gebhart/patrepeval huggingface dataset:
Solid Model Reconstruction of Wireframe CAD Models Based on Topological Embeddings of Planar Graphs (2003)

This paper describes a robust and versatile method based on graph embedding for reconstructing a solid model from a wireframe model. The robustness and versatility of the conventional methods are limited in that: (1) most of them are heuristic and thus less robust, and (2) the rest, deterministic ones, can handle only small class of wireframes. Unlike the conventional methods, our approach is deterministic and covers a larger class of wireframes that are topologically 2-connected planar multigraphs. The class includes wireframes that can be interpreted as a closed two-manifold in multiple ways. The proposed algorithm consists of three steps: (1) all topological solutions are exhaustively generated using triconnected component decomposition; (2) the surface geometries for all the topological solutions are generated; and (3) the solutions are pruned down to geometrically valid ones. We also show the algorithm is extendable to the class of general planar multigraphs. The approach is characterized by generating the complete set of topological solutions without referring to the geometry of the wireframe, which makes the process free from geometric errors and instabilities. The algorithm is also fast, because even when there are many topological solutions, the total number of different faces is very small. The proposed approach provides a method for easy and intuitive geometric modeling as well as a conversion tool for legacy wireframes.
Immunocytochemical localization of a methionine‐enkephalin‐resembling neuropeptide in the central nervous system of the american cockroach, Periplaneta americana L (1985)

Using the peroxidase antiperoxidase immunocytochemical method, we were able to demonstrate within the brain and retrocerebral complex of Periplaneta americana several neuronal structures which were very specifically stained with an anti-methionine-enkephalin antiserum. From the precise localization of this immunoreactive material some speculations about its possible functions could be derived, such as a neurotransmitter- or neuromodulatorlike function and/or a neurohormonal role. These data present new evidence for the recently developed concept that opiate peptides, identical or related to those found in higher species, occur also in invertebrates.
Sulfur in Proteins. (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSulfur in Proteins.John L. WoodCite this: J. Am. Chem. Soc. 1960, 82, 1, 250Publication Date (Print):January 1, 1960Publication History Published online1 May 2002Published inissue 1 January 1960https://pubs.acs.org/doi/10.1021/ja01486a059https://doi.org/10.1021/ja01486a059research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
K-Ras protein as a drug target (2016)

K-Ras proteins are major drivers of human cancers, playing a direct causal role in about one million cancer cases/year. In cancers driven by mutant K-Ras, the protein is locked in the active, GTP-bound state constitutively, through a defect in the off-switch mechanism. As such, the mutant protein resembles the normal K-Ras protein from a structural perspective, making therapeutic attack extremely challenging. K-Ras is a member of a large family of related proteins, which share very similar GDP/GTP-binding domains, making specific therapies more difficult. Furthermore, Ras proteins lack pockets to which small molecules can bind with high affinity, with a few interesting exceptions. However, new insights into the structure and function of K-Ras proteins reveal opportunities for intervention that were not appreciated many years ago, when efforts were launched to develop K-Ras therapies. Furthermore, K-Ras undergoes post-translational modification and interactions with cellular signaling proteins that present additional therapeutic opportunities, such as specific binding to calmodulin and regulation of non-canonical Wnt signaling.
BEHAVIOR GENETICS OF NEST GLEANING IN HONEY BEES. IV. RESPONSES OF F1AND BACKCROSS GENERATIONS TO DISEASE-KILLED BROOD (1964)

animal kingdom lives a more or less soli? tary existence (except for a minimal amount of social life involved in mating activity and reproduction), whereas the honey bee lives in colonies of up to 60,000 individuals. Honey-bee colonies are much more than aggregations, flocks, or herds, for the individuals within one are so dependent upon one another that no individual, nor even a group of a few hundred individuals, can survive and perpetuate the species in nature.
Antitumor cytotoxicity mediated by ligand-activated human V alpha24 NKT cells. (1999)

Human V alpha24 NKT cells bearing an invariant V alpha24J alphaQ antigen receptor, the counterpart of the murine V alpha14 NKT cells, are activated by the specific ligand, alpha-galactosylceramide (alpha-GalCer) in a CD1d-dependent manner. Here, we demonstrate that the alpha-GalCer-activated V alpha24 NKT cells exert a potent perforin-dependent cytotoxic activity against a wide variety of human tumor cell lines. In addition, we demonstrate that V alpha24 NKT cells and dendritic cells (DCs) from melanoma patients are functionally normal, even in the tumor-bearing status. The potential use of alpha-GalCer-activated V alpha24 NKT cells and/or DCs from patients for cancer immunotherapy is discussed.
The Molecular Diversity of Adaptive Convergence (2012)

To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
Directed evolution of homing endonuclease I-SceI with altered sequence specificity (2009)

Homing endonucleases recognize specific long DNA sequences and catalyze double-stranded breaks that significantly stimulate homologous recombination, representing an attractive tool for genome targeting and editing. We previously described a two-plasmid selection system that couples enzymatic DNA cleavage with the survival of host cells, and enables directed evolution of homing endonucleases with altered cleavage sequence specificity. Using this selection system, we successfully evolved mutant I-SceI homing endonucleases with greatly increased cleavage activity towards a new target DNA sequence that differs from the wild-type cleavage sequence by 4 bp. The most highly evolved mutant showed a survival rate approximately 100-fold higher than that of wild-type I-SceI enzyme. The degree of selectivity displayed by a mutant isolated from one round of saturation mutagenesis for the new target sequence is comparable to that of wild-type I-SceI for the natural sequence. These results highlight the ability and efficiency of our selection system for engineering homing endonucleases with novel DNA cleavage specificities. The mutant identified from this study can potentially be used in vivo for targeting the new cleavage sequence within genomic DNA.
Towards patient‐specific tumor antigen selection for vaccination (2002)

In this review, we discuss the possibilities for combining the power of molecular analysis of the antigens expressed in a given individual tumor with the design of a tailored vaccine containing defined antigens. Step 1 is a differential gene expression analysis of tumor and corresponding normal tissue. Step 2 is the analysis of human leukocyte antigen (HLA) ligands on tumor cells. Step 3 is data mining with the aim to select those antigens that might be suitable for tumor attack by the adaptive immune system. Step 4 is the on-the-spot clinical grade production of the constituents of the patient tailored vaccine, e.g. peptides. Step 5 is then vaccination and monitoring. Although it will not be possible to cover all relevant antigens expressed in a tumor, the antigens that can be identified with our present technical possibilities might be enough for improved immunotherapy. The scope of the present review is to explore the possibilities and the formidable technical and logistical challenge for such individual patient-oriented antigen definition to be used for therapeutic immunization.
Apical extracellular calcium/polyvalent cation-sensing receptor regulates vasopressin-elicited water permeability in rat kidney inner medullary collecting duct. (1997)

During antidiuresis, increases in vasopressin (AVP)-elicited osmotic water permeability in the terminal inner medullary collecting duct (tIMCD) raise luminal calcium concentrations to levels (> or = 5 mM) above those associated with the formation of calcium-containing precipitates in the urine. Calcium/polycation receptor proteins (CaRs) enable cells in the parathyroid gland and kidney thick ascending limb of Henle to sense and respond to alterations in serum calcium. We now report the presence of an apical CaR in rat kidney tIMCD that specifically reduces AVP-elicited osmotic water permeability when luminal calcium rises. Purified tIMCD apical membrane endosomes contain both the AVP-elicited water channel, aquaporin 2, and a CaR. In addition, aquaporin 2-containing endosomes also possess stimulatory (G(alpha q)/G(alpha 11) and inhibitory (G(alpha i1, 2, and 3)) GTP binding proteins reported previously to interact with CaRs as well as two specific isoforms (delta and zeta) of protein kinase C. Immunocytochemistry using anti-CaR antiserum reveals the presence of CaR protein in both rat and human collecting ducts. Together, these data provide support for a unique tIMCD apical membrane signaling mechanism linking calcium and water metabolism. Abnormalities in this mechanism could potentially play a role in the pathogenesis of renal stone formation.
In vitro analysis of the E1A-homologous sequences of RIZ (1997)

The RIZ (G3B/MTB-Zf) gene was first isolated based on its ability to bind to the retinoblastoma protein (Rb). An acidic, approximately 100-amino-acid region around the Rb-binding motif of RIZ has structural and antigenic similarity to the conserved sequences of the E1A viral oncogene. We show here that this region interacts specifically with the E1A-binding domain of Rb. This interaction could be disrupted by E1A or by a peptide of RIZ homologous to the CR2 motif of E1A which is involved in binding to Rb family proteins. Also like E1A, RIZ can form a ternary complex with Rb and E2F1. Despite this similarity to E1A, however, RIZ could not bind to the Rb family proteins p107 and p130 in vitro. The data show that the RIZ CR2 motif can mediate differential binding to Rb family proteins. We also mapped the shared antigenic determinant between RIZ and E1A to a conserved sequence, designated CE1, which is located in the C terminus of E1A. Unlike that of ETA, the CE1 motif of RIZ is located next to the CR2 motif. Despite this proximity, CE1 and CR2 appear to act independently. The data show similarities as well as differences between the homologous sequences of RIZ and E1A and contribute to an understanding of the biochemistry of these proteins.
A 40 mV Transformer-Reuse Self-Startup Boost Converter With MPPT Control for Thermoelectric Energy Harvesting (2012)

This paper presents transformer-based self-starting boost converter architecture with low-power maximum power point tracking (MPPT) control for low-voltage thermoelectric generator applications. The minimum working voltage of the proposed boost converter is 40 mV with oscillation through a positive feedback loop formed by a native MOS and transformer. The oscillation autonomously starts up by thermal noise and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OUT</sub> is charged up to 1.2 V by the oscillation so that the control block can operate. After that, the transformer for start-up is reused as an inductor, and the normal boost converter mode is enabled for better energy transfer efficiency. An improved MPPT sensing method is also proposed to simplify the circuit. The prototype chip is implemented in a 0.13-μm CMOS process. It operates with an input voltage range of 40 mV to 300 mV and provides a maximum output power of 2.7 mW with a maximum efficiency of 61% at an output voltage of 2 V.
A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system ofEscherichia coli (1990)

Anaerobically growing Escherichia coli cells contain the enzyme pyruvate formate-lyase which catalyses the non-oxidative cleavage of pyruvate to acetyl-CoA and formate. The enzyme is subject to interconversion between inactive and active forms. The active form contains an oxygen-sensitive organic free radical located on the polypeptide chain which is essential for catalysis. It affords a novel homolytic C-C bond cleavage of the pyruvate substrate. The radical is generated by an iron-dependent converter enzyme which requires reduced flavodoxin and adenosyl methionine as co-substrates and pyruvate as a positive allosteric effector. A second converter enzyme, also iron-dependent, accomplishes the removal of the radical. This post-translational interconversion cycle controls the activity state of pyruvate formate-lyase in the anaerobic cell. Anaerobic conditions also regulate pyruvate formate-lyase at the level of gene expression. Multiple promoters are responsible for effecting a twelve to fifteen fold induction and they are coordinately controlled in response to the oxygen and metabolic status of the cell by sequences which are located far upstream of the pfl coding region. The transcription factor Fnr has been identified as being responsible for part of the anaerobic control of pfl expression, probably through direct interaction with the upstream sequences. In contrast, the expression of the gene encoding the first iron-dependent converter enzyme is unaffected by anaerobiosis and is independent of the Fnr protein.
Release of interleukin 1 inhibitory activity (contra-IL-1) by human monocyte-derived macrophages infected with human immunodeficiency virus in vitro and in vivo. (1988)

Infection of monocyte-macrophages with human immunodeficiency virus may be central to the pathogenesis of the acquired immunodeficiency syndrome. The ability of infected macrophages to prime T cells through IL-1 production was investigated in vitro. Purified human monocytes maintained in suspension culture were infected with strain HIV-DV. Intracellular expression of virus p24 antigen increased from undetectable levels immediately after infection to 13-59% of cells by 10-14 d; infected macrophages remained viable for up to 60 d. Supernatants collected between 14 and 20 d after infection were examined in the murine thymocyte co-mitogenesis assay and demonstrated to contain a potent IL-1 inhibitor, designated contra-IL-1. Contra-IL-1 activity was present in all supernatants examined after 4 d of infection, and peaked coincident with peak p24 antigen expression. Inhibitory activity was not present in uninfected cells. Contra-IL-1 activity eluted after gel filtration with an approximate molecular weight of 9 kD. Inhibitory activity was removed by exposure to heat or acid pH, or by incubation with chymotrypsin or staphylococcal V8 protease. Contra-IL-1 did not inhibit IL-2- or IL-4-dependent proliferation of murine T cell lines. Despite its ability to inhibit IL-1 activity, contra-IL-1 did not interfere with the binding of recombinant IL-1 beta to a fibroblast cell line. Contra-IL-1 inhibited the proliferation of normal peripheral blood mononuclear cells to both concanavalin A and tetanus toxoid; inhibition could be attenuated by the addition of exogenous IL-1. Messenger RNA extracted from infected macrophages was examined by Northern analysis for the presence of message to IL-1 beta. No message was apparent, suggesting that the presence of contra-IL-1 was not obscuring the concomitant release of IL-1. Infected macrophages stimulated with endotoxin generated readily detectable message for IL-1 beta. Spleen macrophages purified from two patients with AIDS complicated by immune thrombocytopenia spontaneously expressed p24 antigen in vitro and released contra-IL-1 activity into the media. Contra-IL-1 may contribute to the immune dysfunction of AIDS.
Herpes Simplex Virus Type 1 Evades the Effects of Antibody and Complement In Vivo (2002)

Herpes simplex virus type 1 (HSV-1) encodes a complement-interacting glycoprotein, gC, and an immunoglobulin G (IgG) Fc binding glycoprotein, gE, that mediate immune evasion by affecting multiple aspects of innate and acquired immunity, including interfering with complement components C1q, C3, C5, and properdin and blocking antibody-dependent cellular cytotoxicity. Previous studies evaluated the individual contributions of gC and gE to immune evasion. Experiments in a murine model that examines the combined effects of gC and gE immune evasion on pathogenesis are now reported. Virulence of wild-type HSV-1 is compared with mutant viruses defective in gC-mediated C3 binding, gE-mediated IgG Fc binding, or both immune evasion activities. Eliminating both activities greatly increased susceptibility of HSV-1 to antibody and complement neutralization in vitro and markedly reduced virulence in vivo as measured by disease scores, virus titers, and mortality. Studies with C3 knockout mice indicated that other activities attributed to these glycoproteins, such as gC-mediated virus attachment to heparan sulfate or gE-mediated cell-to-cell spread, do not account for the reduced virulence of mutant viruses. The results support the importance of gC and gE immune evasion in vivo and suggest potential new targets for prevention and treatment of HSV disease.
Gene targeting in the analysis of mammalian apoptosis and TNF receptor superfamily signaling (1999)

Apoptosis, or programmed cell death (PCD), is the subject of much current investigative interest. Developing embryos and many adult organ systems require the tight coupling of cellular proliferation and PCD to ensure proper organogenesis and optimal tissue function. Over the past decade, our knowledge of the genetic basis underlying the execution of apoptosis in mammals has progressed enormously, thanks largely to groundbreaking studies performed in the nematode Caenorhabditis elegans. In contrast, the components of the signaling apparatus that links the various death stimuli and the receptors they stimulate to the execution mechanism remain relatively unknown. It is only in the past 4 years that studies of signal transduction via members of the tumor necrosis factor (TNF) receptor superfamily have identified a plethora of novel signaling proteins, including molecules that are directly involved in apoptosis signaling, and others that regulate the induction of cell death. This two-part review focuses on the biology of apoptosis and signaling through members of the TNF receptor superfamily as revealed by the study of gene-targeted "knockout" mice. These genetic mutant animals are invaluable tools not only for confirming or refuting a proposed function of a particular gene in an in vivo setting, but also for uncovering novel functions for a gene that were not anticipated from conventional in vitro experiments. In the field of apoptosis, as for many other areas of biomedical research, knockout mice and cell lines can be used as models for studying human disease, with the ultimate goal of developing therapeutic strategies.
Differential fate and functional outcome of lithium chloride primed adult neural progenitor cell transplants in a rat model of Huntington disease (2010)

These initial findings indicate that in vitro priming of adult NPCs with lithium chloride may augment transplant efficiency and accelerate sensorimotor function outcome in vivo.
Partial Reactions Catalyzed by Protein Components of the Acetyl-CoA Decarbonylase Synthase Enzyme Complex from Methanosarcina barkeri (1996)

In methanogens, the acetyl-CoA decarbonylase synthase (ACDS) complex, which has five different subunits, catalyzes synthesis and cleavage of acetyl-CoA according to the reaction: CO2 + 2H+ + 2e- + CH3-H4SPt + CoA <--> acetyl-CoA + H4SPt + H2O, where H4SPt and CH3-H4SPt are tetrahydrosarcinapterin and N5-methyl-tetrahydrosarcinapterin, respectively. We have dissociated the ACDS complex into three protein components by limited proteolytic digestion. Catalysis of acetyl-CoA synthesis was lost in parallel with the loss of the intact beta subunit; however, no decrease in activity was detected in any of three partial reactions found to be catalyzed by distinct protein components of the proteolyzed ACDS complex: (a) CO dehydrogenase, catalyzed by the alpha epsilon component, (b) CH3-H4pteridine:cob(I)amide-protein methyltransferase, catalyzed by the intact gamma subunit and fragments of the delta subunit, and (c) acetyltransferase, catalyzed by a truncated form of the beta subunit. The results indicated that the beta subunit is responsible for binding CoA and acetyl-CoA and suggested that acetyl-enzyme formation occurs on the beta subunit. A value of 5.5 x [H+]-1 M-1 was determined for the equilibrium constant of the following reaction at pH 7.5 and 25 degrees C: CH3-H4SPt + cob(I)amide-protein + H+ <--> H4SPt + CH3-cob(III)amide-protein.
Real-time imaging of tissue vibration using a two-dimensional speckle tracking system (1993)

Tumors in soft tissues are often detected because of their higher stiffness relative to surrounding tissues. A number of groups have constructed systems which attempt to estimate stiffness by imaging the propagation of low frequency (<1 KHz) mechanical waves using modified one-dimensional flow measurement techniques. We have constructed a system which utilizes a two-dimensional speckle tracking technique to measure vibrations in soft tissues in real-time. The vibration source and speckle tracking system are completely synchronous, so phase information is preserved. We describe the system and present the results of initial calibration studies
Carbohydrate analysis: a practical approach (1986)

1: Monosaccharides. 2: Oligosaccharides. 3: Neutral Polysaccharides. 4: Proteoglycans. 5: Glycoproteins. 6: Glycolipids