gebhart/patrepeval huggingface dataset:
Structural and functional characterization of MBS301, an afucosylated bispecific anti-HER2 antibody (2018)

MBS301, a glyco-engineered bispecific anti-human epidermal growth factor receptor 2 (HER2) antibody with a typical IgG1 monoclonal antibody structure, was developed through dual-cell expression and in vitro assembling process. MBS301 consists of two half antibodies engineered from trastuzumab and pertuzumab, respectively. Integrity and purity profiles of MB301 indicated that the heterodimerization of the two half antibodies was successful. The high and similar melting temperatures (Tm1,72.0°C and Tm2, 84.8°C) of MBS301 compared with those of its parental monoclonal antibodies trastuzumab and pertuzumab (in-house made T-mab and P-mab, respectively) revealed its structural compactness. With computer-modeling experiments and Biacore binding and competition kinetics studies, the binding stoichiometry between MBS301 and HER2-ECD was determined to be 1:1 and the two arms of MBS301 were shown to bind to domains II and IV of HER2-ECD antigen simultaneously. MBS301 displayed synergistic bioactivities as the combination of T-mab and P-mab in vitro in multiple cancer cell lines and in vivo in xenograft mouse model studies, and showed more effective activity than T-mab or P-mab used individually. Moreover, fucose-knockout dramatically increased MBS301's binding affinity to low affinity FcγRIIIa allotype 158F (K<sub>D</sub> = 2.35 × 10<sup>-7</sup>M) to near the high affinity level of allotype V158 (K<sub>D</sub> = 1.17 × 10<sup>-7</sup>M). This resulted in far more effective ADCC activity of MBS301 than the combination of T-mab and P-mab in killing HER2-positive cancer cells. Hence, a novel fully afucosylated anti-HER2 bispecific antibody with improved antitumor activities was generated and shown to have the potential to be used for treating HER2-positive but trastuzumab-resistant solid tumors.
The Low Affinity IgE Receptor (CD23) Is Cleaved by the Metalloproteinase ADAM10 (2007)

The low affinity IgE receptor, FcepsilonRII (CD23), is both a positive and negative regulator of IgE synthesis. The proteinase activity that converts the membrane-bound form of CD23 into a soluble species (sCD23) is an important regulator of the function of CD23 and may be an important therapeutic target for the control of allergy and inflammation. We have characterized the catalytic activity of ADAM (a disintegrin and metalloproteinase) 10 toward human CD23. We found that ADAM10 efficiently catalyzes the cleavage of peptides derived from two distinct cleavage sites in the CD23 backbone. Tissue inhibitors of metalloproteinases and a specific prodomain-based inhibitor of ADAM10 perturb the release of endogenously produced CD23 from human leukemia cell lines as well as primary cultures of human B-cells. Expression of a mutant metalloproteinase-deficient construct of ADAM10 partially inhibited the production of sCD23. Similarly, small inhibitory RNA knockdown of ADAM10 partially inhibited CD23 release and resulted in the accumulation of the membrane-bound form of CD23 on the cells. ADAM10 contributes to CD23 shedding and thus could be considered a potential therapeutic target for the treatment of allergic disease.
Neighboring joint density-based JPEG steganalysis (2011)

The threat posed by hackers, spies, terrorists, and criminals, etc. using steganography for stealthy communications and other illegal purposes is a serious concern of cyber security. Several steganographic systems that have been developed and made readily available utilize JPEG images as carriers. Due to the popularity of JPEG images on the Internet, effective steganalysis techniques are called for to counter the threat of JPEG steganography. In this article, we propose a new approach based on feature mining on the discrete cosine transform (DCT) domain and machine learning for steganalysis of JPEG images. First, neighboring joint density features on both intra-block and inter-block are extracted from the DCT coefficient array and the absolute array, respectively; then a support vector machine (SVM) is applied to the features for detection. An evolving neural-fuzzy inference system is employed to predict the hiding amount in JPEG steganograms. We also adopt a feature selection method of support vector machine recursive feature elimination to reduce the number of features. Experimental results show that, in detecting several JPEG-based steganographic systems, our method prominently outperforms the well-known Markov-process based approach.
Prediction of Life-Threatening Arrhythmias – Still an Unresolved Problem (2011)

A major challenge in current cardiology is to predict who will die suddenly from ventricular arrhythmias. Ventricular arrhythmias are the most common cause of sudden cardiac death, occurring in about 1-2:1,000 inhabitants yearly, and is most frequently due to coronary artery disease. Patients with increased risk of ventricular arrhythmias can be offered medical treatment and ultimately an implantable cardioverter defibrillator (ICD). Left ventricular ejection fraction (EF) is currently the main risk stratification tool used to select patients for ICD therapy. However, EF is insufficient in predicting arrhythmic risk. A number of techniques have been presented to improve arrhythmic risk stratification without having reached clinical utility. Conduction abnormalities and dispersion of action potential duration forms the substrate for malignant ventricular arrhythmias in infarcted tissue as in several cardiomyopathies. The ability to assess electrical dispersion in patients noninvasively has been limited. Myocardial strain by echocardiography has been presented as an accurate tool for assessing myocardial function and timing. Inhomogeneous and dispersed myocardial contraction has been related to the occurrence of ventricular arrhythmias and seems to be a promising tool in risk stratification. This review focuses on arrhythmia mechanisms and novel echocardiographic tools for assessing risk of ventricular arrhythmias.
Calix[<i>n</i>]bipyrroles: Synthesis, Characterization, and Anion‐Binding Studies (2003)

Bigger is better: Preliminary anion-binding studies reveal that bipyrrole-containing macrocycle calix[3]bipyrrole 2 binds large halide anions (for example, Br−) with affinities that are substantially enhanced relative to those of the smaller pyrrole-containing calix[4]pyrrole 1. The complexation has been studied by 1H NMR spectroscopy, isothermal titration calorimetry, and X-ray crystallography. In addition, the synthesis of the even larger calix[4]bipyrrole was achieved. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z50941_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mass candidate detection and segmentation in digitized mammograms (2009)

This paper introduces a system for identifying candidate masses in digitized mammograms. Mass identification is a basic component in Computer-Aided Detection (CAD) systems for mammograms. The proposed algorithm is a cascaded filtering process that consists of several stages: First, a new breast fat model is introduced and the fat content in the image is estimated and removed from the image to obtain a fatless image at a standard resolution. Next, a Gabor filter is specially designed and tailored to fit the mass detection problem and then applied to the fatless image. Finally, the resulting image is segmented to obtain iso-contours. Candidate regions are then identified by contour processing and selection. The proposed algorithm obtained 100% sensitivity with 3.4 false positives per image.
A Binuclear Gold(I) Complex with Mixed Bridging Diphosphine and Bis(N‐Heterocyclic Carbene) Ligands Shows Favorable Thiol Reactivity and Inhibits Tumor Growth and Angiogenesis In Vivo (2014)

Abstract In the design of anticancer gold(I) complexes with high in vivo efficacy, tuning the thiol reactivity to achieve stability towards blood thiols yet maintaining the thiol reactivity to target cellular thioredoxin reductase (TrxR) is of pivotal importance. Herein we describe a dinuclear gold(I) complex ( 1 ‐PF 6 ) utilizing a bridging bis(N‐heterocyclic carbene) ligand to attain thiol stability and a diphosphine ligand to keep appropriate thiol reactivity. Complex 1 ‐PF 6 displays a favorable stability that allows it to inhibit TrxR activity without being attacked by blood thiols. In vivo studies reveal that 1 ‐PF 6 significantly inhibits tumor growth in mice bearing HeLa xenograft and mice bearing highly aggressive mouse B16‐F10 melanoma. It inhibits angiogenesis in tumor models and inhibits sphere formation of cancer stem cells in vitro. Toxicology studies indicate that 1 ‐PF 6 does not show systemic anaphylaxis on guinea pigs and localized irritation on rabbits.
Novel Decapeptides that Bind Avidly and Deliver Radioisotope to Colon Cancer Cells (2007)

This experimental approach represents a new example of a strategy, termed peptide binding therapy, for the potential treatment of colorectal and other adenocarcinomas.
Injection of intense pulsed-ion beams into tokamaks with application to plasma heating and current maintenance (1981)

This paper examines various schemes by which an intense pulsed ion beam can be injected into a tokamak. There are several schemes which appear to be viable just as the plasma is being formed, but which cannot work for a steady-state plasma. All schemes considered here use parallel injection. Once the beam is in the plasma, the heating and current maintenance are calculated. It is found that intense pulsed beams with reasonable energy should be capable of heating the plasma to breakeven and ignition.
Development of a Monoclonal Antibody against Ochratoxin A and Its Application in Enzyme-Linked Immunosorbent Assay and Gold Nanoparticle Immunochromatographic Strip (2008)

A monoclonal antibody (mAb) specific to ochratoxin A (OTA) was produced from a stable hybridoma cell line, 9C9H9, generated by the fusion of P3/NS1/1-AG4-1 myeloma cells with spleen cells isolated from a BALB/c mouse immunized with OTA-keyhole limpet hemocyanin. The 9C9H9 mAb belongs to the immunoglobulin G1 (kappa chain) isotype. A competitive direct enzyme-linked immunosorbent assay (cdELISA) and a competitive indirect ELISA were established for antibody characterization. The concentrations causing 50% inhibition of binding of OTA-horseradish peroxidase to the antibody by OTA, OTB, and OTC were found to be 0.32, 0.17, and 0.28 ng/mL, respectively, in the cdELISA. A sensitive and rapid mAb-based gold nanoparticle immunochromatographic strip was also developed using this mAb. This strip has a detection limit of 5 ng/mL for OTA and can be completed in 10 min. Analysis of OTA in coffee samples revealed that data obtained from immunochromatographic strip were in a good agreement with those obtained from cdELISA. The mAb-based cdELISA and immunochromatographic strip assay established in this study were sensitive and accurate for rapid screening of OTA in coffee samples.
Towards an Industrial Strength SQL/XML Infrastructure (2005)

XML has become an attractive data processing model for applications. SQL/XML is a SQL standard that integrates XML with SQL. It introduces the XML datatype as a native SQL datatype and defines XML generation functions in the SQL/XML 2003 standard. The goal for the next version of SQL/XML is integrating XQuery with SQL by supporting XQuery embedded inside SQL functions such as the XMLQuery and XMLTable functions. Starting with the 9i database release, Oracle has supported the XML datatype and various operations on XML instances. In this paper, we present the design and implementation strategies of the SQL/XML standard in Oracle XMLDB. We explore the various critical infrastructures needed in the SQL database kernel to support an efficient native XML datatype implementation and the design approaches for efficient generation, query and update of the XML instances. Furthermore, we also illustrate extensions to SQL/XML that makes Oracle XMLDB a truly industrial strength platform for XML processing.
<title>Innovative algorithm for cast detection</title> (2001)

The paper describes a method for detecting a color cast (i.e. a superimposed dominant color) in a digital image without any a priori knowledge of its semantic content. The color gamut of the image is first mapped in the CIELab color space. The color distribution of the whole image and of the so-called Near Neutral Objects (NNO) is then investigated using statistical tools then, to determine the presence of a cast. The boundaries of the near neutral objects in the color space are set adaptively by the algorithm on the basis of a preliminary analysis of the image color gamut. The method we propose has been tuned and successfully tested on a large data set of images, downloaded from personal web-pages or acquired using various digital and traditional cameras.
An Improved Torque Sharing Function for Torque Ripple Reduction in Switched Reluctance Machines (2018)

An offline torque sharing function (TSF) is introduced in this paper for torque ripple reduction in switched reluctance machines (SRM). This TSF uses static flux linkage characteristics of the machine obtained from finite element analysis or experiments that describe the machine dynamics to determine optimal current profiles such that the torque ripple reduction is achieved with minimal copper losses. Due to this feature, the proposed TSF performs well across a wide speed range. Additionally, the objective function of the proposed TSF uses only one weight parameter, which facilitates the use of this TSF. In this paper, an intuitive justification for the selection of this weight parameter is given, and the performance of this TSF is validated in simulation and experimentally on a 5.2 kW, four phase SRM. To baseline its performance, the proposed TSF has been compared to the offline TSF in the literature, which shows that it has better current tracking performance at higher speeds due to the inclusion of flux linkage characteristics. Finally, it has been compared to conduction angle control at speeds above the base speed to show that it can be a viable alternative for the control of SRM even in an operation region normally not considered for TSF.
Prognostic value of prostate-specific antigen for women with breast cancer: a large United States cohort study. (1998)

Prostate-specific antigen (PSA) is a valuable tumor marker used for diagnosis and management of prostate cancer. Recently, PSA has been found in various female tissues and body fluids. Female breasts, both normal and abnormal, including cancerous tissues, can produce PSA, and this production is regulated by androgens and progestins. Preliminary data suggested that patients with breast tumors positive for PSA may have better prognosis compared to those with PSA-negative breast tumors. This study examines the prognostic value of PSA in a large cohort study of United States patients. Using a PSA assay that has a lower detection limit of 0.001 ng/ml, we measured PSA in tumor cytosolic extracts of 953 women with primary breast cancer. Other information available for this study included age, follow-up time, survival outcome, tumor size, nodal status, steroid hormone receptor levels, DNA analysis by flow cytometry, and postoperative treatment. The median follow-up time was 73 months. During the follow-up, 200 patients relapsed and 188 died. PSA presence was found to be significantly associated with smaller tumors, tumors with low S-phase fraction, diploid tumors, younger patient age, and tumors with lower cellularity. Survival analysis indicated that the relative risks (RRs) for relapse and death were both significantly lower [RR = 0.67 (P = 0.01) for relapse; RR = 0.72 (P = 0.05) for death] in PSA-positive patients (levels higher than the 30th percentile of PSA values) than in PSA-negative patients. The reduced risks for relapse and death remained statistically significant after other clinical and pathological variables were adjusted in the multivariate analysis [RR = 0.68 (P = 0.02) for relapse; RR = 0.65 (P = 0.02) for death]. Our results suggest that the measurement of PSA in breast tumor extracts provides additional information on the prognosis of patients with primary breast cancer.
GNSS-based positioning: Attacks and Countermeasures (2009)

Increasing numbers of mobile computing devices, user-portable, or embedded in vehicles, cargo containers, or the physical space, need to be aware of their location in order to provide a wide range of commercial services. Most often, mobile devices obtain their own location with the help of Global Navigation Satellite Systems (GNSS), integrating, for example, a Global Positioning System (GPS) receiver. Nonetheless, an adversary can compromise location-aware applications by attacking the GNSS-based positioning: It can forge navigation messages and mislead the receiver into calculating a fake location. In this paper, we analyze this vulnerability and propose and evaluate the effectiveness of countermeasures. First, we consider replay attacks, which can be effective even in the presence of future cryptographic GNSS protection mechanisms. Then, we propose and analyze methods that allow GNSS receivers to detect the reception of signals generated by an adversary, and then reject fake locations calculated because of the attack. We consider three diverse defense mechanisms, all based on knowledge, in particular, own location, time, and Doppler shift, receivers can obtain prior to the onset of an attack. We find that inertial mechanisms that estimate location can be defeated relatively easy. This is equally true for the mechanism that relies on clock readings from off-the-shelf devices; as a result, highly stable clocks could be needed. On the other hand, our Doppler Shift Test can be effective without any specialized hardware, and it can be applied to existing devices.
Optimum Topology of Embossed Ribs in Stamped Plates (1998)

Abstract This paper presents a methodology to compute the optimum topology of embossed ribs (also known as beads) in stamped plates. The pattern and orientation of embossed ribs are determined using topology optimization techniques as introduced by Bendsøe and Kikuchi (1988). The particular characteristics of embossed ribs in membrane and pure bending deformations are considered in the analysis model to closely simulate their structural behavior. What makes this approach unique is that the optimum solution is made of two materials, one with orthotopic properties which is optimally distributed within a second material with isotropic properties that model the non-ribbed plate. An example of a vehicle fuel tank is included to illustrate the potential use of this methodology.
Amphiphilic Networks. I. Network Synthesis by Copolymerization of Methacryloyl-Capped Polyisobutylene with 2-(Dimethylamino) Ethyl Methacrylate and Characterization of The Networks (1988)

Abstract New amphiphilic networks have been synthesized by free-radical co-polymerization of hydrophobic methacryloyl-capped polyisobutylenes (MA-PIB-MA) with hydrophilic 2-(dimethylamino)ethyl methacrylate. Two MA-PIB-MAs have been prepared with Mn = 4920 and 10 200, and two series of networks were prepared with MA-PIB-MA contents between 48 and 71.5%. Variation of the molecular weight of MA-PIB-MA and its concentration in the network allows for a wide range of mechanical properties and swellability in hydrophilic and hydrophobic solvents. Differential scanning calorimetry shows the existence of two glass transitions in these networks and thus indicates a phase-separated domain structure. Tensile strengths and elongations were dependent on MA-PIB-MA contents varying from 57.7 to 39.8 kg/cm2 and from 168 to 200%, respectively, with increasing MA-PIB-MA content. Solvent swelling of the networks ranged from 170 to 20% in water and from 40 to 170% in n-heptane with increasing MA-PIB-MA contents.
Flue-Gas Carbon Capture on Carbonaceous Sorbents:  Toward a Low-Cost Multifunctional Carbon Filter for “Green” Energy Producers (2008)

A low-pressure Carbon Filter Process (patent pending) is proposed to capture carbon dioxide (CO2) from flue gas. This filter is filled with a low-cost carbonaceous sorbent, such as activated carbon or charcoal, which has a high affinity (and, hence, high capacity) to CO2 but not to nitrogen (N2). This, in turn, leads to a high CO2/N2 selectivity, especially at low pressures. The Carbon Filter Process proposed in this work can recover at least 90% of flue-gas CO2 of 90%+ purity at a fraction of the cost normally associated with the conventional amine absorption process. The Carbon Filter Process requires neither expensive materials nor flue-gas compression or refrigeration, and it is easy to heat integrate with an existing or grassroots power plant without affecting the cost of the produced electricity too much. An abundant supply of low-cost CO2 from electricity producers is good news for enhanced oil recovery (EOR) and enhanced coal-bed methane recovery (ECBMR) operators, because it will lead to higher oil and gas recovery rates in an environmentally sensitive manner. A CO2-rich mixture that contains some nitrogen is much less expensive to separate from flue-gas than pure CO2; therefore, mixed CO2/N2-EOR and CO2/N2-ECBMR methods are proposed to maximize the overall carbon capture and utilization efficiency.
Pulse-Heat Aerosol Reactor (PHAR): Processing Thermolabile Biomaterials and Biomolecules into Nanoparticles with Controlled Properties (2012)

This work addresses the challenge of processing thermolabile biomaterials and biomolecules into nanoparticles without compromising structural integrity and activity. Control of size, structure, and crystallinity of nanoparticles is desirable for drug targeting and controlled release applications. An innovation using pulse-heat aerosol processing is demonstrated through a design of a pulse-heat aerosol reactor. Nanoparticle aerosol lipid matrices (NALM), of stearic acid, were synthesized under different processing conditions, obtained through pulse heating (fixed duration, three heat-pulse levels) and solvent selection. Operation with continuous heating resulted in ill-conditioned, multimodal size distributions. Pulse heating resulted in the synthesis of NALM with mean mobility diameter in the range of 56-183nm and narrow unimodal size distributions (geometric size distribution, GSD = 1.5-1.7). Under higher pulse levels, particles with larger mean mobility diameter were formed, which had shell-type structures, compared with smaller, solid particles under operation with low level or no heating. NALM with different degree of crystallinity were produced under different processing conditions, at which different drop temperature is expected to result. The activity of glucose oxidase enzyme was preserved, when subjected to high pulse-heat (gas temperature of 110 degrees C) aerosol processing. These results establish pulse-heat aerosol processing as a single-step, continuous method to process heat-sensitive biomaterials and biomolecules into nanoparticles with controlled properties, while avoiding thermal damage. Copyright 2013 American Association for Aerosol Research