gebhart/patrepeval huggingface dataset:
Susceptibility to PNU-140690 (Tipranavir) of Human Immunodeficiency Virus Type 1 Isolates Derived from Patients with Multidrug Resistance to Other Protease Inhibitors (2000)

In our study we examined the anti-human immunodeficiency virus type 1 (anti-HIV-1) activity of a novel HIV-1 protease inhibitor, PNU-140690 (tipranavir), against patient-derived isolates resistant to multiple other protease inhibitors (PIs). The aim of our experiments was to investigate the genotypes and the in vitro phenotypes of drug resistance of PNU-140690. We carried out drug susceptibility tests with peripheral blood mononuclear cells and a fixed amount of infectious virus (1,000 50% tissue culture infective doses) to determine the 50% inhibitory concentration (IC(50)) and IC(90), PCR assays for the detection of drug resistance mutations in RNA in plasma, and direct sequencing of PCR products. Phenotypic resistance to PIs was invariably related to genotypic mutations. The substitutions among the amino acid residues of the protease included L10I, K20R, L24I, M36I, N37D, G48V, I54V, L63P, I64V, A71V, V77I, V82A, I84V, and L90M. Isolates from all of the patients had developed a maximal degree of resistance to indinavir, ritonavir, and nelfinavir (IC(50)s, >0.1 microM). We also compared these mutations with the amino acid changes previously described in association with in vivo tipranavir administration. The mutations included the following: I15V, E35D, N37D, R41K, D60E, and A71T. Infections with IIIB, 14aPre, and N70 were inhibited by an average drug IC(90) of 0.18 +/- 0.02 microM in multiple experiments. The average mean +/- standard error of mean IC(90) for the entire group of multidrug-resistant isolates derived from the mean values for two culture wells with p24 antigen supernatant appeared to be 0.619 +/- 0.055 microM (range, 0.31 to 0.86 microM). Tipranavir retained a sustained antiviral activity against PI-MDR clinical isolates and might be useful in combination regimens with other antiretroviral agents for patients who have already failed other PI-containing therapies.
3-Hydroxyisobutyrate Dehydrogenase fromPseudomonas putidaE23: Purification and Characterization (1996)

The NAD(+)-dependent 3-hydroxyisobutyrate dehydrogenase [EC 1.1.1.31] was purified to homogeneity from Pseudomonas putida E23. The enzyme was a tetramer (molecular mass, 120 kDa) consisted of identical subunits (molecular mass, 30 kDa). The enzyme was specific for NAD+ (Km, 0.44 mM). The maximal activity was obtained at about pH 10. The enzyme was specific for the L-isomer of 3-hydroxyisobutyrate. In addition to L-3-hydroxyisobutyrate, L-serine, 2-methyl-DL-serine, and 3-hydroxypropionate were substrates. The Km for L-3-hydroxyisobutyrate, L-serine, 2-methyl-DL-serine, and 3-hydroxypropionate were 0.12, 18, 44, and 83 mM, respectively. The enzyme was inhibited by p-chloromercuribenzoate, HgCl2, and AgNO3, but not by EDTA, alpha,alpha'-dipyridyl, and o-phenanthroline. The N-terminal 26 amino acid sequence was compared with the sequences deduced from the enzyme genes of rat liver and Pseudomonas aeruginosa.
Kramers–Kronig coherent receiver (2016)

The interest for short-reach links of the kind needed for inter-data-center communications has fueled in recent years the search for transmission schemes that are simultaneously highly performing and cost effective. In this work we propose a direct-detection coherent receiver that combines the advantages of coherent transmission and the cost-effectiveness of direct detection. The working principle of the proposed receiver is based on the famous Kramers–Kronig (KK) relations, and its implementation requires transmitting a continuous-wave signal at one edge of the information-carrying signal spectrum. The KK receiver scheme allows digital postcompensation of linear propagation impairments and, as compared to other existing solutions, is more efficient in terms of spectral occupancy and energy consumption.
Isolation and characterization of cDNA clones for human and bovine fibronectins. (1983)

A bovine fibronectin (FN) cDNA clone (pFB1) was isolated by screening a cDNA library of calf testis fibroblasts with a synthetic oligonucleotide probe. The probe was a mixture of eight 14-base-long oligonucleotides designed from the amino acid sequence Glu-Cys-Phe-Met-Pro present in the Mr 3,000 COOH-terminal fragment of bovine plasma FN [Petersen, T.E., Thøgersen, H.C., Skorstengaard, K., Vibe-Pedersen, K., Sahl, P., Sottrup-Jensen, L. & Magnusson. S. (1983) Proc. Natl. Acad. Sci. USA 80. 137-141]. pFB1 contained a 1,000 base-pair (bp) insert comprising the complete 3' noncoding sequence (690 bp) and approximately equal to 300 bp of the coding region. The clone pFB1 was used as a radioactive probe in the screening of a human cell line (Hs 578T) cDNA library. Eleven positive cDNA clones were detected, one of which, named pFH1, contained a 2,000-bp insert comprising the complete 3' noncoding region (693 bp) and approximately equal to 1,300 bp of the coding region of human FN. The sequences of the clone pFB1 insert and of the homologous region in clone pFH1 were determined. The nucleotide sequences are 90% homologous. Six amino acid changes were found, clustered in an area connecting two structural domains described in bovine plasma FN. Furthermore, the 204 COOH-terminal amino acid sequence of bovine FN was completed by overlapping two peptide fragments (MrS 3,000 and 23,000). Clone pFH1 was used in estimating the size of human fibronectin mRNA (7,900 bases) through blot hybridization analysis. Southern blot studies suggest that human FN is coded by a unique gene.
Purification of properties of Saccharomyces cerevisiae cystathionine β‐synthase (1994)

Cystathionine beta-synthase (beta-CTSase), which catalyses cystathionine synthesis from serine and homocysteine, was purified to homogeneity from Saccharomyces cerevisiae. The molecular mass of the enzyme was estimated to be 235 kDa by gel filtration and 55 kDa by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, indicating that it is a homotetramer. The N-terminal amino acid sequence of the enzyme perfectly coincided with that deduced from the nucleotide sequence of CYS4, except for the absence of initiation The purified beta-CTSase catalysed cysteine synthesis from serine (or O-acetylserine) and H2S. From this finding, we discuss the multifunctional nature and evolutionary divergence of S-metabolizing enzymes.
Metabolic benefits of dietary prebiotics in human subjects: a systematic review of randomised controlled trials (2013)

Complex relationships exist between the gut microflora and their human hosts. Emerging evidence suggests that bacterial dysbiosis within the colon may be involved in the pathogenesis of the metabolic syndrome, type 2 diabetes and CVD. The use of dietary prebiotic supplements to restore an optimal balance of intestinal flora may positively affect host metabolism, representing a potential treatment strategy for individuals with cardiometabolic disorders. The present review aimed to examine the current evidence supporting that dietary prebiotic supplementation in adults has beneficial effects on biochemical parameters associated with the development of metabolic abnormalities including obesity, glucose intolerance, dyslipidaemia, hepatic steatosis and low-grade chronic inflammation. Between January 2000 and September 2013, eight computer databases were searched for randomised controlled trials published in English. Human trials were included if at least one group received a dietary prebiotic intervention. In the present review, twenty-six randomised controlled trials involving 831 participants were included. Evidence indicated that dietary prebiotic supplementation increased self-reported feelings of satiety in healthy adults (standardised mean difference -0.57, 95% CI -1.13, -0.01). Prebiotic supplementation also significantly reduced postprandial glucose (-0.76, 95% CI -1.41, -0.12) and insulin (-0.77, 95% CI -1.50, -0.04) concentrations. The effects of dietary prebiotics on total energy intake, body weight, peptide YY and glucagon-like peptide-1 concentrations, gastric emptying times, insulin sensitivity, lipids, inflammatory markers and immune function were contradictory. Dietary prebiotic consumption was found to be associated with subjective improvements in satiety and reductions in postprandial glucose and insulin concentrations. Additional evidence is required before recommending prebiotic supplements to individuals with metabolic abnormalities. Large-scale trials of longer duration evaluating gut microbial growth and activity are required.
Id-1: Regulator of EGFR and VEGF and potential target for colorectal cancer therapy (2008)

This study revealed that Id-1, EGFR and VEGF took part in development and progression of colorectal carcinomas and that Id-1 was associated with regulations of EGFR and VEGF. The results of this study support the idea that not only EGFR and VEGF but also Id-1 could be new targets in cancer treatment.
Cloning and in vitro expression of a melanoma-associated antigen immunogenic in patients with melanoma (1991)

The purpose of this study was to identify human melanoma-associated Ag (MAA) that are immunogenic in patients, because these molecules may be useful immunogens to implement active specific immunotherapy. To this end, an expression cDNA library constructed from the human melanoma cell line A375 was screened with sera from patients with melanoma. A 1029-bp cDNA (designated D-1) was isolated. Its nucleotide sequence showed no significant homology with viral and mammalian sequences stored in GE-NETYX. cDNA D-1 hybridized to a 2.0-kb mRNA species from human melanoma, neuroblastoma, erythroleukemia, B lymphoid, and T lymphoid cell lines but not from a renal carcinoma cell line, PBL, and cultured skin fibroblasts. The D-1 clone produced a fusion protein that displayed a significantly higher reactivity with sera from patients with melanoma than from healthy controls. Furthermore, D-1 fusion protein induced in mice antibodies that immunoprecipitated a 50-kDa component from cultured human melanoma cells. The structural properties of D-1 MAA are different from those of previously described MAA. These results suggest that the approach we have applied may be useful to identify novel MAA expressed by melanoma cells. Furthermore, the immunogenicity of recombinant D-1 protein suggests that it may be a valuable immunogen to implement active specific immunotherapy in patients with melanoma, if additional experiments show that it has the appropriate tissue distribution.
Joint cartilage repair with transplantation of embryonic chondrocytes embedded in collagen-fibrin matrices. (2000)

Fibrin-collagen gel allowed stable graft fixation and provided an adequate microenvironment for embryonic chondrocytes to generate hyaline-like neocartilage in a full-thickness cartilage defect.
A New Transponder Architecture With On-Chip ADC for Long-Range Telemetry Applications (2006)

We present a new architecture for wireless power and data telemetry that recovers power and a system clock from a weak incident RF signal. A high-efficiency RF-DC converter generates a 3-VDC supply for the system from a -12.3-dBm incident RF signal, gathered by a commercial 50-/spl Omega/ antenna. A system clock is extracted from the same incident signal, by an injection-locked LC oscillator. Sub-harmonic injection-locking facilitates the separation of the incident and the transmit signal frequencies, without need for a PLL. The proposed architecture is used in a long-range telemetry device, incorporating an on-chip ADC, and employing active telemetry for data transmission. Data is transmitted through binary phase-shift-keying of a 900-MHz carrier. The prototype, implemented in 0.25-/spl mu/m CMOS, occupies less than 1 mm/sup 2/. A wireless operation range of more than 18 meters is indicated by anechoic chamber testing.
Temperature differences for trans-glycosylation and hydrolysis reaction reveal an acceptor binding site in the catalytic mechanism of Trypanosoma cruzi trans-sialidase (1997)

Trypanosoma cruzi, the agent of Chagas disease, expresses on its surface a trans-sialidase that catalyzes preferentially the transference of alpha-2,3-linked sialic acid to acceptors containing terminal beta-galactosyl residues, instead of the typical hydrolysis reaction, found in most sialidases. The trans-sialidase is responsible for the acquisition of the host sialic acid by this protozoan parasite, which does not synthesize sialic acids. Here, we have studied some kinetic properties of a recombinant trans-sialidase expressed in Escherichia coli. We found that it has sequential-type kinetics for the transferase reaction, as shown for the parasite-derived enzyme. The rates of sialic acid transfer to water (hydrolysis), and to beta-galactosyl residues have a unique behavior with respect to the reaction temperature. While the hydrolysis rate of sialyllactose increases continuously up to 35 degrees C, the temperature for the maximal rate of trans-glycosylation depends on the acceptor concentration. At low acceptor concentrations the rate of trans-glycosylation is maximal at 13 degrees C and independent of the amount of sialic acid donors. With increasing acceptor concentrations, maximal rates of trans-glycosylation are shifted to higher temperatures. This finding is explained by an 8-fold increase in the Km for the acceptor from 13 degrees C to 33 degrees C. Differences in hydrolysis and transfer rates were also obtained by using 4-methylumbelliferyl-N-acetyl-neuraminic acid. However, its hydrolysis rate is much higher than the rate of transference to lactose, suggesting that a long-lived enzyme-sialosyl intermediate is not formed. In addition, lactose does not increase the rate of methyl-umbelliferone release at any temperature, indicating that the rate limiting step is the aglycon release. Based on these results we propose that transglycosylation in T. cruzi sialidase is favored by the existence of a binding site for beta-galactosyl residues, which accepts the new glycosidic bond as sialic acid is released from the donor. With increasing temperature the affinity for the acceptor decreases, resulting in a concomitant increase in the rate of transfer to water, which, in turn, can be suppressed by increasing the acceptor concentration.
BLADDER EPITHELIAL CELLS FROM PATIENTS WITH INTERSTITIAL CYSTITIS PRODUCE AN INHIBITOR OF HEPARIN-BINDING EPIDERMAL GROWTH FACTOR-LIKE GROWTH FACTOR PRODUCTION (2000)

Bladder epithelial abnormalities in interstitial cystitis may be caused by a negative autocrine growth factor that inhibits cell proliferation by down-regulating HB-EGF production. Furthermore, decreased levels of urine and serum HB-EGF indicate that interstitial cystitis may be a urinary tract manifestation of a systemic disorder.
Nanoscale RRAM-based synaptic electronics: toward a neuromorphic computing device (2013)

Efforts to develop scalable learning algorithms for implementation of networks of spiking neurons in silicon have been hindered by the considerable footprints of learning circuits, which grow as the number of synapses increases. Recent developments in nanotechnologies provide an extremely compact device with low-power consumption.In particular, nanoscale resistive switching devices (resistive random-access memory (RRAM)) are regarded as a promising solution for implementation of biological synapses due to their nanoscale dimensions, capacity to store multiple bits and the low energy required to operate distinct states. In this paper, we report the fabrication, modeling and implementation of nanoscale RRAM with multi-level storage capability for an electronic synapse device. In addition, we first experimentally demonstrate the learning capabilities and predictable performance by a neuromorphic circuit composed of a nanoscale 1 kbit RRAM cross-point array of synapses and complementary metal-oxide-semiconductor neuron circuits. These developments open up possibilities for the development of ubiquitous ultra-dense, ultra-low-power cognitive computers.
Kiwifruit-derived supplements increase stool frequency in healthy adults: a randomized, double-blind, placebo-controlled study (2015)

The worldwide growth in the incidence of gastrointestinal disorders has created an immediate need to identify safe and effective interventions. In this randomized, double-blind, placebo-controlled study, we examined the effects of Actazin and Gold, kiwifruit-derived nutritional ingredients, on stool frequency, stool form, and gastrointestinal comfort in healthy and functionally constipated (Rome III criteria for C3 functional constipation) individuals. Using a crossover design, all participants consumed all 4 dietary interventions (Placebo, Actazin low dose [Actazin-L] [600 mg/day], Actazin high dose [Actazin-H] [2400 mg/day], and Gold [2400 mg/day]). Each intervention was taken for 28 days followed by a 14-day washout period between interventions. Participants recorded their daily bowel movements and well-being parameters in daily questionnaires. In the healthy cohort (n = 19), the Actazin-H (P = .014) and Gold (P = .009) interventions significantly increased the mean daily bowel movements compared with the washout. No significant differences were observed in stool form as determined by use of the Bristol stool scale. In a subgroup analysis of responders in the healthy cohort, Actazin-L (P = .005), Actazin-H (P < .001), and Gold (P = .001) consumption significantly increased the number of daily bowel movements by greater than 1 bowel movement per week. In the functionally constipated cohort (n = 9), there were no significant differences between interventions for bowel movements and the Bristol stool scale values or in the subsequent subgroup analysis of responders. This study demonstrated that Actazin and Gold produced clinically meaningful increases in bowel movements in healthy individuals.
GNOMES: a testbed for low power heterogeneous wireless sensor networks (2003)

Continuing trends in sensor, semiconductor and communication systems technology (smaller, faster, cheaper) make feasible very dense networks of fixed and mobile wireless devices for use in many different sensing and decision-making systems. In this paper we present the design and development of GNOMES, a low-cost hardware and software testbed. This testbed was designed to explore the properties of heterogeneous wireless sensor networks, to test theory in sensor networks architecture, and be deployed in practical application environments. We also present an overview of architectures for extending the lifetime of individual nodes in the network, along with the design tradeoffs that this presents.
Involvement of Ras/Raf/AP-1 in BMP-4 signaling during Xenopus embryonic development. (1996)

Previously, we elucidated the role of bone morphogenetic protein 4 (BMP-4) in the dorsal-ventral patterning of the Xenopus embryo by using a dominant negative mutant of the BMP-4 receptor (DN-BR). The present paper describes the involvement of Ras, Raf, and activator protein 1 (AP-1) in BMP-4 signaling during Xenopus embryonic development. The AP-1 activity was determined by injecting an AP-1-dependent luciferase reporter gene into two-cell-stage Xenopus embryos and measuring the luciferase activity at various developmental stages. We found that injection of BMP-4 mRNA increased AP-1 activity, whereas injection of DN-BR mRNA inhibited AP-1 activity. Similar inhibitory effects were seen with injection of mRNAs encoding dominant negative mutants of c-Ha-Ras, c-Raf, or c-Jun. These results suggest that the endogenous AP-1 activity is regulated by BMP-4/Ras/Raf/Jun signals. We next investigated the effects of Ras/Raf/AP-1 signals on the biological functions of BMP-4. DN-BR-induced dorsalization of the embryo, revealed by the formation of a secondary body axis or dorsalization of the ventral mesoderm explant analyzed by histological and molecular criteria, was significantly reversed by coinjection of [Val12]Ha-Ras, c-Raf, or c-Jun mRNA. Furthermore, the BMP-4-stimulated erythroid differentiation in the ventral mesoderm was substantially inhibited by coinjection with the dominant negative c-Ha-Ras, c-Raf, or c-Jun mutant. Our results suggest the involvement of Ras/Raf/AP-1 in the BMP-4 signaling pathway.
Carbon-nanotube-based nonvolatile memory with oxide–nitride–oxide film and nanoscale channel (2003)

We have fabricated a single-wall carbon-nanotube (CNT)-based nonvolatile memory device using SiO2–Si3N4–SiO2 (ONO) layers as a storage node. The memory device is composed of a top gate structure with a channel width of a few nanometers and the ONO layer embedded between CNT and gate electrode. When the bias voltage between the CNT and gate electrode increases to 4 V, charges are tunneled out from CNT surfaces and captured to the traps in the ONO layers. Stored charges on the trap sites make the threshold voltage shift of 60 mV and is independent of charging time, suggesting that the ONO has traps with a quasiquantized energy state. The quantized state is related to the localized high electric field associated with CNT channel. The CNT-field-effect transistor with an ONO storage node could be used for an ultrahigh-density nonvolatile memory.
Adapting arrays and lab-on-a-chip technology for proteomics (2002)

The impact of proteomics as a discovery engine in life science and in drug discovery has increased tremendously over the last seven years. At the same time, proteomics has expanded from the initial trust as a two-dimensional gel based approach to cover more functional and structural properties of proteins. The development of lab-on-a-chip and protein arrays for proteomics will have to evolve with the changes in proteomics to stay relevant. Here, we review the changes in the field of proteomics and their impact on the development in protein arrays and lab-on-a-chip.
Studies on 2,5-Disubstituted-1,3,4-oxadiazoles. Part-II. Preparation and Antimicrobial Activity of 2-Arylsulphonamido/α-carbamylarylmethylamino-5-(4'-pyridyl)-1,3,4-oxadiazoles (1988)

Department of Chemistry, Saurashtra. University, Rajkot-360 005 <em>Manuscript received 4 February 1988, accepted 21 March 1988</em> Some new 2,6-disubstituted-1,3,4-oxadiazoles have been prepared having 2-arylsulphonamido and 2-α-carbamylarylmethylamino moieties. Structures of the compounds have been supported by ir spectral data The products were screened for their antimicrobial activity.
Dysprosium doped Ga:La:S glass for an efficientoptical fibre amplifier operating at 1.3 µm (1994)

The authors present experimental results which indicate that a Dy3+-doped Ga:La:S glass fibre amplifier may be operated efficiently at 1.3 µm with an optimum device length significantly shorter than a comparable Pr3+-doped glass fibre amplifier. Moreover, the efficiency exceeds that obtained from the Pr3+-doped ZBLAN devices currently available.
Prostasomes are heterogeneous regarding size and appearance but affiliated to one DNA‐containing exosome family (2012)

Reasonably, prostasomes could be included in the exosome family and be regarded as one entity containing chromosomal DNA.