gebhart/patrepeval huggingface dataset:
Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry (2005)

Gene product (gp) 24 of bacteriophage T4 forms the pentameric vertices of the capsid. Using x-ray crystallography, we found the principal domain of gp24 to have a polypeptide fold similar to that of the HK97 phage capsid protein plus an additional insertion domain. Fitting gp24 monomers into a cryo-EM density map of the mature T4 capsid suggests that the insertion domain interacts with a neighboring subunit, effecting a stabilization analogous to the covalent crosslinking in the HK97 capsid. Sequence alignment and genetic data show that the folds of gp24 and the hexamer-forming capsid protein, gp23*, are similar. Accordingly, models of gp24* pentamers, gp23* hexamers, and the whole capsid were built, based on a cryo-EM image reconstruction of the capsid. Mutations in gene 23 that affect capsid shape map to the capsomer's periphery, whereas mutations that allow gp23 to substitute for gp24 at the vertices modify the interactions between monomers within capsomers. Structural data show that capsid proteins of most tailed phages, and some eukaryotic viruses, may have evolved from a common ancestor.
Evaluating maturation and genetic modification of human dendritic cells in a new polyolefin cell culture bag system (2009)

The polyolefin bag-based culture system yields DCs qualitatively and quantitatively comparable to the standard flask preparation. All steps including cryopreservation can be performed in a closed system facilitating standardized, safe, and reproducible preparation of therapeutic cells.
Nonlinear distortion in long wavelength AC bias recording (1979)

Nonlinear distortion due to tape magnetization nonlinearity is analyzed for long wavelength ac bias recording. A normal distribution of particle switching fields is assumed in order to derive a transfer function. Harmonic components are computed by Fourier expansion, not only for idealized uniform magnetization but also for practical nonuniform magnetization throughout tape coating thickness. To calculate harmonics for nonuniform magnetization, the tape coating thickness is divided into thin layers. Even though the vertical magnetization component and the demagnetizing field effect are neglected, the computed results for nonuniform magnetization exhibit excellent quantitative agreement with experimental data.
A broad-band VHF mixer exhibiting high image rejection over a multidecade baseband frequency range (1981)

Image-suppressing frequency converters operating over greater than octave RF and LO input bandwidths in the VHF frequency range are described. The devices, designed for RF to video conversion, exhibit very flat conversion loss response and greater than 34 dB rejection of the undesired sideband at any baseband frequency between 186 kHz and 50 MHz.
Synthetic Routes to 4-Amino-3-carboxy-.beta.-carboline Derivatives: Incidental Formation of Novel Furo[3,4-c]-.beta.-carbolin-2-ones Displaying High Affinities for the Benzodiazepine Receptor (1995)

The synthesis of the first 4-amino-3-carboxy-beta-carboline derivative (35) is described. This synthesis is based on ozonolysis of the 4-vinyl-beta-carboline-3-carboxamide 17 to give the 4-aldehyde 20 and potassium permanganate oxidation of the latter to the 4-carboxylic acid 34 followed by a DPPA-promoted Curtius rearrangement. During the course of these transformations, a number of furo[3,4-c]-beta-carbolin-2-ones, differing in substituents at the C-10 position, were formed. While these beta-carboline lactones (15,25,26,33) generally displayed good affinities for the central type benzodiazepine receptor in vitro (IC50's in the 10-50 nM range), one compound, 29, demonstrated an exceptionally high binding affinity (IC50 = 0.2 nM). Compound 29 was shown in electrophysiological and behavioral studies to act as a benzodiazepine receptor antagonist. The unusually high binding affinity of compound 29 corroborates the hypothesis that the benzodiazepine receptor preferentially recognizes the C-3 carbonyl function of 3-carboxy-beta-carbolines in an s-cis conformation (i.e., the carbonyl oxygen on the same side as the pyridinyl nitrogen).
Effect of Root-Knot Nematodes On the Mineral, Amino Acid and Carbohydrate Concentrations of Almond and Peach Rootstocks (1980)

The mineral concentrations of both roots and leaves of bitter almond were significantly greater in plants infested by Meloidogyne javanica or M. incognita than in uninfested plants. K, Ca, Mn and Cu concentrations of roots and leaves were increased; P concentrations of leaves and N concentrations of roots were also increased. The concentration of Fe was significantly decreased whereas those of Mg and Zn were unaffected. There were no significant differences in mineral concentrations of roots or leaves between nematode-infested Nemaguard peach plants and control, except that the Fe concentration of roots was significantly less in infested plants. No qualitative differences in combined amino acids were found between healthy and nematode-infested bitter almond plants but there were some differences in free amino acid contents. The concentration of total carbohydrates in Nemaguard peach was unaffected by nematode infestation. M. incognita significantly decreased the total carbohydrate concentration of both roots and leaves of bitter almond and M. javanica significantly decreased the total concentration of carbohydrates in roots.
Preparation of Styryl Dyes from Aromatic Heterocyclic Ammonium Salts. X (1949)

In order to observe the physiological properties of styryl dyes, a comparatively simply compounds of photosensitive heterocyclic ammonium salt dyes, over 30 kinds of dyes were obtained by the condensation of aromatic aldehydes and aromatic heterocyclic ammonium salts in EtOH solution under the presence of piperidine. Ammonium salts used were synthesized from lepidine, 6-methoxylepidine, quinaldine, 4-aminoquinaldine, 2, 4-dimethylthiazole, α-picoline, γ-picoline, 2, 4-lutidine and 2, 6-lutidine with alkyl halides such as ethyl, propyl, butyl and octyl bromides and methyl iodide. Aldehydes used were benzaldehyde, piperonal, vanillin, furfural, p-dimethylaminobenzaldehyde and anisaldehyde.
MoS<sub>2</sub>transistors with 1-nanometer gate lengths (2016)

Scaling of silicon (Si) transistors is predicted to fail below 5-nanometer (nm) gate lengths because of severe short channel effects. As an alternative to Si, certain layered semiconductors are attractive for their atomically uniform thickness down to a monolayer, lower dielectric constants, larger band gaps, and heavier carrier effective mass. Here, we demonstrate molybdenum disulfide (MoS<sub>2</sub>) transistors with a 1-nm physical gate length using a single-walled carbon nanotube as the gate electrode. These ultrashort devices exhibit excellent switching characteristics with near ideal subthreshold swing of ~65 millivolts per decade and an On/Off current ratio of ~10<sup>6</sup> Simulations show an effective channel length of ~3.9 nm in the Off state and ~1 nm in the On state.
<title>Interactive computation of coverage regions for indoor wireless communication</title> (1995)

This paper describes a system which assists in the strategic placement of rf base stations within buildings. Known as the site modeling tool (SMT), this system allows the user to display graphical floor plans and to select base station transceiver parameters, including location and orientation, interactively. The system then computes and highlights estimated coverage regions for each transceiver, enabling the user to assess the total coverage within the building. For single-floor operation, the user can choose between distance-dependent and partition- dependent path-loss models. Similar path-loss models are also available for the case of multiple floors. This paper describes the method used by the system to estimate coverage for both directional and omnidirectional antennas. The site modeling tool is intended to be simple to use by individuals who are not experts at wireless communication system design, and is expected to be very useful in the specification of indoor wireless systems.
L-Arginine as an Antihypertensive Agent (1992)

L-Arginine, the precursor of endothelium-derived relaxing factor (EDRF)/nitric oxide (NO), was administered intravenously in five patients with essential hypertension, one with renovascular hypertension, one with primary aldosteronism, and one with Cushing's syndrome. During the administration, the mean arterial pressure decreased concomitantly with an elevation of cardiac output and a fall in total peripheral resistance in all cases. Indicators of NO release in vivo such as plasma concentrations of L-citrulline and urinary excretion of nitrite/nitrate increased simultaneously during the administration. These results suggest that exogenous L-arginine can produce a vasodilatory effect via stimulating NO release in hypertensives.
Synthesis of carboranes containing nucleoside bases. Unexpectedly high cytostatic and cytocidal toxicity towards cancer cells (1992)

5-Carboranyluridine 1, 5-carboranyldeoxyuridine 2 and 5-hydroxymethylcarboranyluridine 3 have been prepared; they show unexpectedly high cytotoxicity towards cancer cells, with IC50 values being ca. 10–5 mol dm–3.
Expandable Liner Hanger Provides Cost-Effective Alternative Solution (2000)

Abstract Establishing and maintaining hydraulic integrity between liner hangers and the base casing in which they are set has long been one of the most problematic areas facing operators. With failure rates on pressure seals in overlaps now exceeding 40% in some regions, the need for a solution to this decades-old problem has reached a critical level. Although new approaches have included turbolizers for cementing overlaps, special cements, and liner-top packers, many problems still remain. An operator and a service company are working together to develop a new drill liner hanger based on patented expandable-casing technology. This technology is being used to diametrically expand solid tubulars for a variety of drilling, completion, and remedial applications. The new liner system is designed to totally eliminate the liner lap by expanding an elastomer-coated casing into intimate contact with the casing from which the liner is being hung. Preliminary results indicate the new hanger design can result in load-carrying and burst capacities that exceed the capacity of the previous casing string. Furthermore, the overlap samples tested to date have all resulted in annular seals that have exceeded 10,000-psi differential capacities. In fact, casing has always failed during large-scale testing before any overlap leaks developed. This paper discusses the design and application of the new liner hanger and presents laboratory and field-test results.
A graphics model building and refinement system for macromolecules (1978)

A model building and refinement system is described for use with a Vector General 3400 display. The system allows the user to build models using guide atoms and angles to arrive at the final conformation. It has been used to assist in difference Fourier map interpretation at medium and high resolution, and to build a protein molecule into a multiple isomorphous replacement phased electron density map.
Antibacterial activity of bactenecin 5 fragments and their interaction with phospholipid membranes (2001)

Bactenecin 5 (Bac 5) is an antibacterial 43mer peptide isolated from bovine neutrophils. It consists of an Arg-rich N-terminal region and successive repeats of Arg-Pro-Pro-Ile (or Phe). We synthesized Bac 5(1-23) and several related peptides to clarify the roles these regions play in antibacterial activity. An assay of antibacterial activity revealed that such activity requires the presence of Arg residues at or near the N-terminus, as well as a chain length exceeding 15 residues. None of the peptides exhibited haemolytic activity. Polyproline II-like CD curves were observed for most of the peptides. Measurements of the membrane perturbation and fusion indicated that the perturbation and fusogenic activities of the peptides were, generally, parallel to their antibacterial activities. Amino acid substitution in the repeating region had some effect on antibacterial activity.
Metabolomics as a Functional Genomic Tool for Understanding Lipid Dysfunction in Diabetes, Obesity and Related Disorders (2006)

With the rise of systems biology, a number of approaches have been developed to globally profile a tier of organization in a cell, tissue or organism. Metabolomics is an approach that attempts to profile all the metabolites in a biological matrix. One of the major challenges of this approach, as with other 'omic' technologies, is that the metabolome is context-dependent and will vary with pathology, developmental stage and environmental factors. Thus, the possibility of globally profiling the metabolome of an organism is a genuine analytical challenge, as by definition this must also take into consideration all relevant factors that influence metabolism. Despite these challenges, the approach has already been applied to understand the metabolism in a range of animal models, and has more recently started to be projected into the clinical situation. In this review, the technologies currently being used in metabolomics will be assessed prior to examining their use to study diseases related to the metabolic syndrome, including Type II diabetes, obesity, cardiovascular disease and fatty liver disease.
EglC, a New Endoglucanase from <i>Aspergillus niger</i> with Major Activity towards Xyloglucan (2002)

A novel gene, eglC, encoding an endoglucanase, was cloned from Aspergillus niger. Transcription of eglC is regulated by XlnR, a transcriptional activator that controls the degradation of polysaccharides in plant cell walls. EglC is an 858-amino-acid protein and contains a conserved C-terminal cellulose-binding domain. EglC can be classified in glycoside hydrolase family 74. No homology to any of the endoglucanases from Trichoderma reesei was found. In the plant cell wall xyloglucan is closely linked to cellulose fibrils. We hypothesize that the EglC cellulose-binding domain anchors the enzyme to the cellulose chains while it is cleaving the xyloglucan backbone. By this action it may contribute to the degradation of the plant cell wall structure together with other enzymes, including hemicellulases and cellulases. EglC is most active towards xyloglucan and therefore is functionally different from the other two endoglucanases from A. niger, EglA and EglB, which exhibit the greatest activity towards beta-glucan. Although the mode of action of EglC is not known, this enzyme represents a new enzyme function involved in plant cell wall polysaccharide degradation by A. niger.
Angiotensin-(1-7) Reduces Fibrosis in Orthotopic Breast Tumors (2010)

Angiotensin-(1-7) [Ang-(1-7)] is an endogenous 7-amino acid peptide hormone of the renin-angiotensin system that has antiproliferative properties. In this study, Ang-(1-7) inhibited the growth of cancer-associated fibroblasts (CAF) and reduced fibrosis in the tumor microenvironment. A marked decrease in tumor volume and weight was observed in orthotopic human breast tumors positive for the estrogen receptor (BT-474 or ZR-75-1) and HER2 (BT-474) following Ang-(1-7) administration to athymic mice. Ang-(1-7) concomitantly reduced interstitial fibrosis in association with a significant decrease in collagen I deposition, along with a similar reduction in perivascular fibrosis. In CAFs isolated from orthotopic breast tumors, the heptapeptide markedly attenuated in vitro growth as well as reduced fibronectin, transforming growth factor-β (TGF-β), and extracellular signal-regulated kinase 1/2 kinase activity. An associated increase in the mitogen-activated protein kinase (MAPK) phosphatase DUSP1 following treatment with Ang-(1-7) suggested a potential mechanism by which the heptapeptide reduced MAPK signaling. Consistent with these in vitro observations, immunohistochemical analysis of Ang-(1-7)-treated orthotopic breast tumors revealed reduced TGF-β and increased DUSP1. Together, our findings indicate that Ang-(1-7) targets the tumor microenvironment to inhibit CAF growth and tumor fibrosis.
Citrus Red Mites: Evaluation of Control Obtained with a New Class of Miticides Containing the Cyclopropane Moiety12 (1978)

Journal Article Citrus Red Mites: Evaluation of Control Obtained with a New Class of Miticides Containing the Cyclopropane Moiety Get access D. K. Reed, D. K. Reed 3 Boyden Entomological Laboratory Agric. Res. Serv. USDA Riverside CA 92502 3Present address: Fruit and Vegetable Insects Research Laboratory, Agric. Res. Serv., USDA, Vincennes, IN 47591. Search for other works by this author on: Oxford Academic PubMed Google Scholar D. S. Moreno D. S. Moreno Boyden Entomological Laboratory Agric. Res. Serv. USDA Riverside CA 92502 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 71, Issue 1, 1 February 1978, Pages 93–96, https://doi.org/10.1093/jee/71.1.93 Published: 01 February 1978 Article history Received: 29 August 1977 Published: 01 February 1978
E2F and Histone Deacetylase Mediate Transforming Growth Factor β Repression of <i>cdc25A</i> during Keratinocyte Cell Cycle Arrest (1999)

cdc25A is a tyrosine phosphatase that activates G1 cyclin-dependent kinases (Cdk's). In human keratinocytes, cdc25A expression is down-regulated after the initial drop in Cdk activity caused by cell exposure to the antimitogenic cytokine transforming growth factor beta (TGF-beta) or removal of serum factors. Here we show that the TGF-beta-inhibitory-response element in the cdc25A promoter maps to an E2F site at nucleotides -62 to -55 from the transcription start site. This site is not required for basal transcription in keratinocytes. We provide evidence that the cell cycle arrest program activated by TGF-beta in human keratinocytes includes the generation of E2F4-p130 complexes that in association with histone deacetylase HDAC1 inhibit the activity of the cdc25A promoter from this repressor E2F site. This mechanism is part of a program that places keratinocytes in the quiescent state following the initial drop in Cdk activity caused by cell exposure to TGF-beta.
Optimized Silicidation Technique for Source and Drain of Fin-Type Field-Effect Transistor (2008)

An optimization of a Ni-silicidation technique for three-dimensional (3-D) structure devices is investigated. For 3-D structure devices, an undesirable deformation of silicide films due to annealing in the deposition chamber occurs at pattern edges. To avoid this deformation, the deposition control of Ni on a 3-D structure and the precise control of annealing conditions are required. In this work, Ni deposition at a higher pressure to improve its uniformity is adopted and controlled silicidation annealing is implemented during the deposition to exclude the deformation. For 300 and 250 °C annealings, metal-rich Ni3Si2 and Ni2Si phases are observed, respectively, with X-ray diffraction (XRD) spectroscopy. However silicide deformation at pattern edges is observed in the former case. On the other hand, this undesirable deformation is suppressed in 250 °C annealing. To obtain the desirable lower-resistivity NiSi film, a method involving a controlled two-step annealing at 250 °C and a subsequent additional annealing at 450 or 500 °C is successfully developed.
Intra picture coding with planar representations (2010)

In this paper we introduce a novel concept for Intra coding of pictures especially suitable for representing smooth image segments. Traditional block based transform coding methods cause visually annoying blocking artifacts for image segments with gradually changing smooth content. The proposed solution overcomes this drawback by defining a fully continuous surface of sample values approximating the original image. The gradient of the surface is indicated by transmitting values for selected control points within the image segment and the surface itself is obtained by interpolating sample values in-between the control points. This approach is found to provide up to 30 percent bitrate reductions in the case of natural imagery and it has also been adopted to the initial HEVC codec design by JCT-VC.
Projective Geometry and Transformations of 2D (2004)

This chapter introduces the main geometric ideas and notation that are required to understand the material covered in this book. Some of these ideas are relatively familiar, such as vanishing point formation or representing conics, whilst others are more esoteric, such as using circular points to remove perspective distortion from an image. These ideas can be understood more easily in the planar (2D) case because they are more easily visualized here. The geometry of 3-space, which is the subject of the later parts of this book, is only a simple generalization of this planar case.
Co‐activator activator (CoAA) prevents the transcriptional activity of Runt domain transcription factors (2009)

Runx proteins are essential for a number of developmental processes and are aberrantly expressed in many human cancers. Runx factors bind DNA and co-factors to activate or repress genes crucial for bone formation, hematopoiesis, and neuronal development. Co-activator activator (CoAA) is a nuclear protein that regulates gene expression, RNA splicing and is overexpressed in many human tumors. In this study, we identified CoAA as a Runx2 binding protein. CoAA repressed Runx factor-dependent activation of reporter genes in a histone deacetylase-independent manner. CoAA also blocked Runx2-mediated repression of the Axin2 promoter, a novel Runx target gene. The carboxy-terminus of CoAA is essential for binding the Runt domains of Runx1 and Runx2. In electophoretic mobility shift assays, CoAA inhibited Runx2 interactions with DNA. These data indicate that CoAA is an inhibitor of Runx factors and can negate Runx factor regulation of gene expression. CoAA is expressed at high levels in human fetal osteoblasts and osteosarcoma cell lines. Suppression of CoAA expression by RNA interference reduced osteosarcoma cell viability in vitro, suggesting that it contributes to the proliferation and/or survival of osteoblast lineage cells.