gebhart/patrepeval huggingface dataset:
Participation of macrophages in atherosclerotic lesion morphology in LDLr−/− mice (2004)

Lystbeige (beige) mice crossed with LDL receptor-deficient (LDLr-/-) mice had a distinct atherosclerotic lesion morphology that was not observed in LDLr-/- mice. This morphology is often associated with a stable plaque phenotype. We hypothesized that macrophage expression of the beige mutation accounted for this distinct morphology. Cultured bone marrow-derived macrophages from LDLr-/- and beige,LDLr-/- mice were compared for their ability to accumulate cholesterol, efflux cholesterol, migrate in response to chemotactic stimuli through Matrigel-coated membranes, and express matrix metalloproteinase 9 (MMP9). No differences in cholesterol metabolism were identified. Beige,LDLr-/- macrophage invasion in vitro appeared to be less than LDLr-/- macrophage invasion but did not achieve significance. Nevertheless, tumor necrosis factor-alpha-induced MMP9 expression, secretion, and enzymatic activity of beige,LDLr-/- macrophages were all significantly decreased compared with those of LDLr-/- macrophages (P < 0.05). For in vivo analyses of macrophage function, bone marrow transplantation (BMT) studies were performed. LDLr-/- mice and beige,LDLr-/- mice were irradiated and reconstituted with wild-type or beige bone marrow from mice expressing green fluorescent protein (GFP). Identification of GFP cells provided for direct identification of donor-derived cells within lesions. Only expression of the beige mutation in the BMT recipients altered the macrophage location and collagen content of the lesions. These results suggested that impaired macrophage function by itself did not account for the stable lesion morphology of beige,LDLr-/- double-mutant mice.
Investigation of the dosimetric characteristics of PRESAGE<sup>TM</sup> (2006)

In this work we perform a detailed investigation of the fundamental dosimetric characteristics of PRESAGETM, to determine its potential for dosimetry. A common problem encountered when attempting to evaluate a new material, is how to efficiently evaluate the large multitude of potential mechanisms and response-characteristics that may affect the practicality and accuracy of that material for dosimetry. We introduce a new method designed to enable rapid, accurate and convenient evaluation of any material which has an optical dose-response, and can be formed into columns of precise dimension (e.g. spectro-photometric cuvettes). The method is also optimised to enable evaluation of dosimetric characteristics with the minimum volume of material, to minimise cost, and problems associated to storage, transportation etc.
High performance database logging using storage class memory (2011)

Storage class memory (SCM), a new generation of memory technology, offers non-volatility, high-speed, and byte-addressability, which combines the best properties of current hard disk drives (HDD) and main memory. With these extraordinary features, current systems and software stacks need to be redesigned to get significantly improved performance by eliminating disk input/output (I/O) barriers; and simpler system designs by avoiding complicated data format transformations. In current DBMSs, logging and recovery are the most important components to enforce the atomicity and durability of a database. Traditionally, database systems rely on disks for logging transaction actions and log records are forced to disks when a transaction commits. Because of the slow disk I/O speed, logging becomes one of the major bottlenecks for a DBMS. Exploiting SCM as a persistent memory for transaction logging can significantly reduce logging overhead. In this paper, we present the detailed design of an SCM-based approach for DBMSs logging, which achieves high performance by simplified system design and better concurrency support. We also discuss solutions to tackle several major issues arising during system recovery, including hole detection, partial write detection, and any-point failure recovery. This new logging approach is used to replace the traditional disk based logging approach in DBMSs. To analyze the performance characteristics of our SCM-based logging approach, we implement the prototype on IBM SolidDB. In common circumstances, our experimental results show that the new SCM-based logging approach provides as much as 7 times throughput improvement over disk-based logging in the Telecommunication Application Transaction Processing (TATP) benchmark.
Specific inhibition of HIV-1 coreceptor activity by synthetic peptides corresponding to the predicted extracellular loops of CCR5 (2003)

We used synthetic peptides to the extracellular loops (ECLs) of CCR5 to examine inhibitory effects on HIV infection/fusion with primary leukocytes and cells expressing recombinant CCR5. We show for the first time that peptides derived from the first, second, or third ECL caused dose-dependent inhibition of fusion and infection, although with varying potencies and specificities for envelope glycoproteins (Envs) from different strains. The first and third ECL peptides inhibited Envs from the R5 Ba-L strain and the R5X4 89.6 strain, whereas the second ECL peptide inhibited Ba-L but not 89.6 Env. None of the peptides affected fusion mediated by Env from the X4 LAV strain. Fusion mediated by Envs from several primary HIV-1 isolates was also inhibited by the peptides. These findings suggest that various HIV-1 strains use CCR5 domains in different ways. Experiments involving peptide pretreatment and washing, modulation of the expression levels of Env and CCR5, analysis of CCR5 peptide effects against different coreceptors, and inhibition of radiolabeled glycoprotein (gp) 120 binding to CCR5 suggested that the peptide-blocking activities reflect their interactions with gp120. The CCR5-derived ECL peptides thus provide a useful approach to analyze structure-function relationships involved in HIV-1 Env-coreceptor interactions and may have implications for the design of drugs that inhibit HIV infection.
ChemInform Abstract: Reaction of Thiazolo(3,2‐a)benzimidazol‐3‐one with Electrophiles. (1989)

Abstract A known reaction of (I) is extended to other benzaldehydes such as (II) (→ (III), no further details given).
Inhibition of growth of experimental prostate cancer with sustained delivery systems (microcapsules and microgranules) of the luteinizing hormone-releasing hormone antagonist SB-75. (1991)

Inhibitory effects of the sustained delivery systems (microcapsules and microgranules) of a potent antagonist of luteinizing hormone-releasing hormone N-Ac-[3-(2-naphthyl)-D-alanine1, 4-chloro-D-phenylalanine2, 3-(3-pyridyl)-D-alanine3, D-citrulline6, D-alanine10]LH-RH (SB-75) on the growth of experimental prostate cancers were investigated. In the first experiment, three doses of a microcapsule preparation releasing 23.8, 47.6, and 71.4 micrograms of antagonist SB-75 per day were compared with microcapsules of agonist [D-Trp6]LH-RH liberating 25 micrograms/day in rats bearing Dunning R3327H transplantable prostate carcinoma. During 8 weeks of treatment, tumor growth was decreased by [D-Trp6]LH-RH and all three doses of SB-75 as compared to untreated controls. The highest dose of SB-75 (71.4 micrograms/day) caused a greater inhibition of prostate cancer growth than [D-Trp6]LH-RH as based on measurement of tumor volume and percentage change in tumor volume. Doses of 23.8 and 47.6 micrograms of SB-75 per day induced a partial and submaximal decrease, respectively, in tumor weight and volume. Tumor doubling time was the longest (50 days) with the high dose of SB-75 vs. 15 days for controls. The body weights were unchanged. The weights of testes, seminal vesicles, and ventral prostate were greatly reduced in all three groups that received SB-75, and testosterone levels were decreased to nondetectable values in the case of the two higher doses of SB-75. LH levels were also diminished. Similar results were obtained in the second experiment, in which the animals were treated for a period of 8 weeks with microgranules of SB-75. Therapy with microgranules of SB-75 significantly decreased tumor growth as measured by the final tumor volume, the percentage change from the initial tumor volume, and the reduction in tumor weight. The results indicate that antagonist SB-75, released from sustained delivery systems, can produce a state of chemical castration and effectively inhibit the growth of experimental prostate cancers. The efficacy of the antagonist SB-75 in inhibiting androgen-dependent Dunning prostatic carcinoma and the absence of side effects suggest its possible usefulness for the treatment of hormone-sensitive tumors.
A Mouse Model of Blast Injury to Brain: Initial Pathological, Neuropathological, and Behavioral Characterization (2011)

The increased use of explosives in recent wars has increased the number of veterans with blast injuries. Of particular interest is blast injury to the brain, and a key question is whether the primary overpressure wave of the blast is injurious or whether brain injury from blast is mostly due to secondary and tertiary effects. Using a shock tube generating shock waves comparable to open-field blast waves, we explored the effects of blast on parenchymatous organs of mice with emphasis on the brain. The main injuries in nonbrain organs were hemorrhages in the lung interstitium and alveolar spaces and hemorrhagic infarcts in liver, spleen, and kidney. Neuropathological and behavioral outcomes of blast were studied at mild blast intensity, that is, 68 ± 8 kPag (9.9 ± 1.2 psig) static pressure, 103 kPag (14.9 psig) total pressure and 183 ± 14 kPag (26.5 ± 2.1 psig) membrane rupture pressure. Under these conditions, we observed multifocal axonal injury, primarily in the cerebellum/brainstem, the corticospinal system, and the optic tract. We also found prolonged behavioral and motor abnormalities, including deficits in social recognition and spatial memory and in motor coordination. Shielding of the torso ameliorated axonal injury and behavioral deficits. These findings indicate that long CNS axon tracts are particularly vulnerable to the effects of blast, even at mild intensities that match the exposure of most veterans in recent wars. Prevention of some of these neurological effects by torso shielding may generate new ideas as to how to protect military and civilian populations in blast scenarios.
Effects of scopolamine upon delayed radial-arm maze performance in rats. (1991)

Behavioral impairment induced by the muscarinic anticholinergic drug, scopolamine (SCP) has been widely used to make preclinical evaluation of nootropic drugs. To further investigate the disruptive effect of SCP on memory-related behavior, male Wistar-Imamichi strain rats were tested in the 8-arm radial maze task with a delay interval between choices 4 and 5. In this task, the animals were first allowed to obtain 4 food rewards out of 8 arms and then removed from the maze. They were replaced on the maze to collect the remaining 4 pellets after a delay interval, during which they were kept in their home cages. In experiment 1, a 1-6 hr delay interval was imposed. SCP (0.5 mg/kg, i.p.) was administered immediately after choice 4. In experiment 2, a delay interval was always 4 hr, but SCP was administered 0-2 hr after choice 4. In both experiments, SCP significantly reduced the number of correct choices in choices 5-8, but did not show any effects depending on delay intervals or drug-administration time. These results suggest that the performance deficits induced by SCP might be due to its effects on the primary stage of information processing rather than those on the consolidation or storage process of memory.
A Novel Splice Variant of Human TGF-β Type II Receptor Encodes a Soluble Protein and Its Fc-Tagged Version Prevents Liver Fibrosis in vivo (2021)

We describe, for the first time, a new splice variant of the human TGF-β type II receptor (TβRII). The new transcript lacks 149 nucleotides, resulting in a frameshift and the emergence of an early stop codon, rendering a truncated mature protein of 57 amino acids. The predicted protein, lacking the transmembrane domain and with a distinctive 13-amino-acid stretch at its C-terminus, was named TβRII-Soluble Endogenous (TβRII-SE). Binding predictions indicate that the novel 13-amino-acid stretch interacts with all three TGF-β cognate ligands and generates a more extensive protein-protein interface than TβRII. TβRII-SE and human IgG1 Fc domain were fused in frame in a lentiviral vector (Lv) for further characterization. With this vector, we transduced 293T cells and purified TβRII-SE/Fc by A/G protein chromatography from conditioned medium. Immunoblotting revealed homogeneous bands of approximately 37 kDa (reduced) and 75 kDa (non-reduced), indicating that TβRII-SE/Fc is secreted as a disulfide-linked homodimer. Moreover, high-affinity binding of TβRII-SE to the three TGF-β isoforms was confirmed by surface plasmon resonance (SPR) analysis. Also, intrahepatic delivery of Lv.TβRII-SE/Fc in a carbon tetrachloride-induced liver fibrosis model revealed amelioration of liver injury and fibrosis. Our results indicate that TβRII-SE is a novel member of the TGF-β signaling pathway with distinctive characteristics. This novel protein offers an alternative for the prevention and treatment of pathologies caused by the overproduction of TGF-β ligands.
Clinical application of PET for the evaluation of brain tumors. (1991)

The combination of FDG and PET has demonstrated clinical utility in the evaluation of patients with brain tumors. At the time of diagnosis, FDG PET provides information concerning the degree of malignancy and patient prognosis. After therapy, FDG PET is able to assess persistence of tumor, determine degree of malignancy, monitor progression, differentiate recurrence from necrosis, and assess prognosis. Other studies using PET provide information that may be clinically useful. Determination of tumor blood flow and permeability of the blood-brain barrier may help in the selection of appropriate therapy. Amino acid imaging using 11C-methionine is being evaluated in patients with brain tumors and provides different information than FDG imaging.
Facile preparation of polyaniline nanofibers modified bentonite nanohybrid for gas sensor application (2013)

We report the preparation of polyaniline (PAni) nanofibers by in situ intercalative polymerization of anilinium salt absorbed onto the nanoclay layers and modification of bentonite to an efficient nanohybrid gas sensor. The nanohybrid exhibited stable dispersion in different organic solvents like tetrahydrofuran, dimethyl acetamide and dimethyl sulphoxide. The Fourier transform infrared (FTIR) spectroscopic analysis indicated the formation of the benzenoid-quinoid structure of PAni in the nanohybrid. The wide angle X-ray diffraction study confirmed the crystallinity of the PAni nanofibers and the increase of d-spacing of the clay gallery on formation of the nanohybrid. The formation of the PAni nanofibers within the porous nanoclay layer was confirmed by the field-emission scanning electron microscopy. The sensitivity of the nanohybrid-based gas sensor towards toxic gases viz., acetone, benzene, ethanol and toluene was investigated. The nanohybrid gas sensor exhibited a high sensitivity to acetone compared to benzene, ethanol and toluene using ruthenium electrode than the silver electrode. Therefore, the prepared nanohybrid has the potential to be used as a promising gas sensor for the detection of toxic gases.
Serum Response Factor-dependent Regulation of the Smooth Muscle Calponin Gene (2000)

Smooth muscle calponin is a multifunctional, thin filament-associated protein whose expression is restricted to smooth muscle cell lineages in developing and postnatal tissues. Although the physiology of smooth muscle calponin has been studied extensively, the cis-elements governing its restricted pattern of expression have yet to be identified. Here we report on smooth muscle-specific enhancer activity within the first intron of smooth muscle calponin. Sequence analysis revealed a proximal consensus intronic CArG box and two distal intronic CArG-like elements, each of which bound recombinant serum response factor (SRF) as well as immunoreactive SRF from smooth muscle nuclear extracts. Site-directed mutagenesis studies suggested that the consensus CArG box mediates much of the intronic enhancer activity; mutating all three CArG elements abolished the ability of SRF to confer enhancer activity on the smooth muscle calponin promoter. Cotransfecting a dominant-negative SRF construct attenuated smooth muscle-specific enhancer activity, and transducing smooth muscle cells with adenovirus harboring the dominant-negative SRF construct selectively reduced steady-state expression of endogenous smooth muscle calponin. These results demonstrate an important role for intronic CArG boxes and the SRF protein in the transcriptional control of smooth muscle calponin in vitro.
A Phase II Trial of a New Combination Chemotherapy (Cisplatin, Bleomycin, VP-16 and Methylprednisolone) in Advanced Recurrent Squamous Cell Carcinoma of the Head and Neck (1988)

this therapeutic regimen improves the CR rate and survival time with a tolerable toxicity.
Robust range alignment algorithm via Hough transform in an ISAR imaging system (1995)

The inverse synthetic aperture radar (ISAR) algorithm for imaging objects moving in a straight line requires range alignment as a preprocessing step since scatterers migrate through the various range bins. The conventional correlation alignment method fails when applied in ground scenarios like an airport due to the clutter environment. A procedure using Hough Transform (HT) alignment is presented which overcomes this disadvantage and provides information for clutter elimination.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019)

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
Action Recognition using Visual Attention (2015)

We propose a soft attention based model for the task of action recognition in videos. We use multi-layered Recurrent Neural Networks (RNNs) with Long Short-Term Memory (LSTM) units which are deep both spatially and temporally. Our model learns to focus selectively on parts of the video frames and classifies videos after taking a few glimpses. The model essentially learns which parts in the frames are relevant for the task at hand and attaches higher importance to them. We evaluate the model on UCF-11 (YouTube Action), HMDB-51 and Hollywood2 datasets and analyze how the model focuses its attention depending on the scene and the action being performed.
Modification of the Dittmer-Lester reagent for the detection of phospholipid derivatives on thin-layer chromatograms. (1979)

A simple modification of the Dittmer-Lester reagent is described that allow the detection of phospholipid derivatives at very low concentrations on silica gel and reversed-phase thin-layer plates. This modification, which involves the addition of acetic acid to the mixture, permits the observation of sharp blue spots on a white background. The specificity and sensitivity of the spray are discussed.
An SIW-Based Large-Scale Corporate-Feed Array Antenna (2015)

A 16 × 16 substrate-integrated waveguide (SIW) cavity-backed array antenna is proposed in this paper. The array consists of two layers. The top layer employs novel SIW-based subarrays with a compact size. The bottom layer is an 8 × 8 SIW corporate-feed network to feed the subarrays. The Chebyshev amplitude weighting is employed in the feed network, which substantially reduces the side lobe level (SLL). The array antenna is fabricated using low-cost printed circuit board technology. The experimental results show that the proposed array antenna has a large bandwidth of 15% from 18.5 to 21.5 GHz with a peak gain of 29.1 dBi at 20.5 GHz. Across the entire band, high radiation efficiency above 62% and a low SLL below -17 dB are realized. The design principle can be used as a guidance for largescale planar array antenna design and the proposed antenna can be used as a receiving antenna located on the ground in satellite communication systems.
Deep Learning Visualization for Underspecification Analysis in Product Design Matching Model Development (2021)

In machine learning model development, the best model for deployment is usually chosen among the models trained during hyperparameter tuning based on the performance on the test data. However, with the underspecification problem, this practice can be shortsighted as the solution may not perform well in the production environment. Hence, developers need a better tool to comprehend model results in both development and production environments to guide the next iteration of development. In this work, we present the novel visualization system for tracking model results with underspecification analysis in mind. In our evaluation, we show both qualitative and quantitative analysis of model development for product design matching problem and the results suggest that our method helps developers gain a better understanding of the models being developed, resulting in better performance in production. Finally, this visualization has been used at Wazzadu.com to help developers make decisions more effectively in model development.
Organic-Guest/Microporous-Host Composite Materials Obtained by Diffusion from a Supercritical Solution (1998)

Diffusion from supercritical CO2 into porous zeolite is demonstrated to be an effective method for incorporating organic compounds into the zeolite's open framework. The advantages of supercritical fluid technology over conventional techniques are described, which include enhanced transport coefficient values. The Figure shows the hydrothermally precipitated aluminophosphate hydrate, VPI-5, used in the investigation.