gebhart/patrepeval huggingface dataset:
Runtime 3-D stacked cache data management for energy minimization of 3-D chip-multiprocessors (2014)

In a 3-D processor-memory system, multiple cache dies can be stacked onto multi-core die to reduce latency and power of the on-chip wires connecting the cores and the cache, which finally increases the power efficiency. However, there are two challenging issues. The first is the high power density (resulting from multiple die stacking) that incurs many temperature-related problems including temperature-dependent leakage power. The second is the processor-cache traffic congestions that occur at through-silicon vias (TSVs) shared by multiple stacked caches. In this paper, a runtime cache data mapping is proposed for 3-D stacked L2 caches to minimize the overall energy of 3-D chip multiprocessors (CMPs). The proposed method considers both temperature distribution and memory traffic of 3-D CMPs. Experimental result shows that the proposed method achieves up to 22.88% energy reduction compared to an existing solution which considers only the temperature distribution.
The Cityscapes Dataset for Semantic Urban Scene Understanding (2016)

Visual understanding of complex urban street scenes is an enabling factor for a wide range of applications. Object detection has benefited enormously from large-scale datasets, especially in the context of deep learning. For semantic urban scene understanding, however, no current dataset adequately captures the complexity of real-world urban scenes. To address this, we introduce Cityscapes, a benchmark suite and large-scale dataset to train and test approaches for pixel-level and instance-level semantic labeling. Cityscapes is comprised of a large, diverse set of stereo video sequences recorded in streets from 50 different cities. 5000 of these images have high quality pixel-level annotations, 20 000 additional images have coarse annotations to enable methods that leverage large volumes of weakly-labeled data. Crucially, our effort exceeds previous attempts in terms of dataset size, annotation richness, scene variability, and complexity. Our accompanying empirical study provides an in-depth analysis of the dataset characteristics, as well as a performance evaluation of several state-of-the-art approaches based on our benchmark.
Efficient route to well‐characterized homo, block, and statistical polymers containing terpyridine in the side chain (2005)

Abstract The incorporation of metal–ligand interactions into macromolecules imparts to them unique and potentially useful properties. We report the synthesis of homo, block, and statistical copolymers with controlled molecular weights, compositions, and relatively narrow polydispersities via atom transfer radical polymerization that contain activated esters for the subsequent incorporation of terpyridine. This approach is universal and allows facile access to macromolecules with rich chemical functions, illustrated here with metal ligands. Comonomers include methyl, n ‐butyl, and poly(ethylene glycol) methyl ether methacrylate as well as styrene. The addition of lanthanide ions to the final copolymers generates emissive materials with blue, green, red, or purple light, depending on the metal used. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5831–5843, 2005
Mammaglobin-Based Strategies for Treatment of Breast Cancer (2004)

Mammaglobin is a gene that is expressed almost exclusively in the normal breast epithelium and human breast cancer. It is a member of the secretoglobin gene family and forms a heterodimer with lipophilin B. We have focused on the tissue-specificity of mammaglobin as a potential mechanism for the specific killing of breast cancer cells. By elucidating the promoter region of mammaglobin, we hope to utilize this site as a method for turning on the apoptosis inducer gene, Bax, in breast cancer cells. The Bax gene will only be expressed at levels necessary to induce apoptosis in mammaglobin positive cells. This would include > 80% of all breast cancers and some normal breast epithelium. This type of targeted killing could be conceptualized as a biochemical mastectomy, that is, genetic ablation of breast tumor cells and perhaps non-malignant breast epithelium while preserving the adipose and stromal components of the breast. Work is also being done to address the binding specificity of the secreted mamaglobin protein. There is early evidence that the mammaglobin heterodimer may in fact bind to breast and breast cancer cells. If this finding is validated, this creates the possibility that mammaglobin can be tagged with radioisotope or toxin, so that binding of the tagged-mammaglobin complex results in the specific killing of that breast cancer cell. Finally, mammaglobin is being explored as a target for immune-based interventions. In vitro studies have demonstrated that T cell-mediated immune responses can be induced against mammaglobin-derived peptides expressed by MHC molecules on tumor cells and antigen-presenting cells.
Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. (1995)

During fertilization in marine invertebrates, fusion between sperm and egg cell membranes occurs at the tip of the sperm acrosomal process. In abalone sperm the acrosomal process is coated with an 18-kDa protein. In situ, this protein has no effect on the egg vitelline envelope, but in vitro it is a potent fusagen of liposomes. Thus, the 18-kDa protein may mediate membrane fusion between the gametes, a step in gamete recognition known to restrict heterospecific fertilization in other species. The cDNA and deduced amino acid sequences of the 18-kDa protein were determined for five species of California abalone. The deduced amino acid sequences exhibit extraordinary divergence; the percent identity varies from 27% to 87%. Analysis of nucleotide substitution shows extremely high frequencies of amino acid-altering substitution compared to silent substitution, demonstrating that positive Darwinian selection promotes the divergence of this protein. However, amino acid replacement is conservative with respect to size and polarity of residue. The data support the developing idea that in free-spawning marine invertebrates, the proteins mediating fertilization may be subjected to intense, and as yet unknown, selective forces. The extraordinary divergence of fertilization proteins may be related to the establishment of barriers to heterospecific fertilization.
Role of βArg211 in the Active Site of Human β-Hexosaminidase B (2000)

Tay-Sachs or Sandhoff disease results from a deficiency of either the alpha- or the beta-subunits of beta-hexosaminidase A, respectively. These evolutionarily related subunits have been grouped with the "Family 20" glycosidases. Molecular modeling of human hexosaminidase has been carried out on the basis of the three-dimensional structure of a bacterial member of Family 20, Serratia marcescens chitobiase. The primary sequence identity between the two enzymes is only 26% and restricted to their active site regions; therefore, the validity of this model must be determined experimentally. Because human hexosaminidase cannot be functionally expressed in bacteria, characterization of mutagenized hexosaminidase must be carried out using eukaryotic cell expression systems that all produce endogenous hexosaminidase activity. Even small amounts of endogenous enzyme can interfere with accurate K(m) or V(max) determinations. We report the expression, purification, and characterization of a C-terminal His(6)-tag precursor form of hexosaminidase B that is 99.99% free of endogenous enzyme from the host cells. Control experiments are reported confirming that the kinetic parameters of the His(6)-tag precursor are the same as the untagged precursor, which in turn are identical to the mature isoenzyme. Using highly purified wild-type and Arg(211)Lys-substituted hexosaminidase B, we reexamine the role of Arg(211) in the active site. As we previously reported, this very conservative substitution nevertheless reduces k(cat) by 500-fold. However, the removal of all endogenous activity has now allowed us to detect a 10-fold increase in K(m) that was not apparent in our previous study. That this increase in K(m) reflects a decrease in the strength of substrate binding was confirmed by the inability of the mutant isozyme to efficiently bind an immobilized substrate analogue, i.e., a hexosaminidase affinity column. Thus, Arg(211) is involved in substrate binding, as predicted by the chitobiase model, as well as catalysis.
Dual-color Proteomic Profiling of Complex Samples with a Microarray of 810 Cancer-related Antibodies (2010)

Antibody microarrays have the potential to enable comprehensive proteomic analysis of small amounts of sample material. Here, protocols are presented for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In addition to measures of array quality, we implemented indicators for the accuracy and significance of dual-color detection. Dual-color measurements outperform a single-color approach concerning assay reproducibility and discriminative power. In the analysis of serum samples, depletion of high-abundance proteins did not improve technical assay quality. On the contrary, depletion introduced a strong bias in protein representation. In an initial study, we demonstrated the applicability of the protocols to proteins derived from urine samples. We identified differences between urine samples from pancreatic cancer patients and healthy subjects and between sexes. This study demonstrates that biomedically relevant data can be produced. As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses.
Hexamethylene bisacetamide stimulates herpes simplex virus immediate early gene expression in the absence of trans-induction by Vmw65 (1992)

Hexamethylene bisacetamide (HMBA) and DMSO are known to induce differentiation of cultured erythroleukaemic cells and to enhance the reactivation of latent herpes simplex virus (HSV) after explantation of ganglia. We report that the presence of these compounds in cell culture medium overcomes the replication defect of in 1814, an HSV-1 mutant with an insertion mutation that inactivates the virion trans-inducing factor, Vmw65 (VP16). The effect of HMBA was not cell type-specific and was attained even by a short exposure (1.5 to 5 h) to the agent early after infection. The presence of HMBA resulted in an increase in immediate early (IE) RNA accumulation after infection of cells in the presence of cycloheximide, such that RNA levels in in 1814-infected cells approached the values observed in wild-type HSV-1-infected cells in the absence of HMBA. Transport of viral DNA to the cell nucleus was not affected by HMBA. The results suggest that HMBA- and DMSO-mediated enhancement of reactivation from latency is due to an increase in IE RNA production. In addition, these studies demonstrate a primary effect of HMBA on gene regulation which may be a paradigm for initial events during erythroleukaemic cell differentiation.
Lipoarabinomannan, a possible virulence factor involved in persistence of Mycobacterium tuberculosis within macrophages (1991)

Mycobacterium tuberculosis and Mycobacterium leprae, the causative agents of tuberculosis and leprosy, respectively, produce large quantities of lipoarabinomannan (LAM), a highly immunogenic, cell wall-associated glycolipid. This molecule has been previously reported to be a potent inhibitor of gamma interferon-mediated activation of murine macrophages. Studies of the mechanism by which this mycobacterial glycolipid down-regulates macrophage effector functions provide evidence that LAM acts at several levels and that it can (i) scavenge potentially cytotoxic oxygen free radicals, (ii) inhibit protein kinase C activity, and (iii) block the transcriptional activation of gamma interferon-inducible genes in human macrophage-like cell lines. These results suggest that LAM can inhibit macrophage activation and triggering and cytocidal activity and that it may represent a chemically defined virulence factor contributing to the persistence of mycobacteria within mononuclear phagocytes.
Antibody facilitation of multiple sclerosis-like lesions in a nonhuman primate. (1995)

In the human disease multiple sclerosis (MS), the immune mechanisms responsible for selective destruction of central nervous system myelin are unknown. In the common marmoset Callithrix jacchus, a unique demyelinating form of experimental allergic encephalomyelitis resembling MS can be induced by immunization with whole myelin. Here we show that the MS-like lesion can be reproduced by immunization against the extracellular domain of a single myelin protein, myelin/oligodendrocyte glycoprotein (MOG). By contrast, immunization against the quantitatively major myelin proteins myelin basic protein or proteolipid protein results in inflammation but little or no demyelination. Furthermore, in the presence of encephalitogenic (e.g., disease-inducing) T cells, the fully demyelinated lesion is reconstructed by systemic administration of IgG purified from whole myelin-, or MOG-immunized animals, and equally by a monoclonal antibody against MOG, but not by control IgG. Encephalitogenic T cells may contribute to the MS-like lesion through disruption of the blood-brain barrier that permits access of demyelinating antibody into the nervous system. The identification of MOG as a major target antigen for autoimmune demyelination in a nonhuman primate should facilitate development of specific immunotherapies for human MS.
A review of abuse-deterrent opioids for chronic nonmalignant pain. (2012)

Chronic nonmalignant pain, which affects millions of people, is the most common reason patients seek medical care. Both current and potential opioid analgesics are discussed, along with new technologies used to prevent abuse.
A 640*480 pixel computer display using pin diodes with device redundancy (2003)

A report is presented of the successful development of a (640*480)-pixel computer monitor display with a 6 in.*8 in. viewing area using pin diode switches with complete device redundancy. This active matrix liquid-crystal display has an area contrast ratio greater than 20:1 near normal viewing, and greater than 3:1 for horizontal viewing angles of +or-70 degrees . The display can be configured as reflective, transmissive, or transflective. Because of the device redundancy, the absence of crossing lines, the simple diode structure, and the use of a large area projection stepper in processing, the displays show very high yield despite the large size. This high yield makes it ideal for high-volume production as a laptop-computer display.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanoporous Gold Catalysts for Selective Gas-Phase Oxidative Coupling of Methanol at Low Temperature (2010)

Gold (Au) is an interesting catalytic material because of its ability to catalyze reactions, such as partial oxidations, with high selectivities at low temperatures; but limitations arise from the low O2 dissociation probability on Au. This problem can be overcome by using Au nanoparticles supported on suitable oxides which, however, are prone to sintering. Nanoporous Au, prepared by the dealloying of AuAg alloys, is a new catalyst with a stable structure that is active without any support. It catalyzes the selective oxidative coupling of methanol to methyl formate with selectivities above 97% and high turnover frequencies at temperatures below 80 degrees C. Because the overall catalytic characteristics of nanoporous Au are in agreement with studies on Au single crystals, we deduced that the selective surface chemistry of Au is unaltered but that O2 can be readily activated with this material. Residual silver is shown to regulate the availability of reactive oxygen.
Mouse Model of Tuberculosis (2014)

This chapter describes how the mouse model has evolved over the past century from the simple but beautiful experiments of Koch to present-day models based on sophisticated gene targeting. In the process, the authors describe the course of the infection in the mouse after inoculation by various routes and their growing picture of how the host immune response is mobilized against the infecting organism. They also describe various mouse models that involve immunodeficiency; these may prove useful not only in the further dissection of the cellular immune response but also in applied strategies of chemotherapy and immunotherapy. The growth of Mycobacterium tuberculosis in mice has been extremely well characterized, with the organism giving rise to highly characteristic distribution patterns in target organs after inoculation. A week or so after inoculation of mice with a sublethal intravenous dose of M. tuberculosis, a population of CD4 cells that are capable of adoptively transferring protective immunity emerges in the spleen. In the mouse model of tuberculosis, enriched populations of immune CD8 T cells transferred some degree of resistance, albeit rather weakly, and in vivo depletion of CD8 T cells by intravenous administration of monoclonal antibody was shown to diminish resistance to some extent. The cytokine response to M. tuberculosis probably begins almost immediately after infection of host macrophages, as these cells begin to transcribe message from a number of early response genes.
Understanding research trends in conferences using paperLens (2005)

PaperLens is a novel visualization that reveals trends, connections, and activity throughout a conference community. It tightly couples views across papers, authors, and references. PaperLens was developed to visualize 8 years (1995-2002) of InfoVis conference proceedings and was then extended to visualize 23 years (1982-2004) of the CHI conference proceedings. This paper describes how we analyzed the data and designed PaperLens. We also describe a user study to focus our redesign efforts along with the design changes we made to address usability issues. We summarize lessons learned in the process of design and scaling up to the larger set of CHI conference papers.
Stromally Derived Lysyl Oxidase Promotes Metastasis of Transforming Growth Factor-β–Deficient Mouse Mammary Carcinomas (2013)

The tumor stromal environment can dictate many aspects of tumor progression. A complete understanding of factors driving stromal activation and their role in tumor metastasis is critical to furthering research with the goal of therapeutic intervention. Polyoma middle T-induced mammary carcinomas lacking the type II TGF-β receptor (PyMT(mgko)) are highly metastatic compared with control PyMT-induced carcinomas (PyMT(fl/fl)). We hypothesized that the PyMT(mgko)-activated stroma interacts with carcinoma cells to promote invasion and metastasis. We show that the extracellular matrix associated with PyMT(mgko) tumors is stiffer and has more fibrillar collagen and increased expression of the collagen crosslinking enzyme lysyl oxidase (LOX) compared with PyMT(fl/fl) mammary carcinomas. Inhibition of LOX activity in PyMT(mgko) mice had no effect on tumor latency and size, but significantly decreased tumor metastasis through inhibition of tumor cell intravasation. This phenotype was associated with a decrease in keratin 14-positive myoepithelial cells in PyMT(mgko) tumors following LOX inhibition as well as a decrease in focal adhesion formation. Interestingly, the primary source of LOX was found to be activated fibroblasts. LOX expression in these fibroblasts can be driven by myeloid cell-derived TGF-β, which is significantly linked to human breast cancer. Overall, stromal expansion in PyMT(mgko) tumors is likely caused through the modulation of immune cell infiltrates to promote fibroblast activation. This feeds back to the epithelium to promote metastasis by modulating phenotypic characteristics of basal cells. Our data indicate that epithelial induction of microenvironmental changes can play a significant role in tumorigenesis and attenuating these changes can inhibit metastasis. Cancer Res; 73(17); 5336-46. ©2013 AACR.
High amplitude short time excitation: A method to form and detect low mass product ions in a quadrupole ion trap mass spectrometer (2005)

Collision induced dissociation (CID) in a quadrupole ion trap mass spectrometer using the conventional 30 ms activation time is compared with high amplitude short time excitation (HASTE) CID using 2 ms and 1 ms activation times. As a result of the shorter activation times, dissociation of the parent ions using the HASTE CID technique requires resonance excitation voltages greater than conventional CID. After activation, the rf trapping voltage is lowered to allow product ions below the low mass cut-off to be trapped. The HASTE CID spectra are notably different from those obtained using conventional CID and can include product ions below the low mass cut-off for the parent ions of interest. The MS/MS efficiencies of HASTE CID are not significantly different when compared with the conventional 30 ms CID. Similar results were obtained with a two-dimensional (linear) ion trap and a three-dimensional ion trap.
Cross‐linking of cell surface immunoglobulins induces epstein‐barr virus in burkitt lymphoma lines (1984)

Anti-human immunoglobulin (Ig) antibodies with single-chain specificities induced Epstein-Barr virus (EBV) in various Burkitt lymphoma lines when the corresponding Ig chain was expressed on the cell surface. The F(ab')2 fragments of IgG antibody were as potent as intact Ig, while the Fab and Fc fragments gave no induction, indicating that cross-linking of surface Ig was required for the induction. Simultaneously with EBV induction, anti-Ig inhibited the uptake of 3H-thymidine. This inhibition was also seen in EBV-genome-negative Burkitt lymphoma lines. In contrast, no effect on virus induction and cell growth was noted in lymphoblastoid lines of non-neoplastic origin. The possible relationship between cell differentiation and latency of EBV-carrier state is discussed.