Miracle-dz/UniFAR-FTUs huggingface dataset:
A Classification System for Predicting RNA Hairpin Loops

RiboNucleic Acid (RNA) molecules fold back over themselves to form secondary structures which determine the RNA’s functionality in living cells. RNA secondary structure can be determined in laboratory by X-ray diffraction and nuclear magnetic resonance (NMR) techniques. However, these techniques are slow and expensive. Therefore, computational approaches are used to predict the secondary structure of RNA molecules. A new approach, RNA-SSP, for predicting RNA secondary structure elements is proposed. It combines computational approaches and machine learning classifiers to predict individual structure elements using a new search heuristic. The approach is implemented and tested for hairpin loops and a methodology for extending the approach to predict the remaining secondary structure elements is proposed. The experiments showed a significant improvement in prediction accuracy to 95% for stem regions and 80% for loops. The overall weighted-average accuracy for predicting hairpin loop sub-structure is 89% with a sensitivity of 85.29%.
A Cloud-Friendly RFID Trajectory Clustering Algorithm in Uncertain Environments

In the emerging environment of the Internet of Things (IoT), through the connection of billions of radio frequency identification (RFID) tags and sensors to the Internet, applications will generate an unprecedented number of transactions and amount of data that require novel approaches in mining useful information from RFID trajectories. RFID data usually contain a considerable degree of uncertainty caused by various factors such as hardware flaws, transmission faults and environment instability. In this paper, we propose an efficient clustering algorithm that is much less sensitive to noise and outliers than the existing methods. To better facilitate the emerging cloud computing resources, our algorithm is designed cloud-friendly so that it can be easily adopted in a cloud environment. The scalability and efficiency of the proposed algorithm are demonstrated through an extensive set of experimental studies.
Overdetermined blind separation for convolutive mixtures of speech based on multistage ICA using subarray processing

We propose a new algorithm for overdetermined blind source separation based on multistage independent component analysis (MSICA). To improve the separation performance, we have proposed MSICA in which frequency-domain ICA and time-domain ICA are cascaded. In the original MSICA, the specific mixing model, where the number of microphones is equal to that of sources, was assumed. However, additional microphones are required to achieve an improved separation performance under reverberant environments. This leads to alternative problems, e.g., a complication of the permutation problem. In order to solve them, we propose a new extended MSICA using subarray processing, where the number of microphones and that of sources are set to be the same in every subarray. The experimental results obtained under the real environment reveal that the separation performance of the proposed MSICA is improved as the number of microphones is increased.
A Practical Evaluation of Popular Volume Rendering Algorithms

This paper evaluates and compares four volume rendering algorithms that have become rather popular for rendering datasets described on uniform rectilinear grids: raycasting, splatting, shear-warp, and hardware-assisted 3D texture-mapping. In order to assess both the strengths and the weaknesses of these algorithms in a wide variety of scenarios, a set of real-life benchmark datasets with different characteristics was carefully selected. In the rendering, all algorithm-independent image synthesis parameters, such as viewing matrix, transfer functions, and optical model, were kept constant to enable a fair comparison of the rendering results. Both image quality and computational complexity were evaluated and compared, with the aim of providing both researchers and practitioners with guidelines on which algorithm is most suited in which scenario. Our analysis also indicates the current weakness in each algorithm's pipeline, and possible solutions to these as well as pointers for future research are offered.
Evidence for increased glutamatergic cortical facilitation in children and adolescents with major depressive disorder.

CONTEXT Converging lines of evidence implicate the glutamate and γ-aminobutyric acid neurotransmitter systems in the pathophysiology of major depressive disorder. Transcranial magnetic stimulation cortical excitability and inhibition paradigms have been used to assess cortical glutamatergic and γ-aminobutyric acid-mediated tone in adults with major depressive disorder, but not in children and adolescents. OBJECTIVE To compare measures of cortical excitability and inhibition with 4 different paradigms in a group of children and adolescents with major depressive disorder vs healthy controls. DESIGN Cross-sectional study examining medication-free children and adolescents (aged 9-17 years) with major depressive disorder compared with healthy controls. Cortical excitability was assessed with motor threshold and intracortical facilitation measures. Cortical inhibition was measured with cortical silent period and intracortical inhibition paradigms. SETTING University-based child and adolescent psychiatry clinic and neurostimulation laboratory. PATIENTS Twenty-four participants with major depressive disorder and 22 healthy controls matched for age and sex. Patients with major depressive disorder were medication naive and had moderate to severe symptoms based on an evaluation with a child and adolescent psychiatrist and scores on the Children's Depression Rating Scale-Revised. MAIN OUTCOME MEASURES Motor threshold, intracortical facilitation, cortical silent period, and intracortical inhibition. RESULTS Compared with healthy controls, depressed patients had significantly increased intracortical facilitation at interstimulus intervals of 10 and 15 milliseconds bilaterally. There were no significant group differences in cortical inhibition measures. CONCLUSIONS These findings suggest that major depressive disorder in children and adolescents is associated with increased intracortical facilitation and excessive glutamatergic activity.
Evidence for an extraterrestrial impact 12,900 years ago that contributed to the megafaunal extinctions and the Younger Dryas cooling

A carbon-rich black layer, dating to ≈12.9 ka, has been previously identified at ≈50 Clovis-age sites across North America and appears contemporaneous with the abrupt onset of Younger Dryas (YD) cooling. The in situ bones of extinct Pleistocene megafauna, along with Clovis tool assemblages, occur below this black layer but not within or above it. Causes for the extinctions, YD cooling, and termination of Clovis culture have long been controversial. In this paper, we provide evidence for an extraterrestrial (ET) impact event at ≅12.9 ka, which we hypothesize caused abrupt environmental changes that contributed to YD cooling, major ecological reorganization, broad-scale extinctions, and rapid human behavioral shifts at the end of the Clovis Period. Clovis-age sites in North American are overlain by a thin, discrete layer with varying peak abundances of (i) magnetic grains with iridium, (ii) magnetic microspherules, (iii) charcoal, (iv) soot, (v) carbon spherules, (vi) glass-like carbon containing nanodiamonds, and (vii) fullerenes with ET helium, all of which are evidence for an ET impact and associated biomass burning at ≈12.9 ka. This layer also extends throughout at least 15 Carolina Bays, which are unique, elliptical depressions, oriented to the northwest across the Atlantic Coastal Plain. We propose that one or more large, low-density ET objects exploded over northern North America, partially destabilizing the Laurentide Ice Sheet and triggering YD cooling. The shock wave, thermal pulse, and event-related environmental effects (e.g., extensive biomass burning and food limitations) contributed to end-Pleistocene megafaunal extinctions and adaptive shifts among PaleoAmericans in North America.
Mining of Sentence Level Opinion Using Supervised Term Weighted Approach of Naïve Bayesian Algorithm

Mining is used to help people to extract valuable information from large amount of data. As the addictive use of computers and 3G high speed internet have taken place in our day to day life, so there are so many user generated opinions on the web for the popular product. Now, from all those opinions , it is so difficult to know, how many opinions are negative, positive. It makes tough for them people to take conform decision about the purchasing of the product. And at the same time it is also difficult for the manufacturer to keep the track of the opinions and manage the opinions. For that, in this paper to help the people for making correct decision for the product, analysis and mining of the opinions are done at sentence level , because by this, we can come to know the views of so many people. This is done by the term counting based approach, in which total no of negative and positive words are count and then compared. If the dictionary is good then, it really gives good result. The algorithm used over here is naïve Bayesian algorithm, which is supervised. And for increasing the accuracy of this algorithm , it is changes in the terms of parameter which are passed to the algorithm.
The Internal Wave Action Model IWAM

This article describes the overall modeling strategy for the Internal Wave Action Model (IWAM), which is a hybrid dynamical model that predicts the internal wave field in a basin or region for given forcing and environmental fields. Large-scale internal tides and near-inertial internal waves will be modeled by integrating appropriate hydrodynamic equations. Intermediate and small-scale internal waves will be modeled by integrating the radiative balance equation (RBE). The RBE describes changes of the action density spectrum along wave group trajectories as a result of forcing, interaction, and dissipation processes; RBE makes the random phase, geometric optics (WKB), and weak interaction approximations. The action density spectrum is a reduced description of the internal wave field; it is a statistical secondorder moment from which all other second-order moments can be calculated. IWAM will combine different dynamical processes into a coherent framework. Methodologically, it is similar to the WAM model developed by the surface wave modeling community. One important task in constructing IWAM is specifying the source terms in the radiation balance equation. The specification of the dissipation source function is discussed in some detail. It involves the “derivation” of a functional form with free parameters and solutions of the RBE for the reflection off a straight slope, where propagation and dissipation are assumed to balance. Comparisons with observations and numerical process studies then allow the calibration of the free parameters. The calibration and validation of the RBE are the first tasks in constructing IWAM. The next tasks include the integration of the radiative balance equations and embedding it into a circulation model. The major issues and problems are discussed.
Inflammatory Response and Barrier Dysfunction by Different e-Cigarette Flavoring Chemicals Identified by Gas Chromatography–Mass Spectrometry in e-Liquids and e-Vapors on Human Lung Epithelial Cells and Fibroblasts

Abstract Recent studies suggest that electronic cigarette (e-cig) flavors can be harmful to lung tissue by imposing oxidative stress and inflammatory responses. The potential inflammatory response by lung epithelial cells and fibroblasts exposed to e-cig flavoring chemicals in addition to other risk-anticipated flavor enhancers inhaled by e-cig users is not known. The goal of this study was to evaluate the release of the proinflammatory cytokine (interleukin-8 [IL-8]) and epithelial barrier function in response to different e-cig flavoring chemicals identified in various e-cig e-liquid flavorings and vapors by chemical characterization using gas chromatography–mass spectrometry analysis. Flavorings, such as acetoin (butter), diacetyl, pentanedione, maltol (malt), ortho-vanillin (vanilla), coumarin, and cinnamaldehyde in comparison with tumor necrosis factor alpha (TNFα), were used in this study. Human bronchial epithelial cells (Beas2B), human mucoepidermoid carcinoma epithelial cells (H292), and human lung fibroblasts (HFL-1) were treated with each flavoring chemical for 24 hours. The cells and conditioned media were then collected and analyzed for toxicity (viability %), lung epithelial barrier function, and proinflammatory cytokine IL-8 release. Cell viability was not significantly affected by any of the flavoring chemicals tested at a concentration of 10 μM to 1 mM. Acetoin and diacetyl treatment induced IL-8 release in Beas2B cells. Acetoin- and pentanedione-treated HFL-1 cells produced a differential, but significant response for IL-8 release compared to controls and TNFα. Flavorings, such as ortho-vanillin and maltol, induced IL-8 release in Beas2B cells, but not in H292 cells. Of all the flavoring chemicals tested, acetoin and maltol were more potent inducers of IL-8 release than TNFα in Beas2B and HFL-1 cells. Flavoring chemicals rapidly impaired epithelial barrier function in human bronchial epithelial cells (16-HBE) as measured by electric cell surface impedance sensing. Our findings suggest that some of the e-cig liquids/aerosols containing flavoring chemicals can cause significant loss of epithelial barrier function and proinflammatory response in lung cells.
Proteolytic exposure of a cryptic site within collagen type IV is required for angiogenesis and tumor growth in vivo

Evidence is provided that proteolytic cleavage of collagen type IV results in the exposure of a functionally important cryptic site hidden within its triple helical structure. Exposure of this cryptic site was associated with angiogenic, but not quiescent, blood vessels and was required for angiogenesis in vivo. Exposure of the HUIV26 epitope was associated with a loss of α1β1 integrin binding and the gain of αvβ3 binding. A monoclonal antibody (HUIV26) directed to this site disrupts integrin-dependent endothelial cell interactions and potently inhibits angiogenesis and tumor growth. Together, these studies suggest a novel mechanism by which proteolysis contributes to angiogenesis by exposing hidden regulatory elements within matrix-immobilized collagen type IV.
Multilingual perspectives on child language disorders

ContributorsAcknowledgments1. Janet L. Patterson: Child Language Disorders Across Languages, Cultural Contexts, and Syndromes Section 1 Language Disorders in Specific Clinical Populations2. Stefka H. Marinova-Todd and Pat Mirenda: Language and Communication Abilities of Bilingual Children with Autism Spectrum Disorders3. Elizabeth Kay-Raining Bird: Bilingualism and Children with Down Syndrome 4. John Thorne and Truman Coggins: Communication in Children with Fetal Alcohol Spectrum Disorders: Impairment and Intervention5. Vesna Stojanovik: Multilingual Perspectives on Language in Children with Williams SyndromeSection 2 Language Disorders in Specific Languages 6. Carol To: Language Disorders in Cantonese-Speaking Children7. Jane Stokes and Nita Madhani: Perspectives on Working with Preschool Children from Panjabi, Gujarati, and Bengali Speaking Families8. Elin Thordardottir: Typical Language Development and Primary Language Impairment in Monolingual French-Speaking Children9. Seyhun Topbas and Ilknur Mavis: Comparing Measures of Spontaneous Speech of Turkish Speaking Children With and Without Language Impairment10. Barbara L. Rodriguez: Linguistic Variation and Assessment Implications for Spanish-Speaking Children in the United States
Enzymatic control of anhydrobiosis-related accumulation of trehalose in the sleeping chironomid, Polypedilum vanderplanki

Larvae of an anhydrobiotic insect, Polypedilum vanderplanki, accumulate very large amounts of trehalose as a compatible solute on desiccation, but the molecular mechanisms underlying this accumulation are unclear. We therefore isolated the genes coding for trehalose metabolism enzymes, i.e. trehalose‐6‐phosphate synthase (TPS) and trehalose‐6‐phosphate phosphatase (TPP) for the synthesis step, and trehalase (TREH) for the degradation step. Although computational prediction indicated that the alternative splicing variants (PvTpsα/β) obtained encoded probable functional motifs consisting of a typical consensus domain of TPS and a conserved sequence of TPP, PvTpsα did not exert activity as TPP, but only as TPS. Instead, a distinct gene (PvTpp) obtained expressed TPP activity. Previous reports have suggested that insect TPS is, exceptionally, a bifunctional enzyme governing both TPS and TPP. In this article, we propose that TPS and TPP activities in insects can be attributed to discrete genes. The translated product of the TREH ortholog (PvTreh) certainly degraded trehalose to glucose. Trehalose was synthesized abundantly, consistent with increased activities of TPS and TPP and suppressed TREH activity. These results show that trehalose accumulation observed during anhydrobiosis induction in desiccating larvae can be attributed to the activation of the trehalose synthetic pathway and to the depression of trehalose hydrolysis.
IL-21: A Pleiotropic Cytokine with Potential Applications in Oncology

Interleukin- (IL-) 21 is a pleiotropic cytokine that regulates the activity of both innate and specific immunity. Indeed, it costimulates T and natural killer (NK) cell proliferation and function and regulates B cell survival and differentiation and the function of dendritic cells. In addition, IL-21 exerts divergent effects on different lymphoid cell leukemia and lymphomas, as it may support cell proliferation or on the contrary induce growth arrest or apoptosis of the neoplastic lymphoid cells. Several preclinical studies showed that IL-21 has antitumor activity in different tumor models, through mechanism involving the activation of NK and T or B cell responses. Moreover, IL-21's antitumor activity can be potentiated by its combination with other immune-enhancing molecules, monoclonal antibodies recognizing tumor antigens, chemotherapy, or molecular targeted agents. Clinical phase I-II studies of IL-21 in cancer patients showed immune stimulatory properties, acceptable toxicity profile, and antitumor effects in a fraction of patients. In view of its tolerability, IL-21 is also suitable for combinational therapeutic regimens with other agents. This review will summarize the biological functions of IL-21, and address its role in lymphoid malignancies and preclinical and clinical studies of cancer immunotherapy.
Quality enhancement of coded transient audio with a post-filter in frequency domain

This paper proposed a post-filter in frequency domain for enhancing the perceptual quality of the coded transient audio. The post-filter is used to filter the frequency coefficients of the coded transient and consists of a short-term post-filter which is derived from the Linear Predictive Coding (LPC) predictor based on the Discrete Cosine Transform (DCT) coefficients of the transient frame. In order to compensate the overall spectral tilt, a spectral tilt compensation filter is used following the short-term post-filter. As a result, the post-filter in frequency domain shapes the temporal noise in time domain while introducing a little distortion in audio. This kind of post-filter doesn't need side information from the encoder and can be used in any audio decoder.
Seasonal variation on the presence of adenoviruses in stools from non-diarrheic patients

Human adenoviruses (HAdV), members of the Adenoviridae family, are excreted through the fecal route and may be present in the feces of humans consuming contaminated food or water. The presence of HAdV from different serotypes in the feces of healthy individuals was already reported using conventional polymerase chain reaction; however, real-time PCR (qPCR) may reveal not only the rates of detection as well as demonstrate the viral loads excreted by healthy persons. Aiming to identify and characterize the presence of adenoviruses in stool samples, 147 fecal samples from patients with no records of diarrhea were analyzed (74 from winter season and 73 from summer) by Real-Time PCR (qPCR) assay and conventional PCR. HAdV genome was present in 43.8% (32/73) of stools samples collected during summer season and 21.6% (16/74) during winter. The rate of detection of genomic copies (gc) ranged from 4.04×102 to 6.72×105gc/g of feces among the 147 samples analyzed, of which the ranged of genomic copies of DNA HAdV was major in summer. All samples were negative when tested for rotaviruses (RV) and noroviruses (NoV) by PCR conventional and qPCR respectively. HAdV is excreted constantly by infected individuals in the absence of clinical signs and the occurrence may vary seasonally.
The Davey-Stewartson System and the Bäcklund Transformations

We consider (coupled) Davey-Stewartson (DS) system and its Backlund transformations (BT). Relations among the DS system, the double Kadomtsev-Petviashvili (KP) system and the Ablowitz-Ladik hierarchy (ALH) are established. The DS system and the double KP system are equivalent. The ALH is the BT of the DS system in a certain reduction. From the BT of coupled DS system we can obtain new coupled derivative nonlinear Schrodinger equations.
The Cooperative Ratio of On-line Algorithms

On-line algorithms are usually analyzed using competitive analysis, in which the performance of an on-line algorithm on a sequence is normalized by the performance of the optimal off-line algorithm on that sequence. In this paper we introduce cooperative analysis as an alternative general framework for the analysis of on-line algorithms. The idea is to normalize the performance of an on-line algorithm by a measure other than the performance of the off-line optimal algorithm OPT. We show that in many instances the perform of OPT on a sequence is a coarse approximation of the difficulty or complexity of a given input. Using a finer, more natural measure we can separate paging and list update algorithms which were otherwise indistinguishable under the classical model. This creates a performance hierarchy of algorithms which better reflects the intuitive relative strengths between them. Lastly, we show that, surprisingly, certain randomized algorithms which are superior to MTF in the classical model are not so in the cooperative case, which matches experimental results. This confirms that the ability of the on-line cooperative algorithm to ignore pathological worst cases can lead to algorithms that are more efficient in practice. ∗Cheriton School of Computer Science, University of Waterloo, Waterloo, Ont. , N2L 3G1, Canada. {rdorrigiv, alopez-o}@uwaterloo.ca.
Adaptive Information Filtering: Learning in the Presence of Concept Drifts

The task of information filtering is to classify texts from a stream of documents into relevant and nonrelevant, respectively, with respect to a particular category or user interest, which may change over time. A filtering system should be able to adapt to such concept changes. This paper explores methods to recognize concept changes and to maintain windows on the training data, whose size is either fixed or automatically adapted to the current extent of concept change. Experiments with two simulated concept drift scenarios based on real-world text data and eight learning methods are performed to evaluate three indicators for concept changes and to compare approaches with fixed and adjustable window sizes, respectively, to each other and to learning on all previously seen examples. Even using only a simple window on the data already improves the performance of the classifiers significantly as compared to learning on all examples. For most of the classifiers, the window adjustments lead to a further increase in performance compared to windows of fixed size. The chosen indicators allow to reliably recognize concept changes.