gebhart/patrepeval huggingface dataset:
Herpes Simplex Virus Type 1 Induces CD83 Degradation in Mature Dendritic Cells with Immediate-Early Kinetics via the Cellular Proteasome (2007)

Mature dendritic cells (DCs) are the most potent antigen-presenting cells within the human immune system. However, Herpes simplex virus type 1 (HSV-1) is able to interfere with DC biology and to establish latency in infected individuals. In this study, we provide new insights into the mechanism by which HSV-1 disarms DCs by the manipulation of CD83, a functionally important molecule for DC activation. Fluorescence-activated cell sorter (FACS) analyses revealed a rapid downmodulation of CD83 surface expression within 6 to 8 h after HSV-1 infection, in a manner strictly dependent on viral gene expression. Soluble CD83 enzyme-linked immunosorbent assays, together with Western blot analysis, demonstrated that CD83 rapidly disappears from the cell surface after contact with HSV-1 by a mechanism that involves protein degradation rather than shedding of CD83 from the cell surface into the medium. Infection experiments with an ICP0 deletion mutant demonstrated an important role for this viral immediate-early protein during CD83 degradation, since this particular mutant strain leads to strongly reduced CD83 degradation. This hypothesis was further strengthened by cotransfection of plasmids expressing CD83 and ICP0 into 293T cells, which led to significantly reduced accumulation of CD83. In strong contrast, transfection of plasmids expressing CD83 and a mutant ICP0 defective in its RING finger-mediated E3 ubiquitin ligase function did not reduce CD83 expression. Inhibition of the proteasome, the cellular protein degradation machinery, almost completely restored CD83 surface expression during HSV-1 infection, indicating that proteasome-mediated degradation and HSV-1 ICP0 play crucial roles in this novel viral immune escape mechanism.
Dispersal and inhibitory roles of mannose, 2‐deoxy‐ d ‐glucose and N ‐acetylgalactosaminidase on the biofilm of Desulfovibrio vulgaris (2017)

Biofilms of sulfate-reducing bacteria (SRB) are often the major cause of microbiologically influenced corrosion. The representative SRB Desulfovibrio vulgaris has previously been shown to have a biofilm that consists primarily of protein. In this study, by utilizing lectin staining, we identified that the biofilm of D. vulgaris also consists of the matrix components mannose, fucose and N-acetylgalactosamine (GalNAc), with mannose predominating. Based on these results, we found that the addition of mannose and the nonmetabolizable mannose analog 2-deoxy-d-glucose inhibits the biofilm formation of D. vulgaris as well as that of D. desulfuricans; both compounds also dispersed the SRB biofilms. In addition, the enzyme N-acetylgalactosaminidase, which degrades GalNAc, was effective in dispersing D. vulgaris biofilms. Therefore, by determining composition of the SRB biofilm, effective biofilm control methods may be devised.
Tailored Nanocomposites of Polypropylene with Layered Silicates (2009)

The melt rheological properties of layered silicate nanocomposites with maleic anhydride (MA) functionalized polypropylene are contrasted to those based on ammonium-terminated polypropylene. While the MA functionalized PP based nanocomposites exhibit solid-like linear viscoelastic behavior, consistent with the formation of a long-lived percolated nanoparticle network, the single-end ammonium functionalized PP based nanocomposites demonstrated liquid-like behavior at comparable montmorillonite concentrations. The differences in the linear viscoelasticity are attributed to the presence of bridging interactions in MA functionalized nanocomposites. Further, the transient shear stress of the MA functionalized nanocomposites in start-up of steady shear is a function of the shear strain alone, and the steady shear response is consistent with that of non-Brownian systems. The weak dependence of the steady first normal stress difference on the steady shear stress suggests that the polymer chain mediated silicate network contributes to such unique flow behavior.
New sugar-based gelators with an amino group, the gelation ability of which is remarkably reinforced by the hydrogen bond and the metal coordination (1999)

Three sugar-integrated gelators bearing a p-aminophenyl group which are expected to exert a hydrogen-bonding effect and a metal coordination effect on the gelation ability were synthesised. α-D-Galactose-based 2b was only soluble or precipitated and β-D-glucose-based 4b gelated only two of 15 solvents tested herein whereas α-D-glucose-based 1b acted as an excellent gelator which could gelate 8 solvents. The sol–gel phase-transition temperature (Tgel) values for 1b were higher by 41–78 °C than those for α-D-glucose-based 1a bearing a p-nitrophenyl group. The spectral studies indicated that this gel reinforcement is due to the hydrogen-bonding interaction including the amino group. The Tgel values for the ethanol gel of 1b were markedly improved by the addition of AgNO3, CoCl2 or CdCl2. The detailed examination of a 1b + CoCl2 gel system in ethanol showed that the gel is stabilised by the ‘cross-link’ of 1b molecules by the Co(II)–amino group interaction. This is the first and a convenient method for the metal reinforcement of organic gels.
ABO3 and A1−xCxB1−yDy(O1−zEz)3: review of experimental optimisation of thin film perovskites by high-throughput evaporative physical vapour deposition (2019)

The development of functional perovskites for future technologies can be achieved though the combinatorial synthetic method of evaporative physical vapour deposition (HT-ePVD) which provides a direct low temperature route to anion stoichiometric materials. When combined with the ability to control and vary precisely the composition of thin film libraries of materials, high-throughput methods of screening and characterisation provides a rapid experimental determination of the structure/function relationship. This review of the use of HT-ePVD shows that controlled cationic substitutions in A and/or B sites can easily be explored, as can the effect of anionic substitution. This is exemplified in using this approach for a wide range of perovskite systems, where the tuning of the functional properties through cation substitution has application in a broad range of technologies.
Optimizing queries over multimedia repositories (1996)

Repositories of multimedia objects having multiple types of attributes (e.g., image, text) are becoming increasingly common. A selection on these attributes will typically produce not just a set of objects, as in the traditional relational query model ( filtering ), but also a grade of match associated with each object, indicating how well the object matches the selection condition ( ranking ). Also, multimedia repositories may allow access to the attributes of each object only through indexes. We investigate how to optimize the processing of queries over multimedia repositories. A key issue is the choice of the indexes used to search the repository. We define an execution space that is search-minimal, i.e., the set of indexes searched is minimal. Although the general problem of picking an optimal plan in the search-minimal execution space is NP-hard, we solve the problem efficiently when the predicates in the query are independent. We also show that the problem of optimizing queries that ask for a few top-ranked objects can be viewed, in many cases, as that of evaluating selection conditions. Thus, both problems can be viewed together as an extended filtering problem.
Discovery of a novel regulator of neuroinflammation: differential roles of SNS-1 in experimental autoimmune encephalomyelitis and lipopolysaccharide-induced neuroinflammation (2018)

Background
Radio-photoluminescence of Ag-doped Li3PO4-Al(PO3)3 Glass (2015)

We report a radio-photoluminescence (RPL) oxide glass with a new composition: 30Li3PO4-70Al(PO3)3-0.5Ag2O. The as-prepared sample, prepared by a conventional melt-quenching method, only shows a PL ...
Abstract P6-14-02: A Phase 3 Randomized, Controlled Trial of Myocet, Trastuzumab and Paclitaxel vs. Trastuzumab and Paclitaxel for 1st Line Therapy of HER2+ Metastatic Breast Cancer (2010)

Abstract Background: Myocet™ (M) is a non-pegylated liposomal doxorubicin which exhibits reduced cardiotoxicity as compared to conventional doxorubicin. A phase 1/2 non-randomized multi-site trial combining M, trastuzumab (H) and paclitaxel (T) has resulted in high response rate, prolonged time to progression and improved overall survival, with no clinical cardiac toxicity in patients (pts) with first line metastatic breast cancer (MBC) over-expressing human epidermal growth factor-2neu (HER2+) (Cortes et al Clin Cancer res 2009:15:307). Methods: This multicenter study was designed to demonstrate the efficacy and cardiac safety of M+ H + T vs. the standard of care, H + T, in pts with HER2+ MBC with no prior chemotherapy for MBC. After stratification by hormone receptor status, prior or no prior anthracycline (A) therapy, age ≥50 or &amp;gt;50 y and geography, patients were randomly allocated to receive either M (50 mg/m2 q 3 wks for 6 cycles), H (4 mg/kg loading dose followed by 2 mg/kg q wk) and T (80 mg/m2 q wk) or H + T until progression or toxicity. The primary efficacy outcome is progression-free survival (PFS), as determined by a blinded independent review committee (IRC). The primary safety outcome is the incidence of NYHA class 3 or 4 heart failure or cardiac death, independently adjudicated. Secondary endpoints are overall survival and tumor response, also determined by the IRC according to RECIST. 332 pts were needed to detect a 30% difference in PFS with 80% power. Results: Between 2006 and 2009, 363 HER2+ women from 12 countries were enrolled. Median age is 53 yr (range 22-79); 80% are Caucasian; with ECOG performance status of 0 (62%) and 1 (38%); 42% are ER and/or PR positive; 40% received adjuvant chemotherapy, 24% hormone therapy, and 37% radiotherapy; 33% received prior A, median lifetime cumulativedoxorubicin and epirubicin dose (range) were 240 (45-360) mg/m2 and 360 (69-600) mg/m2, respectively. The final analysis of PFS is scheduled for 3Q10. Conclusions: The safety and efficacy data will be presented at the meeting. Clinical Trials.Gov Identifier: NCT00294996 Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-14-02.
An efficient encoder–decoder model for portrait depth estimation from single images trained on pixel-accurate synthetic data (2021)

Depth estimation from a single image frame is a fundamental challenge in computer vision, with many applications such as augmented reality, action recognition, image understanding, and autonomous driving. Large and diverse training sets are required for accurate depth estimation from a single image frame. Due to challenges in obtaining dense ground-truth depth, a new 3D pipeline of 100 synthetic virtual human models is presented to generate multiple 2D facial images and corresponding ground truth depth data, allowing complete control over image variations. To validate the synthetic facial depth data, we propose an evaluation of state-of-the-art depth estimation algorithms based on single image frames on the generated synthetic dataset. Furthermore, an improved encoder-decoder based neural network is presented. This network is computationally efficient and shows better performance than current state-of-the-art when tested and evaluated across 4 public datasets. Our training methodology relies on the use of synthetic data samples which provides a more reliable ground truth for depth estimation. Additionally, using a combination of appropriate loss functions leads to improved performance than the current state-of-the-art network performances. Our approach clearly outperforms competing methods across different test datasets, setting a new state-of-the-art for facial depth estimation from synthetic data.
Evidence for widespread, severe brain copper deficiency in Alzheimer's dementia (2017)

Datasets comprising simultaneous measurements of many essential metals in Alzheimer's disease (AD) brain are sparse, and available studies are not entirely in agreement. To further elucidate this matter, we employed inductively-coupled-plasma mass spectrometry to measure post-mortem levels of 8 essential metals and selenium, in 7 brain regions from 9 cases with AD (neuropathological severity Braak IV-VI), and 13 controls who had normal ante-mortem mental function and no evidence of brain disease. Of the regions studied, three undergo severe neuronal damage in AD (hippocampus, entorhinal cortex and middle-temporal gyrus); three are less-severely affected (sensory cortex, motor cortex and cingulate gyrus); and one (cerebellum) is relatively spared. Metal concentrations in the controls differed among brain regions, and AD-associated perturbations in most metals occurred in only a few: regions more severely affected by neurodegeneration generally showed alterations in more metals, and cerebellum displayed a distinctive pattern. By contrast, copper levels were substantively decreased in all AD-brain regions, to 52.8-70.2% of corresponding control values, consistent with pan-cerebral copper deficiency. This copper deficiency could be pathogenic in AD, since levels are lowered to values approximating those in Menkes' disease, an X-linked recessive disorder where brain-copper deficiency is the accepted cause of severe brain damage. Our study reinforces others reporting deficient brain copper in AD, and indicates that interventions aimed at safely and effectively elevating brain copper could provide a new experimental-therapeutic approach.
Computational Opportunities In The Estimation Of Free-living Temporal Gait Parameters From Wearable Accelerometry Data (2020)

Wearable accelereometrs are widely used to monitor free-living physical activity (PA) in the variety of epidemiological and clinical studies. Due to a small size, long battery life and low costs their popularity grew exponentially in recent years. This motivates researchers to seek additional utility of free-living accelerometery outside traditional PA measurements. Arguably, the assessment of mobility and gait parameters is one of the most popular and exciting applications of wearable accelerometers. However, because of the sheer size of free-living, sub-second level accelerometry data, the choice of existing analytical methods and the development of new ones is highly limited by the computational capabilities of modern computers and workstations. In this work, we explore possible solutions to this challenge. Namely, multi-core and graphics processing unit (GPU) computing. As a motivating example, we use the Adaptive Empirical Pattern Transformation (ADEPT), an open-source, dictionary-based pattern recognition method dedicated to the segmentation of walking strides in high-density accelerometry data. PURPOSE: We propose to minimize the computational time of the ADEPT algorithm by application of the GPU computing using inexpensive, desktop workstation equipped with the consumer-grade GPU. METHODS: We use data collected on 5 healthy participants equipped with the wrist-worn tri-axial Actigraph GT3X monitor over 48-hour period at sampling frequency of 100Hz. Next, we deploy the ADEPT algorithm on single-core Intel I9-900K CPU, 8-core CPU and Nvidia RTX 2080 GPU and measure total computation time. RESULTS: Average single-core CPU computation time was equal to 607.70 (sd = 0.3), multicore CPU was 344.40 (sd = 0.8) and GPU was 25.52 (sd = 0.07) seconds. GPU enabled computing allowed for nearly 23 times faster computation with respect to single-core and 14 times with respect to multicore processing. CONCLUSIONS: GPU accelerated computing allows for the application of more complex and time-consuming methods in the statistical analysis of high-density accelerometry data collected in free-living settings over multiple days. Additionally, it creates possibilities for scaling-up computationally intensive methods to much larger samples enabling their application in large epidemiological studies.
Hepatocyte Transfection in Small Pigs After Weaning by Hydrodynamic Intraportal Injection of Naked DNA/Minicircle Vectors (2015)

Liver is an attractive organ for gene delivery in order to correct various genetic (metabolic) diseases. Hydrodynamic vein injection of naked DNA/minicircles devoid of viral or plasmid backbones was demonstrated in, for example, murine phenylketonuria to allow sustained therapeutic transduction of hepatocytes. Here we show successful hepatocyte transfusion in domestic small pigs immediately after weaning upon portal vein catheterization and hydrodynamic injection of naked DNA/minicircle vectors expressing the luciferase gene from the CMV or a liver-specific promoter. First, we established a surgical method allowing hydrodynamic portal vein pressurization up to 120 mmHg and infusion of naked DNA in pigs (n = 5) with long-term survival. No acute adverse effects such as changes in liver transaminases or signs of liver cell damage were observed. We then showed efficiency of stable hepatocyte transfection at 10 and 28 days in single experiments (n = 7) where we found that up to 60% of samples (45/75) were polymerase chain reaction (PCR)-positive for minicircle-DNA. Of these samples, 13% of the positive specimen (6/45) showed low but stable luciferase expression when driven by a liver-specific promoter, as well as appropriate copy numbers per diploid genome. In conclusion, we accomplished a safe procedure for stable transfection of liver cells upon hydrodynamic gene delivery using minicircle vectors in small pigs as a prerequisite to potentially treat infants with genetic liver diseases.
Properties of pyranose dehydrogenase purified from the litter‐degrading fungus Agaricus xanthoderma (2007)

We purified an extracellular pyranose dehydrogenase (PDH) from the basidiomycete fungus Agaricus xanthoderma using ammonium sulfate fractionation and ion-exchange and hydrophobic interaction chromatography. The native enzyme is a monomeric glycoprotein (5% carbohydrate) containing a covalently bound FAD as its prosthetic group. The PDH polypeptide consists of 575 amino acids and has a molecular mass of 65 400 Da as determined by MALDI MS. On the basis of the primary structure of the mature protein, PDH is a member of the glucose-methanol-choline oxidoreductase family. We constructed a homology model of PDH using the 3D structure of glucose oxidase from Aspergillus niger as a template. This model suggests a novel type of bi-covalent flavinylation in PDH, 9-S-cysteinyl, 8-alpha-N3-histidyl FAD. The enzyme exhibits a broad sugar substrate tolerance, oxidizing structurally different aldopyranoses including monosaccharides and oligosaccharides as well as glycosides. Its preferred electron donor substrates are D-glucose, D-galactose, L-arabinose, and D-xylose. As shown by in situ NMR analysis, D-glucose and D-galactose are both oxidized at positions C2 and C3, yielding the corresponding didehydroaldoses (diketoaldoses) as the final reaction products. PDH shows no detectable activity with oxygen, and its reactivity towards electron acceptors is rather limited, reducing various substituted benzoquinones and complexed metal ions. The azino-bis-(3-ethylbenzthiazolin-6-sulfonic acid) cation radical and the ferricenium ion are the best electron acceptors, as judged by the catalytic efficiencies (k(cat)/K(m)). The enzyme may play a role in lignocellulose degradation.
Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery* (2015)

Circulating O-glycoproteins shed from cancer cells represent important serum biomarkers for diagnostic and prognostic purposes. We have recently shown that selective detection of cancer-associated aberrant glycoforms of circulating O-glycoprotein biomarkers can increase specificity of cancer biomarker assays. However, the current knowledge of secreted and circulating O-glycoproteins is limited. Here, we used the COSMC KO "SimpleCell" (SC) strategy to characterize the O-glycoproteome of two gastric cancer SimpleCell lines (AGS, MKN45) as well as a gastric cell line (KATO III) which naturally expresses at least partially truncated O-glycans. Overall, we identified 499 O-glycoproteins and 1236 O-glycosites in gastric cancer SimpleCells, and a total 47 O-glycoproteins and 73 O-glycosites in the KATO III cell line. We next modified the glycoproteomic strategy to apply it to pools of sera from gastric cancer and healthy individuals to identify circulating O-glycoproteins with the STn glycoform. We identified 37 O-glycoproteins in the pool of cancer sera, and only nine of these were also found in sera from healthy individuals. Two identified candidate O-glycoprotein biomarkers (CD44 and GalNAc-T5) circulating with the STn glycoform were further validated as being expressed in gastric cancer tissue. A proximity ligation assay was used to show that CD44 was expressed with the STn glycoform in gastric cancer tissues. The study provides a discovery strategy for aberrantly glycosylated O-glycoproteins and a set of O-glycoprotein candidates with biomarker potential in gastric cancer.
Determining inertial measurement unit placement for estimating human trunk sway while standing, walking and running (2015)

Inertial measurement units (IMU) are often used to estimate medial-lateral (M/L) trunk sway for assessing and treating gait disorders, and IMU sensor placement is an important factor effecting estimation accuracy. This study tracked multi-segment spine movements during standing and ambulation tasks to determine optimal IMU placement. Ten young healthy subjects, wearing markers placed along the spine, left/right acromion, and left/right posterior superior iliac spine performed standing and walking trials in a motion capture laboratory. Results showed that movement at the spine location T7-T8 most closely matched the clinical definition of M/L trunk sway for standing trials (0.5 deg error) and at the spine location T9-T10 for walking trials (1.0 deg error), while movement at the lower spine L2-L4 tended to be the least accurate for standing and ambulation tasks (1.5 deg error and 4.0 deg error, respectively). Based on these results, a second study was performed to develop and validate a trunk sway estimation algorithm during walking trials with a single optimally-placed IMU. IMU trunk sway estimation was compared to the clinical definition of trunk sway from motion capture markers and showed root-mean-square errors of 2.5 deg and peak trunk sway errors of 2.0 deg. The results of this study suggest that IMUs should be placed on the mid-back to reduce errors associated with spine movements not matching clinically-defined M/L trunk motion.