gebhart/patrepeval huggingface dataset:
Joint neighbors approximation of macromolecular solvent accessible surface area (2007)

A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 A2, while for unfolded protein conformations it varies from 1.65 to 1.87 A2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today.
Effect of enterocoated cholestyramine on bowel habit after ileal resection: a double blind crossover study. (1985)

Ileal resection causes malabsorption of bile acid; the increased load of bile acids in the colon induces increased secretion of salt and water and hence diarrhoea. A study was carried out to test the effect of an enterocoated cholestyramine tablet designed to disintegrate in the colon and sequester the bile acids there, thereby minimising diarrhoea induced by bile acids while having no effect on malabsorption of bile acid and jejunal fat absorption. The study comprised 14 patients who had undergone ileal resection of 40-150 cm for Crohn's disease. A double blind crossover trial was performed with placebo and cholestyramine enterocoated with cellulose acetate phthalate. During treatment with cholestyramine the daily faecal output decreased, the number of defecations each week decreased, and the intestinal transit time increased. Acceptability of the tablets was high, in contrast with general clinical experience with cholestyramine powder. No change was observed in the total faecal output of bile acids or fat. Cholestyramine tablets caused a reduction in diarrhoea without noticeably interfering with the metabolism of fat or bile acid.
Investigation of oxidative stress in pterygium tissue. (2011)

These findings indicating oxidative stress in the pterygium tissue suggest that oxidative stress can play a role in pterygium etiopathogenesis.
High performance channel model hardware emulator for 802.11n (2006)

In this paper, the design and implementation of a new high performance hardware channel emulator is presented. The purpose of the developed emulator is to efficiently reproduce in a laboratory environment the accurate behaviour of several effects of the radio channel over a multiple antennas wireless communication system, including AWGN (additive white Gaussian noise), multipath, attenuation and Doppler shift. The main application target is the test and the performance evaluation of a new 802.11n transceiver. The prototype has been implemented on a board including both an ARM processor and a field programmable gate array (FPGA), and it supports the simulation of a 40 MHz radio frequency bandwidth.
Heterophilic antibodies: a problem for all immunoassays. (1988)

We verified that antibody-binding substances in serum that interfere in two-site immunoassays involving murine antibodies are heterophilic antibodies. Incubation of serum containing heterophilic antibodies and a murine monoclonal antibody to human choriogonadotropin (hCG) leads to formation of a series of soluble immune complexes. We investigated the recognition of hCG by reagent antibody in the presence of heterophilic antibodies and found this recognition to be diminished. Consequently, about 30% of serum samples containing heterophilic antibodies falsely appear to contain increased concentrations of hCG. The effect on analyte recognition probably results from steric inhibition of hCG binding to complexed antibody. Heterophilic antibodies detected with a murine antibody also bound immunoglobulin from several other species but did not bind all of those tested.
Smart personal assistant using machine learning (2017)

Assisting users in performing their tasks is the main goal of todays personal assistant applications. Many such applications are being developed, which are capable to discover the user's habits, abilities, preferences, and goals, even more accurately and predicting the user's actions in advance and perform them without user's interaction. The assistant agent has to continuously improve its behavior based on previous experiences. Improvements are achieved in personal assistant applications by learning mechanism. Agents are capable of accessing information from databases to guide people through different tasks, deploying a learning mechanism to acquire new information on user behaviour. Also the resources has to be utilised in highly efficient way leading to less power consumption. In this paper we have proposed a machine learning approach for learning mechanism of personal assistant agent. For better utilization of smartphones battery, the interrupt based broadcast receiver approach has been followed.
Diverse carotenoids protect against chemically induced neoplastic transformation (1991)

The ability of diverse carotenoid to inhibit methylcholanthrene-induced transformation of 10T1/2 cells has been investigated. When delivered using tetrahydrofuran as a novel solvent, all carotenoids were absorbed by cultured cells. When continuously administered to methylcholanthrene-treated cultures 7 days after removal of the carcinogen, canthaxanthin, beta-carotene, alpha-carotene and lycopene inhibited the production of transformed foci in a dose-dependent manner in the above order of potency. This activity was not associated with drug toxicity or antiproliferative effects. Renierapurpurin and bixin did not inhibit transformation at concentrations less than or equal to 10(-5) M. Lutein was inhibitory at 10(-5) M, but was inactive at lower concentrations. Because of differences in stability in culture medium (alpha-carotene less than beta-carotene less than canthaxanthin less than lycopene less than lutein) and structure, cellular levels of drug differed up to 8-fold after administration of identical concentrations of compounds. Carotenoids with polar groups achieved highest cellular levels, however cellular uptake did not correlate with activity. For example, lutein, the most polar and most stable, reached the highest concentration in cells yet required a concentration of 10(-5) M for activity in the transformation assay, while alpha-carotene, the least stable and least concentrated by cells, was comparably active at 3 X 10(6) M. alpha-Tocopherol, a potent lipid-phase antioxidant, was as active as lycopene in the transformation assay but at a 10-fold higher concentration did not approach the activity of beta-carotene or canthaxanthin. Because the most potent of the carotenoids tested (i.e. beta-carotene, alpha-carotene, canthaxanthin) all have the potential for conversion to retinoids (though this has never been demonstrated in mammals for canthaxanthin), it is suggested that these compounds have two components to their action; one related to their antioxidant properties, the other to their pro-vitamin A activities.
Is Cu a stable electrode material in hybrid perovskite solar cells for a 30-year lifetime? (2016)

Here we explored the potential of using copper as the electrode material for long-term stability of perovskite solar cells.
The Predictive Validity of the HERO Scorecard in Determining Future Health Care Cost and Risk Trends (2014)

The HERO Scorecard predicts health care cost trends among employers. More research is needed to determine how well it predicts health risk trends for employees.
Delivery of antioxidative enzyme genes protects against ischemia/reperfusion–induced liver injury in mice (2006)

Hepatic ischemia/reperfusion (I/R) injury is characterized by the generation of reactive oxygen species (ROS), such as superoxide anions and hydrogen peroxide. The aim of this study is to investigate whether antioxidative gene delivery by our polylipid nanoparticles (PLNP) is an effective approach for prevention of the injury. Polyplexes of extracellular superoxide dismutase (EC-SOD) and/or catalase genes were injected via the portal vein 1 day prior to a warm I/R procedure in mice. The effects of the gene delivery were determined 6 hours after starting reperfusion. PLNP-mediated antioxidative gene delivery led to a marked increase in human EC-SOD and catalase gene expression in the liver. Liver superoxide dismutase (SOD) and catalase activity both increased approximately 10-fold. Increased liver superoxide anion levels caused by the I/R procedure were reduced to normal levels by EC-SOD gene delivery. The overexpression of these 2 antioxidative genes significantly suppressed the I/R-induced elevation of serum alanine aminotransferase (ALT) levels, decreased liver malondialdehyde content, restored glutathione reserve, and improved liver histology. In conclusion, EC-SOD or catalase gene delivery by PLNP resulted in high levels of the transgene activity in the liver, and markedly attenuated hepatic I/R injury. The protection is directly associated with elevated antioxidative enzyme activity as the result of the gene delivery. This novel approach may become a potential therapy to improve graft function and survival after liver transplantation.
Characterization of P19 cells during retinoic acid induced differentiation. (2010)

The aim of our study was to characterize mouse embryonal carcinoma (EC) cells P19 in different stages of retinoic acid induced neurodifferentiation by two methods, immunocytochemistry and RT qPCR. The characterization of the cells is crucial before any transplantation into any model, e.g. in our case into the mouse brain with the aim to treat a neurodegenerative disease. Specific protein markers (MAP-2, OCT-4, FORSE-1) were detected by immunocytochemistry in the cell cultures. The mRNA expression levels of PAX-6, MASH-1, Brachyury, GATA-4 and AFP were determined by RT qPCR method. HPRT was used as a housekeeping gene. The degree of differentiation can be characterized by expression of analyzed genes. The presence of OCT-4 and FORSE-1 proteins in undifferentiated pluripotent cells and the presence of dendrite specific MAP-2 in neuroprogenitors was detected. The expression levels of PAX-6 and MASH-1 increased and expression of Brachyury decreased during the neurodifferentiation process. The expression levels of GATA-4 and AFP were the highest after induction of differentiation with retinoic acid. Detailed characterization of cells before transplantation experiments can contribute to better understanding of their effect.
Do G protein subunits associate via a three‐stranded coiled coil? (1992)

We used a computer-based prediction algorithm to identify probable coiled-coil segments at the N-termini of G protein alpha, beta and gamma subunits. This result indicates that G protein trimers may form via a three-stranded coiled coil. Previous biochemical results had shown that the N-termini of alpha and beta are involved in subunit interactions. Here we present a structural model for the N-terminal domain of beta gamma and a hypothesis for the reversible association of alpha to beta gamma.
Civilian and Military Initiatives, 1939–1941 (1992)

Appearances were to prove deceptive. Instead of heralding the final demise of Army education, the new conflict was to see the goals of 1918–20, particularly in the socio-political context, rise phoenix-like from the ashes of the inter-war years, and attain a position of power and influence hitherto undreamt of. This chapter looks at the start of the process by which this transformation took place. The situation was different with the new entrants, eager to do their bit for the war effort. Schoolmasters, WEA tutors, university lecturers, journalists, and anyone else who could possibly be classified as ‘intellectual’ entered the AEC, some unable to join the combat arms for reasons of health or age, others convinced that an Anny education offered the best outlet for their talents. They brought with them a sense of idealistic faith and commitment virtually unseen in the Corps for many years.
MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis (2008)

Our experiments provide the first evidence for a peripheral blood protein signature in IPF to our knowledge. The two main components of this signature, MMP7 and MMP1, are overexpressed in the lung microenvironment and distinguish IPF from other chronic lung diseases. Additionally, increased MMP7 concentration may be indicative of asymptomatic ILD and reflect disease progression.
Position-dependent inhibition of class-switch recombination by PGK-neorcassettes inserted into the immunoglobulin heavy chain constant region locus (1999)

The Ig heavy chain (IgH) constant region (CH) genes are organized from 5' to 3' in the order Cmicro, Cdelta, Cgamma3, Cgamma1, Cgamma2b, Cgamma2a, Cepsilon, and Calpha. Expression of CH genes downstream of Cdelta involves class-switch recombination (CSR), a process that is targeted by germ-line transcription (GT) of the corresponding CH gene. Previously, we demonstrated that insertion of a PGK-neor cassette at two sites downstream of Calpha inhibits, in cultured B cells, GT of and CSR to a subset of CH genes (including Cgamma3, Cgamma2a, Cgamma2b, and Cepsilon) that lie as far as 120 kb upstream. Here we show that insertion of the PGK-neor cassette in place of sequences in the Igamma2b locus inhibits GT of and CSR to the upstream Cgamma3 gene, but has no major effect on the downstream Cgamma2a and Cepsilon genes. Moreover, replacement of the Cepsilon exons with a PGK-neor cassette in the opposite transcriptional orientation also inhibits, in culture, GT of and CSR to the upstream Cgamma3, Cgamma2b, and Cgamma2a genes. As with the PGK-neor insertions 3' of Calpha studied previously, the Cgamma1 and Calpha genes were less affected by these mutations both in culture and in mice, whereas the Cgamma2b gene appeared less affected in vivo. Our findings support the existence of a long-range 3' IgH regulatory region required for GT of and CSR to multiple CH genes and suggest that PGK-neor cassette insertion into the locus short circuits the ability of this region to facilitate GT of dependent CH genes upstream of the insertion.
LOF (2000)

For many KDD applications, such as detecting criminal activities in E-commerce, finding the rare instances or the outliers, can be more interesting than finding the common patterns. Existing work in outlier detection regards being an outlier as a binary property. In this paper, we contend that for many scenarios, it is more meaningful to assign to each object a degree of being an outlier. This degree is called the local outlier factor (LOF) of an object. It is local in that the degree depends on how isolated the object is with respect to the surrounding neighborhood. We give a detailed formal analysis showing that LOF enjoys many desirable properties. Using real-world datasets, we demonstrate that LOF can be used to find outliers which appear to be meaningful, but can otherwise not be identified with existing approaches. Finally, a careful performance evaluation of our algorithm confirms we show that our approach of finding local outliers can be practical.
Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors (1994)

Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding in the recognition pocket of thrombin led to the discovery of (aminoiminomethyl)piperidine (amidinopiperidine) as a weak, but intrinsically selective, thrombin inhibitor. Elaboration of this molecule provided compounds which inhibit thrombin with Ki's in the range of 20-50 nM and with selectivities of 1000-4000 against trypsin. These inhibitor compounds show a new and unexpected binding mode to thrombin. Modification of the central building block and then of one of the hydrophobic substituents led to the discovery of a new family of thrombin inhibitors which has reverted to the former binding mode to thrombin. This last class of compounds shows inhibitory activities in the picomolar range, low toxicity, and a short plasma half life which favors its use for an intravenous application. From this series of thrombin inhibitors, 19f(Ro 46-6240) was selected for clinical development as an antithrombotic agent for intravenous administration.
Frequent inactivation of the p73 gene by abnormal methylation or LOH in non‐Hodgkin's lymphomas (2002)

p73 is a candidate tumor suppressor and imprinted gene that shares significant homology with the p53 gene. It is located on 1p36, a region frequently deleted in neuroblastoma and other tumors. To investigate the pattern of inactivation of this gene in human lymphomas, we studied 59 tumors to identify abnormal methylation in exon 1 and loss of heterozygosity (LOH) at this locus. p73 was methylated in 13/50 (26%) B cell lymphomas. There was no evidence of p73 methylation in the 9 T cell lymphomas analyzed. Burkitt's lymphomas showed the highest proportion of methylated cases (36%), although this alteration also affected other aggressive lymphomas such as diffuse large cell and some marginal zone lymphomas. LOH at the p73 locus was detected in 4/34 (11%) B and 1/9 (11%) T cell lymphomas. The p73 expression analysis showed absence or low level of p73 product in methylated lymphomas, whereas p73 was always detected in unmethylated tumors. We found monoallelic expression in normal peripheral blood samples, consistent with imprinting. None of the tumors showed LOH and methylation of the remaining allele simultaneously, suggesting that alteration of the expressed allele could lead to the total inactivation of the gene. Our results show that deletion or methylation of the p73 gene could be important mechanisms in suppressing p73 expression in B cell non-Hodgkin's lymphomas.
Regulation of a plant pathogenesis-related enzyme: Inhibition of chitinase and chitinase mRNA accumulation in cultured tobacco tissues by auxin and cytokinin (1987)

Two endochitinases (EC 3.2.1.14) of M(r) values of approximately 34,000 and approximately 32,000 have been purified from cultured tissues of Nicotiana tabacum cv. Havana 425. The chitinase content of cloned tobacco pith tissues subcultured on hormone-free medium increases by approximately 5-fold to 8% of the soluble protein over a 7-day period. This induction is inhibited >90% by addition of combinations of the plant hormones auxin and cytokinin to the culture medium. Chitinase is also developmentally regulated in the intact plant. Not detectable in leaves near the top of the plant, it is 1-4% of the soluble protein in roots and lower leaves. A cDNA clone of tobacco chitinase was isolated containing a single, large open reading frame of 310 amino acids that includes the complete amino acid sequence of the mature enzyme. Chitinase and chitinase mRNA measured by RNA blot analysis show similar patterns of regulation indicating that chitinase accumulation is controlled, at least in part, at the mRNA level. The patterns were also similar to those obtained with glucan endo-1,3-beta-glucosidase (EC 3.2.1.39) suggesting that the two enzymes are coordinately regulated.
Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish, Raja eglanteria (2001)

T lymphocytes and B lymphocytes are present in jawed vertebrates, including cartilaginous fishes, but not in jawless vertebrates or invertebrates. The origins of these lineages may be understood in terms of evolutionary changes in the structure and regulation of transcription factors that control lymphocyte development, such as PU.1. The identification and characterization of three members of the PU.1 family of transcription factors in a cartilaginous fish, Raja eglanteria, are described here. Two of these genes are orthologs of mammalian PU.1 and Spi-C, respectively, whereas the third gene, Spi-D, is a different family member. In addition, a PU.1-like gene has been identified in a jawless vertebrate, Petromyzon marinus (sea lamprey). Both DNA-binding and transactivation domains are highly conserved between mammalian and skate PU.1, in marked contrast to lamprey Spi, in which similarity is evident only in the DNA-binding domain. Phylogenetic analysis of sequence data suggests that the appearance of Spi-C may predate the divergence of the jawed and jawless vertebrates and that Spi-D arose before the divergence of the cartilaginous fish from the lineage leading to the mammals. The tissue-specific expression patterns of skate PU.1 and Spi-C suggest that these genes share regulatory as well as structural properties with their mammalian orthologs.
Studies on MHD Interaction in Hypervelocity Ionized Air Flow Over Aero-Surfaces (2003)

The paper presents results of experiments and analysis in the study of MHD interaction around blunt bodies in hypervelocity (M>6) ionized air. One test configuration that was extensively studied was that of transverse hypersonic flow around a right circular cylinder model with an azimuthal magnetic field of the 1.0 Tesla level. The experiments were conducted at the unique MHD accelerator wind tunnel facility of TsAGI. This facility can provide the quasi-stationary hypervelocity flow of ionized air in the Mach number 6 to 15 range. Supportive analysis of the experiments was developed based on the full Navier-Stokes equations coupled with the MHD approximation of the Maxwell equations and set up to optionally included finite rate chemistry kinetics. The results of the analyses and numerical simulations have demonstrated that under conditions typical to experimental facility, the MHD interaction leads to significant changes of the flow field distribution, shock attenuation, gas dynamic characteristics and a marked redistribution of the flow enthalpy. The preliminary results of this project were discussed in previous publications by the authors. This paper is principally devoted to presentation and critique of the experimental results obtained during 2001-2002. The potential field applications of these results are also discussed.
Synthesis and Evaluation of Nitrofuranylamides as Novel Antituberculosis Agents (2004)

In an effort to develop new and more potent therapies to treat tuberculosis, a library of compounds was screened for M. tuberculosis UDP-Gal mutase inhibition. Nitrofuranylamide 1 was identified as a hit in this screen, possessing good antituberculosis activity. This paper describes the synthesis and evaluation of an expanded set of nitrofuranylamides. We have discovered a number of nitrofuranylamides with submicromolar M. tuberculosis MIC values and acceptable therapeutic indexes. The MIC activity did not correlate with UDP-Gal mutase inhibition, suggesting an alternative primary cellular target was responsible for the antituberculosis activity. The compounds were only active against mycobacteria of the tuberculosis complex. On the basis of these results, four compounds were selected for in vivo testing in a mouse model of tuberculosis infection, and of these compounds one showed significant antituberculosis activity.