gebhart/patrepeval huggingface dataset:
Molecule Cascades (2002)

Carbon monoxide molecules were arranged in atomically precise configurations, which we call "molecule cascades," where the motion of one molecule causes the subsequent motion of another, and so on in a cascade of motion similar to a row of toppling dominoes. Isotopically pure cascades were assembled on a copper (111) surface with a low-temperature scanning tunneling microscope. The hopping rate of carbon monoxide molecules in cascades was found to be independent of temperature below 6 kelvin and to exhibit a pronounced isotope effect, hallmarks of a quantum tunneling process. At higher temperatures, we observed a thermally activated hopping rate with an anomalously low Arrhenius prefactor that we interpret as tunneling from excited vibrational states. We present a cascade-based computation scheme that has all of the devices and interconnects required for the one-time computation of an arbitrary logic function. Logic gates and other devices were implemented by engineered arrangements of molecules at the intersections of cascades. We demonstrate a three-input sorter that uses several AND gates and OR gates, as well as the crossover and fan-out units needed to connect them.
The role of cellular glutathione peroxidase redox regulation in the suppression of tumor cell growth by manganese superoxide dismutase. (2000)

Manganese-containing superoxide dismutase (MnSOD) is an essential primary antioxidant enzyme that converts superoxide radical to hydrogen peroxide and molecular oxygen within the mitochondrial matrix. Cytosolic glutathione peroxidase (GPX) converts hydrogen peroxide into water. MnSOD is reduced in a variety of tumor types and has been proposed to be a new kind of tumor suppressor gene, but the mechanism(s) by which MnSOD suppresses malignancy is unclear. According to the enzymatic reactions catalyzed by MnSOD and cytosolic GPX, change in the cellular redox status, especially change attributable to accumulation of hydrogen peroxide or other hydroperoxides, is a possible reason to explain the suppression of tumor growth observed in MnSOD-overexpressing cells. To test this possible mechanism, we transfected human cytosolic GPX cDNA into human glioma cells overexpressing MnSOD. The results showed that GPX overexpression not only reversed the tumor cell growth inhibition caused by MnSOD overexpression but also altered the cellular contents of total glutathione, reduced glutathione, oxidized glutathione, and intracellular reactive oxygen species. Overexpression of GPX also inhibited degradation of the inhibitory subunit alpha of nuclear factor-KB. These results suggest that hydrogen peroxide or other hydroperoxides appear to be key reactants in the tumor suppression by MnSOD overexpression, and growth inhibition correlates with the intracellular redox status. This work suggests that manipulations that inhibit peroxide removal should enhance the tumor suppressive effect of MnSOD overexpression.
The cell biology of receptor-mediated virus entry (2011)

The cell imposes multiple barriers to virus entry. However, viruses exploit fundamental cellular processes to gain entry to cells and deliver their genetic cargo. Virus entry pathways are largely defined by the interactions between virus particles and their receptors at the cell surface. These interactions determine the mechanisms of virus attachment, uptake, intracellular trafficking, and, ultimately, penetration to the cytosol. Elucidating the complex interplay between viruses and their receptors is necessary for a full understanding of how these remarkable agents invade their cellular hosts.
Micelle Formation by Bile Salts (1972)

Bile salts, which are soluble amphiphiles, possess a unique molecular structure when compared with typical detergent molecules. In water, bile salts form small aggregates called micelles. The behavior of bile salt micelles is quite different from micelles formed by detergents. Bile salt micelles are smaller, more highly charged and of different structure than detergent micelles. Bile salts form mixed micelles with a variety of other soluble and insoluble lipidic substances. While bile salts increase slightly the solubility of relatively nonpolar molecules (such as cholesterol or fatty acids), they have a striking capacity to render soluble certain important insoluble molecules of biological importance such as phospholipids and monoglycerides. In fact as little as 1 mole of bile salt can solubilize 2 moles of lecithin. Solubilization takes place in mixed bile salt micelles of unique structure and properties. These mixed micelles incorporate very appreciable amounts of insoluble molecules, such as fat-soluble vitamins
A Comparison of the Cardiovascular Responses to Stimulation of the Aortic and Carotid Sinus Nerves of the Dog (1973)

The maximum decrease in blood pressure and heart rate in response to electrical stimulation of the aortic (AN) and carotid sinus nerves (CSN) of the dog was essentially the same in both cases. Thus, reported difference in the effectiveness of the reflexes served by these nerves must be due to the baroreceptor discharge characteristics in response to a rise in pressure in the respective regions. Both nerves consist of at least two groups of depressor afferents and one fiber group which appears to arise from chemoreceptors. These fiber groups are distinguishable by their threshold to electrical stimulation. The major group of depressor fibers in the AN have a low threshold to stimulation while the major group of depressor fibers in the CSN are of higher threshold and presumably smaller in diameter. Maximal depressor effects to stimulation of the CSN are attained at lower stimulus frequencies (10-20 Hz) than is the case during AN stimulation (60-80 Hz). The chemosensory fibers in both nerves have a higher threshold than either group of depressor fibers. Stimulation of these fibers in the AN causes a rise in pressure and cardiac acceleration which nearly offsets the effects of stimulating the depressor fibers. However, little increase in breathing is observed. Stimulation of the chemosensory fibers in the CSN causes a marked hyperventilation but has relatively little effect on blood pressure and heart rate.
An Oncolytic HSV-1 Mutant Expressing ICP34.5 under Control of a Nestin Promoter Increases Survival of Animals even when Symptomatic from a Brain Tumor (2005)

Oncolytic herpes simplex virus-1 (HSV-1) mutants possessing mutations in the ICP34.5 and ICP6 genes have proven safe through clinical trials. However, ICP34.5-null viruses may grow poorly in cells due to their inability to prevent host-cell shut-off of protein synthesis caused by hyperphosphorylation of eukaryotic initiation factor 2alpha. To increase tumor selectivity, glioma-selective expression of ICP34.5 in the context of oncolysis may be useful. Malignant gliomas remain an incurable disease. One molecular marker of malignant gliomas is expression of the intermediate filament nestin. Expression of nestin mRNA was confirmed in 6 of 6 human glioma lines and in 3 of 4 primary glioma cells. Normal human astrocytes were negative. A novel glioma-selective HSV-1 mutant (rQNestin34.5) was thus engineered by expressing ICP34.5 under control of a synthetic nestin promoter. Replication, cellular propagation, and cytotoxicity of rQNestin34.5 were significantly enhanced in cultured and primary human glioma cell lines compared with control virus. However, replication, cellular propagation, and cytotoxicity of rQNestin34.5 in normal human astrocytes remained quantitatively similar to that of control virus. In glioma cell lines infected with rQNestin34.5, the level of phospho-eukaryotic initiation factor 2alpha was lower than that of cells infected by control rHsvQ1, confirming selective ICP34.5 expression in glioma cells. In vivo, rQNestin34.5 showed significantly more potent inhibition of tumor growth compared with control virus. Treatment in the brain tumor model was instituted on animal's display of neurologic symptoms, which usually led to rapid demise. rQNestin34.5 treatment doubled the life span of these animals. These results show that rQNestin34.5 could be a potent agent for the treatment of malignant glioma.
Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus (1976)

A stable deoxyribonucleic acid (DNA) polymerase (EC 2.7.7.7) with a temperature optimum of 80 degrees C has been purified from the extreme thermophile Thermus aquaticus. The enzyme is free from phosphomonoesterase, phosphodiesterase and single-stranded exonuclease activities. Maximal activity of the enzyme requires all four deoxyribonucleotides and activated calf thymus DNA. An absolute requirement for divalent cation cofactor was satisfied by Mg2+ or to a lesser extent by Mn2+. Monovalent cations at concentrations as high as 0.1 M did not show a significant inhibitory effect. The pH optimum was 8.0 in tris(hydroxymethyl)aminomethane-hydrochloride buffer. The molecular weight of the enzyme was estimated by sucrose gradient centrifugation and gel filtrations on Sephadex G-100 to be approximately 63,000 to 68,000. The elevated temperature requirement, small size, and lack of nuclease activity distinguish this polymerase from the DNA polymerase of Escherichia coli.
Role of the male BmDSX protein in the sexual differentiation of Bombyx mori (2005)

The sex determination pathway is different between Drosophila melanogaster and Bombyx mori in the initial signal. Here we show evidence that the sex determination pathway in B. mori is similar to that of D. melanogaster at the level of the terminal regulator, doublesex (dsx), which is essential for the proper differentiation of the sexually dimorphic somatic features of D. melanogaster. In B. mori, a homolog of dsx (Bmdsx) is expressed in various tissues, and its primary transcript is alternatively spliced in males and females to yield sex-specific mRNAs that encode male-specific (BmDSXM) and female-specific (BmDSXF) polypeptides. In the studies reported here, transgenic silkworms carrying a construct with a Bmdsx male cDNA placed under the control of either an hsp70 promoter or a Bombyx actin3 promoter were generated by piggyBac-mediated germline transformation. Ectopic expression of the male cDNA in females resulted in abnormal differentiation of certain female-specific genital organs and caused partial male differentiation in female genitalia. Transgenic analysis also revealed that the expression of BmDSXM in females caused repression of the female-specifically expressed gene, the vitellogenin gene, and also resulted in activation of the pheromone-binding protein gene that is dominantly expressed in males. These results provide evidence that the role of BmDSXM includes the activation of some aspects of male differentiation as well as the repression of female differentiation. Taken together with our previous data on the function of BmDSXF, we can conclude that Bmdsx is a double-switch gene at the final step in the sex-determination cascade of B. mori.
Human myoblast transplantation: Preliminary results of 4 cases (1992)

Myoblasts from immunocompatible donors have been transplanted into the muscles (tibialis anterior, biceps brachii, and/or extensor carpi radialis longus) of 4 Duchenne patients in the advanced stages of the disease. Although no immunosuppressive treatment was used, none of the patients showed any clinical signs of rejection such as fever, redness, and inflammation. One patient transiently produced antibodies against the donor myoblasts as determined by cytofluorometric analysis. This patient and 2 others were shown to form antibodies against their donor's myotubes. Muscle biopsies of the injected tibialis anterior of 4 patients revealed that 80%, 75%, 25%, and 0% of the muscle fibers, respectively, showed some degree of dystrophin immunostaining. The contralateral noninjected muscles of the latter 3 patients did not contain any dystrophin positive fibers, while that of the first patient showed dystrophin expression in 16% of the fibers examined. Myoblasts were also injected into the extensor carpi radialis longus or the biceps brachii of these patients. A few months subsequent to injection, one patient was shown to have a 143% increase of strength during static wrist extension. This result must be interpreted with caution because a double-blind strength-measuring protocol was not used. Furthermore, we have noted that this change slowly decayed over time. The strength of 2 other patients was increased less remarkably (41% and 51%), while the strength of the fourth patient was unchanged.
Detection of neuron-specific gamma-enolase messenger ribonucleic acid in normal human leukocytes by polymerase chain reaction amplification with nested primers. (1993)

This method exploiting short stretches of nucleotide differences in the coding regions for priming can more generally be applied to the distinction of all isoforms of RNA where nested specific primers can be designed. However, the presence of NSE specific transcripts in normal human leukocytes invalidates the use of this highly sensitive method as a disease marker in neuroblastoma.
CDP-Alcohol Hydrolase, a Very Efficient Activity of the 5′-Nucleotidase/UDP-Sugar Hydrolase Encoded by the ushA Gene of Yersinia intermedia and Escherichia coli (2008)

Nucleoside 5'-diphosphate-X hydrolases are interesting enzymes to study due to their varied activities and structure-function relationships and the roles they play in the disposal, assimilation, and modulation of the effects of their substrates. Few of these enzymes with a preference for CDP-alcohols are known. In Yersinia intermedia suspensions prepared from cultures on Columbia agar with 5% sheep blood, we found a CDP-alcohol hydrolase liberated to Triton X-100-containing medium. Growth at 25 degrees C was deemed optimum in terms of the enzyme-activity yield. The purified enzyme also displayed 5'-nucleotidase, UDP-sugar hydrolase, and dinucleoside-polyphosphate hydrolase activities. It was identified as the protein product (UshA(Yi)) of the Y. intermedia ushA gene (ushA(Yi)) by its peptide mass fingerprint and by PCR cloning and expression to yield active enzyme. All those activities, except CDP-alcohol hydrolase, have been shown to be the properties of UshA of Escherichia coli (UshA(Ec)). Therefore, UshA(Ec) was expressed from an appropriate plasmid and tested for CDP-alcohol hydrolase activity. UshA(Ec) and UshA(Yi) behaved similarly. Besides being the first study of a UshA enzyme in the genus Yersinia, this work adds CDP-alcohol hydrolase to the spectrum of UshA activities and offers a novel perspective on these proteins, which are viewed here for the first time as highly efficient enzymes with k(cat)/K(m) ratios near the theoretical maximum level of catalytic activities. The results are discussed in the light of the known structures of UshA(Ec) conformers and the respective homology models constructed for UshA(Yi), and also in relation to possible biological functions. Interestingly, every Yersinia species with a sequenced genome contains an intact ushA gene, except Y. pestis, which in all its sequenced biovars contains a ushA gene inactivated by frameshift mutations.
Suppression of HMGB1 release by stearoyl lysophosphatidylcholine:an additional mechanism for its therapeutic effects in experimental sepsis (2005)

Stearoyl lysophosphatidylcholine (LPC) has recently been proven protective against lethal sepsis by stimulating neutrophils to eliminate invading pathogens through an H2O2-dependent mechanism. Here, we demonstrate that stearoyl LPC, but not caproyl LPC, significantly attenuates circulating high-mobility group box 1 (HMGB1) levels in endotoxemia and sepsis by suppressing endotoxin-induced HMGB1 release from macrophages/monocytes. Neutralizing antibodies against G2A, a potential cell surface receptor for LPC, partially abrogated stearoyl LPC-mediated suppression of HMGB1 release. Thus, stearoyl LPC confers protection against lethal experimental sepsis partly by facilitating the elimination of the invading pathogens and partly by inhibiting endotoxin-induced release of a late proinflammatory cytokine, HMGB1.
Non-Linear Dimensionality Reduction (1992)

A method for creating a non--linear encoder--decoder for multidimensional data with compact representations is presented. The commonly used technique of autoassociation is extended to allow non--linear representations, and an objective function which penalizes activations of individual hidden units is shown to result in minimum dimensional encodings with respect to allowable error in reconstruction. 1 INTRODUCTION Reducing dimensionality of data with minimal information loss is important for feature extraction, compact coding and computational efficiency. The data can be tranformed into &amp;quot;good&amp;quot; representations for further processing, constraints among feature variables may be identified, and redundancy eliminated. Many algorithms are exponential in the dimensionalityof the input, thus even reduction by a single dimension may provide valuable computational savings. Autoassociating feedforward networks with one hidden layer have been shown to extract the principal components of the data ...
Intranasal Immunization with Pneumococcal Conjugate Vaccines with LT-K63, a Nontoxic Mutant of Heat-Labile Enterotoxin, as Adjuvant Rapidly Induces Protective Immunity against Lethal Pneumococcal Infections in Neonatal Mice (2002)

Immunization with pneumococcal polysaccharides (PPS) conjugated to tetanus toxoid (TT) (Pnc-TT) elicits protective immunity in an adult murine pneumococcal infection model. To assess immunogenicity and protective immunity in early life, neonatal (1 week old) and infant (3 weeks old) mice were immunized intranasally (i.n.) or subcutaneously (s.c.) with Pnc-TT of serotype 1 (Pnc1-TT). Anti-PPS-1 and anti-TT immunoglobulin G (IgG) and IgM antibodies were measured in serum and saliva, and vaccine-induced protection was evaluated by i.n. challenge with serotype 1 pneumococci. Pnc1-TT was immunogenic in neonatal and infant mice when administered s.c. without adjuvant: a majority of the young mice were protected from bacteremia and a reduction of pneumococcal density in the lungs was observed, although antibody responses and protective efficacy remained lower than in adults. The addition of LT-K63, a nontoxic mutant of heat-labile enterotoxin, as adjuvant significantly enhanced PPS-1-specific IgG responses and protective efficacy following either s.c. or i.n. Pnc1-TT immunization. Mucosal immunization was particularly efficient in neonates, as a single i.n. dose of Pnc1-TT and LT-K63 induced significantly higher PPS-1-specific IgG responses than s.c. immunization and was sufficient to protect neonatal mice against pneumococcal infections, whereas two s.c. doses were required to induce complete protection. In addition, i.n. immunization with Pnc1-TT and LT-K63 induced a vigorous salivary IgA response. This suggests that mucosal immunization with pneumococcal conjugate vaccines and LT-K63 may be able to circumvent some of the limitations of neonatal antibody responses, which are required for protective immunity in early life.
Polymer films on electrodes. 8. Investigation of charge-transport mechanisms in Nafion polymer modified electrodes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer films on electrodes. 8. Investigation of charge-transport mechanisms in Nafion polymer modified electrodesHenry S. White, Johna Leddy, and Allen J. BardCite this: J. Am. Chem. Soc. 1982, 104, 18, 4811–4817Publication Date (Print):September 1, 1982Publication History Published online1 May 2002Published inissue 1 September 1982https://pubs.acs.org/doi/10.1021/ja00382a013https://doi.org/10.1021/ja00382a013research-articleACS PublicationsRequest reuse permissionsArticle Views1579Altmetric-Citations294LEARN 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
Technique for obtaining high-energy ultrashort pulses from an additive-pulse mode-locked erbium-doped fiber ring laser (1994)

We report a self-starting stretched-pulse polarization additive-pulse mode-locked erbium-doped fiber ring laser with high output power. By using the light normally absorbed by the intracavity polarizer as the output, we obtained pulses with energies greater than 0.5 nJ at a repetition rate of 48 MHz. External chirp compensation was used to shorten the highly chirped output pulses to durations of less than 100 fs. The power levels suggest that erbium-doped fiber lasers may replace bulk solid-state lasers, such as the color-center laser, for some applications.
Activation of TRPV1 and TRPA1 by Black Pepper Components (2010)

We searched in this study for novel agonists of transient receptor potential cation channel, subfamily V, member 1 (TRPV1) and transient receptor potential cation channel, subfamily A, member 1 (TRPA1) in pepper, focusing attention on 19 compounds contained in black pepper. Almost all the compounds in HEK cells heterogeneously expressed TRPV1 or TRPA1, increased the intracellular Ca(2+) concentration ([Ca(2+)](i)) in a concentration-dependent manner. Among these, piperine, isopiperine, isochavicine, piperanine, pipernonaline, dehydropipernonaline, retrofractamide C, piperolein A, and piperolein B relatively strongly activated TRPV1. The EC(50) values of these compounds for TRPV1 were 0.6-128 microM. Piperine, isopiperine, isochavicine, piperanine, piperolein A, piperolein B, and N-isobutyl-(2E,4E)-tetradeca-2,4-diamide also relatively strongly activated TRPA1, the EC(50) values of these compounds for TRPA1 were 7.8-148 microM. The Ca(2+) responses of these compounds for TRPV1 and TRPA1 were significantly suppressed by co-applying each antagonist. We identified in this study new transient receptor potential (TRP) agonists present in black pepper and found that piperine, isopiperine, isochavicine, piperanine, piperolein A, and piperolein B activated both TRPV1 and TRPA1.
The links between joint damage and disability in rheumatoid arthritis (2000)

Joint damage progresses constantly over the first 20 yr of RA. It accounts for approximately 25% of disability in established RA. The link between damage and disability is strongest in late (>8 yr) RA. However, avoiding or reducing joint damage in both early and established/late RA is likely to maintain function.
Application of Genetic Male Sterility to Recurrent Selection Schemes in Soybeans1 (1973)

Recurrent selection schemes for soybeans [ Glycine max (L.) Merr.] that use a genetic male‐sterile factor to obtain natural crosses are outlined. A basic scheme with three generations per cycle, intermating, advancing, and testing, and modifications of the scheme are discussed. Guidelines for population size and selection intensity are considered. Expected genetic progress is presented for each selection program.