gebhart/patrepeval huggingface dataset:
A Modular Method for the High‐Yield Synthesis of Site‐Specific Protein–Polymer Therapeutics (2016)

A versatile method is described to engineer precisely defined protein/peptide-polymer therapeutics by a modular approach that consists of three steps: 1) fusion of a protein/peptide of interest with an elastin-like polypeptide that enables facile purification and high yields; 2) installation of a clickable group at the C terminus of the recombinant protein/peptide with almost complete conversion by enzyme-mediated ligation; and 3) attachment of a polymer by a click reaction with near-quantitative conversion. We demonstrate that this modular approach is applicable to various protein/peptide drugs and used it to conjugate them to structurally diverse water-soluble polymers that prolong the plasma circulation duration of these proteins. The protein/peptide-polymer conjugates exhibited significantly improved pharmacokinetics and therapeutic effects over the native protein/peptide upon administration to mice. The studies reported here provide a facile method for the synthesis of protein/peptide-polymer conjugates for therapeutic use and other applications.
Cell-free transcription directed by the 422 adipose P2 gene promoter: activation by the CCAAT/enhancer binding protein. (1991)

Previous investigations have shown that CCAAT/enhancer binding protein (C/EBP) can function as a trans-activator of the promoters of several adipocyte-specific genes--i.e., the 422 adipose P2 (422/aP2), stearoyl-CoA desaturase 1 (SCD1), and glucose transporter 4 (GLUT4) genes, in 3T3-L1 mouse preadipocytes. We now describe a cell-free system prepared from nuclei of 3T3-L1 cells that carries out transcription directed by these promoters. To measure transcript formation, we employed a polymerase chain reaction-assisted analysis. Nuclear extract from 3T3-L1 adipocytes that express C/EBP supports a higher rate of transcription of chimeric 422(aP2) promoter-chloramphenicol acetyltransferase (CAT) reporter gene constructs than nuclear extract from preadipocytes that lack C/EBP. A competitor oligonucleotide containing the C/EBP binding site sequence and antibodies raised against C/EBP inhibit transcription directed by the 422(aP2) promoter. The factor limiting transcription by nuclear extract from preadipocytes appears to be C/EBP, since recombinant C/EBP (rC/EBP) markedly activates transcription of the 422(aP2) promoter-CAT gene with preadipocyte extract but not with adipocyte extract. rC/EBP also activates cell-free transcription of SCD1 promoter-CAT and GLUT4 promoter-CAT chimeric genes. Point mutations within the C/EBP binding site in the 422(aP2) promoter markedly decrease transcription activated by rC/EBP. Consistent with activation by cAMP of the 422(aP2) promoter in intact preadipocytes, cAMP-dependent protein kinase activates transcription through this promoter with the cell-free system, this effect being independent of C/EBP. Thus, regulation of transcription directed by the 422(aP2) promoter in the cell-free system resembles that which occurs in intact 3T3-L1 cells.
Waveform Cross-Correlation-Based Differential Travel-Time Measurements at the Northern California Seismic Network (2005)

We processed the complete digital seismogram database for northern California to measure accurate differential travel times for correlated earthquakes observed at common stations. Correlated earthquakes are earthquakes that occur within a few kilometers of one another and have similar focal mechanisms, thus generating similar waveforms, allowing measurements to be made via cross-corre- lation analysis. The waveform database was obtained from the Northern California Earthquake Data Center and includes about 15 million seismograms from 225,000 local earthquakes between 1984 and 2003. A total of 26 billion cross-correlation measurements were performed on a 32-node (64 processor) Linux cluster, using improved analysis tools. All event pairs with separation distances of 5 km or less were processed at all stations that recorded the pair. We computed a total of about 1.7 billion P-wave differential times from pairs of waveforms that had cross- correlation coefficients (CC) of 0.6 or larger. The P-wave differential times are often on the order of a factor of ten to a hundred times more accurate than those obtained from routinely picked phase onsets. 1.2 billion S-wave differential times were mea- sured with CC 0.6, a phase not routinely picked at the Northern California Seismic Network because of the noise level of remaining P coda. We found that approxi- mately 95% of the seismicity includes events that have cross-correlation coefficients of CC 0.7 with at least one other event recorded at four or more stations. At some stations more than 40% of the recorded events are similar at the CC 0.9 level, indicating the potential existence of large numbers of repeating earthquakes. Large numbers of correlated events occur in different tectonic regions, including the San Andreas Fault, Long Valley caldera, Geysers geothermal field and Mendocino triple junction. Future research using these data may substantially improve earthquake lo- cations and add insight into the velocity structure in the crust.
Surgical Technique for Implantation of the Neurocybernetic Prosthesis (1990)

The surgical technique for the implantation of the neurocybernetic prosthesis is described in detail. This procedure is straightforward and is easily carried out by surgeons familiar with carotid surgery.
Multiple Amino Acids Determine the DNA Binding Specificity of the Msx-1 Homeodomain (1995)

This study investigates the sequence features that contribute to the differential DNA binding properties of two divergent homeodomains, Msx-1 and HoxA3. We show that these homeodomains have overlapping, but nonidentical, DNA binding site preferences. We defined the amino acid residues that contribute to the observed differences in DNA binding specificity by producing a series of mutated polypeptides in which selected residues in Msx-1 were replaced with the corresponding ones in HoxA3. These analyses show that the DNA binding specificity of Msx-1 versus HoxA3 results from the cumulative action of multiple residues in all segments of the homeodomain (i.e., the N-terminal arm and helices I, II, and III). Therefore, substitutions of residues in both helix III and the N-terminal arm (but not in either segment alone) produced an Msx-1 polypeptide whose binding site preference was indistinguishable from that of HoxA3. Residues in helices I and II also influence DNA binding activity; these oppositely charged residues (e.g., lysine 19 and glutamate 30) may mediate ionic interactions between helices I and II which stabilize DNA binding by Msx-1. These findings demonstrate a critical interplay between residues in each homeodomain segment for appropriate conformation of the protein-DNA complex.
Real-Time Single-Molecule Imaging of the Infection Pathway of an Adeno-Associated Virus (2001)

We describe a method, based on single-molecule imaging, that allows the real-time visualization of the infection pathway of single viruses in living cells, each labeled with only one fluorescent dye molecule. The tracking of single viruses removes ensemble averaging. Diffusion trajectories with high spatial and time resolution show various modes of motion of adeno-associated viruses (AAV) during their infection pathway into living HeLa cells: (i) consecutive virus touching at the cell surface and fast endocytosis; (ii) free and anomalous diffusion of the endosome and the virus in the cytoplasm and the nucleus; and (iii) directed motion by motor proteins in the cytoplasm and in nuclear tubular structures. The real-time visualization of the infection pathway of single AAVs shows a much faster infection than was generally observed so far.
An N-Way Hybrid Power Divider (1960)

A circularly symmetric power divider is described which splits a signal into n equiphase equiamplitude parts where n can be odd or even. The power divider provides isolation between output terminals and approximately matched terminal impedances over about a 20 per cent band. A theory of operation is given which yields the necessary design parameters, and an experimental model is described which has a minimum isolation of -27 db between output terminals, an output VSWR of 1.6, and an input VSWR of 1.2.
Endogenous Airway Acidification: Implications for Asthma Pathophysiology (2000)

Airway concentrations of many reactive nitrogen and oxygen species are high in asthma. The stability and bioactivities of these species are pH-dependent; however, the pH of the airway during acute asthma has not previously been studied. As with gastric and urinary acidification, asthmatic airway acidification could be expected dramatically to alter the concentrations and bioactivities/cytotoxicities of endogenous nitrogen oxides. Here, we demonstrate that the pH of deaerated exhaled airway vapor condensate is over two log orders lower in patients with acute asthma (5.23 +/- 0.21, n = 22) than in control subjects (7.65 +/- 0.20, n = 19, p < 0. 001) and normalizes with corticosteroid therapy. Values are highly reproducible, unaffected by salivary or therapeutic artifact, and identical to samples taken directly from the lower airway. Further, at these low pH values, the endogenous airway compound, nitrite, is converted to nitric oxide (NO) in quantities sufficient largely to account for the concentrations of NO in asthmatic expired air, and eosinophils undergo accelerated necrosis. We speculate that airway pH may be an important determinant of expired NO concentration and airway inflammation, and suggest that regulation of airway pH has a previously unsuspected role in asthma pathophysiology.
Liquid-vapor interfacial properties of water-ammonia mixtures: Dependence on ammonia concentration (2005)

The equilibrium and dynamical properties of the liquid-vapor interfaces of water-ammonia mixtures are investigated by means of molecular-dynamics simulations. Altogether, we have simulated seven different systems of different concentration of ammonia. The inhomogeneous density, anisotropic orientational profiles, surface tension, and the pattern of hydrogen bonding are calculated for both water and ammonia molecules in order to characterize the location, width, thermodynamic aspects, and microscopic structure of the liquid-vapor interfaces of each of the water-ammonia systems. The dynamical aspects of the interfaces are investigated in terms of the anisotropic diffusion and dipole orientational relaxation of water and ammonia molecules. The properties of the interfaces are compared with those of the corresponding bulk phases. The present theoretical results are also compared with experimental findings wherever available.
Ex Vivo Expansion and Differentiation of Hematopoietic Stem Cells (1992)

Hematopoietic stem cells are phenotypically very heterogeneous, probably reflecting the degree of activation and/or differentiation. This cell population is capable of high-level proliferative activity and multilineage differentiation. Despite its potential for self-renewal, the hematopoietic stem cell exists in a quiescent state for prolonged periods of time. The mechanism(s) involved in triggering these cells to enter the cell cycle is/are not totally clear; however, cytokines (both positive and negative regulators) are implicated. Most, if not all known cytokines that interact at the stem cell level do so not only by inducing proliferation but also differentiation. The ability to maintain a population of truly primitive stem cells for extended periods of time in vitro is currently under investigation by many research groups.
CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression (2017)

The inflammatory CD40-CD40L pathway is implicated in various autoimmune diseases, but the activity status of this pathway in various stages of rheumatoid arthritis (RA) progression is unknown. In this study, we used gene signatures of CD40L stimulation derived from human immature dendritic cells and naive B cells to assess the expression of CD40-downstream genes in synovial tissues from anti-citrullinated protein Ab-positive arthralgia, undifferentiated arthritis (UA), early RA, and established RA cohorts in comparison with healthy donors. Interestingly, the expression of <i>CD40LG</i> and active full-length <i>CD40</i> was increased in the disease tissues, whereas that of a dominant-negative <i>CD40</i> isoform was decreased. Gene set variation analysis revealed that CD40L-responsive genes in immature dendritic cells and naive B cells were significantly enriched in synovial tissues from UA, early RA, and established RA patients. Additionally, CD40L-induced naive B cell genes were also significantly enriched in synovial tissues from arthralgia patients. In our efforts to characterize downstream mediators of CD40L signaling, we have identified <i>GPR120</i> and <i>KDM6B</i> as novel components of the pathway. In conclusion, our data suggest that therapeutic CD40-CD40L blocking agents may prove efficacious not only in early and established RA, but also in inhibiting the progression of the disease from arthralgia or UA to RA.
Overexpression of c-met proto-oncogene but not epidermal growth factor receptor or c-erbB-2 in primary human colorectal carcinomas. (1992)

The epidermal growth factor receptor (EGFR) and the protein products of c-erbB-2 and c-met proto-oncogenes belong to a family of growth factor receptors with tyrosine kinase activity. In human colonic carcinomas, the expression of the EGFR and c-erbB-2 have been studied at the protein level only, while c-met expression has not been reported. We have examined the mRNA expression of these genes in human normal colorectal mucosa and primary carcinomas. The results demonstrate that the normal mucosa shows highly variable levels of EGFR and c-erbB-2 mRNAs, but expresses consistently low amounts of c-met mRNA. Colorectal carcinomas did not express significantly higher levels of the EGFR and c-erbB-2 mRNAs than the normal mucosa. In contrast, c-met was consistently and significantly overexpressed (mean sixfold) in carcinomas as compared with normal mucosa. Seventy percent of paired normal-tumor specimens showed a tumor to normal c-met mRNA ratio of greater than 4. The expression of c-met mRNA was also enhanced in the adenomas, suggesting that over-expression of this proto-oncogene may have mechanistic significance in the early stages of human colorectal carcinogenesis.
Role of fructose in glycation and cross-linking of proteins (1988)

Incubation of carbohydrate-free human serum albumin (HSA) with fructose in an aqueous buffer at pH 7.4 resulted in glycation of epsilon-amino groups of lysyl residues. A recently developed procedure, involving analysis of hexitol amino acids by high-performance liquid chromatography of phenylthiocarbamyl derivatives, was used to show that 85% of the bound hexose was attached to protein via carbon 2 (C-2). The remainder was attached to protein via carbon 1 (C-1). When incubations were conducted with glucose under identical conditions, all the hexose was attached via C-1. Examination of human ocular lens proteins showed that the majority of the covalently bound hexose was connected to epsilon-amino groups of lysyl residues via C-1; this was attributed mainly to nonenzymatic glucosylation in vivo, which has already been documented. A significant proportion (10-20%) of the bound hexose was connected via C-2. In view of the HSA-hexose incubation results (above), this indicated that the lens proteins had reacted with endogenous fructose; i.e., they had undergone nonenzymatic fructosylation in vivo. The model protein bovine pancreatic ribonuclease A reacted with fructose and glucose at similar rates under physiological conditions. However, covalent, non-disulfide cross-linking, which could be inhibited by D-penicillamine, was induced 10 times more rapidly by fructose than by glucose. It is postulated that some of the protein cross-linking that occurs in vivo is fructose-induced. The possible significance of these processes in diabetic subjects is discussed.
Current and future implications of basic and translational research on amyloid-β peptide production and removal pathways (2015)

Inherited variants in multiple different genes are associated with increased risk for Alzheimer's disease (AD). In many of these genes, the inherited variants alter some aspect of the production or clearance of the neurotoxic amyloid β-peptide (Aβ). Thus missense, splice site or duplication mutants in the presenilin 1 (PS1), presenilin 2 (PS2) or the amyloid precursor protein (APP) genes, which alter the levels or shift the balance of Aβ produced, are associated with rare, highly penetrant autosomal dominant forms of Familial Alzheimer's Disease (FAD). Similarly, the more prevalent late-onset forms of AD are associated with both coding and non-coding variants in genes such as SORL1, PICALM and ABCA7 that affect the production and clearance of Aβ. This review summarises some of the recent molecular and structural work on the role of these genes and the proteins coded by them in the biology of Aβ. We also briefly outline how the emerging knowledge about the pathways involved in Aβ generation and clearance can be potentially targeted therapeutically. This article is part of Special Issue entitled "Neuronal Protein".
Overexpression of osteopontin in hepatocellular carcinoma (2002)

Human hepatocellular carcinoma (HCC) is one of the most common and aggressive malignancies. In order to identify genes involved in HCC progression, we conducted a differential display analysis and found osteopontin (OPN) to be overexpressed in HCC. OPN is known to be a secreted adhesive glycoprotein, associated with tumorigenesis and metastasis in several cancers. Quantitative polymerase chain reaction analysis of 30 HCC cases revealed the average ratio of OPN to glyceraldehyde-3-phosphate dehydrogenase in tumors to be significantly higher than that in the surrounding non-cancerous liver (4.7 +/- 1.6 vs 0.18 +/- 0.04, P = 0.0072). Immunohistochemistry confirmed the OPN protein was expressed mainly on cancer cells, and was positive in 12 of 30 HCC, most of which showed transcript overexpression. Both OPN transcript and OPN protein were significantly overexpressed in HCC with capsular infiltration, compared with HCC without capsular infiltration. Moreover, OPN-positive cancer cells were often dispersed in the periphery of cancer nodules and were adjacent to stromal cells. Although OPN overexpression was not related to vascular invasion or intrahepatic metastasis, OPN was suggested to play a role in HCC, especially in cancer-stromal interactions.
An Antimicrobial Peptide Gene Found in the Male Reproductive System of Rats (2001)

Little is known about the innate defense mechanisms of the male reproductive tract. We cloned a 385-base pair complementary DNA and its genomic DNA named Bin1b that is exclusively expressed in the caput region of the rat epididymis and that is responsible for sperm maturation, storage, and protection. Bin1b exhibits structural characteristics and antimicrobial activity similar to that of cationic antimicrobial peptides, beta-defensins. Bin1b is maximally expressed when the rats are sexually mature and can be up-regulated by inflammation. Bin1b appears to be a natural epididymis-specific antimicrobial peptide that plays a role in reproductive tract host defense and male fertility.
The Immune Epitope Database 2.0 (2009)

The Immune Epitope Database (IEDB, www.iedb.org) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. Over the course of 4 years, the data from 180,978 experiments were curated manually from the literature, which covers approximately 99% of all publicly available information on peptide epitopes mapped in infectious agents (excluding HIV) and 93% of those mapped in allergens. In addition, data that would otherwise be unavailable to the public from 129,186 experiments were submitted directly by investigators. The curation of epitopes related to autoimmunity is expected to be completed by the end of 2010. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria. The database structure, as well as its querying, browsing and reporting interfaces, was completely redesigned for the IEDB 2.0 release, which became publicly available in early 2009.
Physical mapping of Mycobacterium bovis BCG Pasteur reveals differences from the genome map of Mycobacterium tuberculosis H37Rv and from M. bovis (1996)

A Dral restriction map of the approximately 4.35 Mb circular chromosome of the vaccine strain Mycobacterium bovis BCG Pasteur was constructed by linking all 21 Dral fragments, ranging in size from 6 to 820 kb, using specific clones that spanned the Dral recognition sites as hybridization probes. The positions of 20 known genes were also established. Comparison of the resultant genome map with that of the virulent tubercle bacillus Mycobacterium tuberculosis H37Rv revealed extensive global conservation of the genomes of these two members of the M. tuberculosis complex. Possible sites of evolutionary rearrangements were localized on the chromosome of M. bovis BCG Pasteur by comparing the Asnl restriction profile with that of M. tuberculosis H37Rv. When selected cosmids from the corresponding areas of the genome of M. tuberculosis H37Rv were used as hybridization probes to examine different BCG strains, wild-type M. bovis and M. tuberculosis H37Rv, a number of deletions up to 10 kb in size, insertions and other polymorphisms were detected. In addition to the known deletions covering the genes for the protein antigens ESAT-6 and mpt64, other genetic loci exhibiting polymorphisms or rearrangements were detected in M. bovis BCG Pasteur.
Inhibition of β-Ketoacyl-Acyl Carrier Protein Synthases by Thiolactomycin and Cerulenin (2001)

The beta-ketoacyl-acyl carrier protein (ACP) synthases are key regulators of type II fatty acid synthesis and are the targets for two natural products, thiolactomycin (TLM) and cerulenin. The high resolution structures of the FabB-TLM and FabB-cerulenin binary complexes were determined. TLM mimics malonyl-ACP in the FabB active site. It forms strong hydrogen bond interactions with the two catalytic histidines, and the unsaturated alkyl side chain interaction with a small hydrophobic pocket is stabilized by pi stacking interactions. Cerulenin binding mimics the condensation transition state. The subtle differences between the FabB-cerulenin and FabF-cerulenin (Moche, M., Schneider, G., Edwards, P., Dehesh, K., and Lindqvist, Y. (1999) J. Biol. Chem. 244, 6031-6034) structures explain the differences in the sensitivity of the two enzymes to the antibiotic and may reflect the distinct substrate specificities that differentiate the two enzymes. The FabB[H333N] protein was prepared to convert the FabB His-His-Cys active site triad into the FabH His-Asn-Cys configuration to test the importance of the two His residues in TLM and cerulenin binding. FabB[H333N] was significantly more resistant to both antibiotics than FabB and had an affinity for TLM an order of magnitude less than the wild-type enzyme, illustrating that the two-histidine active site architecture is critical to protein-antibiotic interaction. These data provide a structural framework for understanding antibiotic sensitivity within this group of enzymes.