gebhart/patrepeval huggingface dataset:
Specific Activation of the Cysteine Protease CPP32 during the Negative Selection of T Cells in the Thymus (1997)

Cysteine proteases of the CED-3 and ICE family have been recently proposed as the ultimate executioners in several mammalian cell death pathways. Among them, the cysteine protease CPP32 has been shown to participate in programmed cell death (PCD), or apoptosis, affecting lymphoid cells in vitro. In the thymus, negative selection is a mechanism through which developing thymocytes expressing a TcR with high affinity for self peptide-MHC complexes are eliminated by PCD. In order to investigate the role of CPP32 in thymic apoptosis, isolated thymocytes were submitted to cell surface CD3 crosslinking by immobilized anti-CD3 mAb or to dexamethasone treatment. Although apoptosis occurred in the absence or after crosslinking with anti-CD3 mAb, specific activation of CPP32, as assessed by the extent of proteolytic cleavage of the p32 zymogen, was only detected in thymocytes cultured in the presence of the immobilized antibody or dexamethasone. This activation was a very early event during apoptosis as it occurred before the exposure of phosphatidyl serine to the upper side of the cell membrane. This was observed both in anti-CD3- and dexamethasone-induced apoptosis. Moreover, using mice transgenic for pigeon cytochrome C (PCC)-specific TcR, we were able to show that, after injection of PCC, the activation of CPP32 and cleavage of its substrate occurred in thymocytes obtained from mice expressing a permissive MHC haplotype for PCC presentation (H-2k). Moreover, PCC induced apoptosis was blocked by the caspase inhibitor zVAD. While spontaneous apoptosis was not accompanied by detectable levels of CPP32 processing, it was characterized by the proteolysis of poly(ADP-ribose) polymerase (PARP) and was blocked by the cysteine protease inhibitor, zVAD-CH2F. Taken together, these results support the concept that CPP32 is among the earliest effectors of the pathway leading to negative selection of autoreactive thymocytes. Our results also suggest the involvement of a distinct CPP32-like cysteine protease in spontaneous apoptosis of thymocytes.
Fabrication Scheme for Obtaining Transparent, Flexible, and Water-Insoluble Silk Films from Apparently Dissolved Silk-Gland Fibroin of <i>Bombyx mori</i> Silkworm (2017)

Films from silk fibroin protein are one of the most promising biomaterials because of their exquisite balance between mechanical properties and biocompatibility. Numerous schemes have been proposed for processing fibroin film, utilizing liquid silk fibroin (LSF) or regenerated silk fibroin (RSF). The films cast from LSF or RSF in the solution state are water-soluble, and therefore require postproduction treatment inducing β-sheet formation, to render them insoluble in water. Many kinds of postproduction treatments, using alcohol-water solution, water vapor, or controlled temperature, have been developed. However, the tuning and reproducibility of such treatments are quite sensitive and frequently render the fibroin films less flexible or even brittle because of the formation of an over content of β-sheet. To overcome this, we developed a novel scheme for fibroin processing using silk-gland fibroin (SGF). The essence of this scheme is to create a softly solidified fibroin-gel state of the silk glands with an imperfect β-sheet structure, by treating them with an ethanol/water mixture. Such a fibroin gel was found to dissolve in 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). The SGF film cast from the HFIP solution shows a flexible and water-insoluble nature with high reproducibility. In addition to this improvement, the SGF film produced by this method contains a significantly low level of residual HFIP molecules compared to the traditional RSF films prepared from an HFIP solution. The mechanism underlying these advantageous characteristics was investigated from the structural viewpoint, by using techniques such as <sup>13</sup>C solid-state NMR, differential scanning calorimetry, and wide-angle X-ray diffraction.
Geo-coding---an application in a local governmental information system (1968)

Across the nation, local governments of suburban communities surrounding major central cities are facing several basic problems: (1) a tremendous explosion in the development of land that is creating chaos in the record keeping and handling systems of these local governmental entities. This is primarily due to the sheer increase in volume; (2) the increasing population of these suburban areas is becoming more affluent, its tax rates are increasing rapidly, and is expecting more and better governmental service to enhance its standard of living.
Resolution-phase macrophages possess a unique inflammatory phenotype that is controlled by cAMP (2008)

Neutralizing injurious stimuli, proinflammatory mediator catabolism, and polymorphonuclear leukocyte (PMN) clearance are determinants of inflammatory resolution. To this, we recently added innate-type lymphocyte repopulation as being central for restoring postinflammation tissue homeostasis with a role in controlling innate immune-mediated responses to secondary infection. However, although macrophages dominate resolution, their phenotype and role in restoring tissue physiology once inflammation abates are unknown. Therefore, we isolated macrophages from the resolving phase of acute inflammation and found that compared with classically activated proinflammatory M1 cells, resolution-phase macrophages (rMs) possess weaker bactericidal properties and express an alternatively activated phenotype but with elevated markers of M1 cells including inducible cyclooxygenase (COX 2) and nitric oxide synthase (iNOS). This phenotype is controlled by cAMP, which, when inhibited, transforms rM to M1 cells. Conversely, elevating cAMP in M1 cells transforms them to rMs, with implications for cAMP in the resolution of systemic inflammation. It transpires that although rMs are dispensable for clearing PMNs during self-limiting inflammation, they are essential for signaling postresolution lymphocyte repopulation via COX 2 lipids. Thus, rM macrophages are neither classically nor alternatively activated but a hybrid of both, with a role in mediating postresolution innate-lymphocyte repopulation and restoring tissue homeostasis.
A region on human chromosome 4 (q35.1→qter) induces senescence in cell hybrids and is involved in cervical carcinogenesis (2005)

Human papillomavirus (HPV) types 16 and 18 are known to play a major role in cervical carcinogenesis. Additional genetic alterations are required for the development and progression of cervical cancer. Previously, we showed that the introduction of an entire human chromosome 4 into HPV-immortalized cells by microcell-mediated chromosome transfer (MMCT) can induce senescence in cell hybrids. In the present study, we established eight new murine donor cell lines harboring different fragments of the human chromosome 4. These were tested for their ability to induce senescence by MMCT into HPV16-immortalized keratinocytes (HPK II) and cervical carcinoma cells (HeLa). By exclusion, we could identify a region for a putative senescence gene or genes at 4q35.1-->qter. Further evidence that this locus may be involved in cervical carcinogenesis was obtained by studying sections of high-grade cervical intraepithelial neoplasias (CIN2/3) and cervical cancers from 87 women using a combination of interphase fluorescence in situ hybridization (I-FISH) and microsatellite PCR. I-FISH indicated copy number loss at 4q34-->qter. Microsatellite analysis showed that loss of one or more alleles at chromosome 4 was more frequent in the cervical carcinomas than in the CINs. Loss of heterozygosity (LOH) affected four areas, D4S412 (4p16.3), D4S2394 (4q28.2), D4S3041 (4q32.3), and D4S408 (4q35.1), and was highest at D4S408. LOH at terminal 4q has been reported previously for cervical carcinomas and other human malignancies. This is the first report associating allelic loss at 4q34-->qter with high-grade intraepithelial neoplasia and cervical carcinoma, and the first experimental evidence that this locus or these loci can induce senescence in cervical carcinoma cells and HPV16-immortalized cells.
A study of the inhibition of catalase by 3-amino-1:2:4-triazole (1958)

down the cell debris. All tissue preparations were made at 40 and used within 1 hr.
A G protein-coupled receptor with low density lipoprotein-binding motifs suggests a role for lipoproteins in G-linked signal transduction. (1994)

We have isolated and analyzed a cDNA from the central nervous system of the mollusc Lymnaea stagnalis encoding a putative receptor, which might be a natural hybrid between two different classes of receptor proteins. Preceded by a signal peptide, two types of repeated sequences are present in the N-terminal part of the protein. The first repeat displays a high sequence similarity to the extracellular binding domains of the low density lipoprotein receptor, which binds and internalizes cholesterol-containing apolipoproteins. The second repeat and the C-terminal part of the Lymnaea receptor are very similar to regions of a specific class of guanine nucleotide-binding protein-coupled receptors, the mammalian glycoprotein hormone receptors. The mRNA encoding the receptor is predominantly expressed in a small number of neurons within the central nervous system and to a lesser extent in the heart.
Genetic Features of the Widespread Plasmid Coding for the Carbapenemase OXA-48 (2011)

Complete sequencing of plasmid pOXA-48a carrying the bla(OXA-48) gene from a Klebsiella pneumoniae isolate was performed. Its backbone corresponded to that of an IncL/M-type plasmid, in which the bla(OXA-48) gene had been integrated through the acquisition of the Tn1999 composite transposon without any other antibiotic resistance gene. Molecular epidemiology using a collection of international OXA-48 producers revealed the wide diffusion of pOXA-48a or closely related plasmids.
Co-registration of pointclouds by 3D least squares matching (2008)

The automatic co-registration of point clouds, representing 3D surfaces, is a relevant problem in 3D modeling. We treat the problem as least squares matching of overlapping surfaces. The surface may have been digitized/sampled point by point using a laser scanner device, a photogrammetric method or other surface measurement techniques. Our proposed method estimates the transformation parameters of one or more 3D search surfaces with respect to a 3D template surface, using the Generalized Gauss-Markoff model, minimizing the sum of squares of the Euclidean distances between the surfaces. This formulation gives the opportunity of matching arbitrarily oriented 3D surfaces. It fully considers 3D geometry. The method derives its mathematical strength from the Least Squares matching concept and offers a high level of flexibility for many kinds of 3D surface correspondence problems. The experiments demonstrate the capabilities of the basic method and the extensions. Examples on the terrain/object modeling, cultural heritage applications, accuracy assessment and change detection are presented.
Adding Semantics to Detectors for Video Retrieval (2007)

In this paper, we propose an automatic video retrieval method based on high-level concept detectors. Research in video analysis has reached the point where over 100 concept detectors can be learned in a generic fashion, albeit with mixed performance. Such a set of detectors is very small still compared to ontologies aiming to capture the full vocabulary a user has. We aim to throw a bridge between the two fields by building a multimedia thesaurus, i.e., a set of machine learned concept detectors that is enriched with semantic descriptions and semantic structure obtained from WordNet. Given a multimodal user query, we identify three strategies to select a relevant detector from this thesaurus, namely: text matching, ontology querying, and semantic visual querying. We evaluate the methods against the automatic search task of the TRECVID 2005 video retrieval benchmark, using a news video archive of 85 h in combination with a thesaurus of 363 machine learned concept detectors. We assess the influence of thesaurus size on video search performance, evaluate and compare the multimodal selection strategies for concept detectors, and finally discuss their combined potential using oracle fusion. The set of queries in the TRECVID 2005 corpus is too small for us to be definite in our conclusions, but the results suggest promising new lines of research.
The effect of imatinib mesylate on patients with Philadelphia chromosome-positive chronic myeloid leukemia with secondary chromosomal aberrations. (2003)

Although some Ph+ CML patients with clonal evolution can have a complete cytogenetic response to imatinib mesylate, responses tend to be brief, and such patients may benefit from subsequent stem cell transplantation. Therefore, CML patients with clonal evolution may require therapy additional to imatinib mesylate for maximal eradication of the Ph+ leukemic cells.
Near-Ohmic Contact of n-GaAs with GaS/GaAs Quasi-Metal-Insulator-Semiconductor Structure (1998)

We report on the current-voltage ( I – V ) characteristics of a metal/ultrathin GaS (thickness<100 Å)/n + -GaAs (carrier concentration=2×10 18 cm -3 ) quasi-metal-insulator-semiconductor (QMIS) structure. The GaS was grown by molecular beam epitaxy (MBE) employing the precursor tertiarybutyl-galliumsulfide-cubane ([(t-Bu)GaS] 4 ). The I – V characteristics of the QMIS structure depend on the work function of various metals (Au, Al, Ti). We discovered that a QMIS structure leads to a reduction of Schottky-barrier height itself. Furthermore, we demonstrated near-ohmic contact (contact resistivity=3.7×10 -3 Ωcm 2 ) for a Ti/97-Å-thick GaS/n + -GaAs QMIS structure. From the relationship between the semiconductor barrier height and the metal work function, we determined that Fermi level pinning was almost eliminated by GaS passivation.
Optical Interconnection Networks Based on Microring Resonators (2010)

Interconnection networks must transport an always increasing information density and connect a rising number of processing units. Electronic technologies have been able to sustain the traffic growth rate, but are getting close to their physical limits. In this context, optical interconnection networks are becoming progressively more attractive, especially because new photonic devices can be directly integrated in CMOS technology. Indeed, interest in microring resonators as switching components is rising, but their usability in full optical interconnection architectures is still limited by their physical characteristics. Indeed, differently from classical devices used for switching, switching elements based on microring resonators exhibit asymmetric power losses depending on the output ports input signals are directed to. In this paper, we study classical interconnection architectures such as crossbar, Benes and Clos networks exploiting microring resonators as building blocks. Since classical interconnection networks lack either scalability or complexity, we propose two new architectures to improve performance of microring based interconnection networks while keeping a reasonable complexity.
Computer-Assisted Orthopedic Surgery: Current State and Future Perspective (2015)

Introduced about two decades ago, computer-assisted orthopedic surgery (CAOS) has emerged as a new and independent area, due to the importance of treatment of musculoskeletal diseases in orthopedics and traumatology, increasing availability of different imaging modalities, and advances in analytics and navigation tools. The aim of this paper is to present the basic elements of CAOS devices and to review state-of-the-art examples of different imaging modalities used to create the virtual representations, of different position tracking devices for navigation systems, of different surgical robots, of different methods for registration and referencing, and of CAOS modules that have been realized for different surgical procedures. Future perspectives will also be outlined.
Aqueous Photodegradation of Polycyclic Aromatic Hydrocarbons (2002)

Photodegradation of 12 polycyclic aromatic hydrocarbons was studied in aerated pure water, solutions of Suwannee River fulvic acid, and natural waters using polychromatic light (>290 nm). Quantum yields in pure water varied from 3.2 x 10(-5) to 9.2 x 10(-3). No obvious relationships were evident among the quantum yields and molecular properties. Photodegradation rate constants in solutions of Suwannee River fulvic acid or natural waters were largely unchanged compared to rate constants in pure water. Estimates of PAH photodegradation rates in natural waters can thus be obtained employing the quantum yields in pure water, PAH absorption, and solar irradiance. Calculated rate constants for photodegradation in surface waters during the summertime at mid-latitude varied from 3.2 x 10(-3) to 7.6 h(-1).
Leptin responsiveness restored by amylin agonism in diet-induced obesity: Evidence from nonclinical and clinical studies (2008)

Body weight is regulated by complex neurohormonal interactions between endocrine signals of long-term adiposity (e.g., leptin, a hypothalamic signal) and short-term satiety (e.g., amylin, a hindbrain signal). We report that concurrent peripheral administration of amylin and leptin elicits synergistic, fat-specific weight loss in leptin-resistant, diet-induced obese rats. Weight loss synergy was specific to amylin treatment, compared with other anorexigenic peptides, and dissociable from amylin's effect on food intake. The addition of leptin after amylin pretreatment elicited further weight loss, compared with either monotherapy condition. In a 24-week randomized, double-blind, clinical proof-of-concept study in overweight/obese subjects, coadministration of recombinant human leptin and the amylin analog pramlintide elicited 12.7% mean weight loss, significantly more than was observed with either treatment alone (P < 0.01). In obese rats, amylin pretreatment partially restored hypothalamic leptin signaling (pSTAT3 immunoreactivity) within the ventromedial, but not the arcuate nucleus and up-regulated basal and leptin-stimulated signaling in the hindbrain area postrema. These findings provide both nonclinical and clinical evidence that amylin agonism restored leptin responsiveness in diet-induced obesity, suggesting that integrated neurohormonal approaches to obesity pharmacotherapy may facilitate greater weight loss by harnessing naturally occurring synergies.
Molecular characterization of VAC1, a gene required for vacuole inheritance and vacuole protein sorting. (1992)

Cell division requires an accurate partitioning of cytoplasmic organelles. The segregation of vacuoles in the budding yeast Saccharomyces cerevisaie occurs at a specific time in the cell cycle and is spatially targeted to the small bud. Several yeast vac mutants have been isolated which are defective in this process. We have now cloned the VAC1 gene, corresponding to the first of these mutants, vac1-1. This gene encodes a protein of 515 amino acids, without homolog in the current data bases. It contains neither long hydrophobic stretches nor a classical leader peptide. The most notable aspect of the sequence is the presence of three zinc fingers. Yeast in which the VAC1 gene has been entirely deleted are viable. However, they grow more slowly than wild-type cells and only form microcolonies when grown on glycerol at 37 degrees C. These yeast are defective in vacuole segregation at both the permissive and nonpermissive temperatures. The vac1 mutant was previously shown to mislocalize carboxypeptidase Y to the cell surface, suggesting that Vac1p is involved in more than one vesicular traffic pathway.
Adaptive Threshold Technique for Bit-Flipping Decoding of Low-Density Parity-Check Codes (2010)

The bit-flipping (BF) algorithm for decoding of low-density parity-check (LDPC) codes requires less complex hardware than other decoding algorithms, but its error correcting performance needs to be improved. In this letter, a threshold adaptation scheme is applied to BF algorithm based decoding of LDPC codes. Our experiments show that the optimal threshold value for BF depends on the error conditions, and threshold adjustment during decoding helps to prevent meaningless no-flipping iterations. Based on these statistical observations, the adaptive threshold technique is proposed to pursue both the maximum error correcting capability and the fastest decoding convergence.
A grammar-based entity representation framework for data cleaning (2009)

Fundamental to data cleaning is the need to account for multiple data representations. We propose a formal framework that can be used to reason about and manipulate data representations. The framework is declarative and combines elements of a generative grammar with database querying. It also incorporates actions in the spirit of programming language compilers. This framework has multiple applications such as parsing and data normalization. Data normalization is interesting in its own right in preparing data for analysis as well as in pre-processing data for further cleansing. We empirically study the utility of the framework over several real-world data cleaning scenarios and find that with the right normalization, often the need for further cleansing is minimized.
Temporal and spatial pattern of RhoA expression in injured spinal cord of adult mice. (2013)

Traumatic spinal cord injury can upregulate RhoA expression in the neurons as well as all the glial cells in the spinal cord. RhoA expression patterns vary with post-injury time, location and among different parenchymal cells in the injured spinal cord.
Effect of tunicamycin on sialomucin and natural killer susceptibility of rat mammary tumor ascites cells. (1990)

The MAT-B1 and MAT-C1 ascites sublines of the 13762 rat mammary adenocarcinoma contain a dominant cell surface "complex" consisting of two glycoproteins: ascites sialoglycoprotein (ASGP)-1, a Mr 600,000-700,000 peanut agglutinin-binding sialomucin, and ASGP-2, a Mr 120,000 concancavalin A-binding glycoprotein (Sherblom et al., J. Biol. Chem., 255: 783-790, 1980; Sherblom and Carraway, J. Biol. Chem., 255: 12051-12059, 1980). Although both cell lines are resistant to lysis by natural killer cells, treatments which result in loss of cell surface ASGP-1 render the cells susceptible to natural killer cell lysis (Sherblom and Moody, Cancer Res., 46:4543-4546, 1986). Treatment of the ascites cells with 5 micrograms/ml tunicamycin for 24 h effectively inhibits glycosylation of ASGP-2 without affecting cell viability or total protein synthesis. Under these conditions, expression of ASGP-1 is depressed by at least 50% in both cell lines, as monitored by [3H]glucosamine incorporation and by binding of peanut agglutinin to intact cells. The size distribution of O-linked oligosaccharides in ASGP-1 from tunicamycin-treated versus control MAT-B1 cells is indistinguishable, as determined by Bio-Gel P-4 chromatography following alkaline-borohydride treatment. Complex isolated from either treated or control cells bands at the same density in a CsCl gradient containing Triton X-100 and contains a diffuse band corresponding to ASGP-2 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Tunicamycin-treated cells, consistent with the reduced expression of ASGP-1, are significantly more susceptible to natural killer cell-mediated lysis, when compared to untreated controls. The results suggest that N-linked glycosylation is a prerequisite for sialomucin synthesis and/or complex formation.