gebhart/patrepeval huggingface dataset:
The software bookshelf (1997)

Legacy software systems are typically complex, geriatric, and difficult to change, having evolved over decades and having passed through many developers. Nevertheless, these systems are mature, heavily used, and constitute massive corporate assets. Migrating such systems to modern platforms is a significant challenge due to the loss of information over time. As a result, we embarked on a research project to design and implement an environment to support software migration. In particular, we focused on migrating legacy PL/I source code to C++, with an initial phase of looking at redocumentation strategies. Recent technologies such as reverse engineering tools and World Wide Web standards now make it possible to build tools that greatly simplify the process of redocumenting a legacy software system. In this paper we introduce the concept of a software bookshelf as a means to capture, organize, and manage information about a legacy software system. We distinguish three roles directly involved in the construction, population, and use of such a bookshelf: the builder, the librarian, and the patron. From these perspectives, we describe requirements for the bookshelf, as well as a generic architecture and a prototype implementation. We also discuss various parsing and analysis tools that were developed and integrated to assist in the recovery of useful information about a legacy system. In addition, we illustrate how a software bookshelf is populated with the information of a given software project and how the bookshelf can be used in a program-understanding scenario. Reported results are based on a pilot project that developed a prototype bookshelf for a software system consisting of approximately 300K lines of code written in a PL/I dialect.
Hepatic Stellate Cells as a Target for the Treatment of Liver Fibrosis (2001)

Following chronic liver injury of any etiology, there is progressive fibrosis. To date, removing the causative agent is the only effective therapy to stop or even reverse liver fibrosis. Therefore, the development of effective antifibrotic therapies represents a challenge for modern hepatology. In the past decade, dramatic advances have been made in the understanding of the cellular and molecular mechanisms underlying liver fibrogenesis. The identification of activated hepatic stellate cells (HSCs) as the major fibrogenic cell type in the injured liver, as well as the recognition of key cytokines involved in this process, have facilitated the design of promising new antifibrotic therapies. These therapies are aimed at inhibiting the accumulation of activated HSCs at the sites of liver injury and preventing the deposition of extracellular matrix. Although many of these approaches are effective in experimental models of liver fibrosis, their efficacy and safety in humans are still unknown. This review describes the current therapeutic approaches for liver fibrosis and discusses different features of activated HSCs as a target to design new treatments to inhibit scar formation in chronic liver diseases.
Phenotype and Homing of CD4 Tumor-Specific T Cells Is Modulated by Tumor Bulk (2005)

Technical difficulties in tracking endogenous CD4 T lymphocytes have limited the characterization of tumor-specific CD4 T cell responses. Using fluorescent MHC class II/peptide multimers, we defined the fate of endogenous Leishmania receptor for activated C kinase (LACK)-specific CD4 T cells in mice bearing LACK-expressing TS/A tumors. LACK-specific CD44(high)CD62L(low) CD4 T cells accumulated in the draining lymph nodes and had characteristics of effector cells, secreting IL-2 and IFN-gamma upon Ag restimulation. Increased frequencies of CD44(high)CD62L(low) LACK-experienced cells were also detected in the spleen, lung, liver, and tumor itself, but not in nondraining lymph nodes, where the cells maintained a naive phenotype. The absence of systemic redistribution of LACK-specific memory T cells correlated with the presence of tumor. Indeed, LACK-specific CD4 T cells with central memory features (IL-2(+)IFN-gamma(-)CD44(high)CD62L(high) cells) accumulated in all peripheral lymph nodes of mice immunized with LACK-pulsed dendritic cells and after tumor resection. Together, our data demonstrate that although tumor-specific CD4 effector T cells producing IFN-gamma are continuously generated in the presence of tumor, central memory CD4 T cells accumulate only after tumor resection. Thus, the continuous stimulation of tumor-specific CD4 T cells in tumor-bearing mice appears to hinder the systemic accumulation of central memory CD4 T lymphocytes.
Quantitative determination of SC-68328 in dog plasma using flow injection and tandem mass spectrometry (2000)

A flow injection/tandem mass spectrometric assay was developed to quantitate SC-68328 in dog plasma using its stable isotopic analog [13C4]SC-68328 as an internal standard (IS). Since SC-68328, a manganese-based superoxide dismutase mimetic, is very unstable, very polar and adheres to silica-based high-performance liquid chromatographic columns, the analyte and IS were derivatized to their bis-isothiocyanate forms followed by a liquid-liquid extraction with methylene chloride and analyzed using positive ion electrospray mass spectrometric detection. SC-68328 was quantitated using the peak-height ratio of SC-68328 to its IS using MS/MS in the multiple reaction monitoring mode. The lower limit of quantitation of the assay was 0.25 microg ml(-1) SC-68328 in dog plasma with an inter-day precision of 11.8% and an accuracy of 113% (n = 12). Acceptable precision and accuracy were also obtained for concentrations in the calibration curve range (0.25-10 microg ml(-1) SC-68328 in dog plasma).
A human immunoglobulin G receptor exists in both polypeptide-anchored and phosphatidylinositol-glycan-anchored forms. (1989)

Several cDNA clones encoding the human immunoglobulin G receptor CD16 were isolated from human lung or peripheral blood leukocyte cDNA libraries. Nucleotide sequence comparisons revealed that the cDNAs could be divided into two groups. cDNA clones in one group encode a protein that terminates 4 amino acids after the putative transmembrane domain. Clones in the second group encode a protein with an extra 21 amino acids that could comprise a cytoplasmic domain. Direct peptide sequencing was used to determine the N terminus of the mature CD16 receptor protein and supported the existence of the two forms of the receptor. Treatment of neutrophils with phosphatidylinositol-specific phospholipase C resulted in the release of a large percentage of the CD16 molecules from the cell surface. In contrast, treatment of natural killer cells with phosphatidylinositol-specific phospholipase C did not release any CD16 from the cell surface. These data demonstrate that both polypeptide-anchored and phosphatidylinositol-glycan-anchored forms of the CD16 molecule exist and that they are differentially expressed on neutrophils and natural killer cells.
How to measure the Mueller matrix of liquid-crystal cells (2001)

The Mueller matrix is the transfer matrix in the Stokes algebra that describes the polarization of natural light. This matrix is very versatile for the task of characterizing the optical properties of liquid-crystal cells, since it can be used for comparison with theoretical calculations, the determination of material parameters and the modelling of the cell as an optical building block for technological use. We have constructed a Mueller-matrix spectrometer, with the ability to perform fast, dynamic measurements of the Mueller matrix of small areas of liquid-crystal cells throughout the visible range. To illustrate the potential of the instrument, dynamic measurements on a ferroelectric-liquid-crystal cell are presented and analysed. The optical measurements indicate that there is an asymmetry between the up and the down state, tilted smectic layers and polarization reversal initiated at the boundaries.
Roles of the Structure and Orientation of Ligands and Ligand Mimics inside the Ligand-Binding Pocket of the Vitamin D-Binding Protein (1997)

1alpha,25-Dihydroxyvitamin D3, the vitamin D hormone, manifests its diverse biological properties by specifically binding to the vitamin D sterol-binding pockets of vitamin D-binding protein (DBP) and vitamin D receptor. In the past, several affinity, photoaffinity, and chemical modification studies have been carried out to probe the vitamin D sterol-binding pocket of DBP and to evaluate the relationship between the structure of this pocket and the functions of the protein. In the present study, we examined the steric requirements inside this pocket by considering conformational structures of various bromoacetate derivatives of 25-hydroxyvitamin D3 and 1alpha,25-dihydroxyvitamin D3 and their abilities to covalently and specifically modify this pocket. We observed that, although 25-hydroxyvitamin D3 3beta-bromoacetate (25-OH-D3-3-BE), 1alpha,25-dihydroxyvitamin D3 3beta-bromoacetate [1alpha,25(OH)2D3-3-BE], 1alpha,25-dihydroxyvitamin D3 1alpha-bromoacetate [1alpha,25(OH)2D3-1-BE], and 1alpha,25-dihydroxyvitamin D3 1alpha,3beta-dibromoacetate [1alpha,25(OH)2D3-1,3-di-BE] bound DBP in a specific manner, only [3H]-25-OH-D3-3-BE and [3H]-1alpha,25(OH)2D3-3-BE affinity labeled the protein. BNPS-skatole cleavages of [3H]-25-OH-D3-3-BE- and 3H-1alpha,25(OH)2D3-3-BE-labeled DBP samples produced the same labeled peptide (N-terminal), demonstrating the specificity of labeling by these analogs. Energy-minimized conformational structures of these bromoacetate derivatives indicated significant changes in the A-ring conformations of these analogs. These structural changes were invoked to explain the inability of [3H]-1alpha,25(OH)2D3-1-BE and [3H]-1alpha,25(OH)2D3-1,3-di-BE to affinity label DBP. Overall, these studies suggested that the vitamin D sterol-binding pocket in DBP is sterically quite restrictive. This information could be potentially important in designing future vitamin D-based drugs for several diseases.
BAFF and APRIL protect myeloma cells from apoptosis induced by interleukin 6 deprivation and dexamethasone (2003)

Identification of growth factors in neoplasias may be a target for future therapies by blocking either growth factor receptor interaction or the induced pathway. Using gene expression profiling, we identified overexpression of 2 receptors for a proliferation-inducing ligand (APRIL) and B-cell activating factor (BAFF) in malignant plasma cells compared with normal plasma cells. APRIL and BAFF are involved in a variety of tumor and autoimmune diseases, including B-cell malignancies. We confirmed the expression of BAFF and APRIL receptors (B-cell maturation antigen [BCMA], transmembrane activator and calcium modulator and cyclophilin ligand interactor [TACI], and BAFF-R) in a majority of 13 myeloma cell lines and in the purified primary myeloma cells of 11 patients. APRIL and BAFF were potent survival factors for exogenous cytokine-dependent myeloma cell lines and were autocrine growth factors for the RPMI8226 and L363 autonomously growing cell lines. These factors activated nuclear factor (NF)-kappaB, phosphatidylinositol-3 (PI-3) kinase/AKT, and mitogen-activated protein kinase (MAPK) kinase pathways and induced a strong up-regulation of the Mcl-1 and Bcl-2 antiapoptotic proteins in myeloma cells. BAFF or APRIL was also involved in the survival of primary myeloma cells cultured with their bone-marrow environment, and protected them from dexamethasone (DEX)-induced apoptosis. Finally, the serum levels of BAFF and APRIL were increased about 5-fold in patients with multiple myeloma (MM) as compared with healthy donors. Altogether, these data suggest that APRIL/BAFF inhibitors may be of clinical value in MM.
Understanding Tradeoffs in Software Transactional Memory (2007)

There has been a flurry of recent work on the design of high performance software and hybrid hardware/software transactional memories (STMs and HyTMs). This paper re-examines the design decisions behind several of these state-of-the-art algorithms, adopting some ideas, rejecting others, all in an attempt to make STMs faster. We created the transactional locking (TL) framework of STM algorithms and used it to conduct a range of comparisons of the performance of non-blocking, lock-based, and Hybrid STM algorithms versus fine-grained hand-crafted ones. We were able to make several illuminating observations regarding lock acquisition order, the interaction of STMs with memory management schemes, and the role of overheads and abort rates in STM performance
A role for cytokines in antigen presentation: IL-1 and IL-4 induce accessory functions of antigen-presenting cells. (1990)

Fixation of APC with 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (ECDI) eliminates their ability to stimulate proliferation of alloreactive T cells or the D10 T cell clone, although a partial response, IL-4 production, was measured. However, if APC were activated before fixation, they could be ECDI-fixed and retain the ability to induce T cell proliferation. IL-1, IL-4 or LPS were capable of activating APC in this way, whereas IFN-gamma was not. This activation step occurred in 6 h, required protein synthesis, and was distinct from increases in Ia or IL-1. This suggests resting APC lack structures that are essential for inducing T cell proliferation.
Production and purification of recombinant human inhibin and activin (2002)

Inhibin and activin are protein hormones with diverse physiological roles including the regulation of pituitary FSH secretion. Like other members of the transforming growth factor-beta gene family, they undergo processing from larger precursor molecules as well as assembly into functional dimers. Isolation of inhibin and activin from natural sources can only produce limited quantities of bioactive protein. To purify large-scale quantities of recombinant human inhibin and activin, we have utilized stably transfected cell lines in self-contained bioreactors to produce protein. These cells produce approximately 200 microg/ml per day total recombinant human inhibin. Conditioned cell media can be purified through column chromatography resulting in dimeric mature 32-34 kDa inhibin A and 28 kDa activin A. The purified recombinant proteins maintain their biological activity as measured by traditional in vitro assays including the regulation of FSH in rat anterior pituitary cultures and the regulation of promoter activity of the activin-responsive promoter p3TP-luc in tissue culture cells. These proteins will be valuable for future analysis of inhibin and activin function and have been distributed to the US National Hormone and Peptide Program.
Hybrid Image and Signal Processing (1988)

Topics presented in these proceedings include: optical processors, bimodal optical computers, systems for geophysical diffraction tomography, parallel image processing, optical image processors, processor arrays, hypercube multiprocessors, border finding in cardiac digital x-ray images, and analysis of ultrasound image sequences by concurrent processing.
Assay of Volatile Oil-Cyclodextrin Complexes by Pyrolyzis Gas-Chromatography (1981)

A pyrolytic gaschromatographic process was developed for the routine assay of both cyclodextrin inclusion complexes, and for the differentiation of the mechanical mixture of the same oil with beta-cyclodextrin. The method is a direct assay of low material demand.
V2X Security & Privacy: The Current State and its Future (2011)

Vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communication is currently a focus of research and standardization in the USA, Europe and Asia. It is believed that V2V safety applications are able to reduce traffic fatalities significantly. Data security was identified as a major technical aspect to resolve before potential deployment. In particular, communication security and privacy are main aspects to consider but also physical security of the microcontroller, key injection, privacy mechanisms implemented by government agencies, and policy questions around security. This article provides an overview of the current state and of open issues.
A Randomized Trial of an N-methyl-D-aspartate Antagonist in Treatment-Resistant Major Depression (2006)

Robust and rapid antidepressant effects resulted from a single intravenous dose of an N-methyl-D-aspartate antagonist; onset occurred within 2 hours postinfusion and continued to remain significant for 1 week.
Description of an In Vitro Platelet Function Analyzer-PFA-100™ (1995)

A new in vitro system for the detection of platelet dysfunction, PFA-100, has been developed. It provides a quantitative measure of platelet function in anticoagulated whole blood. The system comprises a microprocessor-controlled instrument and a disposable test cartridge containing a biologically active membrane. The instrument aspirates a blood sample under constant vacuum from the sample reservoir through a capillary and a microscopic aperture cut into the membrane. The membrane is coated with collagen and epinephrine or adenosine 5'-diphosphate. The presence of these biochemical stimuli, and the high shear rates generated under the standardized flow conditions, result in platelet attachment, activation, and aggregation, slowly building a stable platelet plug at the aperture. The time required to obtain full occlusion of the aperture is reported as the "closure time." We have found that impairment of von Willebrand factor, or inhibition of platelet receptors glycoprotein Ib or IIb/IIIa with monoclonal antibodies or peptides, resulted in abnormal closure times. An antifibrinogen antibody, in contrast, failed to show any effect. The test appears to be sensitive to platelet adherence and aggregation abnormalities. The PFA-100 system has potential applications in routine evaluation of platelet function in the clinical setting because of its accuracy, ease of operation, and rapid turnaround of results.
Determination of the c-MYC DNA-binding site. (1991)

The carboxyl terminus of the protein encoded by the c-MYC protooncogene has similarity to the helix-loop-helix family of DNA-binding proteins and recognizes a six-nucleotide-long DNA sequence. We have used in vitro-translated c-MYC protein to further define its DNA-binding specificity. The hexanucleotide originally identified is necessary for DNA binding by c-MYC, but not sufficient; the c-MYC target site is a 12-nucleotide-long palindrome. This site is present within regulatory regions of genes that are expressed during cell growth. Point mutations within the helix-loop-helix motif of c-MYC abolish DNA-binding and transforming activities, indicating that c-MYC acts as a DNA-binding protein to transform cells. c-MYC may transform cells by activating transcription of genes required for cell division.
Novedades en el IVA para 2007 (2007)

En el presente artículo los autores analizan las principales novedades que se han producido en el Impuesto sobre el Valor Añadido, como consecuencia de los cambios introducidos por diferentes normas aprobadas a lo largo del año 2006 (Leyes 3/2006, 4/2006, 6/2006, 26/2006 y 36/2006 y Orden EHA/3958/2006), estructurándolo en dos partes: en la primera, se comentan las modificaciones normativas que tienen como punto común el hecho de que todas ellas tienen su origen en el Derecho comunitario, que ha obligado a la modificación de diversos preceptos de la Ley 37/1992, analizándose en la segunda parte aquellas modificaciones que tienen como nota común que no se trata de la adaptación de la Ley 37/1992 al Derecho comunitario, sino que consiste en cambios en la normativa del tributo que, supondremos que con cobertura en la norma comunitaria, responden exclusivamente a la voluntas legislatoris interna (no son cambios que resultaran obligatorios desde la perspectiva del acerbo comunitario).
Induction of Type I Diabetes by Interferon-α in Transgenic Mice (1993)

Type I diabetes is an autoimmune disease involving an interaction between an epigenetic event (possibly a viral infection), the pancreatic beta cells, and the immune system in a genetically susceptible host. The possibility that the type I interferons could mediate this interaction was tested with transgenic mice in which the insulin-producing beta cells expressed an interferon-alpha. These mice developed a hypoinsulinemic diabetes associated with a mixed inflammation centered on the islets. The inflammation and the diabetes were prevented with a neutralizing antibody to the interferon-alpha. Thus, the expression of interferon-alpha by the beta cells could be causal in the development of type I diabetes, which suggests a therapeutic approach to this disease.
Dual-Label Time-resolved Immunofluorometric Assay of Free and Total Prostate-specific Antigen Based on Recombinant Fab Fragments (2000)

The performance of this novel assay based on recombinant components is comparable to a conventional assay based on monoclonal antibodies. The more complete control of the essential characteristics of site-specifically derivatized recombinant Fab fragments will be valuable for the design of miniaturized and multianalyte assay concepts where correct antibody orientation, density, and capacity as well as uncompromised binding affinity are required.
A NEW TYPE OF BREAST PROSTHESIS (1970)

From the Department of Surgery (Plastic Surgery) of the UCLA School of Medicine, Los Angeles, Calif.
Role of MEF feeder cells in direct reprogramming of mousetail‐tip fibroblasts (2009)

Pluripotent stem cells can be induced from somatic cells by the transcription factors Oct3/4, Sox2, c-Myc and Klf4 when co-cultured with mouse embryonic fibroblast (MEF) feeder cells. To date, the role of the feeder cells in the reprogramming process remains unclear. In this study, using a comparative analysis, we demonstrated that MEF feeder cells did not accelerate reprogramming or increase the frequency of induced pluripotent stem (iPS) cell colonies. However, feeder conditions did improve the growth of primary iPS colonies and were necessary for passaging the primary colonies after reprogramming was achieved. We further developed a feeder-free culture system for supporting iPS growth and sustaining pluripotency by adding bFGF and activin A (bFA) to the medium. These data will facilitate the generation of human iPS cells without animal feeders for regenerative medicine.
Computer-generated holograms for 3D objects using the Fresnel zone plate (2005)

A new fast algorithm using the “host” Fresnel zone plate was proposed to improve the computational efficiency of computer-generated hologram (CGH) for 3D objects. By reading .3DS files, the spatial position information of each point of the 3D object was obtained directly. With the illumination of plane wave, the “host” Fresnel zone plate of a single point could be equal to all points located in the same depth plane - as the Fresnel zone plate was translated and superimposed along the horizontal and vertical axes. Consequently, the hologram of a 3D object could be built up by superimposing different Fresnel zone plates in the corresponding depth planes. For a digital object composed of 1060 points, it cost about 83s to generate a hologram of 1024*768 pixels. The CGH of 3D objects with the results of the reconstruction was presented in this paper, which proved the feasibility of this algorithm.