gebhart/patrepeval huggingface dataset:
Investigation of anomalous charge variant profile reveals discrete pH-dependent conformations and conformation-dependent charge states within the CDR3 loop of a therapeutic mAb (2020)

During the development of a therapeutic monoclonal antibody (mAb-1), the charge variant profile obtained by pH-gradient cation exchange chromatography (CEX) contained two main peaks, each of which exhibited a unique intrinsic fluorescence profile and demonstrated inter-convertibility upon reinjection of isolated peak fractions. Domain analysis of mAb-1 by CEX and liquid chromatography-mass spectrometry indicated that the antigen-binding fragment chromatographed as two separate peaks that had identical mass. Surface plasmon resonance binding analysis to antigen demonstrated comparable kinetics/affinity between these fractionated peaks and unfractionated starting material. Subsequent molecular modeling studies revealed that the relatively long and flexible complementarity-determining region 3 (CDR3) loop on the heavy chain could adopt two discrete pH-dependent conformations: an "open" conformation at neutral pH where the HC-CDR3 is largely solvent exposed, and a "closed" conformation at lower pH where the solvent exposure of a neighboring tryptophan in the light chain is reduced and two aspartic acid residues near the ends of the HC-CDR3 loop have atypical pKa values. The pH-dependent equilibrium between "open" and "closed" conformations of the HC-CDR3, and its proposed role in the anomalous charge variant profile of mAb-1, were supported by further CEX and hydrophobic interaction chromatography studies. This work is an example of how pH-dependent conformational changes and conformation-dependent changes to net charge can unexpectedly contribute to perceived instability and require thorough analytical, biophysical, and functional characterization during biopharmaceutical drug product development.
Pyrophosphito-bridged diplatinum chemistry (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrophosphito-bridged diplatinum chemistryD. Max Roundhill, Harry B. Gray, and Chi Ming CheCite this: Acc. Chem. Res. 1989, 22, 2, 55–61Publication Date (Print):February 1, 1989Publication History Published online1 May 2002Published inissue 1 February 1989https://pubs.acs.org/doi/10.1021/ar00158a002https://doi.org/10.1021/ar00158a002research-articleACS PublicationsRequest reuse permissionsArticle Views1955Altmetric-Citations400LEARN 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
Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. (2002)

An anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium, strain SI(T), isolated previously from granular sludge in a thermophilic upflow anaerobic sludge blanket (UASB) reactor, was characterized. The strain could grow fermentatively on pyruvate and fumarate in pure culture. The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus strain deltaH(T). The optimum temperature for growth was 55 degrees C and the pH optimum was 7.0. The G+C content of the DNA was 52.8 mol %. Strain SI(T) contained MK-7 and MK-7(H4) as the major quinones and contained iso-C15:0 as the major fatty acid. Based on 16S rDNA sequence analysis, strain SI(T) formed a novel lineage within the gram-positive, spore-forming, sulphate-reducing bacterial group Desulfotomaculum. However, the strain lacked the ability to conduct dissimilatory sulphate reduction. Instead, it could reduce fumarate to succinate with concomitant growth on several organic substances as electron donor. These phenotypic and genetic properties support the formation of a novel species of a new genus, for which the name Pelotomaculum thermopropionicum gen. nov., sp. nov. is proposed. The type strain is strain SI(T) (= DSM 13744T = JCM 10971T).
Self-Organized Macroporous Carbon Structure Derived from Phenolic Resin via Spray Pyrolysis for High-Performance Electrocatalyst (2013)

The synthesis and evaluation of porous carbon derived from phenolic resin using a fast and facile spray pyrolysis method has been studied for use as a new electrocatalyst support material. By adding polystyrene latex nanoparticles as a template to the phenolic resin precursor, self-organized macroporous carbon structure was first developed. The mass ratio of phenolic resin to PSL at 0.625 gave the optimum porous morphology. Pt nanoparticles (∼20 wt %) were grown on the carbon surface using a standard industrial impregnation method. Well-dispersed Pt nanoparticles of average size 3.91 nm were observed on the surface of porous carbon particles. The high catalytic performance of porous Pt/C electrocatalyst was confirmed by the high mass activity and electrochemically active surface area, which were 450.81 mA mg(-1)-Pt and 81.78 m(2) g(-1)-Pt, respectively. The porous Pt/C catalyst obtains two times higher mass activity than that of the commercial Pt/C catalyst and performs excellent durability under acid conditions.
Intestinal Microbiota During Infancy and Its Implications for Obesity (2009)

Obesity is a worldwide epidemic, threatening both industrialized and developing countries, and is accompanied by a dramatic increase in obesity-related disorders, including type 2 diabetes mellitus, hypertension, cardiovascular diseases, and nonalcoholic fatty liver disease. Recent studies have shown that the gut microbial community (microbiota) is an environmental factor that regulates obesity by increasing energy harvest from the diet and by regulating peripheral metabolism. However, there are no data on how obesogenic microbiotas are established and whether this process is determined during infancy. The sterile fetus is born into a microbial world and is immediately colonized by numerous species originating from the surrounding ecosystems, especially the maternal vaginal and fecal microflora. This initial microbiota develops into a complex ecosystem in a predictable fashion determined by internal (eg, oxygen depletion) and external (eg, mode of birth, impact of environment, diet, hospitalization, application of antibiotics) factors. We discuss how the gut microbiota regulates obesity and how environmental factors that affect the establishment of the gut microbiota during infancy may contribute to obesity later in life.
<title>Temperature-insensitive smart optical strain sensor</title> (2000)

An optical strain gage, employing a hollow polyimide-coated glass capillary tube, is currently under development. The capillary tube serves as a waveguide, in which an optical signal is attenuated in an amount proportional to applied bending strain. The capillary is incorporated into an optical fiber link which acts as both the source of signal and as the return path to a photodiode detector. The inherent compatibility of this optical strain sensor with fiber optic telecommunication systems makes it amenable for incorporation into intelligent systems for the continuous monitoring and damage assessment of bridges, highways, piers, airframes, and buildings. By applying various thin films to the interior and/or exterior surfaces of the waveguide, the strain gage can be optimized for specific strain ranges. This optical strain sensor exhibits advantages in comparison to commercially available metal foil (resistance) strain gages, including gage factors 100 times larger and temperature insensitivity for operating temperatures ranging from -25 degrees Celsius to +51 degrees Celsius.
Distinct immunological activities of four variants of one mutation-generated neoepitope of a mouse fibrosarcoma (TUM10P.1023) (2015)

Abstract Passenger mutations in cancer cells can give rise to mutant MHC Class I restricted epitopes, also referred to as neoepitopes. One such neoepitope, Tnpo3 (SYMLQALCI), has been described for the BALB/c Meth A fibrosarcoma, by our laboratory1. Immunization with a peptide corresponding to the Tnpo3 neoepitope elicits antigen specific CD8+ T cells, which are capable of mediating specific rejection of Meth A. Interrogating the site of mutation within the Tnpo3 neoepitope with NetMHC predicts three other variants of Tnpo3 having the same amino terminus but different carboxyl termini. Of these four Tnpo3 variants, three elicit functional CD8+ T cells upon immunization, and of these, only one elicits tumor rejection. Here, the structural and cellular immunological aspects of the differential activities of these four neoepitopes are investigated. 1Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and Bioinformatic Profiling of Mutational Neoepitopes Reveals New Rules to Predict Anticancer Immunogenicity." J Exp Med. 211 (2014): 2231-248. PMID: 25245761
Relationship between obesity and verbal memory performance among top academic achievers in Singapore (2007)

This document may be used for private study or research purpose only. This document or any part of it may not be duplicated and/or distributed without permission of the copyright owner. The Singapore Copyright Act applies to the use of this document.
Liquid Type Nontoxic Photoluminescent Nanomaterials for High Color Quality White-Light-Emitting Diode (2018)

High-brightness white-light-emitting diodes (w-LEDs) with excellent color quality is demonstrated by using nontoxic nanomaterials. Previously, we have reported the high color quality w-LEDs with heavy-metal phosphor and quantum dots (QDs), which may cause environmental hazards. In the present work, liquid-type white LEDs composed of nontoxic materials, named as graphene and porous silicon quantum dots are fabricated with a high color rendering index (CRI) value gain up to 95. The liquid-typed device structure possesses minimized surface temperature and 25% higher value of luminous efficiency as compare to dispensing-typed structure. Further, the as-prepared device is environment friendly and attributed to low toxicity. The low toxicity and high R9 (87) component values were conjectured to produce new or improve current methods toward bioimaging application.
Activation of adenylate cyclase in cultured fibroblasts by trypsin. (1978)

Adenylate cyclase activity measured in membranes of cultured normal rat kidney (NRK) fibroblasts was markedly increased by prior treatment of the intact cells with trypsin. Cell population density influenced the extent of activation observed. Trypsin treatment of sparse cells significantly enhanced adenylate cyclase activity, whereas similar treatment of confluent cells caused only a slight increase in adenylate cyclase activity. The degree of activation noted after trypsin treatment also varied depending on the adenylate cyclase function measured. Activity determined in the presence of GTP alone showed the greatest increase after trypsin treatment. Similar enhancement of adenylate cyclase activity of a washed cell membrane preparation was achieved by the addition of low concentrations of trypsin directly to the adenylate cyclase reaction mixture. The membranes of confluent NRK fibroblasts initially exhibited higher adenylate cyclase activity than did membranes of sparse cells. The present results suggest that this change in adenylate cyclase activity at cell confluence is not due to an increase in the amount of adenylate cyclase in the cell membrane but rather to a change in membrane components that regulate its activity. Proteolytic activation of adenylate cyclase appears to result from degradation of cell membrane proteins that modulate the activity of this enzyme.
Parameter estimation in linear models based on outage probability minimization (2006)

A traditional approach to estimating random unknown signal parameters in a noisy linear model aims at minimizing the mean squared error (MSE) averaged over both the random signal parameters and noise realizations. In this paper, we develop a new estimation approach which minimizes the MSE averaged over the noise only. Moreover, in contrast to the traditional approach, the MSE is minimized only for the most favorable signal parameter realizations. It is assumed that the second- order statistics of the unknown signal parameter and noise vectors are precisely known and the noise is Gaussian, while the probability density function (pdf) of the unknown signal parameter vector may be Gaussian or completely unknown. Two different linear estimators are derived for the latter two cases.
Large-Area Crystalline Microcolumnar LaBr$_{3}$:Ce for High-Resolution Gamma Ray Imaging (2012)

Novel fabrication methods for cost-effective and large-volume production of important lanthanide halide scintillators are currently being explored. Here we report on the growth of LaBr :Ce scintillator films in a novel light conserving morphology known as Crystalline Microcolumnar StructureTM (CMSTM), using Hot Wall Evaporation (HWE) technique. This method produces specimens which preserve the response uniformity over the area of the film, and low attenuation of light throughout its thickness. Using this approach, we have produced LaBr :Ce film samples measuring 3-7 cm in diameter and approaching 2 cm in thickness, with densely packed microcolumns averaging ~15 μm in diameter. Some of these films show bright light emissions compared to their crystalline counterparts, demonstrating energy resolution of ~9.4% at 122 keV ( Co emission) and uniformity in light response across the area of the scintillator. Imaging data acquired using the University of Arizona Bazooka SPECT detector incorporating our CMS LaBr :Ce film demonstrated m spatial resolution ~138 μm at 122 keV in single-photon counting imaging mode. This technique permits fabrication of thick films that can simultaneously provide the high absorption efficiency and high spatial resolution required for small-animal SPECT imaging and other medical and non-medical applications.
Predictors of stent thrombosis after primary stenting for acute myocardial infarction (1999)

The aim of the study was to determine if a hypercoagulable state that may persist for several months after an acute myocardial infarction may contribute to an increased incidence of stent thrombosis. Primary stenting was performed in 104 consecutive patients with acute myocardial infarction using 147 coronary stents. Twenty-eight patients (27%) were diabetic and 55 patients (53%) were smokers. A single stent was placed in 63%, two stents in 33%, and more than two stents in 4% of the patients. Procedural success was obtained in 97% of the patients. All stents were deployed using high-pressure balloon inflation. The reference vessel diameter and minimal lumen diameter after stent deployment were 3.30 ± 0.42 and 3.23 ± 0.42 mm, respectively. Six patients (5.7%) developed stent thrombosis within 1 month after the procedure complicated by reinfarction in five of the six patients. At 1-month follow-up, all patients remained alive. On multivariate analysis, independent predictors of stent thrombosis were diabetes mellitus (relative risk [RR] 5.2; 95% confidence interval [CI] 1.8, 25.1), tobacco use (RR 4.5; 95% CI 1.3, 24.5), number of stents: 1 vs. > 1 (RR 3.7; 95% CI 1.1, 15.9), minimal lumen diameter poststent placement (RR 0.03; 95% CI 0.0002, 0.74), and duration of chest pain before intervention (RR 1.1; 95% CI 1.01, 1.25). Stent thrombosis had not been associated with diabetes mellitus and tobacco use previously but is in agreement with the enhanced platelet aggregability, coagulation factor abnormalities, and impaired fibrinolysis characteristic of these patients. Cathet. Cardiovasc. Intervent. 47:415–422, 1999. © 1999 Wiley-Liss, Inc.
Smoking rates in Pacific islands. (1986)

This study collected data on rates of cigarette smoking in the following Pacific Islands: Cook Islands, Fiji, Kiribati, Nauru, New Caledonia, Niue, Tuvalu, and Western Samoa. The data were collected in 1975-81 as part of a diabetes-cardiovascular diseases survey. A large variation in the prevalence of smoking was found in the populations surveyed. 90% of men and 74% of women on Kiribati were daily smokers compared with 38% of men and 19% of women on the Cook Islands and only 4% of the female population of Fiji. There was no association between age and the prevalence of smoking. Smoking tended to be more common in rural areas than urban areas and was higher among men than women in all populations studied. For both men and women, the prevalence of smoking was higher among lower income groups and those who reported moderate or heavy alcohol consumption. There was no clear association between smoking and marital status. Overall, the data on the prevalence of cigarette smoking indicate that this has become a significant public health problem in Pacific island communities. The data further suggest that the prevalence of smoking differs markedly in culturally and ethnically different populations. Somewhat unexpected was the greater proportion of smokers among traditional communities in rural areas compared with urban areas. This finding can be explained in part by the widespread practice of cultivating tobacco in many rural areas of the Pacific. It is recommended that a reliable survey of smoking patterns in the Pacific islands and prospective surveys that correlate the results of such a study with the distribution of cardiovascular diseases and cancer be conducted.
317 Gb/in2 Recording Areal Density on Strontium Ferrite Tape (2021)

The recording performance of a new prototype magnetic tape based on perpendicularly oriented strontium ferrite particles is investigated using a 29 nm wide tunneling magnetoresistive reader. At a linear density of 702 kbpi, a post-detection byte-error rate (BER) of 2.8e-2 is demonstrated based on measured recording data and a software read channel. The read channel uses a 64-state implementation of an extended version of a data-dependent noise-predictive maximum-likelihood detection scheme that tracks the first- and second-order statistics of the data-dependent noise. At the demonstrated post-detection BER, a post-error-correction-coding BER of less than 1e-20 can be achieved using an iterative decoding architecture. To facilitate aggressive track-density scaling, we made multiple advances in the area of track following. First, we developed a new timing-based servo pattern and implemented a novel quad channel averaging scheme. Second, we developed a new field programmable gate array prototyping platform to enable the implementation of quad channel averaging. Third, we enhanced our low disturbance tape transport with a pair of 20 mm diameter air bearing tape guides and a prototype track-following actuator. Fourth, we developed a novel low friction tape head and, finally, we designed a set of tape speed optimized track-following controllers using the model-based H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> design framework. Combining these technologies, we achieved a position error signal (PES) characterized by a standard deviation ≤ 3.18 nm over a tape speed range of 1.2-4.1 m/s. This magnitude of PES in combination with a 29 nm wide reader enables reliable recording at a track width of 56.2 nm corresponding to a track density of 451.9 ktpi, for an equivalent areal density of 317.3 Gb/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Entwicklungsumgebung mit echtzeitfähigen Gesamtfahrzeugmodellen für sicherheitskritische Fahrerassistenzsysteme (Development Environment with Real-time Models for Safety Assistance Systems) (2004)

Abstract Simulationen gewinnen bei der Funktionsentwicklung für Fahrdynamikregelungen speziell im Stadium der Vorentwicklung immer mehr an Bedeutung. Die Bewertung von Fahrerassistenzsystemen oder Fahrdynamikregelungen ist jedoch aufgrund des subjektiven Fahrgefühls schwierig. Aus diesem Grund wurden ein Force-Feedback-Lenkrad und eine Pedaleinheit mit einem in Fahrversuchen verifizierten echtzeitfähigen Zweispurmodell gekoppelt, die es dem Fahrer ermöglichen, das Gesamtfahrzeugmodell realitätsnah zu steuern. Den aktuellen Fahrzustand erhält der Fahrer über eine 3D-Animation von Fahrzeug und Umgebung in verschiedenen Perspektiven. Mithilfe dieser Entwicklungsumgebung werden neue Ansätze zur Fahrdynamikregelung mit kombiniertem Lenk- und Bremseingriff untersucht.
Fast Holes, Slow Electrons, and Medium Control of Polaron Size and Mobility in the DA Polymer F8BT (2017)

The nature of electron and hole polarons on poly(9,9-di-n-hexylfluorenyl-2,7-diyl) (pF) and a copolymer poly[(9,9-di-n-octylfluorenyl-2,7-diyl)-alt-(benzo[2,1,3]thiadiazol-4,8-diyl)] (F8BT) has been studied by chemical doping, pulse radiolysis, charge modulation spectroscopy, quantum chemical calculations, and microwave conductivity. While pF exhibits very similar behavior in all respects for the electron and the hole, this paper explores the hypothesis that the donor acceptor (push–pull) nature of F8BT will tend to localize charges. Optical spectra and quantum chemical calculations point to an electron localized on the thiadiazole unit in polar liquids but becoming more delocalized as the solvent polarity decreases. Indeed, in the nonpolar solvent benzene, the electron mobility is only 2.7 times lower than that of the hole, which conversely is shown to be delocalized in all environments and has a similar mobility to polarons on the homopolymer polyfluorene. Advantageous modifications to the optoelectronic properties of conjugated polymers that come about by using alternating donor acceptor repeat units have thus been shown to not significantly hinder charge transport despite the corrugated energy landscape along the backbone.
Faculty Opinions recommendation of 1α,25-dihydroxyvitamin D3 modulates the hair-inductive capacity of dermal papilla cells: therapeutic potential for hair regeneration. (2012)

Read the full review for this Faculty Opinions recommended article: 1α,25-dihydroxyvitamin D3 modulates the hair-inductive capacity of dermal papilla cells: therapeutic potential for hair regeneration.
[Future prospects for primary hormone therapy in localized and locally advanced prostate cancer]. (2003)

The authors consider current and future prospects for primary hormone therapy in localized and locally advanced prostate cancer by comparing this form of treatment (hormone monotherapy) with neoadjuvant radiation therapy and radical prostatectomy. Neoadjuvant hormone therapy prior to radiation therapy has been proven effective in recent years, and currently the United States is showing a year-by-year increase in the use of androgen blocking agents during the early stage of prostate cancer. A survey of recent research findings, clearly showed that, for patients with localized prostate cancer, there is no significant difference in survival rate between hormone monotherapy and radical prostatectomy. In the future we can expect to see an increase in available treatment options for localized and locally advanced prostate cancer, with the optimal therapy for each individual patient to be selected by the attending physician in discussion with the patient.