gebhart/patrepeval huggingface dataset:
Imatinib mesylate (STI571) decreases the vascular endothelial growth factor plasma concentration in patients with chronic myeloid leukemia (2004)

Increased angiogenesis in bone marrow (BM) is one of the characteristics of chronic myeloid leukemia (CML), a clonal myeloproliferative disorder that expresses a chimeric Bcr/Abl protein. Recently, the therapeutic strategy in CML has been totally modified with the development of a new drug: imatinib mesylate (STI571), a specific inhibitor of Bcr/Abl tyrosine kinase activity. The aim of our study was to determine, in patients with CML, the capacity of imatinib mesylate to modulate one of the most potent regulators of angiogenesis, the vascular endothelial growth factor (VEGF). In newly diagnosed CML, we observed significantly increased VEGF secretion by CML BM cells and significantly increased VEGF plasma concentrations. We showed that low plasma VEGF concentrations could be one of the characteristics of complete cytogenetic remission. To understand the molecular mechanisms leading to the inhibition of VEGF production by imatinib, we focused our experiments on the human cell line K562, which is Bcr/Abl positive. We demonstrated that imatinib inhibits VEGF gene transcription by targeting the Sp1 and Sp3 transcription factors. Taken together, our results highlight the potential prognostic value of VEGF concentrations in evaluating the evolution of CML patients treated with imatinib.
Precise control of nitric oxide concentration in the inspired gas of continuous flow respiratory devices (1996)

Inhaled NO has become widely used for diagnosis and therapy of pulmonary hypertension. The potential hazards of NO inhalation include the formation of methemoglobin, formation of NO2, and generation of free radicals in the presence of humidity and oxygen. Careful monitoring of NO and NO2 concentration, and titration of the dose according to a patient's clinical response is essential to minimize toxicity. This paper describes a formula and method that permits calculation and precise control of NO concentration in the inspired gas. The accuracy of the delivery system was assessed by a comparison of calculated and measured NO and NO2 concentrations in a continuous flow ventilator circuit. A comparison of electrochemical detector (ECD) versus chemiluminescence detector (CLD) monitoring techniques showed agreement between the instruments within approximately 2 ppm, with the ECD averaging a higher reading than the calculated or CLD measured values. We deemed a 2 ppm discrepancy between instruments clinically acceptable, and concluded that the instruments could be used interchangeably for clinical purposes to measure NO1 and that the ECD was preferable to CLD for measuring NO2. Details about the equipment are given and techniques are discussed to avoid the risk of inhalation of toxic concentrations of NO and NO2. This method provides the possibility of using inhaled NO with appropriate safety precautions in the range 0-60 ppm in a variety of continuous flow respiratory devices.
Type Specific and Type Common Antigens in Cells Infected with Herpes Simplex Virus Type 1 and on the Surfaces of Naked and Enveloped Particles of the Virus (1974)

SUMMARY Of eleven virus-specific antigens detected in cells infected with herpes simplex virus type 1, six have been shown to be type specific, i.e. not present in cells infected with type 2 virus. Two of the five type common antigens are also present in cells infected with pseudorabies virus. Electron microscopic studies of immune agglutination of virus particles have shown that both naked and enveloped particles possess type specific and type common antigenic determinants on their surface. Further, one of the type common determinants on the naked particle surface interacted with antiserum to pseudorabies virus.
Virtual Screening Approach for the Identification of New Rac1 Inhibitors (2009)

Rac1 protein is implicated in several events of atherosclerotic plaque development and represents a new potential pharmacological target for cardiovascular diseases. In this paper we describe a pharmacophore virtual screening followed by molecular docking calculations leading to the identification of five new Rac1 inhibitors. These compounds were shown to be more effective than the reference compound NSC23766 in reducing the intracellular levels of Rac1-GTP, thus supporting this approach for the development of new Rac1 inhibitors.
The osmotic integrity of the yeast cell requires a functional PKC1 gene product. (1992)

Seven temperature-sensitive cell lysis (cly) mutant strains of Saccharomyces cerevisiae were isolated which lyse at the restrictive temperature on hypotonic but not on osmotically supported medium. The seven mutants fell into four complementation groups, CLY12 to CLY15. The wild-type CLY15 gene was isolated by complementation of the cly15 temperature-sensitive growth defect. Sequence analysis revealed that the complementing DNA fragment encoded a partial PKC1 gene, which has previously been isolated as an S. cerevisiae homolog of mammalian protein kinase C genes (D. E. Levin, F. O. Fields, R. Kunisawa, J. M. Bishop, and J. Thorner, Cell 62:213-224, 1990). Subsequent genetic analysis showed that CLY15 and PKC1 represent identical loci in the yeast genome. A truncated PKC1 gene encoding only the predicted catalytic domain of Pkc1p was able to complement pkc1 mutant strains. Similar to what has been reported recently (D. E. Levin and E. Bartlett-Heubusch, J. Cell Biol. 116:1221-1229, 1992), we observed that cells deleted for the PKC1 gene are viable when grown on osmotically stabilized medium but are osmotically fragile and lyse rapidly after a shift to hypotonic medium. As shown by light and electron microscopic examinations, the delta pkc1 strain exhibits many cells with a strongly elongated bud or chains of incompletely budded cells when grown on solid medium.
Inbreeding coefficients and coalescence times (1991)

This paper describes the relationship between probabilities of identity by descent and the distribution of coalescence times. By using the relationship between coalescence times and identity probabilities, it is possible to extend existing results for inbreeding coefficients in regular systems of mating to find the distribution of coalescence times and the mean coalescence times. It is also possible to express Sewall Wright's FST as the ratio of average coalescence times of different pairs of genes. That simplifies the analysis of models of subdivided populations because the average coalescence time can be found by computing separately the time it takes for two genes to enter a single subpopulation and time it takes for two genes in the same subpopulation to coalesce. The first time depends only on the migration matrix and the second time depends only on the total number of individuals in the population. This approach is used to find FST in the finite island model and in one- and two-dimensional stepping-stone models. It is also used to find the rate of approach of FST to its equilibrium value. These results are discussed in terms of different measures of genetic distance. It is proposed that, for the purposes of describing the amount of gene flow among local populations, the effective migration rate between pairs of local populations, M, which is the migration rate that would be estimated for those two populations if they were actually in an island model, provides a simple and useful measure of genetic similarity that can be defined for either allozyme or DNA sequence data.
Adversarial Autoencoders (2015)

In this paper, we propose the "adversarial autoencoder" (AAE), which is a probabilistic autoencoder that uses the recently proposed generative adversarial networks (GAN) to perform variational inference by matching the aggregated posterior of the hidden code vector of the autoencoder with an arbitrary prior distribution. Matching the aggregated posterior to the prior ensures that generating from any part of prior space results in meaningful samples. As a result, the decoder of the adversarial autoencoder learns a deep generative model that maps the imposed prior to the data distribution. We show how the adversarial autoencoder can be used in applications such as semi-supervised classification, disentangling style and content of images, unsupervised clustering, dimensionality reduction and data visualization. We performed experiments on MNIST, Street View House Numbers and Toronto Face datasets and show that adversarial autoencoders achieve competitive results in generative modeling and semi-supervised classification tasks.
FRET-Labeled siRNA Probes for Tracking Assembly and Disassembly of siRNA Nanocomplexes (2012)

The assembly, stability, and timely disassembly of short interfering RNA (siRNA) nanocomplexes have the potential to affect the efficiency of siRNA delivery and gene silencing. As such, the design of new probes that can measure these properties without significantly perturbing the nanocomplexes or their environment may facilitate the study and further development of new siRNA nanocomplexes. Herein, we study Förster resonance energy transfer (FRET)-labeled siRNA probes that can track the assembly, stability, and disassembly of siRNA nanocomplexes in different environments. The probe is composed of two identical siRNAs, each labeled with a fluorophore. Upon nanocomplex formation, the siRNA-bound fluorophores become locally aggregated within the nanocomplex and undergo FRET. A key advantage of this technique is that the delivery vehicle (DV) need not be labeled, thus enabling the characterization of a large variety of nanocarriers, some of which may be difficult or even impossible to label. We demonstrate proof-of-concept by measuring the assembly of various DVs with siRNAs and show good agreement with gel electrophoresis experiments. As a consequence of not having to label the DV, we are able to determine nanocomplex biophysical parameters such as the extracellular apparent dissociation constants (K(D)) and intracellular disassembly half-life for several in-house and proprietary commercial DVs. Furthermore, the lack of DV modification allows for a true direct comparison between DVs as well as correlation between their biophysical properties and gene silencing.
Brightly Luminescent Organically Capped Silicon Nanocrystals Fabricated at Room Temperature and Atmospheric Pressure (2010)

Silicon nanocrystals are an extensively studied light-emitting material due to their inherent biocompatibility and compatibility with silicon-based technology. Although they might seem to fall behind their rival, namely, direct band gap based semiconductor nanocrystals, when it comes to the emission of light, room for improvement still lies in the exploitation of various surface passivations. In this paper, we report on an original way, taking place at room temperature and ambient pressure, to replace the silicon oxide shell of luminescent Si nanocrystals with capping involving organic residues. The modification of surface passivation is evidenced by both Fourier transform infrared spectroscopy and nuclear magnetic resonance measurements. In addition, single-nanocrystal spectroscopy reveals the occurrence of a systematic fine structure in the emission single spectra, which is connected with an intrinsic property of small nanocrystals since a very similar structure has recently been observed in specially passivated semiconductor CdZnSe nanoparticles. The organic capping also dramatically changes optical properties of Si nanocrystals (resulting ensemble photoluminescence quantum efficiency 20%, does not deteriorate, radiative lifetime 10 ns at 550 nm at room temperature). Optically clear colloidal dispersion of these nanocrystals thus exhibits properties fully comparable with direct band gap semiconductor nanoparticles.
Metal‐Chelate Affinity Chromatography (1996)

Recombinant proteins engineered to have six consecutive histidine residues on either the amino or carboxyl terminus can be purified using a resin containing nickel ions (Ni2+) that have been immobilized by covalently attached nitrilotriacetic acid (NTA). This technique, known as metal-chelate affinity chromatography (MCAC), can readily be performed with either native or denatured protein. Techniques are discussed for creating a fusion protein consisting of the protein of interest with a histidine tail attached (for purification by MCAC). The basic protocol describes expression of histidine-tail fusion proteins and their purification in native form by MCAC. Two alternate protocols describe purification of histidine-tail fusion proteins by MCAC under denaturing conditions and their renaturation by either dialysis or solid-phase renaturation. Support protocols are provided for analysis of the purified product and regeneration of the NTA resin. All of these protocols are easily adaptable to any protein expression system.
Uniform constant composition codes derived from repeated‐root cyclic codes (2017)

Uniform constant composition (UCC) codes are introduced, which are p ‐ary constant composition codes with block length mp where each p ‐ary symbol appears exactly m times in each codeword, being m a positive integer and p a prime. UCC codes are derived from a new class of p ‐ary repeated‐root cyclic codes and two constructions are presented. Both constructions are at least asymptotically optimal with increasing p when compared with known best bounds for constant composition codes.
Host-oblivious security for content-based networks (2010)

Network-level security systems rely significantly on network operations. This reliance has led to conventional network-level security systems based on a host-centric architecture because the network operations themselves are based on hosts. However, host-dependent network security schemes are no longer applicable in content-based networks.
Isolation of a New Human Retrovirus from West African Patients with AIDS (1986)

The etiological agent of AIDS, LAV/HTLV-III, is common in Central Africa but is not endemic in other areas of that continent. A novel human retrovirus, distinct from LAV/HTLV-III, has now been isolated from two AIDS patients from West Africa. Partial characterization of this virus revealed that it has biological and morphological properties very similar to LAV but that it differs in some of its antigenic components. Although the core antigens may share some common epitopes, the West African AIDS retrovirus and LAV differ substantially in their envelope glycoproteins. The envelope antigen of the West African virus can be recognized by serum from a macaque with simian AIDS infected by the simian retrovirus termed STLV-IIImac, suggesting that the West African AIDS virus may be more closely related to this simian virus than to LAV. Hybridization experiments with LAV subgenomic probes further established that this new retrovirus, here referred to as LAV-II, is distantly related to LAV and distinct from STLV-IIImac.
ISOLATION AND CHARACTERIZATION OF RECOMBINATION-DEFICIENT MUTANTS OF ESCHERICHIA COLI K12 (1965)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Large vocabulary natural language continuous speech recognition (2003)

A description is presented of the authors' current research on automatic speech recognition of continuously read sentences from a naturally-occurring corpus: office correspondence. The recognition system combines features from their current isolated-word recognition system and from their previously developed continuous-speech recognition system. It consists of an acoustic processor, an acoustic channel model, a language model, and a linguistic decoder. Some new features in the recognizer relative to the isolated-word speech recognition system include the use of a fast match to prune rapidly to a manageable number the candidates considered by the detailed match, multiple pronunciations of all function words, and modeling of interphone coarticulatory behavior. The authors recorded training and test data from a set of ten male talkers. The perplexity of the test sentences was found to be 93; none of sentences was part of the data used to generate the language model. Preliminary (speaker-dependent) recognition results on these talkers yielded an average word error rate of 11.0%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cannabinoids and cancer: potential for colorectal cancer therapy (2005)

Despite extensive research into the biology of CRC (colorectal cancer), and recent advances in surgical techniques and chemotherapy, CRC continues to be a major cause of death throughout the world. Therefore it is important to develop novel chemopreventive/chemotherapeutic agents for CRC. Cannabinoids are a class of compounds that are currently used in the treatment of chemotherapy-induced nausea and vomiting, and in the stimulation of appetite. However, there is accumulating evidence that they could also be useful for the inhibition of tumour cell growth by modulating key survival signalling pathways. The chemotherapeutic potential for plant-derived and endogenous cannabinoids in CRC therapy is reviewed.
Quantitation of chemopreventive synergism between (-)-epigallocatechin- 3-gallate and curcumin in normal, premalignant and malignant human oral epithelial cells (1998)

An in vitro model for oral cancer was used to examine the growth inhibitory effects of chemopreventive agents when used singly and in combination. The model consists of primary cultures of normal oral epithelial cells, newly established cell lines derived from dysplastic leukoplakia and squamous cell carcinoma. Two naturally occurring substances, (-)-epigallocatechin-3-gallate (EGCG) from green tea and curcumin from the spice turmeric were tested. Cells were treated singly and in combination and effects on growth determined in 5-day growth assays and by cell cycle analysis. Effective dose 50s and the combination index were calculated with the computerized Chou-Talalay method which is based on the median-effect principle. Agents were shown to differ in their inhibitory potency. EGCG was less effective with cell progression; the cancer cells were more resistant than normal or dysplastic cells. In contrast, curcumin was equally effective regardless of the cell type tested. Cell cycle analysis indicated that EGCG blocked cells in G1, whereas curcumin blocked cells in S/G2M. The combination of both agents showed synergistic interactions in growth inhibition and increased sigmoidicity (steepness) of the dose-effect curves, a response that was dose and cell type dependent. Combinations allowed for a dose reduction of 4.4-8.5-fold for EGCG and 2.2-2.8-fold for curcumin at ED50s as indicated by the dose reduction index (DRI). Even greater DRI values were observed above ED50 levels. Our results demonstrate that this model which includes normal, premalignant and malignant oral cells can be used to analyse the relative potential of various chemopreventive agents. Two such naturally-occurring agents, EGCG and curcumin, were noted to inhibit growth by different mechanisms, a factor which may account for their demonstrable interactive synergistic effect.
Host Defense Against Neisseria meningitidis Requires a Complement-Dependent Bactericidal Activity (1979)

Some individuals, with severe or recurrent infection with Neisseria species, have been identified as lacking a component in the terminal attack sequence of complement (complement components 5 to 9). The relevance of the terminal attack sequence to various phases of host defense was tested with the use of the C-11 strain of meningococci and human serum genetically deficient in complement component 8 (C8-D). The C8-D serum was comparable to normal serum in supporting ingestion and intracellular killing by leukocytes but was not bactericidal in the fluid phase unless reconstituted with C8. Thus, serum complement-dependent bactericidal activity may be especially critical for the host's defense against invasive Neisseria species.
Inhibition of Major Histocompatibility Complex Class I Antigen Presentation in Pig and Primate Cells by Herpes Simplex Virus Type 1 and 2 ICP47 (1998)

Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) express an immediate-early protein, ICP47, that effectively inhibits the human transporter associated with antigen presentation (TAP), blocking major histocompatibility complex (MHC) class I antigen presentation to CD8+ T cells. Previous work indicated that the mouse TAP is relatively resistant to inhibition by the HSV-1 and HSV-2 ICP47 proteins (ICP47-1 and ICP47-2) and that mouse cells infected with HSV-1 are lysed by anti-HSV CD8+ cytotoxic T lymphocytes (CTL). Therefore, mice are apparently not suitable animals in which to study the in vivo effects of ICP47. In order to find an animal model, we introduced ICP47-1 and ICP47-2 into cells from various animal species-mice, rats, guinea pigs, rabbits, dogs, pigs, cows, monkeys, and humans-and measured TAP activity in the cells. Both proteins were unable to inhibit TAP in mouse, rat, guinea pig, and rabbit cells. In contrast, ICP47-1 and ICP47-2 inhibited TAP in pig, dog, cow, and monkey cells, and the TAP in pig and dog fibroblasts was often more sensitive to both proteins than TAP in human fibroblasts. These results were extended by measuring CD8+-T-cell recognition (CTL lysis) of cells from various species. Cells were infected with recombinant HSV-1 constructed to express murine MHC class I proteins so that the cells would be recognized and lysed by well-characterized murine anti-HSV CTL unless antigen presentation was blocked by ICP47. Anti-HSV CD8+ CTL effectively lysed pig and primate cells infected with a recombinant HSV-1 ICP47- mutant but were unable to lyse pig or primate cells infected with a recombinant HSV-1 that expressed ICP47. Therefore, pigs, dogs, and monkeys may be useful animal models in which to test the effects of ICP47 on HSV pathogenesis or the use of ICP47 as a selective immunosuppressive agent.
Chiral Fluoro Ketones for Catalytic Asymmetric Epoxidation of Alkenes with Oxone (2002)

Two structurally dissimilar, chiral fluoro ketones have been prepared and their potential as enantioselective catalysts for asymmetric epoxidation with Oxone has been evaluated. The tropinone-based ketone (-)-5 was easily prepared and showed excellent reactivity but only modest enantioselectivity. The biphenyl-based ketone (-)-6 was prepared in a somewhat lengthy synthesis (along with its monofluoro and geminal fluoro analogues). This ketone exhibited only modest reactivity; 30 mol % of (-)-6 was needed to bring about complete conversion in a reasonable time. The enantioselectivity of this catalyst was generally much higher, but again very substrate dependent.