Miracle-dz/UniFAR-FTUs huggingface dataset:
Cobra CRISP Functions as an Inflammatory Modulator via a Novel Zn2+- and Heparan Sulfate-dependent Transcriptional Regulation of Endothelial Cell Adhesion Molecules*

Cysteine-rich secretory proteins (CRISPs) have been identified as a toxin family in most animal venoms with biological functions mainly associated with the ion channel activity of cysteine-rich domain (CRD). CRISPs also bind to Zn2+ at their N-terminal pathogenesis-related (PR-1) domain, but their function remains unknown. Interestingly, similar the Zn2+-binding site exists in all CRISP family, including those identified in a wide range of organisms. Here, we report that the CRISP from Naja atra (natrin) could induce expression of vascular endothelial cell adhesion molecules, i.e. intercellular adhesion molecule-1, vascular adhesion molecule-1, and E-selectin, to promote monocytic cell adhesion in a heparan sulfate (HS)- and Zn2+-dependent manner. Using specific inhibitors and small interfering RNAs, the activation mechanisms are shown to involve both mitogen-activated protein kinases and nuclear factor-κB. Biophysical characterization of natrin by using fluorescence, circular dichroism, and x-ray crystallographic methods further reveals the presence of two Zn2+-binding sites for natrin. The strong binding site is located near the putative Ser-His-Glu catalytic triad of the N-terminal domain. The weak binding site remains to be characterized, but it may modulate HS binding by enhancing its interaction with long chain HS. Our results strongly suggest that natrin may serve as an inflammatory modulator that could perturb the wound-healing process of the bitten victim by regulating adhesion molecule expression in endothelial cells. Our finding uncovers a new aspect of the biological role of CRISP family in immune response and is expected to facilitate future development of new therapeutic strategy for the envenomed victims.
Studies of NBTI in pMOSFETs with thermal and plasma nitrided SiON gate oxides by OFIT and FPM methods

NBTI in pMOSFETs with plasma (PNO) and thermal (TNO) nitrided SiON gate oxides are re-investigated using our newly developed on-the-fly interface trap (OFIT) and fast pulse I–V measurement (FPM) methods. The threshold voltage shift ΔVTH is quantitatively decomposed into interface trap and oxide charge components. It is found that the interface trap generation under stress follows the power law with the same power index n and its temperature dependence, indicating the same interface degradation mechanism for both PNO and TNO devices. The NBTI degradation in TNO devices is larger than those in PNO devices, particularly the larger component of oxide charge. The result is explained by the different N profile of TNO from that of PNO devices, as supported by the first principle calculation.
Measurements of Micro-Defects in the Aluminum Thixoformed Part using Computed Tomography(CT) Technology

Computed tomography(CT) has been applied to measure micro-defects in the aluminum knuckle parts manufactured by the thixoforming process. 6061 aluminum alloys were used to form knuckle samples in the semi-solid temperature after the SIMA processing of billets. Tensile specimens were cut from the different locations in a thixoformed knuckle. The size and the distribution of forming defects in tensile specimens were analyzed using CT scanning and image analysis technology before tensile tests. It has been qualitatively shown that the stress-strain curves were significantly affected by the size and the distribution of forming defects although the defect sizes lie in the range of micro-meters.
Abductive Logic Programming in the Clinical Management of HIV/AIDS

This paper presents a new Abductive Logic Programming (ALP) approach for assisting clinicians in the selection of antiretroviral drugs for patients infected with Human Immunodeficiency Virus (HIV). The approach is comparable to laboratory genotypic resistance testing in that it aims to determine which viral mutations a patient is carrying and predict which drugs they are most likely resistant to. But, instead of genetically analysing samples of the virus taken from patients --which is not always practicable --our approach infers likely mutations using the patient's full clinical history and a model of drug resistance maintained by a leading HIV research agency. Unlike previous applications of abduction, our approach does not attempt to find the “best” explanations, as we can never be absolutely sure which mutations a patient is carrying. Rather, the intrinsic uncertainty of this domain means that multiple alternative explanations are inevitable and we must seek ways to extract useful information from them. The computational and pragmatic issues raised by this approach have led us to develop a new ALP methodology for handling numerous explanations and for drawing predictions with associated levels of confidence. We present our in-Silico Sequencing System (iS3) for reasoning about HIV drug resistance as a concrete example of this approach.
Statistical Analyses of Wave Height and Wind Velocity Distributions for the Sea of Marmara

The Sea of Marmara, a relatively small basin located between the Black Sea and the Aegean Sea with narrow seaways of the Bosphorus and the Dardanelles, has vital importance in coastal and ocean engineering activities due to substantial industrial development surrounding it and related sea traffic. Despite this importance, measurements concerning coastal engineering applications, in particular the wave climate, are quite scarce. Lack of essential data impairs the reliability of engineering works such as breakwaters and coastal protection structure designs. For a period of approximately one year between February 2013 and January 2014 Turkish Petroleum International Company (TPIC) carried out wave and wind measurements in the Sea of Marmara. The data were collected in 30-minute intervals throughout the one year span at the location of 41 o 04 ’ N and 28 o 19 ’ E with 50 m water depth. The present work analyses this rather unique data statistically for wind, wave height and energy conditions in the Sea of Marmara.
Asymptotic Per-User Rate Analysis of Downlink MIMO Cellular Networks with Linear Precoding

Extensive studies have been conducted on the rate analysis of downlink multiuser multiple-input-multiple-output (MIMO) systems. Most of them, nevertheless, focused on the sum rate of all the users where the effect of large-scale fading is either ignored or simplified. For interference-limited MIMO cellular networks, users in various locations may achieve drastically different rates due to distinct large-scale fading and interference levels. It is, therefore, of great practical interest to characterize the rate performance of each single user under various power allocation strategies and precoding schemes. This paper presents an asymptotic per-user rate analysis for a 1-tier (i.e., 7-cell) downlink MIMO cellular network with M base-station antennas co-located at the center of each cell and K uniformly distributed users each equipped with N antennas. Explicit expressions of the ergodic rate with two representative linear precoding schemes, singular-value-decomposition (SVD) transmission and block diagonalization (BD), are derived, based on which the effect of power allocation strategies is further evaluated. The analysis shows that the rate performance of each user is sensitive to its position even if the average received power is kept a constant. To achieve a uniform rate all over the cell, an interference-aware power allocation scheme is proposed, with which the transmit power allocated to each user is carefully adjusted according to the large-scale fading coefficients from the user to its own and neighboring base stations. The tradeoff between fairness and sum rate performance is also identified, which highlights the importance of the characterization of per-user rate.
On insomnia analysis using methods of artificial intelligence

Insomnia generally is defined as a subjective report of difficulty falling sleep, difficulty staying asleep, early awakening, or nonrestorative sleep. It is one of the most common health complaints among the general population. in this paper we try to find relationships between different insomnia cases and predisposing, precipitating, and perpetuating factors following by pharmacological treatment.
Discovering automation level of software change request process from qualitative empirical data

This paper presents an approach in discovering automation level of software change request process from qualitative empirical data. In the study is investigated common practice in local very small software companies. Constructivist grounded theory was used as a research method suitable for discovering common practice and for creating explanations that are grounded in empirical data. In the research participated software experts from local very small software companies. Software experts were interviewed individually in their companies or participated in organized focus groups. The process of qualitative research that is used in the study is outlined, followed by the research findings. Analysis of empirical data reveals that very small software companies do not have automated software change request process, or have automated only parts of the process.
Platelet-vessel Wall Interactions with Third-generation Oral Contraceptives: No Evidence of Detrimental Effects

Summary Because of the association of oral contraceptives (OC) and cigarette smoking with an increased thrombotic risk, we evaluated thromboxane (TX) and prostacyclin urinary (u) metabolites, as in vivo indices of platelet-vessel wall interactions, in women assigned to third generation OC. Twenty-eight women (15 smokers) underwent a 6-month trial of 30 μg ethinylestradiol plus 0.150 mg desogestrel. Cotinine plasma levels were elevated only in persons classified as smokers and serum TXB2 determination confirmed the absence of cyclooxygenase inhibition throughout the study. u-TXB2 and 11-dehydro-TXB2 were higher in smokers than in non-smokers. OC decreased u-11-dehydro-TXB2 both in smokers (from (pg/μmol creatinine) 35.1 ± 6.9 to 15.8 ± 2.8; P <0.025) and non-smokers (from 31.7 ± 9.8 to 20.6 ± 4.8, P = N.S.). u-6-keto-prostaglandin(PG)F1α excretion, also higher in smokers compared to non-smokers, was also reduced after OC in smokers (from (pg/μmol creatinine) 24.3 ± 5.2 to 14.8 ± 2.3; P <0.05). Smokers also had a trend to higher u-2,3-dinor-6-keto-PGF1α, marginally reduced by OC. Thus, the OC regimen used here improves – if anything – platelet vessel wall interactions as assessed by prostanoid production in vivo. The prothrombotic tendency associated with the use of OC in smokers does not appear to be mediated by changes in platelet-vessel wall interactions.
Resistance of Potential Plant Growth Promoting Rhizobacteria to Heavy Metals (Ni, Cd, Co, Pb) Isolated from Polluted Areas of Hyderabad

Heavy metal pollution is increases day by day due to industrialization in all over world. Pollution is generated due to metallic ferrous ores mining and smelting, fossil fuels, sewage, municipal wastes, pesticides and fertilizers. The occurrence of these heavy metals in the environment has been a topic of great worry due to their toxicity, nonbiodegradable nature and the long biological half-lives for their removal from biological tissues (Aiking et al., 1984). Their high aquatic solubility triggers bioaccumulation and biomagnifications which eventually leads to insidious and irreversible health hazard International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 08 (2018) Journal homepage: http://www.ijcmas. com
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.
DEPFIX: A System for Automatic Correction of Czech MT Outputs

We present an improved version of DEPFIX (Marecek et al., 2011), a system for automatic rule-based post-processing of English-to-Czech MT outputs designed to increase their fluency. We enhanced the rule set used by the original DEPFIX system and measured the performance of the individual rules. We also modified the dependency parser of McDonald et al. (2005) in two ways to adjust it for the parsing of MT outputs. We show that our system is able to improve the quality of the state-of-the-art MT systems.
Geometry-aware Video Registration

We present a new method for the accurate registration of video sequences of a real object over its dense triangular mesh. The goal is to obtain an accurate video-to-geometry registration to allow the bidirectional data transfer between the 3D model and the video using the perspective projection defined by the camera model. Our solution uses two different approaches: feature-based registration by KLT video tracking, and statistic-based registration by maximizing the Mutual Information (MI) between the gradient of the frame and the gradient of the rendering of the 3D model with some illumination related properties, such as surface normals and ambient occlusion. While the first approach allows a fast registration of short sequences with simple camera movements, the MI is used to correct the drift problem that KLT tracker produces over long sequences, due to the incremental tracking and the camera motion. We demonstrate, using synthetic sequences, that the alignment error obtained with our method is smaller than the one introduced by KLT, and we show the results of some interesting and challenging real sequences of objects of different sizes, acquired under different conditions.
Terpenoids and Their Biosynthesis in Cyanobacteria

Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the MEP pathway are the isomeric five-carbon compounds isopentenyl diphosphate and dimethylallyl diphosphate, which in turn form the basic building blocks for formation of all terpenoids. Many terpenoid compounds have useful properties and are of interest in the fields of pharmaceuticals and nutrition, and even potentially as future biofuels. The MEP pathway, its function and regulation, and the subsequent formation of terpenoids have not been fully elucidated in cyanobacteria, despite its relevance for biotechnological applications. In this review, we summarize the present knowledge about cyanobacterial terpenoid biosynthesis, both regarding the native metabolism and regarding metabolic engineering of cyanobacteria for heterologous production of non-native terpenoids.
Pramipexole reverses Parkinson's disease‐related motivational deficits in rats

Recent evidence suggests that Parkinson's disease affects not only movement, but also cognitive and psychiatric functions. Among these nonmotor complications, apathy, which is defined as a lack of motivation and operationalized as a quantitative reduction in goal‐directed behavior, may even precede motor impairments, disappearing with the introduction of dopaminergic (DA) therapies and possibly reappearing with its discontinuation, suggesting a causal role of DA. We recently developed a lesion‐based model, with stereotaxic infusion of 6‐hydroxydopamine (6‐OHDA) into precise areas of the rat SNc or ventral tegmental area and showed, in several operant tasks, that a partial denervation of the nigrostriatal, but not of the mesocorticolimbic, DA system induced profound motivational deficits during instrumental action. We investigated the time course of the effects of nigrostriatal DA denervation on motivation in rats, by assessing the negative effect of SNc bilateral 6‐OHDA infusion on preacquired operant behavior, and determining whether the induced deficits were sensitive to the introduction and withdrawal of a clinically relevant PD treatment, the DA D2/D3 receptor agonist, pramipexole (PRA). Partial nigrostriatal DA denervation was accompanied by a significant reduction in operant behavior. This deficit, indicative of a decrease in motivation, was fully reversed by PRA and reappeared after treatment withdrawal. This longitudinal preclinical study provides evidence for the implication of the DA nigrostriatal system in PD‐associated apathy. Moreover, by showing a good isomorphy and predictive value, our model highlights the relevance of D2/D3 receptors as potential targets for alleviating apathy in PD. © 2014 International Parkinson and Movement Disorder Society
Parallelized Seeded Region Growing Using CUDA

This paper presents a novel method for parallelizing the seeded region growing (SRG) algorithm using Compute Unified Device Architecture (CUDA) technology, with intention to overcome the theoretical weakness of SRG algorithm of its computation time being directly proportional to the size of a segmented region. The segmentation performance of the proposed CUDA-based SRG is compared with SRG implementations on single-core CPUs, quad-core CPUs, and shader language programming, using synthetic datasets and 20 body CT scans. Based on the experimental results, the CUDA-based SRG outperforms the other three implementations, advocating that it can substantially assist the segmentation during massive CT screening tests.
Intratumoral CD8+ T Lymphocytes as a Prognostic Factor of Survival in Endometrial Carcinoma

Purpose: CTLs are a prominent immune component infiltrating many solid tumors. These cells are considered to be a manifestation of host-immune response to the tumor; however, their prognostic significance remains a subject of considerable debate. The objective of this study was to evaluate the distribution pattern and prognostic value of CD8+ T cells in endometrial carcinoma. Experimental Design: We studied 90 cases of endometrial carcinoma, including 75 endometrioid and 15 papillary serous carcinomas. Immunohistochemical staining for CD8 and granzyme B was performed on paraffin-embedded sections. The number of immunohistochemically staining CD8+ T cells was enumerated in the following four regions: lymphocytes infiltrating the tumor epithelium at the invasive border, within the underlying tumor stroma, within the superficial tumor epithelium, and in the perivascular areas of the myometrium. Results: Patients with >10 CD8+ T lymphocytes/high-power field within the tumor epithelium at the invasive border displayed improved overall survival compared with patients with fewer intraepithelial CD8+ T lymphocytes (87 and 50%, respectively; P = 0.027). Multivariate analysis revealed that stage, vascular invasion, grade, and the number of intraepithelial CD8+ T lymphocytes at the invasive border were the only independent predictors of survival (P < 0.0001, P = 0.001, P = 0.011, and P = 0.025, respectively). Granzyme B+ cytoplasmatic granules were detected in a high proportion of CTLs, confirming their activated cytotoxic phenotype. Conclusions: Our study demonstrates for the first time that increased numbers of CTLs at the invasive border may be a reliable independent prognostic factor of survival in patients with endometrial carcinoma.
Antenatal steroids and fluid balance in very low birthweight infants

Objectives: To determine if insensible water loss (IWL) differed between infants exposed or not exposed antenatally to corticosteroids and to explore possible mechanisms for the early postnatal diuresis associated with antenatal steroid exposure. Design: Retrospective analysis of prospectively collected data. Setting: Level three neonatal intensive care unit. Patients: Ninety six infants, median gestational age 27.5 weeks (range 23–33). Main outcome measures: Comparison of the IWL, urine output and osmolality, fluid input, electrolyte imbalance, respiratory illness severity (as assessed by surfactant requirement, maximum peak inspiratory pressure, and inspired oxygen concentration), and cardiovascular status (as assessed by inotrope requirement) between infants with antenatal corticosteroid exposure and gestational age matched controls. Results: The infants exposed to antenatal steroids differed significantly from the controls in having both a lower IWL (p = 0.0135) and a higher urine output (p = 0.0036) on day 1, and fewer developed hyponatraemia (p = 0.027) on day 2. Fewer of those exposed to antenatal steroids required inotropes (p = 0.06), but their respiratory status was similar to that of the controls. Conclusions: Infants exposed to antenatal corticosteroids have a lower IWL. The results suggest that greater skin maturation, but also better perfusion rather than less severe respiratory status, explains the early diuresis in infants exposed to antenatal steroids.
An operating system for a Reconfigurable Active SSD processing node

We have recently proposed a Distributed Reconfigurable Active SSD computation platform (RASSD) for processing data-intensive applications at the storage node itself, without having to move data over slow networks. In this paper, we present the design of an operating system (OS) for the RASSD node. RASSD OS is a multitasking real-time operating system that runs on the 32-bit MicroBlaze® soft processor core available for Xilinx® FPGA's. We discuss in this paper our OS design features which include initializing the node and configuring the different components of the RASSD node, monitoring the node's activities, and processing middleware requests. RASSD OS provides a set of services to the middleware through which it hides the low-level details of the node's hardware architecture. We describe the functions essential for the data-intensive processing within the RASSD node using examples that capture the common states of the node and various possible requests.