gebhart/patrepeval huggingface dataset:
Knocking Down Liver CCAAT/Enhancer-Binding Protein α by Adenovirus-Transduced Silent Interfering Ribonucleic Acid Improves Hepatic Gluconeogenesis and Lipid Homeostasis indb/dbMice (2006)

CCAAT/enhancer-binding protein-alpha (C/EBPalpha) is a member of the basic leucine zipper transcription factor family and regulates expression of several enzymes in the liver that control glucose and lipid metabolism. Using adenovirus-transduced silent interfering (si)RNA against C/EBPalpha, endogenous liver C/EBPalpha protein was knocked down by 70-80% in 8-wk-old wild-type (WT) and db/db mice. In WT mice, fasting blood glucose concentrations were reduced approximately 24% without changes in plasma free fatty acid and triglycerides, when compared with LacZ adenovirus-treated control mice. Ad-C/EBPalpha siRNA treatment nearly normalized fasting glucose and significantly reduced plasma insulin and free fatty acid content, even though there was no elevation of C/EBPalpha protein in the livers of db/db mice. In parallel with the changes in glucose levels, hepatic glucose production was significantly reduced in C/EBPalpha siRNA-treated WT and db/db mice. mRNA levels of phyosphoenolpyruvate carboxykinase, glucose-6-phosphatase, and liver glycogen synthase were decreased in the C/EBPalpha siRNA-treated WT and db/db mice. Interestingly, the magnitude of reduction in these enzymes was more profound in db/db mice. C/EBPalpha siRNA also decreased mRNA levels of proliferator activator protein-gamma coactivator-1alpha in both the WT and db/db mice but reduced cAMP response element-binding protein only in WT and did not alter hepatic nuclear factor-4alpha and CBP/p300 expression. Expression of genes involved in lipogenesis, such as fatty acid synthase, acetyl-CoA carboxylase, and sterol regulatory element-binding protein-1c was robustly suppressed in the C/EBPalpha siRNA-treated db/db mice. Taken together, these results indicate that C/EBPalpha plays an important role in maintaining glucose and lipid homeostasis in the liver.
Neural networks with a self-refreshing memory: Knowledge transfer in sequential learning tasks without catastrophic forgetting (2000)

19 pages
Fused Structure And Texture (Fst) Features For Improved Pedestrian Detection (2016)

In this paper, we present a pedestrian detection descriptor called Fused Structure and Texture (FST) features based on the combination of the local phase information with the texture features. Since the phase of the signal conveys more structural information than the magnitude, the phase congruency concept is used to capture the structural features. On the other hand, the Center-Symmetric Local Binary Pattern (CSLBP) approach is used to capture the texture information of the image. The dimension less quantity of the phase congruency and the robustness of the CSLBP operator on the flat images, as well as the blur and illumination changes, lead the proposed descriptor to be more robust and less sensitive to the light variations. The proposed descriptor can be formed by extracting the phase congruency and the CSLBP values of each pixel of the image with respect to its neighborhood. The histogram of the oriented phase and the histogram of the CSLBP values for the local regions in the image are computed and concatenated to construct the FST descriptor. Several experiments were conducted on INRIA and the low resolution DaimlerChrysler datasets to evaluate the detection performance of the pedestrian detection system that is based on the FST descriptor. A linear Support Vector Machine (SVM) is used to train the pedestrian classifier. These experiments showed that the proposed FST descriptor has better detection performance over a set of state of the art feature extraction methodologies.
Correlation network analysis for data integration and biomarker selection (2008)

High-throughput biomolecular profiling techniques such as transcriptomics, proteomics and metabolomics are increasingly being used in in vivo studies to recognize and characterize effects of xenobiotics on organs and systems. Of particular interest are biomarkers of treatment-related effects which are detectable in easily accessible biological fluids such as blood. A fundamental challenge in such biomarker studies is selecting among the plethora of biomolecular changes induced by a compound and revealed by molecular profiling, to identify biomarkers which are exclusively or predominantly due to specific processes. In this work we present a cross-compartment correlation network approach, involving no a priori supervision or design, to integrate proteomic, metabolomic and transcriptomic data for selecting circulating biomarkers. The case study we present is the identification of biomarkers of drug-induced hepatic toxicity effects in a rodent model. Biomolecular profiling of both blood plasma and liver tissue from Wistar Hannover rats administered a toxic compound yielded many hundreds of statistically significant molecular changes. We exploited drug-induced correlations between blood plasma analytes and liver tissue molecules across study animals in order to nominate selected plasma molecules as biomarkers of drug-induced hepatic alterations of lipid metabolism and urea cycle processes.
Multihop Optical Wireless Communication Over ${\mathcal {F}}$-Turbulence Channels and Generalized Pointing Errors With Fog-Induced Fading (2022)

Multihop relaying is a potential technique to mitigate channel impairments in optical wireless communications (OWC). In this paper, multiple fixed-gain amplify-and-forward (AF) relays are employed to enhance the OWC performance under the combined effect of atmospheric turbulence, pointing errors, and fog. We consider a long-range OWC link by modeling the atmospheric turbulence by the Fisher-Snedecor <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">${\mathcal {F}}$</tex-math></inline-formula> distribution, pointing errors by the generalized non-zero boresight model, and random path loss due to fog. We also consider a short-range OWC system by ignoring the impact of atmospheric turbulence. We derive novel upper bounds on the probability density function (PDF) and cumulative distribution function (CDF) of the end-to-end signal-to-noise ratio (SNR) for both short and long-range multihop OWC systems by developing exact statistical results for a single-hop OWC system under the combined effect of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">${\mathcal {F}}$</tex-math></inline-formula> -turbulence channels, non-zero boresight pointing errors, and fog-induced fading. Based on these expressions, we present analytical expressions of outage probability (OP) and average bit-error-rate (ABER) performance for the considered OWC systems involving single-variate Fox's H and Meijer's G functions. Moreover, asymptotic expressions of the outage probability in high SNR region are developed using simpler Gamma functions to provide insights on the effect of channel and system parameters. The derived analytical expressions are validated through Monte-Carlo simulations, and the scaling of the OWC performance with the number of relay nodes is demonstrated with a comparison to the single-hop transmission.
Direction-based spatial skylines (2010)

Traditional location-based services recommend nearest objects to the user by considering their spatial proximity. However, an object not only has its distance but also has its direction which originates from the user to it. In this paper, we study direction-based spatial skyline queries (DSS queries) which retrieve nearest objects around the user from different directions. The closer object is better than or dominates the further object if they are in the same direction. The objects that cannot be dominated by any other object are included in the direction-based spatial skyline (DSS). We propose algorithms to answer snapshot queries which find objects on the DSS according to the user's current position. We also develop algorithms to support continuous queries which retrieve objects on the DSS while the user is moving linearly. Extensive experiments verify the performance of our proposed algorithms using both real and synthetic datasets.
Specification of multimedia composition and a visual programming environment (1993)

Multimedia refers to the composition of multiple monomedia which should be synchronized temporally and spatially. Over the past few years, some trials to describe the composition and synchronization have been made in a variety of applications and these descriptions have been used as frameworks in their applications. Although conventional works have succeeded in describing the synchronizations well, we indicate that they do not deal with the interactivity required in Interactive Multimedia Applications(IMA) like coursewares and hypermedia systems. In this paper, we propose a new specification method based on Milner's Calculus of Communicating Systems(CCS) to cope with the interactivity. For showing the effectiveness of the specification, we design and implement a visual programming environment based on the specification mechanism, and propose a simple courseware as a programming example. Our approach has implications that the new specification mechanism can be adapted as a framework in various interactive applications and the visual programming environment acquires the benefits that it can handle user interactions and synchronizations with only visual expressions while additional texts for control commands should be augmented in conventional works.
New Phase-Locked Loop Design: Understanding the Impact of a Phase-Tracking Channel Detector (2010)

We consider design of a phase-locked loop (PLL) that runs in conjunction with a phase-compensating channel detector capable of tracking and compensating for slow-varying phase errors. The main significance of this highly nontraditional timing recovery structure is that unlike the traditional PLLs, the loop's overall tracking ability and the steady-state jitter performance can be controlled more or less separately. The effective bandwidth of the PLL is set much lower than the traditional PLL for given input phase error fluctuations. As a result, the PLL jitter is made considerably smaller than traditional systems. On the other hand, the tracking ability of the overall loop depends largely on the window parameter associated with the phase estimator operating inside the Viterbi-like trellis detector. The window parameter has only a small effect on the loop jitter. The new PLL design is tested via tracking speed, timing jitter and error rate performance comparisons against a timing recovery method based on traditional PLL design. Simulation results in a turbo equalizer setting are also presented that validate the new PLL design methodology proposed.
Transcranial Theranostic Ultrasound for Pre-Planning and Blood-Brain Barrier Opening: A Feasibility Study Using an Imaging Phased Array In Vitro and In Vivo (2021)

TUS as an ultrasound-guided modality for BBB opening could serve as a promising alternative to current FUS-mediated BBB opening configurations in the clinic.
Erratum to: Cerebrovascular mental stress reactivity is impaired in hypertension (2009)

After publication of this work [1], we noted that Figure Two Y axis is labeled incorrectly as CA IMT (mm).The correct label is ''CA Diameter (cm)'' (see figure 1).
CONDYLAR RESORPTION IN PATIENTS WITH TMD. (2009)

The objective of this study is to determine the nature of the difference between condyle morphology of osteoarthritic temporomandibular joint (TMJ) and non-osteoarthritic TMJ, using 3D surface models constructed from cone-beam CT (CBCT) images. Three-dimensional Shape Correspondence was used to localize and quantify condylar morphological differences of 20 patients with RDC/TMD group III (arthralgia, arthritis, arthrosis) compared to 40 asymptomatic subjects. Three-dimensional models of right and left condyles for each subject were constructed from CBCT images and shape analysis performed using the publicly available SPHARM-PDM software. The right and left condyles were normalized using rigid Procrustes alignment to an overall mean condylar surface per group. The mean differences between groups were compared using the Hotelling T2 analysis with permutation-test derived p-values, corrected for False Discovery Rate. The differences between the group mean surfaces were visualized with color-coded magnitude and difference vectors. The condylar morphology of the TMD group was statistically significantly different from the asymptomatic group (p = 0.05, average surface distance differences of 1.9 mm for the right condyles and 2.3 mm for the left condyles). The average condylar morphology in the TMD patients showed resorption of the anterior surface of the lateral pole and flattening of the articular surface compared to the mean morphology in asymptomatic subjects. The condylar morphology and condylar dimensions of the TMD patients were different, on average, from those of the asymptomatic subjects. The preliminary findings in this cross-sectional study will lead to future investigations to elucidate osteoarthritic changes in TMD and their role in the pathophysiology of TMD. Supported by NIDCR DE017727.
Characterization of air ions in boreal forest air during BIOFOR III campaign (2005)

Abstract. The behavior of the concentration of positive small (or cluster) air ions and naturally charged nanometer aerosol particles (aerosol ions) has been studied on the basis of measurements carried out in a boreal forest at the Hyytiälä SMEAR station, Finland, during the BIOFOR III campaign in spring 1999. Statistical characteristics of the concentrations of cluster ions, two classes of aerosol ions of the sizes of 2.5–8 nm and 8–ca 20 nm and the quantities that determine the balance of small ions in the atmosphere have been given for the nucleation event days and non-event days. The dependence of small ion concentration on the ion loss (sink) due to aerosol particles was investigated applying a model of bipolar diffusion charging of particles by small ions. The small ion concentration and the ion sink were closely correlated (correlation coefficient 87%) when the fog events and the hours of high relative humidity (above 97%), as well as nocturnal calms and weak wind (wind speed&lt;0.6 m s-1 had been excluded. In the case of nucleation burst events, variations in the concentration of small positive ions were in accordance with the changes caused by the ion sink due to aerosols; no clear indication of positive ion depletion by ion-induced nucleation was found. The estimated average ionization rate of air at the Hyytiälä station in early spring, when the ground was partly covered with snow, was about 4.8 ion pairs cm-3 s-1. The study of the charging state of nanometer aerosol particles (2.5–8 nm) revealed a strong correlation (correlation coefficient 88%) between the concentrations of particles and their charged fraction (positive air ions) during nucleation bursts. The estimated charged fraction of particles, which varied from 3% to 6% considering various nucleation event days, confirms that these particles are almost quasi-steady state charged. Also the particles and air ions in the size range of 8–ca 20 nm showed a good qualitative consistency; the correlation coefficient was 92%.
Influenza Virus Lung Infection Protects from Respiratory Syncytial Virus–Induced Immunopathology (2000)

The effect of infection history is ignored in most animal models of infectious disease. The attachment protein of respiratory syncytial virus (RSV) induces T helper cell type 2-driven pulmonary eosinophilia in mice similar to that seen in the failed infant vaccinations in the 1960s. We show that previous influenza virus infection of mice: (a) protects against weight loss, illness, and lung eosinophilia; (b) attenuates recruitment of inflammatory cells; and (c) reduces cytokine secretion caused by RSV attachment protein without affecting RSV clearance. This protective effect can be transferred via influenza-immune splenocytes to naive mice and is long lived. Previous immunity to lung infection clearly plays an important and underestimated role in subsequent vaccination and infection. The data have important implications for the timing of vaccinations in certain patient groups, and may contribute to variability in disease susceptibility observed in humans.
Development of Volumetric Independent Dose Calculation System for Verification of the Treatment Plan in Image-Guided Adaptive Brachytherapy (2020)

Purpose: This study aimed to develop a volumetric independent dose calculation (vIDC) system for verification of the treatment plan in image-guided adaptive brachytherapy (IGABT) and to evaluate the feasibility of the vIDC in clinical practice with simulated cases. Methods: The vIDC is based on the formalism of AAPM TG-43. Four simulated cases of cervical cancer were selected to retrospectively evaluate the dose distributions in IGABT. Some reference point-doses, such as point A, B and rectal points, were calculated by vIDC using absolute coordinate. The dose-volume was also calculated to acquire dose-volume histograms (DVHs) with grid resolutions of 1.0 × 1.0 (G1.0), 2.5 × 2.5 (G2.5) and 0.5 × 0.5 mm² (G0.5). Dosimetric parameters such as D90% and D2cc – doses covering 90% of the high-risk critical target volume (HR-CTV) and 2 cc of the organs at risk (OARs), were obtained from DVHs. D90% also converted to equivalent doses in 2 Gy fractions (EQD2) to produce the same radiobiological effect as external beam radiotherapy. In addition, D90% was obtained in two types with or without the applicator volume to confirm the effect of the applicator itself, respectively. Validation of the vIDC was also performed using gamma evaluation by comparison with Monte-Carlo simulation. Results: The average percentage difference of point-doses was less than 2.28%. The DVHs for the HR-CTV and OARs showed no significant differences between the vIDC and the TPS. Without considering the applicator volume, the D90% of the HR-CTV calculated by the vIDC decreases with a decreasing calculated dose-grid size (32.4, 5.65, and -2.20 cGy in G2.5, G1.0, and G0.5, respectively). The overall D90% is higher when considering the applicator volume. The converted D90% by EQD2 ranged from -1.29% to 1.00%. The D2cc of the OARs showed that the averaged dose deviation is less than 10 cGy regardless of the dose-grid size. Based on gamma analysis, the passing rate was 98.81% for 3%/ 3mm criteria. Conclusion: The vIDC was developed as independent dose verification system for verification of the treatment plan in IGABT. We confirmed that the vIDC is suitable for second-check dose validation of the TPS under various conditions.
Opal photonic crystals infiltrated with chalcogenide glasses (2001)

Composite opal structures for nonlinear applications are obtained by infiltration with chalcogenide glasses As2S3 and AsSe by precipitation from solution. Analysis of spatially resolved optical spectra reveals that the glass aggregates into submillimeter areas inside the opal. These areas exhibit large shifts in the optical stop bands by up to 80 nm, and by comparison with modelling are shown to have uniform glass filling factors of opal pores up to 40%. Characterization of the domain structure of the opals prior to infiltration by large area angle-resolved spectroscopy is an important step in the analysis of the properties of the infiltrated regions.
Mechanical property and biological performance of electrospun silk fibroin-polycaprolactone scaffolds with aligned fibers (2015)

The mechanical strength, biocompatibility, and sterilizability of silk fibroin allow it to be a possible candidate as a natural bone regenerate material. To improve mechanical character and reinforce the cell movement induction, silk fibroin (SF)-polycaprolactone (PCL) alloy was fabricated by electrospinning techniques with a rotating collector to form aligned fibrous scaffolds and random-oriented scaffolds. The scanning electron microscope image of the scaffold and the mechanical properties of the scaffold were investigated by tensile mechanical tests, which were compared to random-oriented scaffolds. Furthermore, mesenchymal stem cells were planted on these scaffolds to investigate the biocompatibility, elongation, and cell movement in situ. Scanning electron microscopy shows that 91% fibers on the aligned fibroin scaffold were distributed between the dominant direction ±10°. With an ideal support for stem cell proliferation in vitro, the aligned fibrous scaffold induces cell elongation at a length of 236.46 ± 82 μm and distribution along the dominant fiber direction with a cell alignment angle at 6.57° ± 4.45°. Compared with random-oriented scaffolds made by artificial materials, aligned SF-PCL scaffolds could provide a moderate mesenchymal stem cell engraftment interface and speed up early stage cell movement toward the bone defect.
Glass-transition behavior of Ni: Calculation, prediction, and experiment (2008)

Vitrification of metals and alloys has received much attention in the field of materials science. Although some progress has been made, this phenomenon has yet to be fully understood. Herein, we investigate the vitrification process of pure Ni using an ab initio molecular dynamics simulation. The results of the molecular dynamics simulation and predictions from the specific volume and density diagrams as well as a casting experiment indicate that Ni may have a high reduced glass transition temperature but due to kinetic reasons is not a good glass former. The results of the present work provide new information about the glass-transition phenomenon and suggest that the reduced glass transition temperature is only an indicator of how easily can glass be formed and that its stability is a significantly more important feature.
Structural and Mechanical Characteristics of Healing Myocardial Scar Tissue (2004)

An anteroapical transmural myocardial infarction was created in Dorset sheep and resulting scar tissues were excised two (Group A, n=5, 10.6 ± 1.2 weeks) and eight months (Group B, n=6, 36.8 ± 1.4 weeks) post infarction [1]. Samples were oriented in longitudinal and circumferential directions in a biaxial stretcher, preconditioned and tested in displacement control at room temperature in BDM solution. Stress-strain plots were obtained for samples. Histology was performed by cryo-sectioning specimens into 8 μm slices and staining using Hematoxylin &amp; Eosin. Stress-strain analyses show that circumsferential direction was stiffer than longitudinal for Group A. Group B samples show a reverse trend and are stiffer than Group A. Stained sections show more collagen in the endocardial surface for Group B samples while Group A samples have added collagen in the epicardial side. A high density of fat cells was seen in Group B samples that may affect stiffness trends.