gebhart/patrepeval huggingface dataset:
Self- and Nonself-Recognition by C-Type Lectins on Dendritic Cells (2004)

Dendritic cells (DCs) are highly efficient antigen-presenting cells (APCs) that collect antigen in body tissues and transport them to draining lymph nodes. Antigenic peptides are loaded onto major histocompatibility complex (MHC) molecules for presentation to naive T cells, resulting in the induction of cellular and humoral immune responses. DCs take up antigen through phagocytosis, pinocytosis, and endocytosis via different groups of receptor families, such as Fc receptors for antigen-antibody complexes, C-type lectin receptors (CLRs) for glycoproteins, and pattern recognition receptors, such as Toll-like receptors (TLRs), for microbial antigens. Uptake of antigen by CLRs leads to presentation of antigens on MHC class I and II molecules. DCs are well equipped to distinguish between self- and nonself-antigens by the variable expression of cell-surface receptors such as CLRs and TLRs. In the steady state, DCs are not immunologically quiescent but use their antigen-handling capacities to maintain peripheral tolerance. DCs are continuously sampling and presenting self- and harmless environmental proteins to silence immune activation. Uptake of self-components in the intestine and airways are good examples of sites where continuous presentation of self- and foreign antigens occurs without immune activation. In contrast, efficient antigen-specific immune activation occurs upon encounter of DCs with nonself-pathogens. Recognition of pathogens by DCs triggers specific receptors such as TLRs that result in DC maturation and subsequently immune activation. Here we discuss the concept that cross talk between TLRs and CLRs, differentially expressed by subsets of DCs, accounts for the different pathways to peripheral tolerance, such as deletion and suppression, and immune activation.
PRODRG: a tool for high-throughput crystallography of protein–ligand complexes (2004)

The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG-generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors.
An experimentation framework for evaluating disassembly and decompilation tools for C++ and java (2004)

The inherent differences between C++ and Javaprograms dictate that the methods used for reverseengineering their compiled executables will be language-specific. This paper looks at the history of decompilers,disassemblers, and obfuscators in C++ and Java andpresents the current state of the art for binary reverseengineering. An experimentation framework forevaluating tools is described, including methodology,benchmark programs, metrics, and reverse engineeringtasks. Preliminary results of experiments conducted sofar to assess the capability of a small select set of chosenpopular tools are given. These results reveal language-specific differences in the feasibility of the binary reverseengineering tasks on input programs with varying degreesof obfuscation (e.g., stripped vs. unstripped binaries). Inaddition, the results reveal the relative effort required tocomplete a task and an assessment of the value of thetools and techniques.
The Effect of Thiazolidinediones on Plasma Adiponectin Levels in Normal, Obese, and Type 2 Diabetic Subjects (2002)

The insulin-sensitizing effects of thiazolidinediones are thought to be mediated through peroxisome proliferator-activated receptor-gamma, a nuclear receptor that is highly abundant in adipose tissue. It has been reported that adipocytes secrete a variety of proteins, including tumor necrosis factor-alpha, resistin, plasminogen activator inhibitor-1, and adiponectin. Adiponectin is a fat cell-secreted protein that has been reported to increase fat oxidation and improve insulin sensitivity. Our aim was to study the effects of troglitazone on adiponectin levels in lean, obese, and diabetic subjects. Ten diabetic and 17 nondiabetic subjects (8 lean, BMI <27 kg/m(2) and 9 obese, BMI >27 kg/m(2)) participated in the study. All subjects underwent an 80 mU. m(-2). min(-1) hyperinsulinemic-euglycemic glucose clamp before and after 3 months' treatment with the thiazolidinedione (TZD) troglitazone (600 mg/day). Fasting plasma glucose significantly decreased in the diabetic group after 12 weeks of treatment compared with baseline (9.1 +/- 0.9 vs. 11.1 +/- 0.9 mmol/l, P < 0.005) but was unchanged in the lean and obese subjects. Fasting insulin for the entire group was significantly lower than baseline (P = 0.02) after treatment. At baseline, glucose disposal rate (R(d)) was lower in the diabetic subjects (3.4 +/- 0.5 mg. kg(-1). min(-1)) than in the lean (12.3 +/- 0.4) or obese subjects (6.7 +/- 0.7) (P < 0.001 for both) and was significantly improved in the diabetic and obese groups (P < 0.05) after treatment, and it remained unchanged in the lean subjects. Baseline adiponectin levels were significantly lower in the diabetic than the lean subjects (9.0 +/- 1.7 vs. 16.7 +/- 2.7 micro g/ml, P = 0.03) and rose uniformly in all subjects (12.2 +/- 2.3 vs. 25.7 +/- 2.6 micro g/ml, P < 10(-4)) after treatment, with no significant difference detected among the three groups. During the glucose clamps, adiponectin levels were suppressed below basal levels in all groups (10.2 +/- 2.3 vs. 12.2 +/- 2.3 micro g/ml, P < 0.01). Adiponectin levels correlated with R(d) (r = 0.46, P = 0.016) and HDL cholesterol levels (r = 0.59, P < 0.001) and negatively correlated with fasting insulin (r = -0.39, P = 0.042) and plasma triglyceride (r = -0.61, P < 0.001). Our findings show that TZD treatment increased adiponectin levels in all subjects, including normal subjects in which no other effects of TZDs are observed. Insulin also appears to suppress adiponectin levels. We have confirmed these results in normal rats. These findings suggest that adiponectin can be regulated by obesity, diabetes, TZDs, and insulin, and it may play a physiologic role in enhancing insulin sensitivity.
Pigmented villonodular synovitis of the knee. The results of total arthroscopic synovectomy, partial, arthroscopic synovectomy, and arthroscopic local excision. (1992)

Twenty-five patients who had had a diagnosis of pigmented villonodular synovitis of the knee were followed for an average of four and one-half years (range, two to ten years) after arthroscopic treatment. Five patients had had localized lesions and had been managed with local resection; all five had improvement, with no apparent recurrence. The remaining twenty patients had had diffuse disease. Of these twenty, eleven had had a complete arthroscopic synovectomy. All eleven had definite improvement in pain and function, and almost all had a decrease in synovitis and an increase in the range of motion of the knee; the disease recurred in only one. The other nine patients had had a partial arthroscopic synovectomy. Although most had some improvement in function and range of motion and a decrease in pain and synovitis, the disease recurred in five of the nine. Thus, in the patients who had had diffuse pigmented villonodular synovitis, the rate of recurrence was lower in those who had had a complete arthroscopic synovectomy than in those who had had a partial arthroscopic synovectomy (p = 0.01).
Full color natural light holographic camera (2013)

Full-color, three-dimensional images of objects under incoherent illumination are obtained by a digital holography technique. Based on self-interference of two beam-split copies of the object's optical field with differential curvatures, the apparatus consists of a beam-splitter, a few mirrors and lenses, a piezo-actuator, and a color camera. No lasers or other special illuminations are used for recording or reconstruction. Color holographic images of daylight-illuminated outdoor scenes and a halogen lamp-illuminated toy figure are obtained. From a recorded hologram, images can be calculated, or numerically focused, at any distances for viewing.
Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays (2003)

Whole genome DNA microarrays were constructed and used to investigate genomic diversity in 18 Campylobacter jejuni strains from diverse sources. New algorithms were developed that dynamically determine the boundary between the conserved and variable genes. Seven hypervariable plasticity regions (PR) were identified in the genome (PR1 to PR7) containing 136 genes (50%) of the variable gene pool. When comparisons were made with the sequenced strain NCTC11168, the number of absent or divergent genes ranged from 2.6% (40 genes) to 10.2% (163) and in total 16.3% (269) of the genes were variable. PR1 contains genes important in the utilisation of alternative electron acceptors for respiration and may confer a selective advantage to strains in restricted oxygen environments. PR2, 3 and 7 contain many outer membrane and periplasmic proteins and hypothetical proteins of unknown function that might be linked to phenotypic variation and adaptation to different ecological niches. PR4, 5 and 6 contain genes involved in the production and modification of antigenic surface structures.
Crystal and molecular structure of a 4,5-dimethyoxbilindione derived from etiobiliverdin-IVγ: a possible model compound for the phytochrome chromophore (1982)

The structure of a synthetic bile pigment, 3,8,12,17-tetraethyl-4,5-dimethoxy-2,7,13,18-tetramethyl-4,5-dihydrobilin-1,19(21H,24H)-dione, C33H44N4O4, has been determined using three-dimensional diffractometer data. It crystallizes in the triclinic space group P with a= 12,755 (2), b= 12.944(s), c= 12.615(2)A, α= 112.27°(2), β= 113.76°(2), γ= 75.45°(2), Z= 2. There is one-half of an n-hexane molecule of crystallization present per formula unit. The structure was solved by direct methods and refined by full-matrix least squares to yield a final R factor of 0.105. The compound, which could be considered as a model for the far-red form (Pfr) of the phytochrome chromphore, belongs to the class of bile pigments known trivially as bilipurpurins. Three of the four pyrrole rings form a conjugated system which is not strictly planar, but is quasi-helical in nature. The fourth ring which is joined to the others by an sp3 carbon atom, is considerably out of the plane of the other three. Bond lengths and angles show a large degree of bond fixation. There is intermolecular hydrogen bonding so that the molecules form hydrogen-bonded dimers.
Dewetting Effects on Polymer-Coated Surface Acoustic Wave Vapor Sensors (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDewetting Effects on Polymer-Coated Surface Acoustic Wave Vapor SensorsJay W. Grate and R. Andrew. McGillCite this: Anal. Chem. 1995, 67, 21, 4015–4019Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ac00117a031https://doi.org/10.1021/ac00117a031research-articleACS PublicationsRequest reuse permissionsArticle Views386Altmetric-Citations60LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of Si-Ge buffer layer for low-temperature Si epitaxial growth on Si substrate by rf plasma chemical vapor deposition (1983)

Silicon epitaxial growth on the Si-Ge buffer layer at a low substrate temperature by the rf plasma chemical vapor deposition using SiH4 and GeH4 has been investigated. The electron Hall mobility of the homoepitaxial layer grown at 750 °C with a growth rate of 14 Å/sec coincides with that of bulk Si, but for a high growth rate of 33 Å/sec, the mobility was limited to within half the value of bulk Si. However, a small amount of Ge introduced in an initial stage of growth to form the Si-Ge buffer layer improved the crystalline quality of the ensuing Si epitaxial layer with a high growth rate. The electron Hall mobility of the Si layer grown on the Si-Ge buffer layer was a similar value of bulk Si in a low carrier concentration of 6×1015 cm−3. The crystalline quality of the grown Si layers was examined by the combination of Rutherford backscattering spectrometry and transmission electron microscopy.
Optical properties of waveguide-coupled nanowires for sub-wavelength detection in microspectrometer applications (2015)

In this paper we experimentally investigate optical interactions between gold nanowires and fs-laser written waveguides in a view of applications for stationary-wave integrated Fourier-transform spectrometers in a movable mirror configuration. For this purpose we fabricated gold nanowires of widths in the range from 40 to 130 nm and of 25 nm in thickness directly on the surface of a borosilicate glass containing fs-laser written optical waveguides beneath. The out-coupling efficiency and the radiation pattern angular distribution were investigated at the wavelength of 850 nm, dependent on the geometrical size of the nanowires, the position of the waveguides under the surface, and the light polarization. We also report measured plasmonic scattering spectra of the nanowires in the wavelength range of 400 to 900 nm. Our findings show that the chosen geometries and material systems are promising candidates for the use in integrated focal plane array spectrometer devices. Finally, we demonstrate the successful operation of a waveguide spectrometer modified by a movable mirror with a stroke of more than 10 &lt;I&gt;μ&lt;/I&gt;m.
Carboxypeptidase M as a marker of macrophage maturation (1998)

During terminal maturation of blood monocytes (MO) into macrophages (MAC), a multitude of phenotypic and functional changes occur: cells increase in size and enhance their capacity for phagocytosis and tumor cytotoxicity, but decrease their ability for T-lymphocyte stimulation. The pattern of secreted cytokines is shifted as is the profile of surface antigens. The identity of the MAC maturation-associated antigen MAX.I/MAX.II with carboxypeptidase M (CPM), a phosphoinositol-linked endopeptidase, was recently described. CPM is able to process a multitude of different substrates, among them immunologically important peptides such as bradykinin, anaphylatoxins and enkephalins. It was previously shown to be expressed in placenta, lung and kidney. CPM as detected by MAX.I/II shows a strong expression on MO-derived MAC in vitro and on MAC in vivo accompanying T-lymphocyte activation such as during allogeneic transplant rejection or allergic alveolitis. In contrast, its expression is suppressed on MAC by some types of tumor cells. A synchronous expression of CPM together with MAC cytotoxic function makes a functional relationship very well possible. However, the biological importance of CPM expression on MAC in vivo is difficult to predict, since a wide range of biologically active peptides are substrates for CPM, and the relevance for most of those peptides to be processed by CPM during an immune reaction is only poorly understood at present.
Overexpression of Rad51 protein stimulates homologous recombination and increases resistance of mammalian cells to ionizing radiation (1998)

Rad51 proteins share both structural and functional homologies with the bacterial recombinase RecA. The human Rad51 (HsRad51) is able to catalyse strand exchange between homologous DNA molecules in vitro . However the biological functions of Rad51 in mammals are largely unknown. In order to address this question, we have cloned hamster Rad51 cDNA and overexpressed the corresponding protein in CHO cells. We found that 2-3-fold overexpression of the protein stimulated the homologous recombination between integrated genes by 20-fold indicating that Rad51 is a functional and key enzyme of an intrachromosomal recombination pathway. Cells overexpressing Rad51 were resistant to ionizing radiation when irradiated in late S/G2phase of the cell cycle. This suggests that Rad51 participate in the repair of double-strand breaks most likely by homologous recombination involving sister chromatids formed after the S phase.
Immunohistochemical Methods for Predicting Cell of Origin and Survival in Patients With Diffuse Large B-Cell Lymphoma Treated With Rituximab (2010)

The Tally algorithm showed the best concordance with the microarray data while maintaining prognostic significance and ease of use.
Hyaluronan in joint disease (1997)

Hyaluronan is a major component of synovial fluid. It is synthesized in the joint and partly degraded in joint capsule and partly carried by lymph to lymph nodes and the general circulation. During various joint disorders, especially inflammatory ones, the amount of hyaluronan in the joint and its turnover rate are increased leading to pathologically high serum levels of the polysaccharide. These levels are a complex function of synovitis mass and the physical activity of the patient. Intra-articular injection of hyaluronan has been used in the treatment of osteoarthritis. Although it results in a relief of pain, controlled clinical trials have not yet convincingly shown any beneficiary effects of the treatment.
A preformed, ordered structure of a 25-residue peptide derived from a major histocompatibility complex class I antigen is required to affect insulin receptor function (1991)

It was recently shown that a 25-residue peptide, Dk-(61-85), derived from the alpha 1 domain of a murine major histocompatibility class I molecule (H-2Dk), affects insulin receptor functions (Hansen, T., Stagsted, J., Pedersen, L., Roth, R. A., Goldstein, A., and Olsson, L. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 3123-3126; Stagsted, J., Reaven, G. M., Hansen, T., Goldstein, A., and Olsson, L. (1990) Cell 62, 297-307). We now report that this peptide can reversibly assume a biologically active or inactive state as measured in the rat adipocyte glucose uptake assay, implying that the peptide has at least two interconvertible conformations. The peptide has an ordered conformation in 0.1 M HCl or 0.1 M NaCl stock solution as shown by circular dichroism, but has a disordered molecular structure and is inactive when dissolved in H2O. The biologically active peptide forms liquid crystals at the stock solution concentration (1 mM), so the CD spectra do not provide information on the secondary structure. Under all conditions tested, biological activity (measured after transfer to assay buffer) is associated with an ordered conformation in stock solution. Biological activity and an ordered conformation of the peptide in H2O stock solution can be induced by increasing ionic strength (greater than 100 mM NaCl for maximal effect) or increasing pH (greater than 5 for maximal effect). The induction rate of the ordered conformation is slow with a half-maximal value obtained after approximately 20 min. Both biological activity and the ordered structure are lost upon heating of stock solution to 90 degrees C or upon transfer to assay buffer. A similar correlation of ordered structure with biological activity was observed with two truncated peptides derived from Dk-(61-85). It is inferred from these results that the Dk-(61-85) peptide and related peptides only affect insulin-stimulated glucose uptake in rat adipocytes if they have assumed an ordered conformation in stock solution prior to transfer to assay buffer and exposure to cells.
DC-STAMP is essential for cell–cell fusion in osteoclasts and foreign body giant cells (2005)

Osteoclasts are bone-resorbing cells that play a pivotal role in bone remodeling. Osteoclasts form large multinuclear giant cells by fusion of mononuclear osteoclasts. How cell fusion is mediated, however, is unclear. We identify the dendritic cell-specific transmembrane protein (DC-STAMP), a putative seven-transmembrane protein, by a DNA subtraction screen between multinuclear osteoclasts and mononuclear macrophages. DC-STAMP is highly expressed in osteoclasts but not in macrophages. DC-STAMP-deficient mice were generated, and osteoclast cell fusion was completely abrogated in homozygotes despite normal expression of osteoclast markers and cytoskeletal structure. As osteoclast multinucleation was restored by retroviral introduction of DC-STAMP, loss of cell fusion was directly attributable to a lack of DC-STAMP. Defects in osteoclast multinucleation reduce bone-resorbing activity, leading to osteopetrosis. Similar to osteoclasts, foreign body giant cell formation by macrophage cell fusion was also completely abrogated in DC-STAMP-deficient mice. We have thus identified an essential regulator of osteoclast and macrophage cell fusion, DC-STAMP, and an essential role of osteoclast multinucleation in bone homeostasis.
A Novel Bioluminescence Orthotopic Mouse Model for Advanced Lung Cancer (2011)

Lung cancer is the leading cause of cancer-related death in the United States despite recent advances in our understanding of this challenging disease. An animal model for high-throughput screening of therapeutic agents for advanced lung cancer could help promote the development of more successful treatment interventions. To develop our orthotopic lung cancer model, luciferase-expressing A549 cancer cells were injected into the mediastinum of athymic nude mice. To determine whether the model would allow easy monitoring of response to therapeutic interventions, tumors were treated with 30 mg/kg Paclitaxel or were irradiated with 5 fractions of 2 Gy, and tumor burden was monitored using bioluminescence imaging. Evidence of radiation-induced lung injury was assessed using immunohistochemical staining for phospho-Smad2/3 and cleaved caspase-3. We found that tumor implantation recapitulated advanced human lung cancer as evidenced by tumor establishment and proliferation within the mediastinum. The tumor responded to Paclitaxel or radiation as shown by decreased tumor bioluminescence and improved overall survival. Immunohistochemistry revealed increased phospho-Smad2/3 and cleaved caspase-3 in irradiated lungs, consistent with radiation-induced lung injury. This orthotopic lung cancer model may help provide a method to assess therapeutic interventions in a preclinical setting that recapitulates locally advanced lung cancer.