systems based on vector norms approach

In the present paper a new stability analysis and stabilization of continuous-time uncertain switched linear systems is considered. This approach is based on the comparison, the overvaluing principle, the application of Borne-Gentina criterion and the Kotelyanski conditions. The stability conditions issued from vector norms correspond to a vector Lyapunov function. Indeed, the switched system to be controlled will be represented in the Companion form. A comparison system relative to regular vector norms is used in order to get the simple arrow form of the state matrix that yields to a suitable use of Borne-Gentina criterion for the establishment of sufficient conditions as function of the uncertain parameters for global asymptotic stability.
A comparison of lithium and T(3) augmentation following two failed medication treatments for depression: a STAR*D report.

OBJECTIVE More than 40% of patients with major depressive disorder do not achieve remission even after two optimally delivered trials of antidepressant medications. This study compared the effectiveness of lithium versus triiodothyronine (T(3)) augmentation as a third-step treatment for patients with major depressive disorder. METHOD A total of 142 adult outpatients with nonpsychotic major depressive disorder who had not achieved remission or who were intolerant to an initial prospective treatment with citalopram and a second switch or augmentation trial were randomly assigned to augmentation with lithium (up to 900 mg/day; N=69) or with T(3) (up to 50 mug/day; N=73) for up to 14 weeks. The primary outcome measure was whether participants achieved remission, which was defined as a score < or =7 on the 17-item Hamilton Depression Rating Scale. RESULTS After a mean of 9.6 weeks (SD=5.2) of treatment, remission rates were 15.9% with lithium augmentation and 24.7% with T(3) augmentation, although the difference between treatments was not statistically significant. Lithium was more frequently associated with side effects (p=0.045), and more participants in the lithium group left treatment because of side effects (23.2% versus 9.6%; p=0.027). CONCLUSIONS Remission rates with lithium and T(3) augmentation for participants who experienced unsatisfactory results with two prior medication treatments were modest and did not differ significantly. The lower side effect burden and ease of use of T(3) augmentation suggest that it has slight advantages over lithium augmentation for depressed patients who have experienced several failed medication trials.
Understanding Why Probiotic Therapies Can be Effective in Treating IBD

Probiotics, for the treatment of inflammatory bowel disease, are a group of specific nonpathogenic bacteria that are functionally and genetically defined by their ability to reduce inflammation in the intestine. Although probiotics also seem to have broad beneficial effects in humans, both as a food and as a therapeutic agent, there are specific identified mechanisms in some, but not all, of these bacteria that are important relative to the pathogenesis of inflammatory bowel disease. Recently, studies relative to the mechanism of action of probiotics have identified that these organisms can have a direct effect on epithelial cell function and intestinal health, including enhancing epithelial barrier function, modulating epithelial cytokine secretion into an anti-inflammatory dominant profile, altering mucus production, changing bacterial luminal flora, modifying the innate and systemic immune system, and inducing regulatory T-cell effects. For probiotics to have a therapeutic role in the management of clinical inflammatory bowel disease, their therapeutic mechanism of action must be aligned with the pathogenic mechanism of action of the disease. In this regard, the role of probiotics for the clinical treatment of inflammatory bowel disease is emerging as the mechanisms and pathogenesis are being unraveled. It remains clear that probiotics are able to reduce gastrointestinal inflammation by exerting positive effects on epithelial cell and mucosal immune dysfunction.
Approximation of non-boolean 2CSP

We develop a polynomial time Ω (1/R log R) approximate algorithm for Max 2CSP-R, the problem where we are given a collection of constraints, each involving two variables, where each variable ranges over a set of size R, and we want to find an assignment to the variables that maximizes the number of satisfied constraints. Assuming the Unique Games Conjecture, this is the best possible approximation up to constant factors. Previously, a 1/R-approximate algorithm was known, based on linear programming. Our algorithm is based on semidefinite programming. The Semidefinite Program that we use has an almost-matching integrality gap. For the more general Max kCSP-R, in which each constraint involves k variables, each ranging over a set of size R, it was known that the best possible approximation is of the order of k/Rk-1, provided that k is sufficiently large compared to R; our algorithm shows that the bound k/Rk-1 is not tight for k = 2.