gebhart/patrepeval huggingface dataset:
Characterization of protein-ligand interaction sites using experimental and computational methods. (2006)

The ability to identify the sites of a protein that can bind with high affinity to small, drug-like compounds has been an important goal in drug design. Accurate prediction of druggable sites and the identification of small compounds binding in those sites have provided the input for fragment-based combinatorial approaches that allow for a more thorough exploration of the chemical space, and that have the potential to yield molecules that are more lead-like than those found using traditional high-throughput screening. Current progress in experimental and computational methods for identifying and characterizing druggable ligand binding sites on protein targets is reviewed herein, including a discussion of successful nuclear magnetic resonance, X-ray crystallography and tethering technologies. Classical geometric and energy-based computational methods are also discussed, with particular focus on two powerful technologies, that is, computational solvent mapping and grand canonical Monte Carlo simulations (as used by Locus Pharmaceuticals Inc). Both methods can be used to reliably identify druggable sites on proteins and to facilitate the design of novel, low-nanomolar-affinity ligands.
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach (2005)

The metagenomic approach allowed us to detect a reduced complexity of the bacterial phylum Firmicutes as a signature of the faecal microbiota in patients with CD. It also indicated the presence of new bacterial species.
Improved acoustic viscosimeter technique (1976)

An improved technique has been developed for studies of the shear viscosity of fluids. It utilizes an acoustic resonator as a four-terminal electrical device; the resonator’s amplitude response may be determined directly and simply related to the fluid’s viscosity. The use of this technique is discussed briefly and data obtained in several fluids is presented. Subject Classification: [43]35.10, [43]35.68; [43]85.52.
THE QUANTITATIVE DETERMINATION OF INFLUENZA VIRUS AND ANTIBODIES BY MEANS OF RED CELL AGGLUTINATION (1942)

1. The agglutination titer for chicken red cells of freshly prepared or carefully stored suspensions of PR8 influenza virus, that is to say virus of maximum pathogenicity, was found to be proportional to the mouse lethal titer of the same preparations. 2. The agglutination titer of infected allantoic fluid procured in a standard way is relatively constant, regardless of the influenza strain used and its pathogenicity for mice. 3. Virus preparations inactivated by heat or storage may retain their agglutinating power. 4. Certain animal sera contain a partially heat-labile factor which, in low dilution, inhibits the agglutination of chicken red cells by influenza A and influenza B viruses. 5. The agglutination inhibition test, using ferret and human sera, gives qualitative data regarding influenza antibodies which are similar to the information obtained on the same sera by means of the virus neutralization test. 6. There is a definite relationship between the agglutination inhibition titer and the virus neutralization titer of a serum. On a logarithmic scale of both variables, this relationship is essentially linear within the range investigated. 7. The agglutination inhibition titer of immune ferret serum is inversely proportional to the amount of virus used in the test.
Understanding nonpolar GaN growth through kinetic Wulff plots (2008)

In this paper we provide explanations to the complex growth phenomena of GaN heteroepitaxy on nonpolar orientations using the concept of kinetic Wulff plots (or v-plots). Quantitative mapping of kinetic Wulff plots in polar, semipolar, and nonpolar angles are achieved using a differential measurement technique from selective area growth. An accurate knowledge of the topography of kinetic Wulff plots serves as an important stepping stone toward model-based control of nonpolar GaN growth. Examples are illustrated to correlate growth dynamics based on the kinetic Wulff plots with commonly observed features, including anisotropic nucleation islands, highly striated surfaces, and pentagonal or triangular pits.
ASAP, a Novel Protein Complex Involved in RNA Processing and Apoptosis (2003)

Different isoforms of a protein complex termed the apoptosis- and splicing-associated protein (ASAP) were isolated from HeLa cell extract. ASAP complexes are composed of the polypeptides SAP18 and RNPS1 and different isoforms of the Acinus protein. While Acinus had previously been implicated in apoptosis and was recently identified as a component of the spliceosome, RNPS1 has been described as a general activator of RNA processing. Addition of ASAP isoforms to in vitro splicing reactions inhibits RNA processing mediated by ASF/SF2, by SC35, or by RNPS1. Additionally, microinjection of ASAP complexes into mammalian cells resulted in acceleration of cell death. Importantly, after induction of apoptosis the ASAP complex disassembles. Taken together, our results suggest an important role for the ASAP complexes in linking RNA processing and apoptosis.
<i>Burkholderia</i> and <i>Paraburkholderia</i> are Predominant Soybean Rhizobial Genera in Venezuelan Soils in Different Climatic and Topographical Regions (2019)

The climate, topography, fauna, and flora of Venezuela are highly diverse. However, limited information is currently available on the characterization of soybean rhizobia in Venezuela. To clarify the physiological and genetic diversities of soybean rhizobia in Venezuela, soybean root nodules were collected from 11 soil types located in different topographical regions. A total of 395 root nodules were collected and 120 isolates were obtained. All isolates were classified in terms of stress tolerance under different concentrations of NaCl and Al<sup>3+</sup>. The tolerance levels of isolates to NaCl and Al<sup>3+</sup> varied. Based on sampling origins and stress tolerance levels, 44 isolates were selected for further characterization. An inoculation test indicated that all isolates showed the capacity for root nodulation on soybean. Based on multilocus sequence typing (MLST), 20 isolates were classified into the genera Rhizobium and Bradyrhizobium. The remaining 24 isolates were classified into the genus Burkholderia or Paraburkholderia. There is currently no evidence to demonstrate that the genera Burkholderia and Paraburkholderia are the predominant soybean rhizobia in agricultural fields. Of the 24 isolates classified in (Para) Burkholderia, the nodD-nodB intergenic spacer regions of 10 isolates and the nifH gene sequences of 17 isolates were closely related to the genera Rhizobium and Bradyrhizobium, respectively. The root nodulation numbers of five (Para) Burkholderia isolates were higher than those of the 20 α-rhizobia. Furthermore, among the 44 isolates tested, one Paraburkholderia isolate exhibited the highest nitrogen-fixation activity in root nodules.
Evaluating the accuracy of functional biomarkers for detecting histological changes in chronic allograft nephropathy (2007)

The most common cause of late kidney transplant failure is chronic allograft nephropathy (CAN). Much research has focused on identifying biomarkers (or correlates) that would predict subsequent CAN and allow timely intervention. Functional biomarkers such as serum creatinine and estimated glomerular filtration rate (eGFR) have been widely adopted, even though they have not been rigorously evaluated as surrogate markers. This study evaluated serum creatinine and eGFR for predicting the early histopathological changes seen in transplant protocol biopsies (TPB). We prospectively followed 289 kidney transplant patients in the Southern Alberta Transplant Program who had TPB at 6-12 months post-transplant. Tissue samples (n = 280) were independently examined by renal pathologists. The ability of serum creatinine or eGFR to predict the threshold level for abnormal histopathology was evaluated by calculating the area under the receiver operator characteristic curve. Serum creatinine and eGFR had poor predictive value (most confidence intervals included 0.5, indicating no predictive ability) for ten individual histological measurements (Banff 97 scores), and the Chronic Allograft Damage Index. We conclude that serum creatinine and eGFR have a limited clinical role in predicting the early histopathological changes that precede CAN and should not be used for this purpose.
Methylnaltrexone prevents morphine-induced delay in oral-cecal transit time without affecting analgesia: A double-blind randomized placebo-controlled trial* (1996)

Methylnaltrexone is a quaternary opioid antagonist with limited ability to cross the blood-brain barrier and the potential to antagonize the peripherally mediated effects of opioids. The effectiveness of methylnaltrexone in preventing morphine-induced changes in gastrointestinal motility and transit without affecting analgesia was evaluated in humans. Twelve healthy volunteers were given intravenous placebo, placebo plus 0.05 mg/kg morphine, or 0.45 mg/kg methylnaltrexone plus 0.05 mg/kg morphine. Oral-cecal transit time was assessed by the pulmonary hydrogen measurement technique, and analgesia was measured with use of the cold-pressor test. Morphine significantly increased oral-cecal transit time from 104.6 +/- 31.1 minutes (mean +/- SD) to 163.3 +/- 39.8 minutes (p < 0.01). Methylnaltrexone prevented 97% of morphine-induced increase in oral-cecal transit time (106.3 +/- 39.8 minutes; not significant compared with baseline; p < 0.01 compared with morphine alone). Methylnaltrexone did not affect the analgesic effect of morphine on both pain intensity and pain bothersomeness ratings. At a higher dose of morphine (0.1 mg/kg), our preliminary results indicated that 0.45 mg/kg methylnaltrexone also prevented the morphine-induced delay in oral-cecal transit time, with no effect on analgesia. Methylnaltrexone may be a useful adjunct to opioids for the relief of opioid-induced constipation.
Identification of Conserved Residues Contributing to the Activities of Adenovirus DNA Polymerase (2000)

Adenovirus codes for a DNA polymerase that is a member of the DNA polymerase alpha family and uses a protein primer for initiation of DNA synthesis. It contains motifs characteristic of a proofreading 3'-5'-exonuclease domain located in the N-terminal region and several polymerase motifs located in the C-terminal region. To determine the role of adenovirus DNA polymerase in DNA replication, 22 site-directed mutations were introduced into the conserved DNA polymerase motifs in the C-terminal region of adenovirus DNA polymerase and the mutant forms were expressed in insect cells using a baculovirus expression system. Each mutant enzyme was tested for DNA binding activity, the ability to interact with pTP, DNA polymerase catalytic activity, and the ability to participate in the initiation of adenovirus DNA replication. The mutant phenotypes identify functional domains within the adenovirus DNA polymerase and allow discrimination between the roles of conserved residues in the various activities carried out by the protein. Using the functional data in this study and the previously published structure of the bacteriophage RB69 DNA polymerase (J. Wang et al., Cell 89:1087-1099, 1997), it is possible to envisage how the conserved domains in the adenovirus DNA polymerase function.
Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides:  Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2‘-O-Ribonucleic Acid Modifications, (2005)

The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.
Quantitative Structure—Activity Analysis and Database-Aided Bioisosteric Structural Transformation Procedure as Methodologies of Agrochemical Design (1995)

We have been intensively studying the Hansch-type QSAR applications to a number of agrochemical series of compounds. Because the QSAR procedure utilizes principles of physical organic chemistry, clues for the molecular mechanism of action have been disclosed in many cases. From the QSAR models, new congeneric structures having the optimum activity profiles have been successfully predicted for some series. For generation of non-congeneric novel structures, we have been constructing a system named EMIL, which incorporates a database for structural "evolution" examples and a data-processing engine. In fact, the QSAR and EMIL procedures are complementary to each other under a category of computer-assisted empirical methodologies. In the QSAR procedure, the empirical model is built by mathematical equations describing correlations between variations in structure and bioactivity with use of physicochemical substituent and (sub)structural parameters. In the EMIL procedure, structural modification patterns, including those which are non-isometric, collected from the past structural evolution examples are used as empirical "rules" for "bioisosteric" structural transformations in a broader sense. The rules are applied to the primary lead structure to generate candidate structures having elaborated features. In this chapter, methodological backgrounds as well as characteristic distinctions of these procedures are presented on the basis of succesful topics for the agrochemical design.
Near-unity broadband absorption designs for semiconducting nanowire arrays via localized radial mode excitation (2014)

We report design methods for achieving near-unity broadband light absorption in sparse nanowire arrays, illustrated by results for visible absorption in GaAs nanowires on Si substrates. Sparse (<5% fill fraction) nanowire arrays achieve near unity absorption at wire resonant wavelengths due to coupling into 'leaky' radial waveguide modes of individual wires and wire-wire scattering processes. From a detailed conceptual development of radial mode resonant absorption, we demonstrate two specific geometric design approaches to achieve near unity broadband light absorption in sparse nanowire arrays: (i) introducing multiple wire radii within a small unit cell array to increase the number of resonant wavelengths, yielding a 15% absorption enhancement relative to a uniform nanowire array and (ii) tapering of nanowires to introduce a continuum of diameters and thus resonant wavelengths excited within a single wire, yielding an 18% absorption enhancement over a uniform nanowire array.
Estilos de decisión y patrón de conducta tipo A (1997)

La determinacion de las causas subyacentes de las alteraciones cardiovasculares ha conducido al estudio del Patron de conducta Tipo A. Los estudios mas recientes parecen concluir que dicho Patron esta formado por factores diversos, apareciendo dos dimensiones: Ambicion-Competitividad e Irritabilidad-Impaciencia, los cuales contribuyen de forma diferente a la explicacion de la patologia coronaria. Los estilos de decision presentan concomitancias divergentes con las dos dimensiones mencionadas. 

El objetivo del presente trabajo es comprobar el compromiso que los diversos factores de estilo de decision tienen con las dimensiones constituyentes del Patron de conducta Tipo A. En el estudio tomaron parte 115 universitarios de la Universidad de La Laguna. Los resultados son concordantes con los que se observan en la literatura, mostrando una contribucion distinta de los diversos estilos de decision en el Patron de conducta Tipo A.
JMJD5 regulates PKM2 nuclear translocation and reprograms HIF-1α–mediated glucose metabolism (2013)

JMJD5, a Jumonji C domain-containing dioxygenase, is important for embryonic development and cancer growth. Here, we show that JMJD5 is up-regulated by hypoxia and is crucial for hypoxia-induced cell proliferation. JMJD5 interacts directly with pyruvate kinase muscle isozyme (PKM)2 to modulate metabolic flux in cancer cells. The JMJD5-PKM2 interaction resides at the intersubunit interface region of PKM2, which hinders PKM2 tetramerization and blocks pyruvate kinase activity. This interaction also influences translocation of PKM2 into the nucleus and promotes hypoxia-inducible factor (HIF)-1α-mediated transactivation. JMJD5 knockdown inhibits the transcription of the PKM2-HIF-1α target genes involved in glucose metabolism, resulting in a reduction of glucose uptake and lactate secretion in cancer cells. JMJD5, along with PKM2 and HIF-1α, is recruited to the hypoxia response element site in the lactate dehydrogenase A and PKM2 loci and mediates the recruitment of the latter two proteins. Our data uncover a mechanism whereby PKM2 can be regulated by factor-binding-induced homo/heterooligomeric restructuring, paving the way to cell metabolic reprogram.
Polarization holography 1: A new high-efficiency organic material with reversible photoinduced birefringence (1984)

A new organic material for polarization holographic recording--azo-dye methyl-orange, introduced in polyvinyl alcohol (PVA)--is fabricated and investigated. It possesses all the good characteristics of the known polarization-sensitive materials--high sensitivity, reversibility, etc.--but excels them substantially in the magnitude of the photoinduced birefringence: delta n > 10(-3). This makes possible the recording of reversible polarization gratings with diffraction efficiency over 30%. Depending on the conditions of production and subsequent mechanical and thermal treatments the layers of methyl orange/PVA may also have intrinsic birefringence. In this paper the results of experimental investigations into the properties of this new material are reported.
Expert systems applications in integrated network management (1989)

While many books focus on the broader, socially ethical topics of widening participation and promoting equal opportunities, this text focuses specifically on the lecturer's professional responsibilities. It covers everyday, real-life moral dilemmas which confront university teachers when dealing with students and colleagues - whether arising from facilitated discussion in the classroom, deciding whether it is fair to extend a deadline, investigating suspected plagiarism or dealing with complaints.
Surround-screen projection-based virtual reality (1993)

Article Surround-screen projection-based virtual reality: the design and implementation of the CAVE Share on Authors: Carolina Cruz-Neira View Profile , Daniel J. Sandin View Profile , Thomas A. DeFanti View Profile Authors Info & Claims SIGGRAPH '93: Proceedings of the 20th annual conference on Computer graphics and interactive techniquesSeptember 1993 Pages 135–142https://doi.org/10.1145/166117.166134Online:01 September 1993Publication History 1,193citation11,681DownloadsMetricsTotal Citations1,193Total Downloads11,681Last 12 Months516Last 6 weeks72 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Stimulation of glucose transport by insulin and norepinephrine in isolated rat brown adipocytes (1989)

The effects of insulin and norepinephrine on glucose transport, glucose uptake, and cell respiration were investigated in isolated rat brown adipocytes. Glucose transport and uptake were determined using [U-14C]-D-glucose and 2-deoxy-[1,2-3H]-D-glucose, respectively. Brown adipocyte respiration was measured polarographically. Dose-response experiments revealed that insulin stimulated D-glucose transport and 2-deoxyglucose uptake between 10(-11) and 10(-7) M with a maximal four- to sixfold stimulation. In the absence of insulin, norepinephrine concentrations ranging from 10(-7) to 10(-7) M also enhanced glucose transport and uptake with a maximal two- to fourfold stimulation. Experiments with alpha- and beta-adrenergic agonists and antagonists showed that the effect of norepinephrine was predominantly mediated via beta-adrenergic pathways. Dibutyryl cyclic AMP and 3-isobutyl-1-methylxanthine also increased glucose transport, suggesting that the effects of norepinephrine are cyclic AMP dependent. Moreover, norepinephrine (10(-8) M) enhanced insulin sensitivity for glucose transport [half-maximum velocity constant (1/2 V max)] but failed to potentiate insulin responsiveness (Vmax). On the other hand, insulin (10(-9) M) had no effect on basal respiration but rapidly inhibited the calorigenic effect of norepinephrine (10(-7) M) by greater than 50%. These results demonstrate that 1) in the absence of insulin, physiological concentrations of norepinephrine stimulate glucose transport via beta-adrenergic pathways, 2) the neurohormone synergistically potentiates brown adipocyte submaximal insulin responses for glucose transport, and 3) insulin counteracts the effects of norepinephrine on brown adipocyte thermogenesis despite the fact that both hormones enhance glucose uptake.
Prenatal diagnosis of alpha-1-antitrypsin deficiency using polymerase chain reaction (PCR). Comparison of conventional RFLP methods with PCR used in combination with allele specific oligonucleotides or RFLP analysis. (1989)

Prenatal diagnosis of alpha 1-antitrypsin (AAT) deficiency can be performed in the 1st trimester of pregnancy. These diagnoses have been based on DNA technology using either RFLP analysis or hybridization with allele specific oligonucleotides. Several RFLPs within and flanking the AAT gene have been found to render most families informative. The polymerase chain reaction allows specific DNA sequences to be amplified up to ten million fold. Both sequences containing a specific mutation or an RFLP can be amplified by this method. We have compared conventional RFLP methods with PCR used in combination with allele specific oligonucleotides or RFLP analysis, in a case of prenatal diagnosis of AAT deficiency of the ZZ type.