gebhart/patrepeval huggingface dataset:
Memory management for dataflow programming of multirate signal processing algorithms (1994)

Managing the buffering of data along arcs is a critical part of compiling a synchronous dataflow (SDF) program. This paper shows how dataflow properties can be analyzed at compile-time to make buffering more efficient. Since the target code corresponding to each node of an SDF graph is normally obtained from a hand-optimized library of predefined blocks, the efficiency of data transfer between blocks is often the limiting factor in how closely an SDF compiler can approximate meticulous manual coding. Furthermore, in the presence of large sample-rate changes, straightforward buffering techniques ran quickly exhaust limited on-chip data memory, necessitating the use of slower external memory. The techniques presented in this paper address both of these problems in a unified manner.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lipophilic Antifolates as Agents against Opportunistic Infections. 1. Agents Superior to Trimetrexate and Piritrexim against Toxoplasma gondii and Pneumocystis carinii in in Vitro Evaluations (1996)

2,4-Diaminopteridines (21 compounds) and 2,4-diamino-5-methyl-5-deazapteridines (34 compounds) along with three 2,4-diamino-5-unsubstituted-5-deazapteridines and four 2,4-diaminoquinazolines, each with an aryl groups attached to the 6-position of the heterocyclic moiety through a two-atom bridge (either CH2NH, CH2N(CH3),CH2S, or CH2CH2), were synthesized and evaluated as inhibitors of the growth of Toxoplasma gondii in culture and as inhibitors of dihydrofolate reductase enzymes from T. gondii, Pneumocystis carinii, and rat liver. Exceptionally high levels of combined potency and selectivity as growth inhibitors of T. gondii and as inhibitors of the microbial enzymes relative to the mammalian enzyme were found among the 5-methyl-5-deazapteridines but not for the other heterocyclic types. Thirty of the 34 5-methyl-5-deaza compounds gave growth inhibition IC50 values lower than that of pyrimethamine (0.4 microM) with 14 compounds below 0.1 microM, values that compare favorably with those for piritrexim and trimetrexate (both near 0.02 microM). As inhibitors of T gondii DHFR, all but three of the 34 5-methyl-5-deaza compounds gave IC50 values in the order of magnitude with those of piritrexim (0.017 microM) and trimetrexate (0.010 microM), and 17 compounds of this group gave IC50 values versus P. carinii DHFR similarly comparable with those of piritrexim (0.031 microM) and trimetrexate (0.042 microM). Thirteen of these congeners gave both T. gondii growth inhibition and DHFR inhibition IC50 values of 0.10 microM or less, thus indicating facile penetration of the cell membrane. Eleven of these inhibitors of both T. gondii growth and DHFR have selectivity ratios (IC50 rat liver divided by IC50 T. gondii) of 5 or greater for the parasite DHFR. The highest selectivity ratio of nearly 100 belongs to the 5-methyl-5-deaza compound whose 6-substituent is CH2CH2C6H3(OCH3)2-2,5. This compound is over 10(3)-fold more selective for T. gondii DHFR than bridge homologue piritrexim (selectivity ratio 0.088), a compound now in clinical trials. The candidate with CH2NHC6H3(CH3)2-2,5 in the 6-position gave the highest P. carinii DHFR selectivity ratio of 4.0, which is about 60-fold more selective than trimetrexate (0.071) and 80-fold more selective than piritrexim (0.048) toward this enzyme. The 10 best compounds with respect to potency and selectivity includes six compounds bearing 2,5-disubstituted phenyl groups in the side chain (with little, if any, difference in effects of methyl, methoxy, or ethoxy), two side chains bearing 1-naphthyl groups, and two with 5,6,7,8-tetrahydro-1-naphthyl groups. Bridge groups represented in the 10 choice compounds are CH2NH, CH2N(CH3), CH2CH2, and CH2S. The high levels of both potency and selectivity among these agents suggest that in vivo studies now underway may lead to agents that could replace trimetrexate and piritrexim in treatment of toxoplasmosis and P. carinii pneumonia.
cGMP produced in response to ANP and CNP regulates proliferation and differentiation of osteoblastic cells (1996)

The effects of natriuretic peptides on the proliferation and differentiation of osteoblast-like cells from rat calvariae were examined. Natriuretic peptides are physiological agonists that activate receptor guanylate cyclases, namely, natriuretic peptide receptor (NPR)-A and NPR-B. Exposure of cells to atrial natriuretic peptide (ANP) and C-type natriuretic peptide (CNP) resulted in large increases in the rate of intracellular production of guanosine 3',5'-cyclic monophosphate (cGMP). Moreover, CNP-like immunoreactivity was detected in the conditioned medium from osteoblast-like cells, while ANP was undetectable. In cells exposed to natriuretic peptides, a dose-dependent reduction in the rate of DNA synthesis was observed. Natriuretic peptides also stimulated the activity of alkaline phosphatase (ALPase) and the expression of mRNA for ALPase and osteocalcin and the mineralization of nodules by the cultured cells. These results could be reproduced by treating cells with 8-bromo-cGMP. Endothelin-1, whose physiological functions are the opposite of those of natriuretic peptides, decreased the ALPase activity and the mineralization of nodules. In the present study, natriuretic peptides were demonstrated to promote bone formation via the action of cGMP in a signal-transduction pathway mediated by specific receptors in osteoblast-like cells.
Modeling the Fluid Dynamics of Electrowetting on Dielectric (EWOD) (2006)

This paper discusses the modeling and simulation of a parallel-plate Electrowetting On Dielectric (EWOD) device that moves fluid droplets through surface tension effects. We model the fluid dynamics by using Hele-Shaw type equations with a focus on including the relevant boundary phenomena. Specifically, we show that contact angle saturation and hysteresis are needed to predict the correct shape and time scale of droplet motion. We demonstrate this by comparing our simulation to experimental data for a splitting droplet. Without these boundary effects, the simulation shows the droplet splitting into three pieces instead of two and the motion is over 15 times faster than the experiment. We then show how including the saturation characteristics of the device, and a simple model of contact angle hysteresis, allows the simulation to better predict the splitting experiment. The match is not perfect and suffers mainly because contact line pinning is not included. This is followed by a comparison between our simulation, whose parameters are now frozen, and a new experiment involving bulk droplet motion. Our numerical implementation uses the level set method, is fast, and is being used to design algorithms for the precise control of microdroplet motion, mixing, and splitting
Infection of influenza virus neuraminidase-vaccinated mice with homologous influenza virus leads to strong protection against heterologous influenza viruses (2014)

Vaccination is the best measure to prevent influenza pandemics. Here, we studied the protective effect against heterologous influenza viruses, including A/reassortant/NYMC X-179A (pH1N1), A/Chicken/Henan/12/2004 (H5N1), A/Chicken/Jiangsu/7/2002 (H9N2) and A/Guizhou/54/89×A/PR/8/34 (A/Guizhou-X) (H3N2), in mice first vaccinated with a DNA vaccine of haemagglutinin (HA) or neuraminidase (NA) of A/PR/8/34 (PR8) and then infected with the homologous virus. We showed that PR8 HA or NA vaccination both protected mice against a lethal dose of the homologous virus; PR8 HA or NA DNA vaccination and then PR8 infection in mice offered poor or excellent protection, respectively, against a second, heterologous influenza virus challenge. In addition, before the second heterologous influenza infection, the highest antibody level against nucleoprotein (NP) and matrix (M1 and M2) proteins was found in the PR8 NA-vaccinated and PR8-infected group. The level of induced cellular immunity against NP and M1 showed a trend consistent with that seen in antibody levels. However, PR8 HA+NA vaccination and then PR8 infection resulted in limited protection against heterologous influenza virus challenge. Results of the present study demonstrated that infection of the homologous influenza virus in mice already immunized with a NA vaccine could provide excellent protection against subsequent infection of a heterologous influenza virus. These findings suggested that NA, a major antigen of influenza virus, could be an important candidate antigen for universal influenza vaccines.
Defect reduction in nonpolar a-plane GaN films using in situ SiNx nanomask (2006)

We report on the use of in-situ SiNx nanomask for defect reduction in nonpolar a-plane GaN films, grown by metal-organic chemical vapor deposition. High-resolution x-ray diffraction analysis revealed that there was a monotonic reduction in the full width at half maximum, both on-axis and off-axis, with the increase in the SiNx thickness. Atomic force microscopy images revealed a significant decrease in the root-mean-square roughness and the density of submicron pits. Cross-section and plan-view transmission electron microscopy on the samples showed that the stacking fault density decreased from 8×105to3×105cm−1 and threading dislocation density decreased from 8×1010to9×109cm−2. Room temperature photoluminescence measurement revealed that the band-edge emission intensity increased with the insertion of the SiNx layer, which suggests reduction in the nonradiative recombination centers.
Pharmaceutic Development: Mesalazine (1990)

Sulfasalazine is composed of mesalazine and sulfapyridine linked by an azo bond. It has been shown that the clinical activity of sulfasalazine in the treatment of inflammatory bowel disease is derived from the mesalazine moiety, whereas most of the side effects are associated with the sulfapyridine component. To avoid the side effects associated with sulfapyridine, researchers have developed dosage forms that deliver mesalazine to the site of inflammation. The preparations were developed by combining two mesalazine molecules, by joining mesalazine with a carrier molecule that has a low side-effect profile, and by formulating controlled and slow-release mesalazine products. Claversal is a controlled-release product that contains 250 mg or 500 mg of mesalazine plus buffered adjuvants in a tablet core surrounded by a special acrylic polymer. The polymer coating starts to dissolve at pH 6.0, and, as a result, mesalazine is reliably released in the distal small bowel and colon. Thus this product can be useful in the treatment of patients with ulcerative colitis and Crohn's disease.
Mechanisms involved in the processing of the p55 and the p75 tumor necrosis factor (TNF) receptors to soluble receptor forms. (1994)

The two tumor necrosis factor (TNF) receptors (TNF-R55 and TNF-R75) can release soluble TNF-binding proteins (TNF-R55-BP and TNF-R75-BP) by proteolytic cleavage. The proteolytic processing of the TNF receptors was investigated in monoblastic THP-1 and promyelocytic HL-60-10 leukemic cell lines. The release of soluble forms of both receptors was rapidly stimulated by staurosporine-sensitive protein kinase C activation by phorbol myristate acetate (PMA) and more slowly stimulated by TNF. No receptor release was seen below a temperature of 16 degrees C. NH4Cl (10 mmol/liter) and monensin (1 mumol/liter), known to increase intracellular pH, inhibited to some extent PMA- and TNF-induced release of both TNF-R55-BP and TNF-R75-BP. The inhibitory effect of monensin might be explained by a diminished translocation of newly synthesized receptor to the plasma membrane. The weak inhibitory effect of NH4Cl on PMA-induced release of soluble receptor forms could be due to effects on a pH-sensitive compartment. PMA-induced down-regulation of receptors was not dependent on acidity as it occurred also in the presence of monensin and NH4Cl when the release of TNF-BPs is partially blocked. Dibutyryl cAMP inhibited the PMA-induced release of TNF-R55-BP but not of TNF-R75-BP in both cell lines investigated. In addition, dibutyryl cAMP alone stimulated the release of both receptors but only in THP-1 cells. Our data show that the generation of soluble forms of both TNF receptors can be regulated by both PKC and PKA.
PPARδ regulates glucose metabolism and insulin sensitivity (2006)

The metabolic syndrome is a collection of obesity-related disorders. The peroxisome proliferator-activated receptors (PPARs) regulate transcription in response to fatty acids and, as such, are potential therapeutic targets for these diseases. We show that PPARdelta (NR1C2) knockout mice are metabolically less active and glucose-intolerant, whereas receptor activation in db/db mice improves insulin sensitivity. Euglycemic-hyperinsulinemic-clamp experiments further demonstrate that a PPARdelta-specific agonist suppresses hepatic glucose output, increases glucose disposal, and inhibits free fatty acid release from adipocytes. Unexpectedly, gene array and functional analyses suggest that PPARdelta ameliorates hyperglycemia by increasing glucose flux through the pentose phosphate pathway and enhancing fatty acid synthesis. Coupling increased hepatic carbohydrate catabolism with its ability to promote beta-oxidation in muscle allows PPARdelta to regulate metabolic homeostasis and enhance insulin action by complementary effects in distinct tissues. The combined hepatic and peripheral actions of PPARdelta suggest new therapeutic approaches to treat type II diabetes.
The influence of slaughter method on the residual blood content of meat (1978)

Abstract The effect of slaughter method on the residual haemoglobin content of the M. longissimus dorsi and the amount of blood lost at exsanguination of sheep was investigated. The influence of stunning method (electrical, 90 V, or captive bolt pistol), pithing and bleeding‐out position were examined. Sheep bled lying lost more blood than those bled hanging and electrically‐stunned animals lost more blood than those stunned with a captive bolt pistol; pithing had no effect. The residual haemoglobin content of the muscle did not vary significantly between methods and there was no relationship between it and the amount of blood lost at slaughter.
The Imaging of Apoptosis with the Radiolabeled annexin V: Optimal Timing for Clinical Feasibility (2004)

In recent years, the imaging of drug-induced apoptosis has become one of the centers of interest in experimental and clinical research. In particular, the accurate monitoring of chemosensitivity as well as the early prediction of chemoresistance in response to various pro-apoptotic interventions are critical requirements for the best management of oncology patients. The use of technetium [(99m)Tc]-labeled annexin V on animal and human models of cancers provides a proof of principle for the feasibility of a non-invasive, in vivo detection of an apoptotic signal and then for the early assessment of tumor response in the course of chemotherapy. Although promising, however, the initial clinical data point out on the technical limitations that are still to be resolved in terms of tumor-to-background ratio and optimal timing for the imaging of apoptosis. In the present review article, we report the results of animal studies aimed to the evaluation of apoptotic peaks following chemotherapy. In the light of these basic research works, we analyze the profiles of radiolabeled annexin V uptake over time as observed in clinical trials. We then discuss possible new imaging strategies designed to optimize the visualization of apoptotic changes within tumor tissues using the [(99m)Tc]-labeled annexin V. We also suggest longer lived forms of radiolabeled annexin V designed to better understand the temporal patterns of apoptotic tumor response, which in turn, may help to capture the best time-window for the imaging of cell death.
Coimmunization with IL-15 plasmid enhances the longevity of CD8 T cells induced by DNA encoding hepatitis B virus core antigen (2006)

DNA vaccine constructed by HBc Ag 1-144 amino acid induces effective cell immunity, and cytokine plasmid-delivered IL-15 enhances the longevity of CD8(+) T cells.
Substrate Binding Stabilizes S-Adenosylhomocysteine Hydrolase in a Closed Conformation (2000)

Comparison of crystal structures of S-adenosylhomocysteine (AdoHcy) hydrolase in the substrate-free, NAD(+) form [Hu, Y., Komoto, J., Huang, Y., Gomi, T., Ogawa, H., Takata, Y., Fujioka, M., and Takusagawa, F. (1999) Biochemistry 38, 8323-8333] and a substrate-bound, NADH form [Turner, M. A., Yuan, C.-S., Borchardt, R. T., Hershfield, M. S., Smith, G. D., and Howell, P. L. (1998) Nat. Struct. Biol. 5, 369-376] indicates large differences in the spatial arrangement of the catalytic and NAD(+) binding domains. The substrate-free, NAD(+) form exists in an "open" form with respect to catalytic and NAD(+) binding domains, whereas the substrate-bound, NADH form exists in a closed form with respect to those domains. To address whether domain closure is induced by substrate binding or its subsequent oxidation, we have measured the rotational dynamics of spectroscopic probes covalently bound to Cys(113) and Cys(421) within the catalytic and carboxyl-terminal domains. An independent domain motion is associated with the catalytic domain prior to substrate binding, suggesting the presence of a flexible hinge element between the catalytic and NAD(+) binding domains. Following binding of substrates (i.e., adenosine or neplanocin A) or a nonsubstrate (i.e., 3'-deoxyadenosine), the independent domain motion associated with the catalytic domain is essentially abolished. Likewise, there is a substantial decrease in the average hydrodynamic volume of the protein that is consistent with a reduction in the overall dimensions of the homotetrameric enzyme following substrate binding and oxidation observed in earlier crystallographic studies. Thus, the catalytic and NAD(+) binding domains are stabilized to form a closed active site through interactions with the substrate prior to substrate oxidation.
Human immunodeficiency virus type 1 variants with increased replicative capacity develop during the asymptomatic stage before disease progression (1994)

We examined the replicative properties of a series of sequential isolates and biological clones of human immunodeficiency virus type 1 (HIV-1) obtained from an individual who progressed from seroconversion to AIDS in approximately 5 years. HIV-1 isolated soon after seroconversion replicated slowly and to low levels in cultures of peripheral blood mononuclear cells; however, subsequent isolates obtained during asymptomatic infection showed a marked increase in replication kinetics. This was examined in more detail by using a panel of 35 biological clones of HIV-1 generated from sequential patient peripheral blood mononuclear cell samples. Each clone was evaluated for replication in primary macrophages and CD4+ T lymphocytes and for the ability to induce syncytium formation in MT-2 cell cultures. Consistent with earlier observations, we found that all of the clones isolated just after seroconversion were slowly replicating and non-syncytium inducing (NSI). However, NSI variants with increased replication kinetics in macrophages were identified soon thereafter. These variants preceded the appearance of NSI and syncytium-inducing variants, with rapid replication in both macrophages and CD4+ T lymphocytes. To determine whether changes in the rate of replication could be traced to the early stages of the virus life cycle, PCR assays were used to evaluate entry and reverse transcription of selected biological clones in macrophages and CD4+ T lymphocytes. We found there was no inherent block to entry or reverse transcription for the slowly replicating variants; however, this does not preclude the possibility that small differences in the rate of entry may account for larger differences in the replication kinetics over many cycles. Overall, our results demonstrate that rapidly replicating variants of HIV-1 emerge during the asymptomatic period in a patient who subsequently progressed clinically, suggesting that these variants may play an important role in HIV-1 pathogenesis.
Trustless Machine Learning Contracts; Evaluating and Exchanging Machine Learning Models on the Ethereum Blockchain (2018)

Using blockchain technology, it is possible to create contracts that offer a reward in exchange for a trained machine learning model for a particular data set. This would allow users to train machine learning models for a reward in a trustless manner. The smart contract will use the blockchain to automatically validate the solution, so there would be no debate about whether the solution was correct or not. Users who submit the solutions won't have counterparty risk that they won't get paid for their work. Contracts can be created easily by anyone with a dataset, even programmatically by software agents. This creates a market where parties who are good at solving machine learning problems can directly monetize their skillset, and where any organization or software agent that has a problem to solve with AI can solicit solutions from all over the world. This will incentivize the creation of better machine learning models, and make AI more accessible to companies and software agents.
The mycobacterial secreted antigen 85 complex possesses epitopes that are differentially expressed in human leprosy lesions and Mycobacterium leprae-infected armadillo tissues (1993)

The granulomatous skin lesions in leprosy are thought to be initiated by the immune response to certain antigens of the causative agent, Mycobacterium leprae. The antigen 85 complex is one of the major targets in the immune response to M. leprae infection. In the present study, a panel of previously characterized monoclonal antibodies (MAbs) (3A8, Rb2, A4g4, A2h11, Pe12, and A3c12) reacting with different epitopes of the 85 complex proteins of Mycobacterium tuberculosis and M. leprae was employed in a comparative immunohistological analysis to demonstrate the in situ expression of 85 complex antigenic epitopes in leprosy lesions across the clinical spectrum and in M. leprae-infected armadillo liver tissues. These MAbs showed a heterogeneous staining pattern in a given leprosy lesion. In highly bacilliferous borderline and lepromatous leprosy lesions, MAbs Rb2, A4g4, A2h11, and Pe12 stained clear rod-shaped M. leprae bacilli within macrophages, and the degree of staining correlated with the bacillary index of the lesion. On the other hand, MAbs 3A8 and A3c12 staining was mostly seen as a diffuse staining pattern within interstitial spaces and on the membranes of the infiltrated cells but not the bacilli. In paucibacillary borderline and tuberculoid leprosy lesions, only 3A8, Rb2, and A3c12 showed distinct staining in association with infiltrates in the granuloma. None of these MAbs showed any detectable reaction with control nonleprosy skin lesions, while MAb A3c12 positively stained the granulomas of both leprosy and control specimens. In situ reactivity of these MAbs with M. leprae-infected armadillo liver tissues also showed a heterogeneous staining pattern. Interestingly, a clear difference in expression of these epitopes was observed between armadillo tissues and human leprosy lesions. By immunogold ultracytochemistry, we further showed the differential localization of these MAb-reactive epitopes on the cell surface, in the cytosol, and at the vicinity of M. leprae within Kupffer cells of armadillo liver tissues. Our results indicate that these antigenic epitopes of the antigen 85 complex are differentially expressed in leprosy lesions and infected armadillo tissues and that they could be target determinants in the immunopathological responses during M. leprae infection.