gebhart/patrepeval huggingface dataset:
Fast protein sequencing of monoclonal antibody by real-time digestion on emitter during nanoelectrospray (2019)

Growth in the pharmaceutical industry has led to an increasing demand for rapid characterization of therapeutic monoclonal antibodies. The current methods for antibody sequence confirmation (e.g., N-terminal Edman sequencing and traditional peptide mapping methods) are not sufficient; thus, we developed a fast method for sequencing recombinant monoclonal antibodies using a novel digestion-on-emitter technology. Using this method, a monoclonal antibody can be denatured, reduced, digested, and sequenced in less than an hour. High throughput and satisfactory protein sequence coverage were achieved by using a non-specific protease from Aspergillus saitoi, protease XIII, to digest the denatured and reduced monoclonal antibody on an electrospray emitter, while electrospray high voltage was applied to the digestion mixture through the emitter. Tandem mass spectrometry data was acquired over the course of enzyme digestion, generating similar information compared to standard peptide mapping experiments in much less time. We demonstrated that this fast protein sequencing method provided sufficient sequence information for bovine serum albumin and two commercially available monoclonal antibodies, mouse IgG1 MOPC21 and humanized IgG1 NISTmAb. For two monoclonal antibodies, we obtained sequence coverage of 90.5-95.1% for the heavy chains and 98.6-99.1% for the light chains. We found that on-emitter digestion by protease XIII generated peptides of various lengths during the digestion process, which was critical for achieving sufficient sequence coverage. Moreover, we discovered that the enzyme-to-substrate ratio was an important parameter that affects protein sequence coverage. Due to its highly automatable and efficient design, our method offers a major advantage over N-terminal Edman sequencing and traditional peptide mapping methods in the identification of protein sequence, and is capable of meeting an ever-increasing demand for monoclonal antibody sequence confirmation in the biopharmaceutical industry.
Clinicopathological study on submucosal injection of collagenase in the treatment of submucous fibrosis in the oral cavity. (1986)

Sufferers of submucous fibrosis (often a condition thought to have resulted from the frequent chewing of betel nut) in its later stages may have difficulty opening their mouths, may experience alterations in mucosal sensations, such as sensitivity to spices, sour, cold, and heat, and can even develop malignant squamous cell carcinoma. 
In performing this study, we first injected a 4% phenol solution into the submucosa of 5 New Zealand rabbits (weights ranging from 1.5－2.0 kgs), a method that we found would successfully induce beautiful submucous fibrosis, and then utilized collagenase to lyse this dense fibrous tissue. 
The collagenase injections resulted in significant clinical improvements of the submucous fibrosis and also decreased significantly the incidence of malignancy.
The current treatments of submucous fibrosis have several disadvantages: 1) medical method: injection of steroids. This can only decrease the inflammatory reaction, whereas collagenase can directly lyse the persisting submucous fibrous tissue. 2) surgical method: by the usage of tissue graft. This involves the possibility of rejection, or a fibrotic change in the suture edge that will eventually result in the contraction of the repair portion and sometimes even a keloid formation. In addition to this, the graft procedure is more difficult than our submucosal collagenase injection. In an experimental study on animals, followed by a clinical application, we obtained exciting therapeutic results with the injection of a 1.0 ml solution of collagenase (SIGMA) into the submucous fibrosis patients. As far as we know, this may be the most convenient and readily available treatment in the submucous fibrosis patients.
Mutations in the <i>uncE</i> gene affecting assembly of the <i>c</i>-subunit of the adenosine triphosphatase of <i>Escherichia coli</i> (1983)

The amino acid substitutions in the mutant c-subunits of Escherichia coli F1F0-ATPase coded for by the uncE429, uncE408 and uncE463 alleles affect the incorporation of these proteins into the cell membrane. The DNA sequence of the uncE429 allele differed from normal in that a G leads to A base change occurred at nucleotide 68 of the uncE gene, resulting in glycine being replaced by aspartic acid at position 23 in the c-subunit. The uncE408 and uncE463 mutant DNA sequences were identical and differed from normal in that a C leads to T base change occurred at nucleotide 91 of the uncE gene, resulting in leucine being replaced by phenylalanine at position 31 in the c-subunit. An increased gene dosage of the uncE408 or uncE463 alleles resulted in the incorporation into the membranes of the mutant c-subunits. The results are discussed in terms of the 'Helical Hairpin Hypothesis' of Engelman & Steitz [(1981) Cell 23,411-422].
[4-(n-Dimethylaminostyryl)-1-methylpyridinium fluorescence in a living cell]. (1981)

A fluorescent compound 4-(p-dimethylinostyryl)-1-methylpyridinium (DSM) has been synthesized, having the absorption maximum about 450 nm and the fluorescence maximum about 590 nm in a water solution. A considerable increase of its fluorescence intensity is found in DNA solutions. The binding of DSM with membranes leads to a shift of its fluorescence maximum to 550 nm. Polychromatic properties of DSM (green fluorescence in membranes, rich yellow - in energized mitochondria, red-orange - in nuclei) are found in DSM stained cells. DSM fluorescence is sensitive to changes in the energized state of cells; the uncupler dinitrophenol or respiration inhibitors-cyanide and amital-cause a strong decrease in the DSM fluorescence intensity in mitochondria. It is ascertained that DSM itself has a low toxicity with respect to cell energy: it had no influence on the mobility of Tetrahymena pyriformis during 23 hours after staining. Thus, DSM may be used as a fluorescent probe for live cells.
Interferon Alfacon-1 Protects Hamsters from Lethal Pichinde Virus Infection (2005)

Hemorrhagic fever of arenaviral origin is a frequently fatal infectious disease of considerable priority to the biodefense mission. Historically, the treatment of arenaviral infections with alpha interferons has not yielded favorable results. Here we present evidence that interferon alfacon-1, a nonnaturally occurring bioengineered alpha interferon approved for the treatment of chronic hepatitis C, is active against Pichinde and Tacaribe arenaviruses in cell culture. In the hamster model of Pichinde virus (PCV) infection, interferon alfacon-1 treatment significantly protected animals from death, prolonged the survival of those that eventually died, reduced virus titers, and limited liver damage characteristic of PCV-induced disease. Moreover, interferon alfacon-1 also demonstrated therapeutic activity, to a lesser degree, when the initiation of treatment was delayed up to 2 days post-virus challenge. Despite the observed advantages of interferon alfacon-1 therapy, efforts to stimulate the immune system with the known interferon inducer poly(I:C12U) (Ampligen) offered only limited protection against lethal PCV challenge. Taken together, these data suggest that the increased potency of the bio-optimized interferon alfacon-1 molecule may be critical to the observed antiviral effects. These data are the first report demonstrating efficacious treatment of acute arenaviral disease with alpha interferon therapy, and further study is warranted.
The Reaction of Dialkyl Sulfates with ROMgBr Compounds (1934)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reaction of Dialkyl Sulfates with ROMgBr CompoundsArthur C. CopeCite this: J. Am. Chem. Soc. 1934, 56, 6, 1342–1346Publication Date (Print):June 1, 1934Publication History Published online1 May 2002Published inissue 1 June 1934https://pubs.acs.org/doi/10.1021/ja01321a030https://doi.org/10.1021/ja01321a030research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-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
Antioxidant Activity of Phosvitin in Phosphatidylcholine Liposomes and Meat Model Systems (2002)

ABSTRACT: Phosvitin, an iron‐chelating protein, was tested for its ability to inhibit lipid oxidation in phosphatidylcholine (PC) liposomes and meats. Inhibition of thiobarbituric acid reactive substances (TBARS) formation increased with increasing phosvitin concentrations with maximal inhibition occurring at 40 and 15 mM in PC liposomes and pork muscle homogenates, respectively. Phosvitin lost only 2 to 15% of its antioxidant activity after being heated for 10 min at 60 to 100 °C. The ability of phosvitin to inhibit TBARS formation was maximal at pH 7.0. Phosvitin was a more effective antioxidant in cooked ground pork with 20 mM inhibiting 11 to 39% of oxidation compared with 0 to 20% inhibition in uncooked, salted ground pork containing 60 mM phosvitin.
Spider Silk Protein Refolding Is Controlled by Changing pH (2004)

Spidroins, the major silk proteins making up the spider's dragline silk, originate in two distinct tissue layers (A and B) in the spider's major ampullate gland. Formation of the complex thread from spidroins occurs in the lumen of the duct connected to the gland. Using pH-sensitive microelectrode probes, we showed that the spidroins traveling through the gland and duct experience a monotonic decrease in pH from 7.2 to 6.3. In addition, circular dichroism spectroscopy of material extracted from the gland showed a structural refolding concomitant with position in the gland and post-extraction changes in pH. We demonstrate that lowering the pH in vitro causes a dramatic conformational change in the protein from the A zone, converting it irreversibly from a coil to a predominantly beta-sheet structure. Furthermore, amino acid analyses have indicated that there are at least two distinct, though similar, proteins secreted in the A and B zones suggesting a potential factor in the progressive acidification as well as a pH sensitivity of the folding of spidroins in the gland. Thus, we provide, for the first time, a quantitative map of the pH value and position correlated with molecular structural folding in the silk gland characterizing the crucial role that pH plays in spider silk formation.
Regional surveys using a helicopter-suspended gravimeter (1998)

Although gravimetry is arguably the most basic of the potential field methods that can map subsurface geology, its use has been restricted by its cost. The reason is that gravimeter measurements, per se, are meaningless unless accompanied by an accurate determination of the relative elevation of each station. To be consistent with the accuracy of modern gravimeters, the determination of station elevation requires optical leveling, which is slow and costly for widely spaced (1 km or more apart) stations in rugged or forested areas.
Investigation of Size Dependence on Sensitivity for Nanowire FET Biosensors (2011)

Label-free electrical detection of biomolecules is demonstrated with a double-gate (DG) nanowire (NW) field-effect transistor (FET). Experimental results confirm that detection sensitivity is favorably improved by the increment of NW size in the DG-NWFET, whereas it is enhanced by the decrement of NW size in a conventional single-gate (SG) NWFET. Sensitivity improvement by the augmentation of the NW size in the DG-FET paves the way to overcome technical challenges we face in achieving ultimate miniaturization of the NW size in the SG-FET. This result is comprehensively understood by simple capacitive modeling. The proposed model explains the observed experimental data and provides a design guideline for highly sensitive NW biosensors.
Multicenter trial of the quantitative BTA TRAK assay in the detection of bladder cancer. (1999)

Because of its relatively high sensitivity, the BTA TRAK assay could complement cytology as an adjunct to cystoscopy in the diagnosis and follow-up of most patients with bladder cancer.
Synthesis and antithrombogenicity of anionic polyurethanes and heparin‐bound polyurethanes (1986)

Two kinds of novel antithrombogenic polyurethane materials were synthesized. One of them is a polyetherurethane with anionic charges on the film surface, and the other is a polyetherurethaneurea to which heparin was covalently bound. The mechanism of their antithrombogenicity was investigated. The anionic polyetherurethane selectively adsorbed albumin, did not cause a conformational change of plasma proteins adsorbed, and suppressed the adherence and deformation of platelets but did not deactivate the blood-clotting system, thus leading to a moderate antithrombogenicity. The heparin-bound polyetherurethaneurea was not favorable for the selective adsorption of albumin, caused the denaturation of plasma proteins adsorbed, and induced the adherence and deformation of platelets but deactivated the blood-clotting system, leading to excellent antithrombogenicity. For the investigation of blood-material interaction, the importance of a multiparameter estimation of the activation of platelets and the blood-clotting system was indicated.
PEGA supports for combinatorial peptide synthesis and solid-phase enzymatic library assays (1998)

Permeable resins cross-linked with long PEG chains were synthesized for use in solid-phase enzyme library assays. High molecular weight bis-amino-polyethylene glycol (PEG) 4000, 6000, 8000 were synthesized by a three-step reaction starting from PEG-bis-OH. Macromonomers were synthesized by partial or di-acryloylation of bis-amino-PEG derivatives. Bis/mono-acrylamido-PEG were copolymerized along with acrylamide by inverse suspension copolymerization to yield a less cross-linked resin (Type I, compounds 6-9). Furthermore, acryloyl-sarcosin ethyl ester was co-polymerized along with bis-acrylamido PEG to obtain more crosslinked capacity resin (Type II, compounds 13-19). N,N-Dimethylacrylamide was used as a co-monomer in some cases. The polymer was usually obtained in a well-defined beaded form and was easy to handle under both wet and dry conditions. The supports showed good mechanical properties and were characterized by studying the swelling properties, size distribution of beads, and by estimating the amino group capacity. Depending on the PEG chain length, the monomer composition and the degree of cross-linking the PEGA supports showed a high degree of swelling in a broad range of solvents, including water, dichloromethane, DMF, acetonitril, THF and toluene: no swelling was observed in diethyl ether. The PEGA resins (Type I) with an amino acid group capacity between 0.07 and 1.0 mmol/g could be obtained by variation of the monomer composition in the polymerization mixture. Fluorescent quenched peptide libraries were synthesized on the new polymer using a multiple column library synthesizer and incubated with the matrix metalloproteinase MMP-9 after it had been activated by 4-aminophenyl mercuric acetate resulting in 67/83 kDa active enzyme. The bright beads were separated manually under a fluorescence microscope and sequenced to obtain peptide substrates for MMP-9. After treatment with ethylene diamine, high-loaded resins (Type II) have been employed in continuous flow peptide synthesis to yield peptides in excellent yield and purity.
Photoinduction of UV-absorbing compounds in six species of marine phytoplankton (1998)

High fluence PAR (photosynthetically active radiation, 400-700 nm), UV-A (320-400 nm), and UV-B (280-320 nm) radiation were tested for their ability to stimulate the production of UV-absorbing mycosporine-like amino acids (MAAs) in 6 diverse species of marine phytoplankton. Dunaliella tertiolecta, Thalassiosira weissflogii, Pyramimonas parkeae. Pavlova gyrans and Isochrysis sp. were grown under (1) low fluence PAR (LL, 23 to 75 pm01 photons m-2 S-'), (2) high fluence PAR (HL, 255 to 290 11mol photons m-2 S-'), (3) PAR+UV-A (240 to 268 pm01 photons m-' S-' and 4910 mW m-', respectively) and ( Amphidinium carterae was grown under similar conditions in LL but reduced levels of PAR and UV radiation were used in the other treatments UV-B supplementation caused a significant depression (23-57 %) in the chl a-specific growth rate of all species except P gyrans, which received the second lowest UV-B dose. The quantum yield of fluorescence for photosystem I1 declined by 4-17 % with exposure to UV-A and/or UV-A+UV-B. The 2 prymnesiophytes exhibited the highest and the dinoflagellate the lowest resistance to UV-B radiation. In vivo absorption spectra indicated that only P. gyrans has a pronounced UV maximum. Of the 3 MAA compounds detected in P. gyrans, only 1 with peak absorption in the UV-A range was photoinducible. The other species examined exhibited relatively small in vlvo UV absorption peaks. In these species, only 1 MAA was detected, a compound with peak absorption in the UV-B range and limited inducibility. UV-B radiation more effectively induced MAAs than UV-A or HL in 4 of the 6 species. In P. gyrans large increases in the concentration of the inducible MAA were obtained with HL and with UV-A+UV-B radiation. Relative to LL cells, UV-B-exposed P. gyrans exhibited a 145-fold MAA increase accompanied by an l l-fold increase in the in vivo UV absorption. In all other species HL had minimal or no effect on MAA production. UV-A radiation effectively increased the chl a-specific MAA content in Isochrysis sp. (77%). T weissflogii (73%), and P. parkeae (43%), and UV-B supplementation increased it by a further 141 % in Isochrysis sp. and 95% in P. parkeae. On a cell volume basis, UV-B also approximately doubled the MAA concentration in the latter 2 species. We conclude that, although MAAs may be commonly present in phytoplankton cells, an ability to produce significant amounts of these compounds through photoinduction is limited to certain species or taxa, particularly some prymnesiophytes and dinoflagellates
Glycerolysis of Crude Methyl Esters with Crude Glycerol from Biodiesel Production (2013)

Abstract Glycerolysis of crude fatty acid methyl esters (FAME) with crude glycerol derived from biodiesel production was performed. The reaction was accomplished at temperatures ranging between 160 and 200 °C and molar ratios of FAME to glycerol ranging between 1.5 and 3.0. Increasing the temperature improved the formation rate of monoglycerides (MG) and diglycerides (DG). However, increasing both the temperature and the molar ratio of glycerol to FAME diminished the formation of MG. Best results (43 % MG and 26 % DG in 10 min) were obtained at 200 °C using the lowest concentration of glycerol. The effects of soap and NaOH present in crude glycerol were controlled by carrying out the reaction with pure glycerol. In comparison with NaOH‐catalyzed reactions, soap‐catalyzed reactions resulted in a slower formation rate of products. However, soap‐catalyzed reactions were less prone to secondary reactions, affording maximum yields of MG and DG, which were higher than those obtained with NaOH‐catalyzed reactions at 180 and 200 °C.
Interpolation, wavelet compression, and neural network analysis for hazardous waste characterization (2002)

Large amounts of hazardous waste is stored at both government and private sites around the world. Within the United States, Department of Energy (formerly Atomic Energy Commission) locations contain an estimated 2.1 million cubic yards of buried hazardous radioactive, heavy metal, and other waste types. In many locations, this material is at risk for contaminating areas outside the burial site. To prevent this problem, materials must either be removed to a safer location or treated in situ. Either approach first requires a careful characterization of the buried materials. This paper describes an ongoing effort to use a neural network to assist in the interpretation of noninvasive sensor information used to characterize buried waste sites. This project to date contained three primary components: (1) using geophysical interpolation to correct for missing or noisy sensor data, (2) compressing the data using wavelets, and (3) construction of two neural networks that used the results of steps (1) and (2) to determine the depth and nature of buried objects. This work is a proof-of-concept study that demonstrates the feasibility of this approach. The resulting system was able to determine the nature of buried objects correctly 79% of the time and was able to locate a buried object to within an average error of 0.85 feet. These statistics were gathered based on a large test set and so can be considered reliable. Considering the limited nature of this study, these results strongly indicate the feasibility of this approach, and the importance of appropriate preprocessing of neural network input data.
Structural effects on the rates of formation and the stability of enols of cyclic benzyl ketones (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural effects on the rates of formation and the stability of enols of cyclic benzyl ketonesSherif Eldin, Ralph M. Pollack, and Dale L. WhalenCite this: J. Am. Chem. Soc. 1991, 113, 4, 1344–1349Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/ja00004a041https://doi.org/10.1021/ja00004a041research-articleACS PublicationsRequest reuse permissionsArticle Views599Altmetric-Citations17LEARN 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
A scalable multiphase buck converter with average current share bus (2003)

The paper presents a scalable multiphase synchronous buck converter which meets the tight requirements of the next generation microprocessors. Flexibility in the number of phases (1-16 phases) accommodates requirements of various applications. The converter can be easily expanded or paralleled with other voltage regulator modules (VRM) through an average current share bus. The distributed control IC architecture allows for local phase current signal processing, which minimizes induced noise and facilitates layout while reducing the gate driver to power stage impedance. The experimental results are given to show the advantages of the converter.