gebhart/patrepeval huggingface dataset:
High-energy x-ray diffraction study of pure amorphous silicon (1999)

Medium and high-energy x-ray diffraction has been used to study the atomic structure of pure amorphous Si prepared by MeV Si implantation into crystalline silicon. Both as-implanted and annealed samples were studied. The inelastically scattered x rays were removed by fitting the energy spectrum for the scattered x rays. The atomic scattering factor of silicon, previously known reliably up to 20 ${\mathrm{\AA{}}}^{\mathrm{\ensuremath{-}}1}$, has been extended to 55 ${\mathrm{\AA{}}}^{\mathrm{\ensuremath{-}}1}$. The radial distribution function of amorphous Si, before and after annealing, has been determined through an unbiased Fourier transformation of the normalized scattering data. Gaussian fits to the first neighbor peak in these functions shows that scattering data out to at least 40 ${\mathrm{\AA{}}}^{\mathrm{\ensuremath{-}}1}$ is required to reliably determine the radial distribution function. The first-shell coordination number increases from 3.79 to 3.88 upon thermal annealing at 600 \ifmmode^\circ\else\textdegree\fi{}C, whereas that of crystalline Si determined from similar measurements on a Si powder analyzed using the same technique is 4.0. Amorphous Si is therefore under coordinated relative to crystalline Si. Noise in the distribution function, caused by statistical variations in the scattering data at high-momentum transfer, has been reduced without affecting the experimental resolution through filtering of the interference function after subtracting the contribution of the first-neighbor peak. The difference induced by thermal annealing in the remainder of the radial distribution functions, thus revealed, is much smaller than previously believed.
Insulin regulation of a novel WD-40 repeat protein in adipocytes (2001)

A 400 bp PCR product generated with degenerate primers derived from the glucagon-like peptide-1 receptor was used to screen a rat skeletal muscle cDNA library. The predicted amino acid sequence of the 978 bp open reading frame has a predicted M(r) of 35 804, an estimated isoelectric point (pI) of 5.31 and contains seven WD-40 repeats, which are common to G-protein beta subunits (Gbeta). Although chemically and structurally similar to Gbeta subunits, the predicted amino acid sequence, when compared with the previously cloned Gbeta isoforms, was found to be only 31-41% similar and thus was named Gbeta-like (GbetaL, 'Gable'). Western blotting of whole-cell lysates and immunoprecipitates of membrane and cytosolic fractions of HEK 293 cells stably overexpressing a carboxy-terminal His-tagged GbetaL indicates that the protein is cytosolic and that it migrates at 42 kDa. A 4 kb transcript was detected in all tissues surveyed by northern blotting; however, an additional 2 kb transcript was detected in testis. Expression of GbetaL mRNA was highest in the brain and testis, followed by lung, heart, kidney, skeletal muscle, spleen and liver. In addition, reverse transcriptase/PCR showed that several other tissues and cell lines express GbetaL. The ubiquitous nature of the tissue expression pattern of GbetaL is similar to that of the insulin receptor, which suggests that insulin may influence GbetaL expression. Indeed, GbetaL protein and mRNA levels, in fully differentiated 3T3-L1 adipocytes, were upregulated by insulin in a concentration-dependent fashion. These changes were highly sensitive to insulin stimulation, being minimally affected by doses as low as 0.1 nM and maximally elevated by 1 nM doses. These data suggest that insulin regulates GbetaL production and imply that some of the actions of insulin may be mediated, in part, by this novel intracellular protein.
Complete MHC Haplotype Sequencing for Common Disease Gene Mapping (2004)

The future systematic mapping of variants that confer susceptibility to common diseases requires the construction of a fully informative polymorphism map. Ideally, every base pair of the genome would be sequenced in many individuals. Here, we report 4.75 Mb of contiguous sequence for each of two common haplotypes of the major histocompatibility complex (MHC), to which susceptibility to >100 diseases has been mapped. The autoimmune disease-associated-haplotypes HLA-A3-B7-Cw7-DR15 and HLA-A1-B8-Cw7-DR3 were sequenced in their entirety through a bacterial artificial chromosome (BAC) cloning strategy using the consanguineous cell lines PGF and COX, respectively. The two sequences were annotated to encompass all described splice variants of expressed genes. We defined the complete variation content of the two haplotypes, revealing >18,000 variations between them. Average SNP densities ranged from less than one SNP per kilobase to >60. Acquisition of complete and accurate sequence data over polymorphic regions such as the MHC from large-insert cloned DNA provides a definitive resource for the construction of informative genetic maps, and avoids the limitation of chromosome regions that are refractory to PCR amplification.
Antiproliferative effect of intravitreal a-tocopherol and a-tocopheryl-acid-succinate in a rabbit model of PVR (1997)

Alpha-tocopherol and alpha-tocopheryl-acid-succinate in saline solution showed retardation of proliferative vitreoretinopathy traction retinal detachments. In silicone oil, alpha-tocopherol is slowly released and decreases the severity of proliferative vitreoretinopathy, especially during the second week of follow-up.
Tool development for Prediction of pIC50 values from the IC50 values - A pIC50 value calculator (2011)

Half maximal inhibitory concentration (IC50) value measures the effectiveness of compound inhibition towards biological or biochemical utility. Quantitative measure indicates the quantity required for particular inhibitor to inhibit a given biological process (i.e. an enzyme, cell, cell receptor or microorganism) by half. Occasionally, it is also converted to the pIC50 scale (−log IC50), in which higher values indicate exponentially greater potency. These are the experimental values which are predicted and coded in Nanomolar (nM-10−9) and micromolar (μM10−6). These IC50 values differs in wide range of molecules. So, there are Varity of ranges of applications in molecular modeling techniques especially 3D-QSAR, CoMFA, CoMSIA, Pharmacophore Mapping and many more applications. So, to predict the narrow value from the experimental value, the successful formula is described here to calculate the pIC50 value. As of now, no tool available as open source software to provide the value of pIC50 from IC values as pICcalculator In this work 5050. we developed the tool for the prediction of pIC50 values from the IC50 in nanomolar and micromolar using the JavaScript programming language, which is available at the Sanjeevslab webpage: http://www.skysanjeev.110mb.com/index.php?p=1_7_Tools
Epitopes of human interferon-alpha defined by the reaction of monoclonal antibodies with alpha interferons and interferon analogues. (1987)

Five monoclonal antibodies reactive with human interferon (HuIFN)-alpha 2, but not with HuIFN-alpha 1, have been analyzed for their reaction with a series of IFN analogues and hybrid IFN molecules. Using analogues containing alpha 1 or gamma substitutions, it was shown that amino acids in the 107 to 113 region are implicated in the epitopes recognized by four of the five antibodies tested. Surprisingly, two of the antibodies that did not react with [alpha 1(113 to 114)112 to 113]alpha 2 also did not react with a truncated IFN-alpha 2(4 to 155). The presence of an epitope determined by amino acids at 112 and 113 and by the amino and carboxyl ends of the molecule supports a model for IFN where the carboxyl- and amino-terminals are adjacent to the proposed reverse turn around amino acid 110 to 115. The fifth alpha 2 specific antibody whose reaction with HuIFN-alpha 2 is not affected by the above substitutions and truncations recognizes IFN or IFN hybrids that, like alpha 2, have arginine at position 120, but does not react with IFN that, like alpha 1, have lysine at position 120. Amino acids 107 to 113 and 120 lie in regions of the molecule that have high hydrophilicity and are probably structurally involved in the epitopes recognized by the antibodies. Under conditions of antibody excess, the antibodies described here inhibit binding of HuIFN-alpha 2 to both human and bovine cells.
MOLECULAR AND EVOLUTIONARY BASIS OF THE CELLULAR STRESS RESPONSE (2004)

The cellular stress response is a universal mechanism of extraordinary physiological/pathophysiological significance. It represents a defense reaction of cells to damage that environmental forces inflict on macromolecules. Many aspects of the cellular stress response are not stressor specific because cells monitor stress based on macromolecular damage without regard to the type of stress that causes such damage. Cellular mechanisms activated by DNA damage and protein damage are interconnected and share common elements. Other cellular responses directed at re-establishing homeostasis are stressor specific and often activated in parallel to the cellular stress response. All organisms have stress proteins, and universally conserved stress proteins can be regarded as the minimal stress proteome. Functional analysis of the minimal stress proteome yields information about key aspects of the cellular stress response, including physiological mechanisms of sensing membrane lipid, protein, and DNA damage; redox sensing and regulation; cell cycle control; macromolecular stabilization/repair; and control of energy metabolism. In addition, cells can quantify stress and activate a death program (apoptosis) when tolerance limits are exceeded.
The antibody-linked chelating polymers for nuclear therapy and diagnostics. (1991)

This review deals with the problem of protein modification with chelating polymers. The main purpose of this approach is the preparation of monoclonal antibodies labeled with heavy metal isotopes (alpha-, beta-, and delta-emitting metals and metals used for NMR-tomography). Traditional binding of metals with proteins via chelating agents directly coupled to protein molecule does not allow binding a high number of metal atoms per single protein molecule and can also alter protein specific properties. At the same time, metal-to-protein binding via intermediate chelating polymer makes possible the binding of several dozen metal atoms per single protein without affecting its specific properties. Moreover, the variations in polymer properties and molecular weight allow controlled modified antibody biodistribution and clearance rate. Modified antibodies can be used successfully for nuclear and NMR diagnostics and for nuclear therapy. The following problems are discussed: the chemistry of the coupling of chelating groups to polymer backbone; the binding of chelating polymers to proteins, including monoclonal antibodies; the ability of chelating polymer-to-protein conjugates to bind heavy metals; the influence of the modification on protein conformation and specific properties; the behavior of metal-containing conjugates in vivo; the practical use of conjugates obtained for radioimmunoimaging, radioimmunotherapy, NMR-tomography, and in vitro immunoassays. Future prospects of the approach are also discussed.
Silicon−Hydrogen Bond Activation and Hydrosilylation of Alkenes Mediated by CpCo Complexes: A Theoretical Study (2009)

Using DFT techniques, we show that triplet cyclopentadienylcobalt activates Si-H bonds to generate singlet silylcobalt hydrides without the intervention of sigma-silanes. The cobalt is configurationally unstable, as evidenced by the diastereoisomerization of derivatives bearing chiral silyl ligands. Inversion at the metal proceeds in the singlet state via a bridging hydride. We demonstrate that a two-state mechanism for the transformation of silyl hydride cobalt complexes into disilyl dihydride cobalt species is feasible. Our calculations predict that catalytic hydrosilylation of alkenes should be achievable in the coordination sphere of cyclopentadienylcobalt.
Non-Catalytic Site HIV-1 Integrase Inhibitors Disrupt Core Maturation and Induce a Reverse Transcription Block in Target Cells (2013)

HIV-1 integrase (IN) is the target for two classes of antiretrovirals: i) the integrase strand-transfer inhibitors (INSTIs) and ii) the non-catalytic site integrase inhibitors (NCINIs). NCINIs bind at the IN dimer interface and are thought to interfere primarily with viral DNA (vDNA) integration in the target cell by blocking IN-vDNA assembly as well as the IN-LEDGF/p75 interaction. Herein we show that treatment of virus-producing cells, but not of mature virions or target cells, drives NCINI antiviral potency. NCINIs target an essential late-stage event in HIV replication that is insensitive to LEDGF levels in the producer cells. Virus particles produced in the presence of NCINIs displayed normal Gag-Pol processing and endogenous reverse transcriptase activity, but were defective at initiating vDNA synthesis following entry into the target cell. NCINI-resistant virus carrying a T174I mutation in the IN dimer interface was less sensitive to the compound-induced late-stage effects, including the reverse transcription block. Wild-type, but not T174I virus, produced in the presence of NCINIs exhibited striking defects in core morphology and an increased level of IN oligomers that was not observed upon treatment of mature cell-free particles. Collectively, these results reveal that NCINIs act through a novel mechanism that is unrelated to the previously observed inhibition of IN activity or IN-LEDGF interaction, and instead involves the disruption of an IN function during HIV-1 core maturation and assembly.
Dynamic Image Networks for Action Recognition (2016)

We introduce the concept of dynamic image, a novel compact representation of videos useful for video analysis especially when convolutional neural networks (CNNs) are used. The dynamic image is based on the rank pooling concept and is obtained through the parameters of a ranking machine that encodes the temporal evolution of the frames of the video. Dynamic images are obtained by directly applying rank pooling on the raw image pixels of a video producing a single RGB image per video. This idea is simple but powerful as it enables the use of existing CNN models directly on video data with fine-tuning. We present an efficient and effective approximate rank pooling operator, speeding it up orders of magnitude compared to rank pooling. Our new approximate rank pooling CNN layer allows us to generalize dynamic images to dynamic feature maps and we demonstrate the power of our new representations on standard benchmarks in action recognition achieving state-of-the-art performance.
Functional Genomics Approach to Identifying Genes Required for Biofilm Development by Streptococcus mutans (2002)

Streptococcus mutans, the primary etiological agent of human dental caries, is an obligate biofilm-forming bacterium. The goals of this study were to identify the gene(s) required for biofilm formation by this organism and to elucidate the role(s) that some of the known global regulators of gene expression play in controlling biofilm formation. In S. mutans UA159, the brpA gene (for biofilm regulatory protein) was found to encode a novel protein of 406 amino acid residues. A strain carrying an insertionally inactivated copy of brpA formed longer chains than did the parental strain, aggregated in liquid culture, and was unable to form biofilms as shown by an in vitro biofilm assay. A putative homologue of the enzyme responsible for synthesis of autoinducer II (AI-2) of the bacterial quorum-sensing system was also identified in S. mutans UA159, but insertional inactivation of the gene (luxS(Sm)) did not alter colony or cell morphology or diminish the capacity of S. mutans to form biofilms. We also examined the role of the homologue of the Bacillus subtilis catabolite control protein CcpA in S. mutans in biofilm formation, and the results showed that loss of CcpA resulted in about a 60% decrease in the ability to form biofilms on an abiotic surface. From these data, we conclude that CcpA and BrpA may regulate genes that are required for stable biofilm formation by S. mutans.
Differential activation of the c-Jun N-terminal kinase/stress-activated protein kinase and p38 mitogen-activated protein kinase signal transduction pathways in the mouse brain upon infection with neurovirulent influenza A virus (2003)

The temporal and spatial distribution of active c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) in the brain was investigated in an experimental virus–mouse system in which neurovirulent influenza A virus caused lethal acute encephalitis. Following stereotaxic microinjection into the olfactory bulb, virus-infected neurons appeared in several midbrain structures, including the ventral tegmental area, amygdala and the pyramidal layer of the hippocampus. Infected neurons exhibited apoptosis on day 5, as demonstrated by in situ detection of DNA fragmentation and active caspase-3. The stress-responsive JNK signal transduction pathway was activated in virus-infected neurons. Activation of p38 MAPK was widespread and occurred in astrocytes on day 7 after infection. Active p38 MAPK in astrocytes showed no association with apoptosis but appeared to be involved in regulation of TNF-α production. These results indicate that these two stress-activated protein kinases may play distinct roles during the course of lethal acute influenza virus encephalitis.
Synthesis and in vitro pharmacology of arpromidine and related phenyl(pyridylalkyl)guanidines, a potential new class of positive inotropic drugs (1989)

Replacement of the cimetidine moiety in impromidine (1,N1-[3-(1H-imidazol-4-yl)propyl]-N2-[2-[[(5-methyl-1H-imidazol-4- yl)methyl]thio]ethyl]guanidine) by more lipophilic H2-nonspecific pheniramine-like structures resulted in potent H2 agonists with up to 160 times the activity of histamine in the isolated, spontaneously beating guinea pig right atrium. Additionally, the compounds proved to be moderate H1 antagonists. Highest H2-agonistic potency was found in compounds characterized by a three-membered carbon chain connecting the aromatic rings and the guanidine group. The activity in the atrium was increased 2-4-fold by halogen substituents in the meta or para position of the phenyl ring. Highest H1-antagonistic potency resides in the group of para-halogenated compounds, p-F representing the optimal substituent in both receptor models. The corresponding guanidine 52 (arpromidine, N1-[3-(4-fluorophenyl)-3-pyridin-2-ylpropyl]-N2-[3-(1H-imidazol-4- yl)propyl]guanidine) combines about 100 times the activity of histamine at the H2 receptor with H1-antagonistic potency in the range of pheniramine. Further increase in the activity on the atrium was achieved by disubstitution with halogen on the phenyl ring, such as 3,4-F2, 3,5-F2, and 3,4-Cl2 (63-65). The 2-pyridyl group in arpromidine was replaced by 3-pyridyl without significant change in H2 agonistic activity, whereas the 4-pyridyl and phenyl analogues were less active. The rank order of potency in the atrium was in good agreement with the positive inotropic effects found in isolated, perfused guinea pig hearts, where 63-65 were the most potent compounds as well.
Looking Out for the Watchdogs: A Legislative Proposal Limiting the Newsgathering Privilege to Journalists in the Greatest Need of Protection for Sources and Information (2002)

In 1999, North Carolina became the thirty-first state to enact a statute granting journalists a privilege to withhold information from compelled disclosure. The North Carolina law, like other journalist's privilege statutes across the United States, applies to persons, companies, or other entities engaged in the business of gathering or disseminating news. Further, by defining the privileged group in terms of news gathering and disseminating functions, the General Assembly continued the time-honored practice of state legislatures in limiting the testimonial privilege to those who work for traditional news media.
Proteomics in human disease: Cancer, heart and infectious diseases (1999)

In recent years, genomics has increased the understanding of many diseases. Proteomics is a rapidly growing research area that encompasses both genetic and environmental factors. The protein composition represents the functional status of a biological compartment. The five approaches presented here resulted in the detection of disease-associated proteins. Calgranulin B was upregulated in colorectal cancer, and hepatoma-derived aldose reductase-like protein was reexpressed in a rat model during hepatocarcinogenesis. In these two investigations, attention was focused on one protein, obviously differing in amount, directly after two-dimensional electrophoresis (2-DE). Additional methods, such as enzyme activity measurements and immunohistochemistry, confirmed the disease association of the two candidates resulting from 2-DE subtractive analysis. The following three investigations take advantage of the holistic potential of the 2-DE approach. The comparison of 2-DE patterns from dilated cardiomyopathy patients with those of controls revealed 25 statistically significant intensity differences, from which 12 were identified by amino acid analysis, Edman degradation or matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). A human myocardial 2-DE database was constructed, containing 3300 protein spots and 150 identified protein species. The number of identified proteins was limited by the capacity of our group, rather than by the principle of feasibility. Another field where proteomics proves to be a valuable tool in identifying proteins of importance for diagnosis is proteome analysis of pathogenic microorganisms such as Borrelia burgdorferi (Lyme disease) and Toxoplasma gondii (toxoplasmosis). Sera from patients with early or late symptoms of Lyme borreliosis contained antibodies of various classes against about 80 antigens each, containing the already described antigens OspA, B and C, flagellin, p83/100, and p39. Similarly, antibody reactivity to seven different marker antigens of T. gondii allowed differentiation between acute and latent toxoplasmosis, an important diagnostic tool in both pregnancy and immunosuppressed patients.
Isolation of tumour stem-like cells from benign tumours (2009)

This study for the first time indicates that stem-like cells are present in benign tumours. The conclusions from this study may have applications to understanding pituitary tumour biology and therapies, as well as implications for the notion of tumour-initiating cells in general.
Chirality-dependent G-band Raman intensity of carbon nanotubes (2001)

The chirality-dependent G-band Raman intensity of single wall carbon nanotubes is calculated using a nonresonant theory for the Raman tensor. We obtain six or three intense Raman modes, respectively, for chiral or achiral nanotubes, whose relative intensities depend on the chiral angle of the nanotube. The longitudinal and transverse optical phonon modes in two-dimensional graphite become, respectively, transverse and longitudinal optical phonon modes in a one-dimensional nanotube. Confocal micro-Raman measurements of individual single wall carbon nanotubes show chirality-dependent spectra of the G-band intensity, as predicted by this theory.
Low-Level Right Vagal Stimulation: Anticholinergic and Antiadrenergic Effects (2011)

LL-RVS suppressed AF inducibility and the chronotropic responses to parasympathetic and sympathetic stimulation. Inhibition of neural activity in the GP may be a mechanism underlying these results.