Miracle-dz/UniFAR-FTUs huggingface dataset:
Guanine-Modified Inhibitory Oligonucleotides Efficiently Impair TLR7- and TLR9-Mediated Immune Responses of Human Immune Cells

Activation of TLR7 and TLR9 by endogenous RNA- or DNA-containing ligands, respectively, is thought to contribute to the complicated pathophysiology of systemic lupus erythematosus (SLE). These ligands induce the release of type-I interferons by plasmacytoid dendritic cells and autoreactive antibodies by B-cells, both responses being key events in perpetuating SLE. We recently described the development of inhibitory oligonucleotides (INH-ODN), which are characterized by a phosphorothioate backbone, a CC(T)XXX3–5GGG motif and a chemical modification of the G-quartet to avoid the formation of higher order structures via intermolecular G-tetrads. These INH-ODNs were equally or significantly more efficient to impair TLR7- and TLR9-stimulated murine B-cells, macrophages, conventional and plasmacytoid dendritic cells than the parent INH-ODN 2088, which lacks G-modification. Here, we evaluate the inhibitory/therapeutic potential of our set of G-modified INH-ODN on human immune cells. We report the novel finding that G-modified INH-ODNs efficiently inhibited the release of IFN-α by PBMC stimulated either with the TLR7-ligand oligoribonucleotide (ORN) 22075 or the TLR9-ligand CpG-ODN 2216. G-modification of INH-ODNs significantly improved inhibition of IL-6 release by PBMCs and purified human B-cells stimulated with the TLR7-ligand imiquimod or the TLR9-ligand CpG-ODN 2006. Furthermore, inhibition of B-cell activation analyzed by expression of activation markers and intracellular ATP content was significantly improved by G-modification. As observed with murine B-cells, high concentrations of INH-ODN 2088 but not of G-modified INH-ODNs stimulated IL-6 secretion by PBMCs in the absence of TLR-ligands thus limiting its blocking efficacy. In summary, G-modification of INH-ODNs improved their ability to impair TLR7- and TLR9-mediated signaling in those human immune cells which are considered as crucial in the pathophysiology of SLE.
A Maximum Entropy Approach to Sentence Boundary Detection of Vietnamese Texts

We present for the first time a sentence boundary detection system for identifying sentence boundaries in Vietnamese texts. The system is based on a maximum entropy model. The training procedure requires no hand-crafted rules, lexicon, or domain-specific information. Given a corpus annotated with sentence boundaries, the model learns to classify each occurrence of potential end-of-sentence punctuations as either a valid or invalid sentence boundary. Performance of the system on a Vietnamese corpus achieved a good recall ratio of about 95%. The approach has been implemented to create a software tool named vnSentDetector, a plug-in of the open source software framework vnToolkit which is intended to be a general framework integrating useful tools for processing of Vietnamese texts.
StingyCD: Safely Avoiding Wasteful Updates in Coordinate Descent

Coordinate descent (CD) is a scalable and simple algorithm for solving many optimization problems in machine learning. Despite this fact, CD can also be very computationally wasteful. Due to sparsity in sparse regression problems, for example, often the majority of CD updates result in no progress toward the solution. To address this inefficiency, we propose a modified CD algorithm named “StingyCD. ” By skipping over many updates that are guaranteed to not decrease the objective value, StingyCD significantly reduces convergence times. Since StingyCD only skips updates with this guarantee, however, StingyCD does not fully exploit the problem’s sparsity. For this reason, we also propose StingyCD+, an algorithm that achieves further speed-ups by skipping updates more aggressively. Since StingyCD and StingyCD+ rely on simple modifications to CD, it is also straightforward to use these algorithms with other approaches to scaling optimization. In empirical comparisons, StingyCD and StingyCD+ improve convergence times considerably for `1-regularized optimization problems.
Effects of food on bacterial community composition associated with the copepod Acartia tonsa Dana

The estuarine copepod Acartia tonsa naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food per se did not much affect BCC associated with the copepod. In xenic algal treatments, however, copepod-associated BCC differed with each alga fed, even though the same bacterial source was used to inoculate the algae. In addition, starved copepods taken at the same location but at different times significantly differed in their BCC. Algal species composition and copepod life history therefore serve to regulate BCC associated with copepods, and spatial and temporal variations in algal species composition and copepod origin would alter bacteria–copepod interactions.
Trauma Exposure, PTSD Symptoms, and Presenting Clinical Problems Among Male Perpetrators of Intimate Partner Violence

Objective: This study explores trauma exposure, posttraumatic stress disorder (PTSD) symptoms and diagnosis, and PTSD symptom associations with key presenting problems in male intimate partner violence (IPV) perpetrators. The goal is to elucidate the implications of trauma and PTSD for understanding the presenting clinical problems of partner violent men. Method: Male IPV perpetrators (n = 293) at a community-based agency completed assessments of their past traumatic event exposures; current PTSD symptoms; depression; alcohol problems; illicit drug use; relationship problems; and perpetration of physical assault, psychological aggression, injury, sexual coercion, and general (nonrelationship) violence. Results: Seventy-seven percent of participants reported past trauma exposure, 62% reported multiple trauma exposures, and 11% screened positive for a probable diagnosis of PTSD. PTSD symptom levels were significantly correlated with depression, alcohol and drug use, general violence, and all indicators of relationship maladjustment and abuse. In multivariate analyses, PTSD symptoms uniquely predicted relationship dysfunction and relationship abuse over and above the influence of alcohol problems, drug use, and depression, and all 3 PTSD symptom clusters had some unique associations with relationship abuse scales. Conclusion: Trauma exposure and PTSD symptoms should be routinely assessed in IPV perpetrator treatment. More research is needed to determine whether PTSD symptoms influence treatment response and to investigate trauma-informed interventions for this population.
Polymorphisms in Pilin Glycosylation Locus of Neisseria meningitidis Expressing Class II Pili

ABSTRACT We have located a locus, pgl, in Neisseria meningitidis strain NMB required for the glycosylation of class II pili. Between five and eight open reading frames (ORFs) (pglF, pglB, pglC, pglB2, orf2, orf3, orf8, and avtA) were present in the pgl clusters of different meningococcal isolates. The Class I pilus-expressing strains Neisseria gonorrhoeae MS11 and N. meningitidis MC58 each contain a pgl cluster in which orf2 andorf3 have been deleted. Strain NMB and other meningococcal isolates which express class II type IV pili contained pglclusters in which pglB had been replaced bypglB2 and an additional novel ORF, orf8, had been inserted between pglB2 and pglC. Insertional inactivation of the eight ORFs of the pglcluster of strain NMB showed that pglF, pglB2, pglC, andpglD, but not orf2, orf3, orf8, andavtA, were necessary for pilin glycosylation. Pilin glycosylation was not essential for resistance to normal human serum, as pglF and pglD mutants retained wild-type levels of serum resistance. Although pglB2 andpglC mutants were significantly sensitive to normal human serum under the experimental conditions used, subsequent examination of the encapsulation phenotypes revealed that pglB2 andpglC mutants expressed almost 50% less capsule than wild-type NMB. A mutation in orf3, which did not affect pilin glycosylation, also resulted in a 10% reduction in capsule expression and a moderately serum sensitive phenotype. On the basis of these results we suggest that pilin glycosylation may proceed via a lipid-linked oligosaccharide intermediate and that blockages in this pathway may interfere with capsular transport or assembly.
Collaborative Annotation of Dialogue Acts: Application of a New ISO Standard to the Switchboard Corpus

This article reports some initial results from the collaborative work on converting SWBD-DAMSL annotation scheme used in the Switchboard Dialogue Act Corpus to ISO DA annotation framework, as part of our on-going research on the interoperability of standardized linguistic annotations. A qualitative assessment of the conversion between the two annotation schemes was performed to verify the applicability of the new ISO standard using authentic transcribed speech. The results show that in addition to a major part of the SWBD-DAMSL tag set that can be converted to the ISO DA scheme automatically, some problematic SWBD-DAMSL tags still need to be handled manually. We shall report the evaluation of such an application based on the preliminary results from automatic mapping via machine learning techniques. The paper will also describe a user-friendly graphical interface that was designed for manual manipulation. The paper concludes with discussions and suggestions for future work.
A Current-Feedback Instrumentation Amplifier With 5 $\mu{\hbox{V}}$  Offset for Bidirectional High-Side Current-Sensing

This paper describes an instrumentation amplifier for bidirectional high-side current-sensing applications. It uses a multipath indirect current-feedback topology. To achieve low offset, the amplifier employs a combination of chopping and auto-zeroing in a low frequency path to cancel the offset of a wide-band amplifier in a high frequency path. With a 60 kHz chopper clock and a 30 kHz auto-zero clock, this offset-stabilization scheme results in an offset voltage of less than 5 muV , a CMRR of 143 dB and a common-mode input voltage range from 1.9 to 30 V. The input voltage-to-current (V-I) converters required by the current-feedback topology are implemented with composite transistors, whose transconductance is determined by laser-trimmed resistors. This results in a less than 0.1% gain inaccuracy. The instrumentation amplifier was realized in a 0.8 mum BiCMOS process with high voltage transistors, and has an effective chip area of 2.5 mm2 .
Log-linear dialog manager

We design a log-linear probabilistic model for solving the dialog management task. In both planning and learning we optimize the same objective function: the expected reward. Rather than performing full policy optimization, we perform on-line estimation of the optimal action as a belief-propagation inference step. We employ context-free grammars to describe our variable spaces, which enables us to define rich features. To scale our approach to large variable spaces, we use particle belief propagation. Experiments show that the model is able to choose system actions that yield a high expected reward, outperforming its POMDP-like log-linear counterpart and a hand-crafted rule-based system.
Boundaries and Overlap between Hypochondriasis and Other Disorders: Differential Diagnosis and Patterns of Co-occurrence

Abstract: Hypochondriasis has common features with a number of other mental disorders, its boundaries are not always easy to draw and it occurs frequently with several psychiatric conditions. This review examines the relationships between hypochondriasis and other psychopathology in two ways. First, it discusses the differential diagnosis of hypochondriasis by identifying both the similarities and differences between hypochondriasis and organic diseases, psychotic disorders, depression, panic disorder, obsessive-compulsive disorder, generalized anxiety disorder, specific phobia of illness and somatization disorder. The greatest overlap seems to exist between hypochondriasis and panic disorder, but hypochondriasis can still be distinguished from it, as well as from other disorders. The diagnosis of hypochondriasis is not warranted in the presence of psychotic features, but it can be made alongside diagnoses of most other disorders, provided that hypochondriacal features are not better explained by them. In the second part, the article reviews studies of the co-occurrence of hypochondriasis and other disorders. The literature reveals some inconsistencies and discrepant findings, which is largely due to different settings in which studies have been conducted and various other methodological issues. Still, it appears that hypochondriasis is more likely to co-occur with depression, panic disorder and somatization disorder than with other psychiatric conditions, suggesting a closer relationship with them. The implications of these findings for the conceptualization of hypochondriasis, its diagnostic status and classification are briefly considered.
Phosphatidylserine Receptors: Role of CD36 in Binding of Anionic Phospholipid Vesicles to Monocytic Cells*

Exposure of phosphatidylserine (PtdSer) has been implicated in the recognition and phagocytosis of senescent and apoptotic cells, and CD36 has been proposed as one receptor protein that recognizes PtdSer and other anionic phospholipids. We investigated the binding of phospholipid vesicles to the monocytic leukemia cell lines THP-1 and J774A.1 with a flow cytometric assay; vesicles contained 50 mol% PtdSer, phosphatidylinositol (PtdIns), or phosphatidylglycerol (PtdGro), with the balance being phosphatidylcholine. Specific, high affinity binding was observed for vesicles containing PtdSer, PtdIns, or PtdGro. Specificity of the assay was confirmed by control experiments with erythrocytes, which showed minimal vesicle binding, and with annexin V, which blocked the binding of PtdSer, PtdGro, and PtdIns vesicles to the THP-1 cells. However, O-phospho-l-serine (to 1 mm) had no effect on the binding of PtdSer vesicles, indicating that high affinity binding requires a surface containing multiple phosphoserine groups rather than a single molecule. A monoclonal antibody to CD36 blocked up to 60% of the specific binding of PtdSer vesicles but had minimal to no effect on the binding of PtdGro or PtdIns vesicles. This antibody also selectively inhibited the phagocytosis of PtdSer-containing vesicles as measured by fluorescence microscopy, indicating that CD36 is functionally significant for phagocytosis of this vesicle type. In addition, collagen and thrombospondin, two other putative ligands of CD36, were unable to inhibit the binding of PtdSer vesicles. We conclude that CD36 is the primary protein responsible for the high affinity binding of PtdSer vesicles to these monocyte-like cells. In addition, CD36 appears to be specific for PtdSer among anionic phospholipids, and non-phospholipid ligands of CD36 do not share binding sites with PtdSer on CD36.
A comparative Study of Machine Learning Classifiers over Gene expressions towards Cardio Vascular Diseases Prediction

Contemporary solutions in genetic technologies like the NGS and GWS are playing a vital role in identifying the complex disease genetic mapping, and in the process of evaluating the genetic structure for complex diseases, machine learning methods are turning out to be a potential solution. In the implementation of machine learning methods, feature selection models are very important in attaining optimal results and accuracy from the machine learning models. In this paper, emphasis is on getting insights in to the varied kinds of machine learning methods, feature selection models that could make significant difference in terms of improving the quality and outcome for the process. An explorative study of varied feature learning models and the performance analysis of feature selection models for machine learning algorithms were carried out, and it is evident that despite of the efficacy shown by certain models, still there is considerable scope for improvement.
UHECR observations and lensing in the magnetic field of the Virgo cluster

We discuss how lensing by magnetic fields in galaxy clusters affects ultrahigh energy cosmic ray (UHECR) observations. As specific example, we use Virgo together with the cluster magnetic fields obtained earlier in a constrained simulation of structure formation including MHD processes. We find that, if M87 is the single source of UHECRs from Virgo, the emitted flux is strongly anisotropic in the most interesting energy range, (50–100) EeV, and differs from the average value by a factor five or more for a significant fraction of observers. Since magnetic lensing is energy dependent, the external energy spectrum as seen by different observers varies strongly too. These anisotropies are averaged out in the case that all active galactic nuclei in Virgo emit UHECRs. In both cases, the anisotropies of the emitted UHECR flux may introduce an important bias in the interpretation of UHECR data like, e.g., the determination of the source density ns and the source energy spectrum of UHECRs.
THE PERFORMANCE OF LEARNING ALGORITHMS ON REDUCED DATA SETS

Knowledge discovery is the process of extracting useful and previously unknown information from the very large data set. But extracting knowledge from a large data set is computationally inefficient. Using a sample from the original data can speed up the data mining process, but this is only acceptable if it does not reduce the quality of the induced information. We thus investigate the behavior of learning algorithms on different sampling sizes to decide which sample is sufficiently similar to the original data. We observe the accuracy of the induced rules extracted from training samples of decreasing sizes and use these results to determine when a sample is sufficiently small, yet maintain the acceptable accuracy rate. We evaluate random and stratified sampling methods on data from the UCI repository with three learning algorithms.
Block-Parallel IDA* for GPUs (Extended Manuscript)

We investigate GPU-based parallelization of Iterative-Deepening A* (IDA*). We show that straightforward thread-based parallelization techniques which were previously proposed for massively parallel SIMD processors perform poorly due to warp divergence and load imbalance. We propose Block-Parallel IDA* (BPIDA*), which assigns the search of a subtree to a block (a group of threads with access to fast shared memory) rather than a thread. On the 15-puzzle, BPIDA* on a NVIDIA GRID K520 with 1536 CUDA cores achieves a speedup of 4.98 compared to a highly optimized sequential IDA* implementation on a Xeon E5-2670 core.
In vivo human crystalline lens topography

Custom high-resolution high-speed anterior segment spectral domain optical coherence tomography (OCT) was used to characterize three-dimensionally (3-D) the human crystalline lens in vivo. The system was provided with custom algorithms for denoising and segmentation of the images, as well as for fan (scanning) and optical (refraction) distortion correction, to provide fully quantitative images of the anterior and posterior crystalline lens surfaces. The method was tested on an artificial eye with known surfaces geometry and on a human lens in vitro, and demonstrated on three human lenses in vivo. Not correcting for distortion overestimated the anterior lens radius by 25% and the posterior lens radius by more than 65%. In vivo lens surfaces were fitted by biconicoids and Zernike polynomials after distortion correction. The anterior lens radii of curvature ranged from 10.27 to 14.14 mm, and the posterior lens radii of curvature ranged from 6.12 to 7.54 mm. Surface asphericities ranged from −0.04 to −1.96. The lens surfaces were well fitted by quadrics (with variation smaller than 2%, for 5-mm pupils), with low amounts of high order terms. Surface lens astigmatism was significant, with the anterior lens typically showing horizontal astigmatism (Z22 ranging from −11 to −1 µm) and the posterior lens showing vertical astigmatism (Z22 ranging from 6 to 10 µm).
Neuritic Deposits of Amyloid-β Peptide in a Subpopulation of Central Nervous System-Derived Neuronal Cells

ABSTRACT Our goal is to understand the pathogenesis of amyloid-β (Aβ) deposition in the Alzheimer's disease (AD) brain. We established a cell culture system where central nervous system-derived neuronal cells (CAD cells) produce and accumulate within their processes large amounts of Aβ peptide, similar to what is believed to occur in brain neurons, in the initial phases of AD. Using this system, we show that accumulation of Aβ begins within neurites, prior to any detectable signs of neurodegeneration or abnormal vesicular transport. Neuritic accumulation of Aβ is restricted to a small population of neighboring cells that express normal levels of amyloid-β precursor protein (APP) but show redistribution of BACE1 to the processes, where it colocalizes with Aβ and markers of late endosomes. Consistently, cells that accumulate Aβ appear in isolated islets, suggesting their clonal origin from a few cells that show a propensity to accumulate Aβ. These results suggest that Aβ accumulation is initiated in a small number of neurons by intracellular determinants that alter APP metabolism and lead to Aβ deposition and neurodegeneration. CAD cells appear to recapitulate the biochemical processes leading to Aβ deposition, thus providing an experimental in vitro system for studying the molecular pathobiology of AD.
Script recognition using inhomogeneous P2DHMM and hierarchical search space reduction

Pseudo-2D hidden Markov models (P2DHMMs) manage the assignment of observations to states quite well, whereas the calculation of probabilities is a great problem. To overcome some of the defects of P2DHMMs, we propose the inhomogeneous P2DHMM (IP2DHMM). In contrast to other approaches, it is consistently able to model state duration and observation matrices of fixed height at no additional cost in computational load and number of parameters. At the same time, it enables an efficient pruning mechanism and allows a considerable reduction in decoding time. In order to further reduce the computational load, a combination scheme is presented for multiple recognition stages, using lexical tree beam searching at different resolutions and with models of different complexities (IP2DHMM and 1DHMM). The resulting system is evaluated on three different databases from different application fields: cursive script recognition, recognition of German legal amounts and recognition of city names from live mail.
Inhibition of Interferon Signaling by the New York 99 Strain and Kunjin Subtype of West Nile Virus Involves Blockage of STAT1 and STAT2 Activation by Nonstructural Proteins

ABSTRACT The interferon (IFN) response is the first line of defense against viral infections, and the majority of viruses have developed different strategies to counteract IFN responses in order to ensure their survival in an infected host. In this study, the abilities to inhibit IFN signaling of two closely related West Nile viruses, the New York 99 strain (NY99) and Kunjin virus (KUN), strain MRM61C, were analyzed using reporter plasmid assays, as well as immunofluorescence and Western blot analyses. We have demonstrated that infections with both NY99 and KUN, as well as transient or stable transfections with their replicon RNAs, inhibited the signaling of both alpha/beta IFN (IFN-α/β) and gamma IFN (IFN-γ) by blocking the phosphorylation of STAT1 and its translocation to the nucleus. In addition, the phosphorylation of STAT2 and its translocation to the nucleus were also blocked by KUN, NY99, and their replicons in response to treatment with IFN-α. IFN-α signaling and STAT2 translocation to the nucleus was inhibited when the KUN nonstructural proteins NS2A, NS2B, NS3, NS4A, and NS4B, but not NS1 and NS5, were expressed individually from the pcDNA3 vector. The results clearly demonstrate that both NY99 and KUN inhibit IFN signaling by preventing STAT1 and STAT2 phosphorylation and identify nonstructural proteins responsible for this inhibition.