gebhart/patrepeval huggingface dataset:
IL10 and PD-1 Cooperate to Limit the Activity of Tumor-Specific CD8+ T Cells (2015)

Immune checkpoint inhibitors show great promise as therapy for advanced melanoma, heightening the need to determine the most effective use of these agents. Here, we report that programmed death-1(high) (PD-1(high)) tumor antigen (TA)-specific CD8(+) T cells present at periphery and at tumor sites in patients with advanced melanoma upregulate IL10 receptor (IL10R) expression. Multiple subsets of peripheral blood mononucleocytes from melanoma patients produce IL10, which acts directly on IL10R(+) TA-specific CD8(+) T cells to limit their proliferation and survival. PD-1 blockade augments expression of IL10R by TA-specific CD8(+) T cells, thereby increasing their sensitivity to the immunosuppressive effects of endogenous IL10. Conversely, IL10 blockade strengthened the effects of PD-1 blockade in expanding TA-specific CD8(+) T cells and reinforcing their function. Collectively, our findings offer a rationale to block both IL10 and PD-1 to strengthen the counteraction of T-cell immunosuppression and to enhance the activity of TA-specific CD8(+) T cell in advanced melanoma patients.
The Bioelectric Factors in Amphibian-Limb Regeneration (1961)

Department of Orthopaedics, State University of New York, Upstate Medical Center, and Orthopaedic Section, Veterans Administration Hospital, Syracuse
Domain kernels for text categorization (2005)

In this paper we propose and evaluate a technique to perform semi-supervised learning for Text Categorization.
<title>Real-time computation of depth from defocus</title> (1996)

A new range sensing method based on depth from defocus is described. It uses illumination pattern projection to give texture to the object surface. Then the image of the scene is split into two images with different focus settings and sensed simultaneously. The contrast map of the two images are computed and compared pixel by pixel to produce a dense depth map. The illumination pattern and the focus operator to extract the contrast map are designed to achieve finest spatial resolution of the computed depth map and to maximize response of the focus operator. As the algorithm uses only local operations such as convolution and lookup table, the depth map can be computed rapidly on a data-flow image processing hardware. As this projects an illumination pattern and detects the two images with different focus setting from exactly the same direction, it does not share the problem of shadowing and occlusion with triangulation based method and stereo. Its speed and accuracy are demonstrated using a prototype system. The prototype generates 512 by 480 range maps at 30 frame/sec with a depth resolution of 0.3% relative to the object distance. The proposed sensor is composed of off-the-shelf components and outperforms commercial range sensors through its ability to produce complete three-dimensional shape information at video rate.
Therapy of Mouse Lymphoma with Monoclonal Antibodies to Glycolipid: Selection of Low Antigenic Variants in Vivo (1981)

Growth of mouse lymphoma L5178Y, which contains large quantitites of the gangliotriosylceramide (GgOs3Cer), in DBA/2 mice was suppressed by passive immunization with monoclonal immunoglobulin G3 antibodies to GgOS3Cer, but not by immunoglobulin M antibodies with or without added complement. Most groups of mice treated with monoclonal immunoglobulin G3 antibodies did not develop tumors, but the tumor that appeared in a treated animal had a much lower amount of the GgOS3Cer than the cells used for inoculation. Thus, passive immunization either prevented growth of the lymphoma or caused selection of a variant with a lower quantity of the antigen GgOS3Cer.
Recovery of the in vivo cytotoxic T-cell response in cyclophosphamide-treated mice by injection of mixed-lymphocyte-culture supernatants. (1981)

Mice given injections of high antileukemic doses of cyclophosphamide lost the capacity to generate cytotoxic T-cells in vivo to allogeneic tumor cells. These low responses were not due to the elimination of cytotoxic T-lymphocyte precursors because normal cytotoxic responses were obtained in vivo after cyclophosphamide treatment by injection of helper factor derived from mixed-lymphocyte-culture supernatants.
Inducible down-regulation of MHC class I results in natural killer cell tolerance (2018)

Natural killer (NK) cells are innate lymphocytes that are thought to kill cells that down-regulate MHC class I (MHC-I) through "missing-self" recognition. NK cells from <i>B2m<sup>-/-</sup></i> mice that lack surface MHC-I, however, are not autoreactive as predicted by the missing-self hypothesis. As a result, it is unclear if MHC-I down-regulation in vivo induces NK cell reactivity or tolerance to missing-self. Here, we generated a floxed <i>B2m</i> mouse to acutely down-regulate MHC-I in vivo in a host that normally expresses MHC-I. Global down-regulation of MHC-I induced NK cell hyporesponsiveness and tolerance to missing-self without overt missing-self reactivity. In contrast, down-regulation of MHC-I on a small fraction of hematopoietic cells triggered missing-self reactivity. Surprisingly, down-regulation of MHC-I only on CD4<sup>+</sup> T cells predominately induced tolerance to missing-self without resetting NK cell responsiveness. In this setting, inflammation triggered substantial missing-self reactivity. These results show that MHC-I down-regulation can induce either NK cell tolerance or killing in vivo and that inflammation promotes missing-self reactivity.
Memory Systems: Cache, DRAM, Disk (2007)

Is your memory hierarchy stopping your microprocessor from performing at the high level it should be? Memory Systems: Cache, DRAM, Disk shows you how to resolve this problem. The book tells you everything you need to know about the logical design and operation, physical design and operation, performance characteristics and resulting design trade-offs, and the energy consumption of modern memory hierarchies. You learn how to to tackle the challenging optimization problems that result from the side-effects that can appear at any point in the entire hierarchy.As a result you will be able to design and emulate the entire memory hierarchy. . Understand all levels of the system hierarchy -Xcache, DRAM, and disk. . Evaluate the system-level effects of all design choices. . Model performance and energy consumption for each component in the memory hierarchy.
Structure–function studies of the HIV-1 coreceptors (1998)

Ten seven-transmembrane-domain G protein-coupled receptors have been identified that are functional HIV-1, HIV-2 and SIV coreceptors. However, the specific structures these receptors have in common that enable them to mediate HIV entry are unknown. Structure-function analyses have revealed that the determinants of coreceptor activity are distinct for each coreceptor, coreceptor activity is dependent on multiple extracellular domains, and various envelope proteins may interact differently with the same coreceptor. G protein coupling and receptor internalization are not required for fusion and infection of established cell lines, or for inhibition of infection by chemokines. The structure-function studies have also helped determine the mechanism by which previously described small molecules inhibit HIV-1 entry. Finally, these studies have led to a hypothesis as to how coreceptor utilization evolves during the course of an infection.
Skeletal effects of oral oestrogen compared with subcutaneous oestrogen and testosterone in postmenopausal women. (1988)

Subcutaneous oestrogen is more effective than oral oestrogen in preventing osteoporosis, probably owing to the more physiological (premenopausal) serum oestradiol concentrations achieved. It also avoids problems of compliance that occur with oral treatment.
N1-Benzyl substituted cambinol analogues as isozyme selective inhibitors of the sirtuin family of protein deacetylases (2011)

The human deacetylase SIRT2 is believed to promote neurodegeneration with recent studies demonstrating that a reduction in the activity of SIRT2 can rescue alpha synuclein toxicity in Parkinson's disease models. In contrast, a second member of the sirtuin family, SIRT1, is believed to play a neuroprotective role. This dichotomy places an additional challenge in the path of sirtuin inhibitor development as a need for isozyme selectivity arises. By combining computational methods with assessment of the biological activity of novel N1-substituted cambinol analogues, further insights that are relevant to this challenge are obtained.
Phase-change recording medium that enables ultrahigh-density electron-beam data storage (2005)

http://aip.scitation.org/doi/pdf/10.1063/1.4996993
Role of Innate Immune Factors in the Adjuvant Activity of Monophosphoryl Lipid A (2003)

Monophosphoryl lipid A (MPL) is a nontoxic derivative of lipopolysaccharide (LPS) that exhibits adjuvant properties similar to those of the parent LPS molecule. However, the mechanism by which MPL initiates its immunostimulatory properties remains unclear. Due to the involvement of Toll-like receptors in recognizing and transducing intracellular signals in response to LPS, the aim of the present study was to determine the ability of MPL to utilize the Toll-like receptor 2 (TLR2) and TLR4. We provide evidence that MPL differentially utilizes TLR2 and TLR4 for the induction of tumor necrosis factor alpha, interleukin 10 (IL-10), and IL-12 by purified human monocytes as well as by human peripheral blood mononuclear cells. Assessment of NF-kappa B activity demonstrated that MPL utilized TLR2 and especially TLR4 for the activation of NF-kappa B p65 by human monocytes. In addition, stimulation of human monocytes by MPL led to an up-regulation of the costimulatory molecules CD80 and CD86, an effect that could be reduced by pretreatment of cells with a monoclonal antibody to TLR2 or TLR4. Analysis of MPL-induced activation of the extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein (MAP) kinases revealed that MPL utilized both TLR2 and TLR4 for the phosphorylation of ERK1/2, while TLR4 was the predominant receptor involved in the ability of MPL to phosphorylate p38. Moreover, using selective inhibitors for MAP kinase kinase (PD98059) and p38 (SB203580), we show that ERK1/2 exhibited differential effects on production of TNF-alpha and IL-12 p40 by human monocytes, whereas MPL-induced activation of p38 appeared to be predominantly involved in production of IL-10 and IL-12 p40 by MPL-stimulated monocytes. Taken together, these findings aid in understanding the cellular mechanisms by which MPL induces host cell activation and subsequent adjuvant properties.
Identification of a novel serine protease-like gene, the expression of which is down-regulated during breast cancer progression. (1996)

In an effort to isolate genes with down-regulated expression at the mRNA level during oncogenic transformation of human mammary epithelial cells (MECs), we performed subtractive hybridization between normal MEC strain 76N and its radiation-transformed tumorigenic derivative 76R-30. Here, we report the isolation of cDNA clones corresponding to a 1.4-kb mRNA species that is abundantly expressed in 76N cells but is drastically reduced in 76R-30 cells. Based on its selective expression in MECs compared with fibroblasts, the corresponding gene is designated NES1 (normal epithelial cell-specific 1). Sequence analysis of the full-length NES1 cDNA clones revealed it to be a novel gene with a predicted polypeptide of 30.14 kilodaltons; in vitro transcription and translation confirmed this prediction. Database searches revealed a 50-63% similarity and 34-42% identity with several families of serine proteases, in particular the trypsin-like proteases, members of the glandular kallikrein family (including prostate-specific antigen, nerve growth factor gamma, and epidermal growth factor-binding protein) and the activators for the kringle family proteins (including the human tissue plasminogen activator and human hepatocyte growth factor activator). Importantly, all of the residues known to be crucial for substrate binding, specificity, and catalysis by the serine proteases are conserved in the predicted NES1 protein, suggesting that it may be a protease. An antipeptide antibody directed against a unique region of the NES1 protein (amino acids 120-137) detected a specific 30-kilodalton polypeptide almost exclusively in the supernatant of the mRNA-positive MECs, suggesting that NES1 is a secreted protein. The 1.4-kb NES1 mRNA was expressed in several organs (thymus, prostate, testis, ovary, small intestine, colon, heart, lung, and pancreas) with highest levels in the ovary; a 1.1-kb transcript was found in the pancreas. Although expression of the NES1 mRNA was observed in all normal and immortalized nontumorigenic MECs, the majority of human breast cancer cell lines showed a drastic reduction or a complete lack of its expression. The structural similarity of NES1 to polypeptides known to regulate growth factor activity and a negative correlation of NES1 expression with breast oncogenesis suggest a direct or indirect role for this novel protease-like gene product in the suppression of tumorigenesis.
Differential effects of CTLA-4 substitutions on the binding of human CD80 (B7-1) and CD86 (B7-2) (1996)

CTLA-4 expressed on activated T cells binds to CD80 (B7-1) and CD86 (B7-2) molecules present on APC with high avidity and appears to deliver a negative regulatory signal to the T cell. We have investigated the kinetics of CTLA-4 binding to CD80 and CD86, together with the effects of selected CTLA-4 mutations on binding activity. The dissociation constants (Kd) for binding of CTLA-4-Ig to CD80 and CD86 transfectants were 8.1 and 6.7 nM, respectively. Surface plasmon resonance was used to determine kinetic parameters of CTLA-4-Ig binding to CD80-Ig and CD86-Ig fusion proteins and revealed enhanced association (ka) and dissociation (kd) rate constants for CD86-Ig compared with CD80-Ig. Furthermore, CD80-Ig and CD86-Ig fusion molecules demonstrated variable abilities to cross-compete for binding to several modified forms of CTLA-4-Ig. Differential binding of CD80 and CD86 to CTLA-4 was further revealed by analysis of 10 discrete CTLA-4 mutants. Five single amino acid substitutions within the CTLA-4 MYPPPY domain exerted modest effects on CD80 binding, but each of these substitutions completely abrogated CD86 binding. In addition, substitutions just N-terminal of the MYPPPY region, and within the CDR1-like region of CTLA-4, eliminated both CD80 and CD86 binding. Hence, CD80 and CD86 bind with different association/dissociation kinetics to similar, but distinct, sites on CTLA-4.
The problems facing labor-based road programs and what to do about them : evidence from Ghana (1996)

The literature gives two explanations for contractors' reluctance to adopt labor-based methods. First, contractors believe the cost of learning this new technology is high. Programs designed to promote labor-based methods have always included subsidized training to address this problem. This study argues that focusing on training often diverts attention away from more substantive problems inherent in adopting labor-based methods. Second, the more fundamental, some have argued that the cost of managing large labor forces, which is difficult to quantify in unit-cost comparisons, makes labor-based methods less competitive than equipment-based methods. This study shows that although labor-based methods can be financially more attractive to Ghanaian contractors, market-structure conditions thwart their use. Unit-rate cost comparisons of labor-based and equipment-based methods, therefore, cannot predict firm behavior. In particular, there is a very important distinction between small and large contractors. Labor-based methods are more attractive to small firms than to large firms. Small firms, because they are small, can supervise their sites themselves and thus find it easier to develop strategies to increase worker productivity and control truancy. Moreover, unlike large firms, small firms who wish to use equipment-based methods face high variable costs: they either own older, less-efficient equipment-with high maintenance costs-or must rent equipment at a high cost. Large firms, in contrast, find labor-based methods much less attractive. Large firms have high monitoring costs because of their size and because they often undertake many projects simultaneously.
Image Retrieval using 2D Dual-Tree Discrete Wavelet Transform (2011)

The large amount of image collections available from a variety of sources has posed increasing technical challenges to computer systems to store/transmit and index/manage the image data to make such collections easily accessible. Here to search and retrieve the expected images from the database we need Content Based Image Retrieval system. This paper proposes a new feature vector based on 2D Dual-tree Discrete Wavelet Transform. One of the advantages of the dual-tree complex wavelet transform is that it can be used to implement 2D wavelet transforms that are more selective with respect to orientation than is the separable 2D DWT. Most of the natural images have short span high frequencies and low frequencies extending for larger span. Hence, the design of our feature vector is such that it provides higher spatial localization and lower frequency resolution at higher frequencies and the reverse for lower frequencies. The energy and mean of the frequency content of the image at various sub bands and different spatial resolution (higher for higher frequency bands) is stored as feature vector. Thus, the given feature vector encodes high frequency information as well.
An Arabidopsis Peptide Transporter Is a Member of a New Class of Membrane Transport Proteins (1994)

Henry-York Steiner, Wei Song, Larry Zhang, Fred Naider, Jeffrey M. Becker, Gary Stacey, An Arabidopsis Peptide Transporter Is a Member of a New Class of Membrane Transport Proteins, The Plant Cell, Vol. 6, No. 9 (Sep., 1994), pp. 1289-1299
Cross-polarized backscatter in optical coherence tomography of biological tissue (1998)

We have observed that cross-polarized backscatter measured by optical coherence tomography of human skin in vivo is surprisingly strong. We identify and give evidence of its main origins: single scattering from nonspherical particles and multiple scattering by particles with sizes much larger than a wavelength. Our findings show that depolarized light scattered by dense large-diameter particles maintains a high degree of temporal coherence and that differential-polarization imaging improves contrast between particles of different sizes.
Homozygous deletion of the PTEN tumor suppressor gene in a subset of prostate adenocarcinomas. (1998)

A novel tumor suppressor gene, PTEN, which encodes a dual-specificity protein phosphatase, has recently been identified on chromosome 10q23. We have previously shown that both alleles of this gene are inactivated in three of four prostate cancer cell lines tested. To evaluate the role of inactivation of this gene in primary stage B prostate cancers, 60 cases were analyzed using Southern blotting with PTEN probes and microsatellites on 10q23. Eight of 60 cases had homozygous deletions by Southern blotting. In three of these cases, homozygous deletion was confirmed by apparent retention of heterozygosity at PTEN with loss of heterozygosity at telomeric and centromeric loci. In the remaining five cases, microsatellite analysis was consistent with homozygous deletion. Loss of heterozygosity at PTEN was found in only two cases both by microsatellite analysis and quantitative Southern blotting. No small mutations within PTEN exons were found in any tumors exhibiting alterations on 10q23. Thus, inactivation of the PTEN gene by homozygous deletion occurs in approximately 10-15% of primary stage B prostate carcinomas.
Water Cooling Method to Improve the Performance of Field-Mounted, Insulated, and Concentrating Photovoltaic Modules (2014)

The installation rate of crystalline silicon photovoltaic (PV) modules worldwide is at an all-time high and is projected to continue to grow as the cost of PV technology is reduced. It is important to note that PV power generation is heavily influenced by the local climate. In particular, for crystalline silicon-based PV devices, as the operating temperature of the panel increases, the efficiency decreases. Higher operating temperatures also lead to accelerated material and mechanical degradation, potentially compromising system effectiveness over the lifetime of the panels. In addition, atmospheric pollution can cause particle deposition on the surface of PV modules (soiling), reducing the amount of solar irradiance that reaches the PV material and reducing panel efficiency. Various cooling and cleaning methods have been proposed in the literature to mitigate these problems. In this study, a uniform film of water was continuously recirculated by pumping over the surface of a solar panel using an emitter head attached to the top of the panel. The water cooling technique was able to maintain panel temperature below 40 °C while adjacent untreated panels were operating near 55 °C. Besides the efficiency improvements due to cooling, the film of water also kept the panels clean, avoiding any reduced power output caused by panel soiling. Additional studies were carried out with artificially chilled cooling fluid, insulating materials, and side mirrors to examine the cooling system performance under different installation scenarios. Water cooling is concluded to be an effective means of increasing the efficiency of monocrystalline silicon photovoltaic panels. Under normal operating conditions, the increased energy output from the panels is more than sufficient to compensate for the energy required to pump the water.
Role of Nrf2 in the regulation of the Mrp2 (ABCC2) gene (2006)

The Nrf2 (nuclear factor-erythroid 2 p45-related factor 2) transcription factor regulates gene expression of the GCLC (glutamate-cysteine ligase catalytic subunit), which is a key enzyme in glutathione synthesis, and GSTs (glutathione S-transferases) via the ARE (antioxidant-response element). The Mrp2 (multidrug-resistance protein 2) pump mediates the excretion of GSH and GSSG excretion as well as endo- and xeno-biotics that are conjugated with GSH, glucuronate or sulphate. Considering that Mrp2 acts synergistically with these enzymes, we hypothesized that the regulation of Mrp2 gene expression is also dependent on Nrf2. Using BHA (butylated hydroxyanisole), which is a classical activator of the ARE-Nrf2 pathway, we observed an increase in the transcriptional activity of Mrp2, GCLC and Gsta1/Gsta2 genes in the mouse liver. A similar pattern of co-induction of Mrp2 and GCLC genes was also observed in mouse (Hepa 1-6) and human (HepG2) hepatoma cells treated with BHA, beta-NF (beta-naphthoflavone), 2,4,5-T (trichlorophenoxyacetic acid) or 2AAF (2-acetylaminofluorene), suggesting that these genes share common mechanism(s) of transcriptional activation in response to exposure to xenobiotics. To define the mechanism of Mrp2 gene induction, the 5'-flanking region of the mouse Mrp2 gene (2.0 kb) was isolated, and two ARE-like sequences were found: ARE-2 (-1391 to -1381) and ARE-1 (-95 to -85). Deletion analyses demonstrated that the proximal region (-185 to +99) contains the elements for the basal expression and xenobiotic-mediated induction of the Mrp2 gene. Gel-shift and supershift assays indicated that Nrf2-protein complexes bind ARE sequences of the Mrp2 promoter, preferentially to the ARE-1 sequence. Overexpression of Nrf2 increased ARE-1-mediated CAT (chloramphenicol acetyltransferase) gene activity, while overexpression of mutant Nrf2 protein repressed the activity. Thus Nrf2 appears to regulate Mrp2 gene expression via an ARE element located at the proximal region of its promoter in response to exposure to xenobiotics.
Zygote score and status 1 or 2 days after cleavage and assisted reproduction outcome (2008)

Combined with embryo morphology evaluation on Days 2 and 3, a scoring system based on pronuclear morphology seems to provide a good criterion when selecting embryos for transfer.