gebhart/patrepeval huggingface dataset:
A Dominant Mutation in the Pea PHYA Gene Confers Enhanced Responses to Light and Impairs the Light-Dependent Degradation of Phytochrome A (2004)

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.
Polyphosphoprotein from the Adhesive Pads of Mytilus edulis (2001)

Achieving a satisfactory biochemical explanation for the opportunistic underwater adhesion of marine invertebrates such as mussels and barnacles requires a detailed characterization of proteins extracted from holdfast structures produced by these organisms. Mefp-5 is an adhesive protein derived from the foot of the common mussel, Mytilus edulis, and deposited into the byssal attachment pads. Purification and primary structure of mefp-5 was determined by peptide mapping and cDNA sequencing. The protein is 74 residues long and has a mass of about 9500 Da. Mefp-5 composition shows a strong amino acid bias: aromatic amino acids, lysine, and glycine represent 65 mol % of the composition. More than a third of all the residues in the protein are posttranslationally modified by hydroxylation or phosphorylation. The conversion of tyrosine to 3, 4-dihydroxyphenyl-L-alanine (DOPA) and serine to O-phosphoserine accounts for the hydroxylation and phosphorylation, respectively. Neither modification is complete since variations in the extent of phosphorylation and hydroxylation can be detected by mass spectrometry. More than 75% of the DOPA is adjacent to basic residues, e.g., Lys-DOPA and DOPA-Lys. Phosphoserine occurs in sequences strikingly reminiscent of acidic mineral-binding motifs that appear in statherin, osteopontin, and others. This may be an adaptation for adhesion to the most common substrata for mussels, i.e., calcareous materials.
The effects of temperature on biological membranes and their models. (1987)

The physical effects of temperature on biological membranes are reviewed. Our current understanding of membrane structure is based on a model in which proteins are inserted in or are attached to a lipid bilayer structure. The lipid composition varies between cell types. Phospholipid bilayers undergo phase transitions at temperatures which are dependent on chain length and the structure of the headgroup. These factors also affect the miscibility of phospholipid types. Cholesterol orders the phospholipid chains above their phase transition temperature but disorders them below this temperature. Cerebrosides, which are important constituents of the myelin membrane, form metastable states under certain conditions. The activities of membrane-bound enzymes may be affected by the physical state of the lipid bilayer which, in turn, is affected by temperature. The interactions between the lipid and protein components of membranes have been investigated by a variety of techniques.
Intracellular phospho‐protein staining techniques for flow cytometry: Monitoring single cell signaling events (2003)

Measuring phosphorylation events by flow cytometry provides a rapid and efficient way to measure kinase cascades in individual cells. Stability of phospho-epitopes in methanol allows long-term storage of samples prior to analysis. Multiple signaling cascades can be monitored simultaneously through the use of different fluorophore labels to determine specificity of ligands or inhibitors. Application of optimized techniques to heterogeneous cell types such as peripheral blood or murine splenocytes may allow signaling to be analyzed simultaneously in immune cell subsets.
The FliP and FliR proteins of Salmonella typhimurium, putative components of the type III flagellar export apparatus, are located in the flagellar basal body (1997)

Most of the structural components of the flagellum of Salmonella typhimurium are exported through a flagellum-specific pathway, which is a member of the family of type III secretory pathways. The export apparatus for this process is poorly understood. A previous study has shown that two proteins, about 23 and 26 kDa in size and of unknown genetic origin, are incorporated into the flagellar basal body at a very early stage of flagellar assembly. In the present study, we demonstrate that these basal body proteins are FliP (in its mature form after signal peptide cleavage) and FliR respectively. Both of these proteins have homologues in other type III secretion systems. By placing a FLAG epitope tag on FliR and the MS-ring protein FliF and immunoblotting isolated hook basal body complexes with anti-FLAG monoclonal antibody, we estimate (using the FLAG-tagged FliF as an internal reference) that the stoichiometry of FliR is fewer than three copies per basal body. An independent estimate of stoichiometry was made using data from an earlier quantitative radiolabelling analysis, yielding values of around four or five subunits per basal body for FliP and around one subunit per basal body for FliR. Immunoelectron microscopy using anti-FLAG antibody and gold-protein A suggests that FliR is located near the MS ring. We propose that the flagellar export apparatus contains FliP and FliR and that this apparatus is embedded in a patch of membrane in the central pore of the MS ring.
Characterization of Soluble Hepatitis C Virus RNA-Dependent RNA Polymerase Expressed in Escherichia coli (1999)

Production of soluble full-length nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) has been shown to be problematic and requires the addition of salts, glycerol, and detergents. In an effort to improve the solubility of NS5B, the hydrophobic C terminus containing 21 amino acids was removed, yielding a truncated NS5B (NS5BDeltaCT) which is highly soluble and monodispersed in the absence of detergents. Fine deletional analysis of this region revealed that a four-leucine motif (LLLL) in the hydrophobic domain is responsible for the solubility profile of the full-length NS5B. Enzymatic characterization revealed that the RNA-dependent RNA polymerase (RdRp) activity of this truncated NS5B was comparable to those reported previously by others. For optimal enzyme activity, divalent manganese ions (Mn2+) are preferred rather than magnesium ions (Mg2+), whereas zinc ions (Zn2+) inhibit the RdRp activity. Gliotoxin, a known poliovirus 3D RdRp inhibitor, inhibited HCV NS5B RdRp in a dose-dependent manner. Kinetic analysis revealed that HCV NS5B has a rather low processivity compared to those of other known polymerases.
Preferential Escape of Subdominant CD8+ T Cells During Negative Selection Results in an Altered Antiviral T Cell Hierarchy (2003)

Negative selection is designed to purge the immune system of high-avidity, self-reactive T cells and thereby protect the host from overt autoimmunity. In this in vivo viral infection model, we show that there is a previously unappreciated dichotomy involved in negative selection in which high-avidity CD8(+) T cells specific for a dominant epitope are eliminated, whereas T cells specific for a subdominant epitope on the same protein preferentially escape deletion. Although this resulted in significant skewing of immunodominance and a substantial depletion of the most promiscuous T cells, thymic and/or peripheral deletion of high-avidity CD8(+) T cells was not accompanied by any major change in the TCR V beta gene family usage or an absolute deletion of a single preferred complementarity-determining region 3 length polymorphism. This suggests that negative selection allows high-avidity CD8(+) T cells specific for subdominant or cryptic epitopes to persist while effectively deleting high-avidity T cells specific for dominant epitopes. By allowing the escape of subdominant T cells, this process still preserves a relatively broad peripheral TCR repertoire that can actively participate in antiviral and/or autoreactive immune responses.
Analysis of Bi-Metal Thermostats (1925)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. Timoshenko, "Analysis of Bi-Metal Thermostats," J. Opt. Soc. Am. 11, 233-255 (1925) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Purification and Characterization of a Novel Restricted Antigen Expressed by Normal and Transformed Human Colonic Epithelium (1996)

A cell surface antigen that is expressed by normal and 95% of transformed colonic epithelium and is recognized by the monoclonal antibody A33 (Welt, S., Divgi, C. R., Real, F. X., Yeh, S. D., Garin-Chesa, P., Finstad, C. L., Sakamoto, J., Cohen, A., Sigurdson, E. R., Kemeny, N., Carswell, E. A., Oettgen, H. F., and Old, L. J. (1990) J. Clin. Oncol. 8, 1894-1906) has been purified to homogeneity from the human colonic carcinoma cell line LIM1215. The A33 protein was purified from Triton X-114 extracts of LIM1215 cells under nondenaturing conditions. These extracts were applied sequentially to Green-Sepharose HE-4BD, Mono-Q HR 10/10, Superose 12 HR 10/30, and micropreparative Brownlee Aquapore RP 300. The purification was monitored by biosensor analysis using surface plasmon resonance detection with a F(ab')2 fragment of the humanized A33 monoclonal antibody immobilized on the sensor surface and Western blot analysis following SDS-polyacrylamide gel electrophoresis (PAGE) under nonreducing conditions using humanized A33 monoclonal antibody. The purified A33 antigen has a Mr on SDS-PAGE of 43,000 under nonreducing conditions. By contrast, the purified protein displayed a Mr of approximately 180,000 under native conditions on both size exclusion chromatography and native PAGE, possibly due to the formation of a homotetramer. N-terminal amino acid sequence analysis of the purified protein identified 34 amino acid residues of a unique sequence: ISVETPQDVLRASQGKSVTLPXTYHTSXXXREGLIQWD. A polyclonal antibody was raised against a synthetic peptide corresponding to residues 2-20 of this sequence. The antipeptide serum recognized the purified protein using Western blot analysis under both nonreducing (Mr 43,000) and reducing (Mr 49,000) conditions.
TILLING in Grass Species (2009)

The reverse genetics detection of single base changes in genes of interest, whether induced or endogenous, is an extremely powerful tool for functional genomics. Two major thrusts of research in the grasses are characterizing the function of all the genes in various genomes and then comparing those
Guide to Industrial Control Systems (ICS) Security (2015)

3541 et seq., Public Law (P.L.) 113-283. NIST is responsible for developing information security standards and guidelines, including minimum requirements for federal information systems, but such standards and guidelines shall not apply to national security systems without the express
Inhibition of Severe Acute Respiratory Syndrome-Associated Coronavirus (SARSCoV) by Calpain Inhibitors and β-D-N4-Hydroxycytidine (2004)

We evaluated two types of compounds for efficacy in inhibiting SARSCoV replication in vitro: calpain inhibitors (a class of cellular cysteine proteinases) and a number of nucleoside analogues. Cytopathic effect reduction assays visually determined with spectrophotometric verification by neutral red (NR) uptake assay were used to evaluate cytotoxicity and antiviral potency of the compounds. Significantly inhibitory compounds were then evaluated in virus yield reduction assays. Two calpain inhibitors, Val-Leu-CHO (calpain inhibitor VI) and Z-Val-Phe-Ala-CHO (calpain inhibitor III), were the most potent inhibitors of SARSCoV. By virus yield reduction assay, calpain inhibitor VI had a 90% effective concentration (EC90) of 3 microM and calpain inhibitor III had an EC90 of 15 microM. Beta-D-N4-hydroxycytidine was the most selective nucleoside analogue inhibitor with an EC90 of 6 microM by virus yield reduction assay. These compounds or analogues warrant further evaluation as potential therapies for treating SARS or could be used as lead compounds for discovery of more potent SARSCoV inhibitors.
Promoting Neurological Recovery in the Post-Acute Stroke Phase: Benefits and Challenges (2014)

The key supporting data have so far been obtained using in vivo models in animals, underscoring the need to validate these findings in humans. For human studies, several potentially confounding variables should be kept in mind, including age, and the presence of risk factors and comorbidities (such as hyperlipidemia and diabetes). Stroke patients vary considerably in age and genetic background, as well as in the etiology, localization and size of brain infarcts. The choice of patient population is a critical factor in the success of clinical trials, as patient heterogeneity could mask any potential therapeutic benefits.
Parameter estimation of spiral waves from atrial electrograms (2004)

The problem of retrieving spiral wave parameters (frequency, radial velocity, and center location) using a minimal number (4) of spatial sensors is considered. The problem has the important application of localization of spiral wave sources of atrial fibrillation from basket catheter electrograms. Numerical simulations demonstrate that our algorithm works effectively for a wide range of parameters, and for spiral waves generated by a cellular automaton model of cardiac wave propagation.
Inhibition of tumor growth by targeting tumor endothelium using a soluble vascular endothelial growth factor receptor. (1998)

Vascular endothelial growth factor (VEGF) is a leading candidate for an endogenous mediator of tumor angiogenesis. Recently, two endothelial cell surface receptors, flk-1 and flt-1, have been shown to mediate the angiogenic activities of VEGF. In this study, we have evaluated whether a soluble VEGF receptor could suppress tumor angiogenesis and thereby inhibit tumor growth. A soluble VEGF receptor was constructed by fusing the entire extracellular domain of murine flk-1 to a six-histidine tag at the COOH terminus (ExFlk.6His). In vitro, recombinant ExFlk.6His protein bound VEGF with high affinity (Kd, 16 nM) and blocked receptor activation in a dose-dependent manner and inhibited VEGF-induced endothelial cell proliferation and migration. ExFlk.6His bound to endothelial cells only in the presence of VEGF, and cell surface cross-linking yielded a high molecular weight complex consistent with the VEGF-mediated formation of a heterodimer between ExFlk.6His and the endogenous VEGF receptor. In vivo, ExFlk.6His potently inhibited corneal neovascularization induced by conditioned media from a rat mammary carcinoma cell line (R3230AC). Moreover, when ExFlk.6His protein was administered into a cutaneous tumor window chamber concomitantly with R3230AC carcinoma transplants, tumor growth was inhibited by 75% (P < 0.005) and vascular density was reduced by 50% (P < 0.002) compared with control-treated tumors. These results demonstrate the potential of ExFlk.6His to inhibit VEGF action by a potent "dominant-negative" mechanism and suggest that targeting VEGF action using a soluble receptor may be an effective antiangiogenic therapy for cancer and other "angiogenic" diseases.
[Clinical investigation of different routes of administration of dexamethasone on sudden deafness]. (2008)

The conventional drug treatment with taking dexamethasone orally or intravenous dexamethasone injection had no obvious effect on sudden deafness with PTA > 70 dB, but the conventional drug treatment with intratympanic dexamethasone injection is a useful treatment for sudden deafness. Comparison with whole body administration, intratympanic dexamethasone injection is more convenient to use in clinic, and with less prohibitions and complications. Patients with PTA > 70 dB should take intratympanic dexamethasone injection in early days.
Primary diffuse large B-cell lymphoma in the maxilla (2018)

Non-specific symptoms, such as unclear primary dental pain and unresolved periapical swelling, can make an accurate diagnosis of DLBCL difficult, which frequently lead to delayed diagnosis. A CT or cone beam computed tomography (CBCT) scan of the maxilla and immunohistochemical staining of the biopsy specimen is recommended. Combination therapy including radiotherapy and chemotherapy is the optimal treatment for NHL.
Influence of active site and tyrosine modification on the secretion and activity of the Aeromonas hydrophila lipase/acyltransferase. (1994)

Aeromonas sp. secrete a lipase/acyltransferase that shares several properties with the mammalian plasma enzyme lecithin:cholesterol acyltransferase. Reaction of the enzyme with tetranitromethane led to modification of 2 tyrosines and a nearly 80% decline in enzyme activity. Replacing Tyr230 with Phe altered the activity of the enzyme in the same way as did treatment with tetranitromethane. Unlike the wild type enzyme, which preferentially hydrolyzes the 2-position acyl chain of phosphatidylcholine, the Y230F mutant enzyme did not discriminate between the 1- and 2-positions of the phospholipid. Tyr230 may be necessary to correctly position phospholipid substrates at the active site. Several amino acids around the active site Ser16 of the were also changed. Replacing Ser18 with Gly, bringing the enzyme's sequence into line with the lipase consensus sequence, resulted in reduced secretion of the protein and complete loss of activity. Changing this serine to Val led to an inactive protein that was not secreted at all. Substituting Phe13 in the hydrophobic region of the consensus sequence with Ser also prevented secretion, although the mutant protein appeared to be active. The Aeromonas may represent a distinct group of lipolytic enzymes which have a novel active site structure.
Rabies virus nucleoprotein expressed in and purified from insect cells is efficacious as a vaccine. (1991)

A cDNA copy of the RNA gene that encodes the nucleoprotein N of rabies virus Evelyn-Rokitnicki-Abelseth strain was cloned into baculovirus. The recombinant baculovirus expressed the N protein abundantly in Spodoptera frugiperda cells. The N protein was extracted from infected Spodoptera frugiperda cells and purified to near homogeneity by affinity chromatography. The purified N protein reacted with 31 of 32 monoclonal antibodies that recognize native rabies virus ribonucleoprotein. Like the ribonucleoprotein, the purified N protein was a major antigen capable of inducing virus-specific helper T cells. Priming of mice with the purified N protein prior to a booster inoculation with inactivated Evelyn-Rokitnicki-Abelseth virus vaccine resulted in a 20-fold increase in the production of virus-neutralizing antibodies. After immunization with the purified N protein, mice developed a strong anti-ribonucleoprotein antibody response and were protected against a lethal challenge of rabies virus. These data indicate that the N protein expressed in insect cells is antigenically and immunogenically comparable to the authentic rabies virus ribonucleoprotein and therefore represents a potential source of an effective and economical vaccine for large-scale immunization of humans and animals against rabies.
Low-Complexity Low-Latency Architecture for Matching of Data Encoded With Hard Systematic Error-Correcting Codes (2013)

A new architecture for matching the data protected with an error-correcting code (ECC) is presented in this brief to reduce latency and complexity. Based on the fact that the codeword of an ECC is usually represented in a systematic form consisting of the raw data and the parity information generated by encoding, the proposed architecture parallelizes the comparison of the data and that of the parity information. To further reduce the latency and complexity, in addition, a new butterfly-formed weight accumulator (BWA) is proposed for the efficient computation of the Hamming distance. Grounded on the BWA, the proposed architecture examines whether the incoming data matches the stored data if a certain number of erroneous bits are corrected. For a (40, 33) code, the proposed architecture reduces the latency and the hardware complexity by ~32% and 9%, respectively, compared with the most recent implementation.
Molecular cloning and expression of a G25K cDNA, the human homolog of the yeast cell cycle gene CDC42. (1990)

G25K is a low-molecular-mass GTP-binding protein with a broad distribution in mammalian tissues. A cDNA clone was isolated by using oligonucleotides corresponding to the partial amino acid sequence of purified human G25K. The cDNA encodes an 191-amino-acid polypeptide containing GTP-binding consensus sequences and a putative farnesylation site at the C terminus. The sequence exhibits 50 and 70% identities to the mammalian rho and rac proteins, respectively, and an 80% identity to the Saccharomyces cerevisiae CDC42 gene product. Insect Sf9 cells infected with recombinant baculovirus vectors expressing the G25K cDNA produced a 25-kDa protein that bound GTP and was recognized by antibodies specifically reactive to G25K. G25K appears to be the human homolog of the CDC42 gene product, since expression of the G25K cDNA in S. cerevisiae suppressed both cdc42-1 and cdc24-4 temperature-sensitive lethal mutations.
Human Cathepsin O2, a Novel Cysteine Protease Highly Expressed in Osteoclastomas and Ovary Molecular Cloning, Sequencing and Tissue Distribution (1995)

A 1.6-kilobase full-length cDNA of a novel human cysteine protease has been isolated and sequenced. The nucleotide sequence encodes a polypeptide of 329 amino acids composed of a 15-residue N-terminal signal peptide, a 99-residue propeptide, and a mature protein of 215 amino acids. The deduced amino acid sequence contains two potential N-glycosylation sites, one located in the proregion and one in the mature enzyme. Comparison of the amino acid sequence of cathepsin O2 with that of known human lysosomal cysteine proteases revealed a substantial degree of similarity to cathepsins L and S. Northern blot analysis indicates predominant levels of expression in osteoclastomas and ovary and therefore the enzyme was named cathepsin O2. The extremely high expression levels of human cathepsin O2 in osteoclastomas suggest a major role of this novel enzyme in bone remodelling and bone related diseases.
THE PREPARATION, PURIFICATION, AND AMINO ACID SEQUENCE OF A POLYPEPTIDE RENIN SUBSTRATE (1957)

A purified preparation of a polypeptide renin substrate prepared by tryptic degradation of the protein renin substrate has been analyzed by the fluorodinitrobenzene method and after degradation with renin, carboxypeptidase, and phenylisothiocyanate, has been found to possess the amino acid sequence; asp-arg-val-tyr-ileu-his-pro-phe-his-leu-leu-val-tyr-ser. The first 10 of these amino acids constitutes hypertensin I which is released by cleavage of the leucyl-leucine bond by renin. The remaining 4 amino acids, leu, val, tyr, ser, apparently link hypertensin I to the protein renin substrate.