gebhart/patrepeval huggingface dataset:
Identifying and quantifying printed circuit board inductance (2002)

The concepts of inductance and partial inductance play a key role in printed circuit board (PCB) modeling. The inductance of the signal path is an important parameter in high-speed signal integrity calculations. Delta I noise modeling, crosstalk calculations, and common-mode source identification all rely heavily on accurate estimations of the partial inductance associated with traces, vias, and signal return paths on printed circuit boards. The paper begins by identifying and quantifying the parameters that affect the inductance of typical PCB geometries. Closed-form equations are provided for estimating the partial inductances of simple trace, via, and ground plane configurations. Finally, the issue of current "crowding" around via connections in planes and its affect on the partial inductance of the plane is addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Discovery and Characterization of Small Molecule Inhibitors of the BET Family Bromodomains (2011)

Epigenetic mechanisms of gene regulation have a profound role in normal development and disease processes. An integral part of this mechanism occurs through lysine acetylation of histone tails which are recognized by bromodomains. While the biological and structural characterization of many bromodomain containing proteins has advanced considerably, the therapeutic tractability of this protein family is only now becoming understood. This paper describes the discovery and molecular characterization of potent (nM) small molecule inhibitors that disrupt the function of the BET family of bromodomains (Brd2, Brd3, and Brd4). By using a combination of phenotypic screening, chemoproteomics, and biophysical studies, we have discovered that the protein-protein interactions between bromodomains and acetylated histones can be antagonized by selective small molecules that bind at the acetylated lysine recognition pocket. X-ray crystal structures of compounds bound into bromodomains of Brd2 and Brd4 elucidate the molecular interactions of binding and explain the precisely defined stereochemistry required for activity.
Ischemic Stroke Injury Is Reduced in Mice Lacking a Functional NADPH Oxidase (1997)

Brain injury was reduced in mice lacking a functional NADPH oxidase in both the central nervous system and peripheral leukocytes, suggesting a pivotal role for the NADPH oxidase in the pathogenesis of ischemia-reperfusion injury in the brain.
Tissue-Specific and Developmentally Regulated Expression of a Cluster of Tandemly Arrayed Cell Wall-Associated Kinase-Like Kinase Genes in Arabidopsis (2003)

The Arabidopsis cell wall-associated kinase (WAK) and WAK-like kinase (WAKL) family of receptor-like kinase genes encodes transmembrane proteins with a cytoplasmic serine/threonine kinase domain and an extracellular region containing epidermal growth factor-like repeats. Previous studies have suggested that some WAK members are involved in plant defense and heavy metal responses, whereas others are required for cell elongation and plant development. The WAK/WAKL gene family consists of 26 members in Arabidopsis and can be divided into four groups. Here, we describe the characterization of group 2 members that are composed of a cluster of seven tandemly arrayed WAKL genes. The predicted WAKL proteins are highly similar in their cytoplasmic region but are more divergent in their predicted extracellular ligand-binding region. WAKL7 encodes a truncated WAKL isoform that is predicted to be secreted from the cytoplasm. Ratios of nonsynonymous to synonymous substitutions suggest that the extracellular region is subject to diversifying selection. Comparison of the WAKL and WAK gene clusters suggests that they arose independently. Protein gel-blot and immunolocalization analyses suggest that WAKL6 is associated with the cell wall. Histochemical analyses of WAKL promoters fused with the beta-glucuronidase reporter gene have shown that the expressions of WAKL members are developmentally regulated and tissue specific. Unlike WAK members whose expressions were found predominately in green tissues, WAKL genes are highly expressed in roots and flowers. The expression of WAKL5 and WAKL7 can be induced by wounding stress and by the salicylic acid analog 2,6-dichloroisonicotinic acid in an nonexpressor of pathogenesis-related gene 1-dependent manner, suggesting that they, like some WAK members, are wound inducible and can be defined as pathogenesis-related genes.
A heterophilic adhesion mechanism for platelet/endothelial cell adhesion molecule 1 (CD31). (1992)

The molecular nature of cell adhesion mediated by platelet/endothelial cell adhesion molecule 1 (PECAM-1; CD31) was examined using stably transfected L cells in a PECAM-dependent aggregation assay. This adhesion was temperature sensitive and divalent cation dependent, with Mg2+ supporting aggregation to a greater degree than Ca2+. PECAM-dependent aggregation was heterophilic: PECAM-1 transfectants bound as readily to control-transfected L cells as to other PECAM-1 transfectants, demonstrating that a molecule endogenously expressed on the L cells serves as the ligand for PECAM in this system and presumably substitutes for the natural human ligand.
Apoptosis in seborrheic keratoses: an open door to a new dermoscopic score (2012)

The aetiology of seborrheic keratoses (SK), the most common benign epithelial tumours, and any relationship with malignancy are not yet known. As a protective anti-cancer mechanism, apoptosis reflects cellular loss as a reaction to proliferative activity. The objective of this study was to quantify apoptosis in different SK types (acanthotic, hyperkeratotic, reticulated, irritated and clonal) and correlate the dermoscopic picture with apoptosis rate. After a qualitative and quantitative analysis of dermoscopic images, we defined a new quantitative dermoscopic score (C3V2F, crypts, millia cysts, colours, hairpin vessels, irregular vessels, fissures) from 0 to 22, which enabled us to establish cut-offs correlating with apoptosis rates. All five SK forms were associated with lower apoptosis rates compared with normal skin. A C3V2F score >10 and greater number of crypts and colours reflected a higher apoptosis rate, which implies a benign character of evolution. In contrast, the presence of irregular vessels on more than 50% of the lesion surface implied a lower rate of apoptosis and probably associated with a risk of malignant transformation. On the basis of dermoscopic information, we used multiple regression to establish a model for estimating the rate of apoptosis with a 0.7 prediction interval (approximately 1S.D.). The new C3V2F score could be valuable for the clinical evaluation of possible SK prognosis and decisions regarding excision.
Immunoprophylaxis with palivizumab, a humanized respiratory syncytial virus monoclonal antibody, for prevention of respiratory syncytial virus infection in high risk infants: a consensus opinion (1999)

MEISSNER, H. CODY MD; WELLIVER, ROBERT C. MD; CHARTRAND, STEPHAN A. MD; LAW, BARBARA J. MD; WEISMAN, LEONARD E. MD; DORKIN, HENRY L. MD; RODRIGUEZ, WILLIAM J. MD Author Information
Vector quantization of images using modified adaptive resonance algorithm for hierarchical clustering (2001)

A modified adaptive resonance theory (ART2) learning algorithm, which we employ in this paper, belongs to the family of NN algorithms whose main goal is the discovery of input data clusters, without considering their actual size. This feature makes the modified ART2 algorithm very convenient for image compression tasks, particularly when dealing with images with large background areas containing few details. Moreover, due to the ability to produce hierarchical quantization (clustering), the modified ART2 algorithm is proved to significantly reduce the computation time required for coding, and therefore enhance the overall compression process. Examples of the results obtained are presented, suggesting the benefits of using this algorithm for the purpose of VQ, i.e., image compression, over the other NN learning algorithms.
Effect of recombinant human macrophage colony-stimulating factor 1 on immunopathology of experimental brucellosis in mice (1992)

Brucella abortus injected into CBA mice replicated primarily in the spleen and liver, reaching a peak bacterial count in both organs about 7 days postinfection. The organism was eliminated from the liver but declined to a chronic phase in the spleen. The infection caused hepatosplenomegaly. An influx of macrophages into the two organs was monitored by quantitative Northern (RNA blot) analysis of the macrophage-specific marker lysozyme mRNA. Lysozyme mRNA was detectable in spleen and increased three- to fourfold during infection. In liver, lysozyme mRNA was initially undetectable, but at about the peak of infection it reached a level comparable to that in the spleen. Macrophage colony-stimulating factor 1 (CSF-1) has been reported to be elevated in the circulation of animals infected with B. abortus and is known to stimulate monocytopoiesis. To investigate the role of CSF-1 in pathogenesis, we studied the effect of further increasing the CSF-1 concentration by administration of recombinant human CSF-1. Since the infection is characterized by several distinct phases, recombinant human CSF-1 was administered at defined times relative to these phases. Pronounced effects were observed only when CSF-1 administration was begun during the developing acute phase. The consequences were decreased bacterial numbers in the spleen but an increase in the liver, reduced antibody generation, and increased hepatosplenomegaly. A feature of many chronic intracellular infections is immunosuppression. B. abortus caused a substantial diminution of responsiveness of spleen cells to T-cell mitogens, particularly concanavalin A. This action was mimicked by CSF-1 treatment of the animals prior to spleen cell isolation. The results suggest that CSF-1 plays a role in macrophage recruitment in brucellosis and that recruited macrophages contribute to the immunopathology and immunosuppression.
New Efficient Synthesis of 3(5)-Carbomethoxy-4-Aryl Pyrazoles from 3-Aryl-2,3-Dehydroamino Acid Derivatives (1987)

Abstract 3(5)-Carbomethoxy-4-arylpyrazoles can be easily obtained by aromatization with boron trifluoride etherate of 4-aryl-3-acetamido(or benzamido)-3-carbo-methoxy-Δ-pyrazolines synthesized by 1,3-dipolar cyclo addition of diazomethane with 3-aryl-2,3-dehydroamino acid derivatives.
G-protein-coupled Receptor Rhodopsin Regulates the Phosphorylation of Retinal Insulin Receptor (2007)

We have shown previously that phosphoinositide 3-kinase in the retina is activated in vivo through light-induced tyrosine phosphorylation of the insulin receptor (IR). The light effect is localized to photoreceptor neurons and is independent of insulin secretion (Rajala, R. V., McClellan, M. E., Ash, J. D., and Anderson, R. E. (2002) J. Biol. Chem. 277, 43319-43326). These results suggest that there exists a cross-talk between phototransduction and other signal transduction pathways. In this study, we examined the stage of phototransduction that is coupled to the activation of the IR. We studied IR phosphorylation in mice lacking the rod-specific alpha-subunit of transducin to determine if phototransduction events are required for IR activation. To confirm that light-induced tyrosine phosphorylation of the IR is signaled through bleachable rhodopsin, we examined IR activation in retinas from RPE65(-/-) mice that are deficient in opsin chromophore. We observed that IR phosphorylation requires the photobleaching of rhodopsin but not transducin signaling. To determine whether the light-dependent activation of IR is mediated through the rod or cone transduction pathway, we studied the IR activation in mice lacking opsin, a mouse model of pure cone function. No light-dependent activation of the IR was found in the retinas of these mice. We provide evidence for the existence of a light-mediated IR pathway in the retina that is different from the known insulin-mediated pathway in nonneuronal tissues. These results suggest that IR phosphorylation in rod photoreceptors is signaled through the G-protein-coupled receptor rhodopsin. This is the first study demonstrating that rhodopsin can initiate signaling pathway(s) in addition to its classical phototransduction.
Amplification of 11q13 in ovarian carcinoma (2008)

Amplification at the 11q13 locus is commonly observed in breast, ovarian, head and neck, oral, and esophageal cancer. Studies of this region led to the identification of multiple amplicons containing several potential oncogenes including EMSY, PAK1, RSF1, and GAB2. Here, we investigate the amplification of the above four genes and their prognostic significance in histologically and clinically defined subsets of ovarian cancer. Amplification of all four genes was assessed by fluorescent in situ hybridization in tissue microarrays containing 538 clinically annotated ovarian carcinomas with 12 years of follow-up data. Overall, for the entire cohort, EMSY was amplified in 44 (16%) of 269 cases, PAK1 was amplified in 38 (15%) of 255 cases, RSF1 was amplified in 37 (12%) of 310 cases, and GAB2 was amplified in 41 (16%) of 255 cases. Amplification of EMSY, PAK1, RSF1, and GAB2 were all highly correlated with each other and with a serous histology. Univariate survival analysis showed that tumors with EMSY and RSF1 amplification were associated with a significantly worse outcome. A molecular inversion probe array was then used to study the 11q13 amplicon in 33 high grade serous carcinomas. The core of the amplicon mapped to a 6-Mb region encompassing EMSY, PAK1, RSF1, and GAB2. However, a second more telomeric amplicon was also observed for which no candidate genes have been identified. In summary, amplification of these four putative oncogenes from 11q13 in early ovarian cancer is associated with a serous histology and in the case of EMSY and RSF1 a poor outcome. These findings support the hypothesis that the11q13 amplicon in ovarian cancer is likely driven by a cassette of genes rather than by a single oncogene. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
High quality Fe-doped semi-insulating InP epitaxial layers grown by low-pressure organometallic vapor phase epitaxy using tertiarybutylphosphine (1991)

High quality Fe-doped semi-insulating InP epitaxial layers were grown by low-pressure organometallic vapor phase epitaxy using tertiarybutylphosphine (TBP) and triethylindium (TEI) as the reactant sources. Semi-insulating InP epitaxial layers with specular surface morphology and low defect density were obtained at TBP partial pressure higher than 0.38 Torr. Electrical measurements on these layers showed the resistivity of TBP-grown materials to be comparable to that of PH3-grown materials over a measurement temperature range of 25 to 110 °C. A premature reaction between TEI and TBP was observed upstream from the substrate in which things such as TEI:TBP adducts and/or polymers could have been formed. This reaction occurred under low pressure, high gas flow conditions which effectively suppressed analogous reactions for TEI:PH3. As a result, the growth rate of Fe-doped semi-insulating InP layers grown at low pressure with TBP in our reactor decreased by 35% as the V/III ratio was increased from 15 to 46.
The RNA Modification Database: 1999 update (1999)

The RNA Modification Database (http://medlib.med.utah.edu/RNAmods/) provides a comprehensive listing of naturally modified nucleosides in RNA. Each file includes: chemical structure; common name and symbol; type(s) of RNA in which found and corresponding phylogenetic distribution; Chemical s registry number and index name; and initial literature citations for structure characterization and chemical synthesis. New features include capability to search database files by name or substructural features, modifications in tmRNA, and links to related data and sites.
Magnetic circular dichroism studies on the active-site flavin of lipoamide dehydrogenase (1980)

The magnetic circular dichroic (MCD) spectra of oxidized and reduced flavins are recorded in various solvents. They are shown to be sensitive to flavin environment. The MCD spectra of oxidized and reduced lipoamide dehydrogenase are reported. In the oxidized enzyme the sign of the B term associated with the 27 000-cm-1 band is reversed from free flavins. This is attributed to interaction of the disulfide with the short-axis dipole of FAD. The sign reversal is also present in a closely related disulfide enzyme, glutathione reductase, but absent in glucose oxidase. In the half-reduced enzyme, the appearance of an A term at 18 180 cm-1 is attributable to a charge-transfer complex with a thiolate anion as donor. Insensitivity of the term's energy and intensity to the redox state of flavin suggests that a protein residue may accept or stabilize the thiolate charge transfer.
Gabapentin in the prophylaxis of chronic daily headache (2003)

Gabapentin represents a therapeutic option for chronic daily headache.
<title>Issues in mobile robotics: the unmanned ground vehicle program teleoperated vehicle</title> (1991)

Key system and supporting technology issues associated with the design and development of effective general-purpose unmanned mobile robots for operation in unstructured outdoor environments are examined within the context of an advanced telerobotic mobile system developed by the Naval Ocean Systems Center (NOSC) -- The Unmanned Ground Vehicle Program Teleoperated Vehicle (TOy).
Monoclonal antibody characterization of the 195-kilodalton major surface glycoprotein of Plasmodium falciparum malaria schizonts and merozoites: identification of additional processed products and a serotype-restricted repetitive epitope. (1987)

The gp195 from Camp strain parasites was characterized with eight monoclonal antibodies (MAb) that recognize different epitopes on gp195 and three of its merozoite-associated processed products. Four MAb (3H7, 3B10, 7F1, and 4G12) reacted with different epitopes on the 45-kDa glycosylated product (gp45), shown by differences in their reactivities with soluble and immunoblotted gp45. One MAb (7H10) reacted with a conformational epitope probably formed as a result of the interaction of gp45 with a nonglycosylated 45-kDa product (p45). Three other MAb (3D3, 7B11, and 7B2) reacted with different epitopes on a nonglycosylated 83-kDa product (p83), shown by differences in their reactivities against various parasite isolates in immunofluorescent antibody assays. Immunoprecipitation of antigens that were pulse-labeled with [3H]isoleucine and chased with cold isoleucine showed that p45 and gp45 were processed products of gp195 and p83 was sequentially processed into smaller fragments of 73 and 67 kDa (p73 and p67). Immunoblots showed that the 7B11 and 7B2 epitopes were present on p83, p73, and p67, but that the 3D3 epitope was present only on p83 and p73. A two-site immunoassay showed the 3D3 epitope to be repetitive. The 3D3 and 7B11 epitopes were serotype restricted (present in seven and 24 of 33 isolates, respectively), but the other five epitopes were common to all isolates tested. The gp195 and its processed products have Mr that are consistent with the Mr of a number of antigens shown previously to be associated with the immune complexes that are formed when merozoites are agglutinated by antibodies contained in some growth inhibitory immune sera.
The alpha1beta1 integrin is expressed during neointima formation in rat arteries and mediates collagen matrix reorganization. (1996)

Remodeling of the extracellular matrix by activated mesenchymal cells (myofibroblasts) is a critical aspect of wound repair in all adult organs. Collagen-dependent gel contraction, a process requiring integrin function, is an established in vitro assay thought to mimic in vivo matrix remodeling. Numerous data have implicated the alpha2beta1 integrin in various cell types as the primary collagen receptor responsible for collagen gel contraction. However, evidence from the literature suggests that the major collagen binding integrin expressed on mesenchymally derived cells in situ is the alpha1beta1 integrin, not the alpha2beta1 integrin. In this report, we use a rat vascular injury model to illustrate that the alpha1beta1 integrin is the major collagen receptor expressed on vascular smooth muscle cells after injury. Using two smooth muscle cell lines, expressing either the alpha1beta1 integrin alone or both the alpha1beta1 and alpha2beta1 integrins, along with Chinese hamster ovary cells transfected with the alpha1 integrin, we demonstrate that alpha1beta1 supports not only collagen-dependent adhesion and migration, but also gel contraction. These data suggest that in vivo the alpha1beta1 integrin is a critical collagen receptor on mesenchymally derived cells potentially involved in matrix remodeling after injury.
SURFACE BRIGHTNESS AND MASS DISTRIBUTION OF THE LATE TYPE SPIRAL GALAXY NGC 2403 (1989)

Luminosity profile of the late type spiral galaxy NGC 2403 was obtained using the PDS scan of the plate. Some physical parameters (scale length, total magnitude, central brightness, disk to bulge ratio and concentric indices) were calculated from the brightness distribution. Total mass and the mass to luminosity ratio were estimated from the fitting of various mass models.
ECA: Energy-Efficient FPGA-based Convolutional Neural Networks Architecture for Single Image Super-Resolution (2018)

Convolutional neural networks (CNNs) demonstrate excellent performance in various computer vision applications. In recent years, FPGA-based CNN accelerators have been proposed for optimizing performance and power efficiency. Most accelerators are designed for object detection and recognition algorithms that are performed on low-resolution (LR) images. However, real-time image super-resolution (SR) cannot be implemented on a typical accelerator because of the long execution cycles required to generate high-resolution (HR) images, such as those used in ultra-high-definition (UHD) systems. In this paper, we propose a novel CNN accelerator with efficient parallelization methods for SR applications. First, we propose a new methodology for optimizing the deconvolutional neural networks (DCNNs) used for increasing feature maps. Secondly, we propose a novel method to optimize CNN dataflow so that the SR algorithm can be driven at low power in display applications. Finally, we quantize and compress a DCNN-based SR algorithm into an optimal model for efficient inference using on-chip memory. We present an energy-efficient architecture for SR and validate our architecture on a mobile panel with quad-high-definition (QHD) resolution. Our experimental results show that, with the same hardware resources, the proposed DCNN accelerator achieves a throughput up to 108 times greater than that of a conventional DCNN accelerator. In addition, our SR system achieves an energy efficiency of 144.9 GOPS/W, 293.0 GOPS/W, and 500.2 GOPS/W at SR scale factors of 2, 3, and 4, respectively. Furthermore, we demonstrate that our system can restore HR images to a high quality while greatly reducing the data bit-width and the number of parameters compared to conventional SR algorithms.
Treatment of Extranodal Marginal Zone B-Cell Lymphoma of Mucosa-Associated Lymphoid Tissue Type With Cladribine: A Phase II Study (2002)

Our data demonstrate that 2-CdA is highly effective in inducing CR in 84% of patients with MALT-type lymphoma.