gebhart/patrepeval huggingface dataset:
Power efficient FIR folding transformation for wireline digital communications (2002)

A new algorithm is introduced for power efficient implementation of the folding algorithm transformation for the adaptive FIR filters. The algorithm is based on the known minimum spanning tree problem which is a modification of the traveling sales person NP-hard problem. A sub-optimal solution can be obtained leading to dramatic reduction in the folded architecture switching activities. The optimum ordering within the folding sets is done in the steady state condition of the filtering operation. For a typical word length, and for large enough folding factor, the projected reduction in switching activity can be as large as 60%. The hierarchical energy analysis too (HEAT) was used to simulate the effect of this reduction on a typical Baugh-Wooley (1973) multiplier and reduction in power consumption for a typical wireline equalization implementation was found to be between 25% and 60%. The new algorithm is based on a simple breadth first search approach and can be easily performed for one time only when the filter is geared to the steady state mode. Dramatic improvement in power consumption can be achieved with minimal overhead.
Activation of Activator Protein 1 and Stress Response Kinases in Epithelial Cells Colonized by Helicobacter pylori Encoding the cag Pathogenicity Island (1999)

Helicobacter pylori interacts with the apical membrane of the gastric epithelium and induces a number of proinflammatory cytokines/chemokines. The subsequent infiltration of macrophages and granulocytes into the mucosa leads to gastric inflammation accompanied by epithelial degeneration. Gastric diseases, e.g. peptic ulcer or gastric adenocarcinoma, are more common among people infected with H. pylori strains producing VacA (vacuolating cytotoxin A) and possessing a cag (cytotoxin-associated antigen A) pathogenicity island. For the induction of the cytokine/chemokine genes in response to H. pylori, we studied the signaling leading to the nuclear activation of the early response transcription factor activator protein 1 (AP-1). We found that H. pylori strains carrying the pathogenicity island induce activation of AP-1 and nuclear factor kappaB. In contrast to the wild type or an isogenic strain without the vacA gene, isogenic H. pylori strains with mutations in certain cag genes revealed only weak AP-1 and nuclear factor kappaB activation. In respect to the molecular components that direct AP-1 activity, our results indicate a cascade of the cellular stress response kinases c-Jun N-terminal kinase, MAP kinase kinase 4, and p21-activated kinase, and small Rho-GTPases including Rac1 and Cdc42, which contributes to the activation of proinflammatory cytokines/chemokines induced by H. pylori encoding the cag pathogenicity island.
Strategies and Methods for Purifying Organic Compounds and Combinatorial Libraries (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Compiler blockability of dense matrix factorizations (1997)

The goal of the LAPACK project is to provide efficient and portable software for dense numerical linear algebra computations. By recasting many of the fundamental dense matrix computations in terms of calls to an efficient implementation of the BLAS (Basic Linear Algebra Subprograms), the LAPACK project has, in large part, achieved its goal. Unfortunately, the efficient implementation of the BLAS results often in machine-specific code that is not portable across multiple architectures without a significant loss in performance or a significant effort to reoptimize them. This article examines wheter most of the hand optimizations performed on matrix factorization codes are unnecessary because they can (and should) be performed by the compiler. We believe that it is better for the programmer to express algorithms in a machine-independent form and allow the compiler to handle the machine-dependent details. This gives the algorithms portability across architectures and removes the error-prone, expensive and tedious process of hand optimization. Although there currently exist no production compilers that can perform all the loop transformations discussed in this article, a description of current research in compiler technology is provided that will prove beneficial to the numerical linear algebra community. We show that the Cholesky and optimized automaticlaly by a compiler to be as efficient as the same hand-optimized version found in LAPACK. We also show that the QR factorization may be optimized by the compiler to perform comparably with the hand-optimized LAPACK version on modest matrix sizes. Our approach allows us to conclude that with the advent of the compiler optimizations dicussed in this article, matrix factorizations may be efficiently implemented in a BLAS-less form
Specific recognition of lamivudine-resistant HIV-1 by cytotoxic T lymphocytes (2000)

CTL can specifically recognize lamivudine-resistant HIV-1 variants. Therefore, the cellular immune response could have an important influence on the control of drug-resistant virus. Furthermore, this demonstrates that the immune system can generate new CTL specificities even in patients with advanced disease, as the M184V HIV variants emerges only after drug treatment. Specific immunotherapy against this epitope might be helpful in delaying or preventing lamivudine resistance.
In vitro model of angiogenesis using a human endothelium‐derived permanent cell line: Contributions of induced gene expression, G‐proteins, and integrins (1992)

The EA hy926 cell line is a continuous, clonable, human cell line that displays a number of features characteristic of vascular endothelial cells (Edgell et al., 1983). Here we report that when EA hy926 cells (EA cells) are plated on an extracellular matrix material [Matrigel], they undergo a process of morphological re-organization leading to the formation of a complex network of cord or tubelike structures. These events seem to resemble, in some respects, an in vitro process of angiogenesis. The morphological re-arrangement occurs within a 12-16 hr period and seems to require expression of new messenger RNA and protein, since it is completely blocked when actinomycin D or cycloheximide are present at the time the cells are plated on Matrigel. This is not due to overt toxicity of the drugs, since exposure of cells to actinomycin D at 2 hr or more after plating on Matrigel has little effect on the formation of the tubelike structures. The process of Matrigel-induced tube formation also apparently involves a G-protein mediated signal. Treatment of the EA cells with pertussis toxin completely blocks the process and causes the ADP-ribosylation of a 42 kD protein that is recognized by an antibody to Gi-alpha subunits. In contrast, concentrations of pertussis toxin sufficient to block tube formation have only modest effects on the adhesion or motility of EA cells on purified matrix components such as laminin or collagen IV. The process of Matrigel-induced tube formation also involves integrins since monoclonal antibodies to integrin alpha 6 or beta 1 subunits can completely block the process. The concentrations of anti-integrin antibodies needed to block tube formation are much lower than those required to block cell adhesion on purified matrix components and are sufficient to occupy less than 10% of the alpha 6 or beta 1 subunits available at the cell surface. These results suggest that integrins may be involved in this potential model of angiogenesis in processes beyond their usual role in cell adhesion. Based on these results, it seems likely that the EA hy 926 cell line will prove to be a useful model for in vitro study of angiogenic processes.
Exposure biomarkers in chemoprevention studies of liver cancer. (2001)

Hepatocellular carcinoma (HCC) is the most common type of liver cancer, the major risk factors being hepatitis B and C viruses and aflatoxins; other factors such as alcohol are also of importance in some populations. Aflatoxin exposure biomarkers include urinary aflatoxin metabolites and aflatoxin-albumin adducts in peripheral blood. These biomarkers are well validated and have been applied in studies of many populations worldwide. They are proving to be valuable end-points in intervention studies, including chemoprevention studies. The biomarkers permit assessment of primary prevention measures to reduce aflatoxin intake. In addition, the determination of individual urinary aflatoxin metabolite profiles means that the effectiveness of chemopreventive agents designed to modulate aflatoxin metabolism can also be evaluated. Both aflatoxin-albumin adducts and urinary aflatoxin metabolites have been associated with increased HCC risk in prospective studies, indicating the predictive value of these biomarkers at the group level. However, given the multifactorial and multistep nature of HCC, it is unlikely that these exposure biomarkers will be predictive at the individual level or be of value as surrogate end-points in longer-term intervention trials aimed at reducing disease incidence. Aflatoxin-related mutations at codon 249 of the p53 gene in plasma may be more relevant in this regard but their application requires further understanding of the temporal appearance of this biomarker in relation to the natural history of the disease.
Distribution and Heritability of Iris Thickness and Pupil Size in Chinese: The Guangzhou Twin Eye Study (2009)

Iris thickness is thinner in girls but is not associated with age in children. The variation is largely attributable to additive genetic effects.
Synthesis of metalloproteases and interleukin 6 (IL-6) in human osteoarthritic synovial membrane is an IL-1 mediated process. (1995)

We investigated the nature of cytokines synthesized by human osteoarthritic (OA) synovium, particularly interleukin 1 alpha (IL-1 alpha), interleukin 1 beta (IL-1 beta), and tumor necrosis factor alpha (TNF alpha). We examined the capacity of recombinant human interleukin 1 receptor antagonist (rhIL-1ra) to block the synthesis of metalloproteases (collagenase and stromelysin), IL-1 beta, and IL-6 in osteoarthritis (OA) synovium. Human OA synovium were incubated in the presence or absence of lipopolysaccharide (LPS) or increasing concentrations of rhIL-1ra. The determinations of IL-1 alpha, IL-1 beta, TNF alpha, IL-6, and IL-1ra in culture medium were carried out using specific ELISA. Although both IL-1 isoforms and TNF alpha could be produced by OA synovium, IL-1 beta was the predominant cytokine synthesized either in the presence or absence of LPS. Treatment of the OA synovium with an increasing concentration of rhIL-1ra (0-10 micrograms/ml) showed a dose dependent reduction of both metalloproteases and IL-6. Maximal inhibition was 70% for collagenase, 80% for stromelysin, and 76% for IL-6. LPS treated synovium also showed a consistent suppression of metalloproteases and IL-6, although a higher IL-1ra concentration was required. Conversely, IL-1 beta production was not inhibited by IL-1ra, irrespective of the concentration used and whether the membranes were LPS stimulated. These data showed that IL-1 appears to be the major autocrine cytokine involved in the stimulation of metalloproteases and IL-6 synthesis in OA synovium.
Universal Pathogen-Reduced Plasma in Elective Open-Heart Surgery and Liver Resection (2006)

ABO-incompatible transfusions and transfusion-related lung injury are today the leading transfusion-related causes of death in the developed world. Since anti-A and anti-B antibodies in plasma can give rise to serious, even fatal, transfusion reactions, ABO-identical/compatible plasma is indicated, but presents a logistical challenge and a risk for transfusion of incorrect plasma. In an effort to circumvent these problems, an ABO-independent universally applicable, pathogen-reduced plasma, Uniplas, has been developed and proven safe and efficacious for use in adults through prospective, randomized, controlled open-heart surgery studies and in prospective, parallel group, controlled liver resection studies. The results of these trials are presented and discussed in relation to solvent/detergent (SD) treated plasma, in general. The cost effectiveness of pathogen-reduced plasma is low because of the very low risk for transfusion transmitted viral infections in the developed world (US 2 to 9 million dollars per quality-adjusted life year). However, taking into account the combined safety of Uniplas with regard to transfusion-related lung injury, pathogen reduction and independence of ABO blood groups, the cost per gained life year is reduced to US 40,000 dollars to 100,000 dollars.
Superresolution microscopy for microbiology (2012)

This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of superresolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate superresolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments.
Superresolved imaging in digital holography by superposition of tilted wavefronts (2006)

A technique based on superresolution by digital holographic microscopic imaging is presented. We used a two dimensional (2-D) vertical-cavity self-emitting laser (VCSEL) array as spherical-wave illumination sources. The method is defined in terms of an incoherent superposition of tilted wavefronts. The tilted spherical wave originating from the 2-D VCSEL elements illuminates the target in transmission mode to obtain a hologram in a Mach-Zehnder interferometer configuration. Superresolved images of the input object above the common lens diffraction limit are generated by sequential recording of the individual holograms and numerical reconstruction of the image with the extended spatial frequency range. We have experimentally tested the approach for a microscope objective with an exact 2-D reconstruction image of the input object. The proposed approach has implementation advantages for applications in biological imaging or the microelectronic industry in which structured targets are being inspected.
The Splash 2 software environment (2002)

Splash 2 is an attached special purpose parallel processor in which the computing elements are user programmable FPGA devices. The architecture of Splash 2 is designed to accelerate the solution of problems which exhibit at least modest amounts of temporal or data parallelism. Applications are developed by writing behavioral descriptions of algorithms in VHDL, which are then iteratively refined and debugged within the Splash 2 simulator. Once an application is determined to be functionally correct in simulation, it is compiled to a gate list and optimized by logic synthesis. The gate list is then mapped onto the FPGA architecture by automatic placement and routing tools to form a loadable FPGA object module. A C language library and a symbolic debugger comprise the execution environment. The Splash 2 system has been shown to be effective on a variety of applications, including text searching, sequence analysis, and image processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automatic Generation of Architecture Model for Reconfigurable Build Tools (2013)

The wide spread of application specific processors like network or communication processors generated the need of optimizing retargetable software development tools such as compiler, linker, debugger, assembler and simulator. In order to quickly develop these tools for multiple design points under consideration, it is highly desirable to have them synthesized from formal processor descriptions written in Architecture Description Languages (ADLs). The ADL should be both simple and covering. The simplicity is translated into less effort to describe an architecture and the coverage means that the description provides enough information to the development tools. In this paper we focus on the challenges faced trying to accomplish these two main characteristics taking into account different classes of processors DSP, MCU, MPU. We propose a flat description generated from a sketch of the architecture. We show that the flat description is reducing the compilation time especially in optimizing parts (code generation, register allocation, encoding, instruction scheduling).
Non-sticky translocation of bio-molecules through Tween 20-coated solid-state nanopores in a wide pH range (2016)

Nanopore-based sensing technology is considered high-throughput and low-cost for single molecule detection, but solid-state nanopores have suffered from pore clogging issues. A simple Tween 20 coating method is applied to ensure long-term (several hours) non-sticky translocation of various types of bio-molecules through SiN nanopores in a wide pH range (4.0–13.0). We also emphasize the importance of choosing appropriate concentration of Tween 20 coating buffer for desired effect. By coating nanopores with a Tween 20 layer, we are able to differentiate between single-stranded DNA and double-stranded DNA, to identify drift-dominated domain for single-stranded DNA, to estimate BSA volume and to observe the shape of individual nucleosome translocation event without non-specific adsorption. The wide pH endurance from 4.0 to 13.0 and the broad types of detection analytes including nucleic acids, proteins, and biological complexes highlight the great application potential of Tween 20-coated solid-state nanopores.
in vivo inhibition of PC-3 human androgen-independent prostate cancer by a targeted cytotoxic bombesin analogue, AN-215 (2000)

The effectiveness of chemotherapy targeted to bombesin (BN) receptors was evaluated in nude mice bearing PC-3 human androgen-independent prostate cancers. Cytotoxic BN analogue AN-215, consisting of 2-pyrrolinodoxorubicin (AN-201) linked to BN-like carrier peptide RC-3094, was injected i.v. at 150 nmol/kg on days 1, 11 and 21. After treatment with AN-215, tumor volume was 69% (p < 0.01) smaller than that in controls and tumor doubling time was extended from 8.5 +/- 0.7 days to 20.3 +/- 3.5 days (p < 0.05). Cytotoxic radical AN-201, carrier RC-3094 and their unconjugated mixture administered at the same dosage were ineffective. The mortality rate was 12.5% in the AN-201 group and 16.7% in the group treated with the mixture, but no deaths occurred in mice receiving AN-215. Because the ester bond linking AN-201 to the carrier molecule is hydrolyzed much faster in mouse serum than in human serum, in the second experiment we investigated the tolerance to AN-215 and its effect in nude mice bearing PC-3 tumors after pharmacological inhibition of serum carboxylesterases. Two applications of AN-201 at 200 nmol/kg were lethal, whereas no mortality was observed after 4 injections of AN-215 at the same dose. Administration of 200 nmol/kg AN-215 on days 1, 7, 17 and 26 again produced 69% tumor inhibition. BN receptors on membranes of PC-3 tumors were detected by (125)I-[Tyr(4)]BN binding, and expression of mRNA for BRS-3 and GRP-R subtypes was also found. AN-215 showed a high affinity to PC-3 tumors, displacing the radioligand at an IC(50) of 12.95 +/- 0.35 nM. Because BN receptors are present on primary and metastatic prostate cancer, targeted chemotherapy with AN-215 might benefit patients with advanced prostatic carcinoma who relapsed androgen ablation.
Bacterial lipopolysaccharide acts as an adjuvant to induce autoimmune arthritisin mice (2000)

We investigated the ability of lipopolysaccharide (LPS) as an adjuvant to induce autoimmune arthritis. LPS from Escherichia coli was intraperitoneally injected into DBA/1J mice together with the joint cartilage component type II collagen (CII) on day 0. Thereafter, the injection of CII and LPS was continued every 2 weeks up to day 56. The results showed that mice injected with CII plus LPS had signs of arthritis on day 55 and the joint inflammation reached a peak on day 75. Injection of CII or LPS alone induced no arthritis. Histologically, marked oedema of synovium and intense infiltration of inflammatory cells, including neutrophils, were observed 3 days after the onset of joint inflammation. Twenty-one days later, there were marked proliferation of synovial tissues with many mononuclear cells and destruction of cartilage. Anti-CII immunoglobulin G (IgG) and IgG2a antibodies were markedly produced in mice injected with CII plus LPS. Pronounced secretion of cytokines, including interleukins-12 and -1beta, interferon-gamma and tumour necrosis factor-alpha, was also observed in these animals. Arthritis was passively transferred into naive syngeneic mice with sera but not with lymphoid cells from mice given CII with LPS. Other types of LPS from Salmonella enteritidis, Salmonella typhimurium and Klebsiella pneumoniae as well as lipid A from E. coli, induced inflammation in joints when administered with CII. Polymixin B sulphate mixed with LPS or lipid A blocked the induction of joint inflammation. These results indicate that LPS appears to play an important role as an adjuvant in the induction of arthritis in which autoimmunity to CII is involved.
Sequencing of bovine enamelin (“tuftelin”) a novel acidic enamel protein (1991)

Enamelins are a major group of 28-70-kDa acidic proteins rich in aspartic acid, glutamic acid, serine, and glycine found in developing and mature extracellular enamel; a unique and highly mineralized ectodermal tissue covering vertebrate teeth. They have been associated with the mineralization and structural organization of this tissue. In an attempt to elucidate the primary structure of enamelin, a 2674-base pair cDNA isolated from a bovine ameloblast-enriched, lambda Zap 2 expression library, was sequenced. The identity and localization of the deduced protein was confirmed by amino acid composition, enzyme-linked immunosorbent assay, Western blotting, indirect immunohistochemistry, and high resolution protein-A gold immunocytochemistry. The immunological techniques were employed using antibodies directed against synthetic peptides corresponding to the protein sequence deduced from the cloned cDNA sequence. The results reveal the deduced protein to be a novel acidic enamel protein. It contains 389 amino acids and has a calculated molecular weight of 43,814. Its amino acid composition is similar to that of "tuft" proteins (enamel matrix protein fragments remaining in the mature tissue). It contains one potential N-glycosylation site and 5 cysteine residues. Southern hybridization of the cloned cDNA with genomic bovine DNA indicated the existence of a single gene with one or more introns.