gebhart/patrepeval huggingface dataset:
Re‐engineering the Immune Response to Metastatic Cancer: Antibody‐Recruiting Small Molecules Targeting the Urokinase Receptor (2016)

Abstract Developing selective strategies to treat metastatic cancers remains a significant challenge. Herein, we report the first antibody‐recruiting small molecule (ARM) that is capable of recognizing the urokinase‐type plasminogen activator receptor (uPAR), a uniquely overexpressed cancer cell‐surface marker, and facilitating the immune‐mediated destruction of cancer cells. A co‐crystal structure of the ARM‐U2/uPAR complex was obtained, representing the first crystal structure of uPAR complexed with a non‐peptide ligand. Finally, we demonstrated that ARM‐U2 substantially suppresses tumor growth in vivo with no evidence of weight loss, unlike the standard‐of‐care agent doxorubicin. This work underscores the promise of antibody‐recruiting molecules as immunotherapeutics for treating cancer.
Effect of Hardness and Thickness of Nonoriented Electrical Steel Sheets on Iron Loss Deterioration by Shearing Process (2015)

The influence of the shearing process on the iron loss of nonoriented electrical steels with the thickness of 0.20-0.50 mm and the hardness of HV150-220 was investigated. The deterioration ratio of iron loss was clearly smaller in thinner or harder samples. The deterioration of iron loss and the droop height, reflecting the amount of plastic deformation, displayed a good relationship irrespective of the material thickness and the hardness. This is a well-known statement that an elastic stress affects losses of steel sheets. The effective plastic strain distribution through the thickness of the sheet calculated by the elastic-plastic analysis based on the finite-element method (FEM) coincided with the actual measurement result of hardness increase, reflecting the distribution of plastic deformation. From the evaluation of elastic-plastic deformation by the FEM, it was also shown that the material thickness and hardness influence the elastic strain distribution as a plastic strain, and that the droop height reflects both the amount of plastic strain and the amount of elastic strain.
System and device technologies for coherent optical communications (2018)

We review the recent advancement in the system and device technologies for coherent optical communications. One major topic is high-dimensional modulation, and in particular the nonlinearity-tolerant modulation format family, based on four-dimensional 2A8PSK. This family, covering 5, 6, 7 bits/4D symbol, outperforms most known corresponding modulation formats in the linear and nonlinear region. We also review our recent progress on forward error correction including polar codes, and monolithic narrow linewidth semiconductor lasers.
Lasing in alkali atoms pumped by the dissociation of alkali-rare gas exciplexes (excimers) (2009)

Lasing on the 6<sup>2</sup>P<sub>1/2</sub>→6<sup>2</sup>S<sub>1/2</sub>(D1) resonance transition of atomic Cs at 894.3 nm has been demonstrated in mixtures of Ar, ethane, and Cs vapor by the photoexcitation of ground state Cs-Ar collision pairs and subsequent dissociation of diatomic, electronically-excited CsAr molecules (exciplexes or excimers). The blue satellites of the alkali D<sub>2</sub> lines provide a pathway for optically pumping atomic alkali lasers on the principal series (resonance) transitions with broad linewidth (>2 nm) semiconductor diode lasers. In this paper we discuss different variations of this new laser system and the experiments of the initial demonstration.
Purification and composition of the human tumor-associated glycoprotein (TAG-72) defined by monoclonal antibodies CC49 and B72.3. (1988)

Human mammary and other carcinoma cells secrete and express on their cell surfaces complex, mucin-like glycoproteins (Mr greater than 10(6] that are recognized as tumor-associated antigens by a variety of monoclonal antibodies (MAbs). One such MAb, B72.3, has been extensively studied as to range of reactivity for a variety of carcinomas versus normal tissues. The B72.3-reactive antigen, designated tumor-associated glycoprotein (TAG)-72, which is a high-molecular-weight mucin, was partially purified and used as immunogen to produce second generation anti-TAG-72 MAbs. One of these second generation MAbs, CC49, was chosen to be used to develop a procedure to yield preparative amounts of purified antigen suitable for analyzing amino acid sequence. One of the reasons for the selection of CC49 for these studies is that it demonstrated a higher Ka for TAG-72 compared with B72.3. Xenografts of LS174T cells (a human colon carcinoma cell line) grown in nude mice were solubilized, extracted with several chaotropic agents and treated with perchloric acid. The acid soluble antigen was subjected to MAb CC49 affinity chromatography, gel filtration, and ion-exchange chromatography using fast protein liquid chromatography and high-performance liquid chromatography methodologies. A double-determinant liquid competition radioimmunoassay for TAG-72 showed greater than a 1000-fold purification. Radiolabeled protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated an apparently homogeneous high molecular weight mucin and a small amount of an additional protein with an apparent Mr of 63,000. Chemical deglycosylation using trifluoromethanesulfonic acid yielded low molecular weight proteins, which could be analyzed for amino acid sequence, and also became susceptible to tryptic digestion. The amino acid composition of the purified TAG-72 mucin was similar to that of other purified mucins.
Decoupling of Multiple Antennas in Terminals With Chassis Excitation Using Polarization Diversity, Angle Diversity and Current Control (2012)

Excitation of the chassis enables single-antenna terminals to achieve good bandwidth and radiation performance, due to the entire chassis being utilized as the main radiator. In contrast, the same chassis excitation phenomenon complicates the design of multiple antennas for MIMO applications, since the same characteristic mode of the chassis may be effectively excited by more than one antenna, leading to strong mutual coupling and severe MIMO performance degradation. In this paper, we introduce a design concept for MIMO antennas to mitigate the chassis-induced mutual coupling, which is especially relevant for frequency bands below 1 GHz. We illustrate the design concept on a dual-antenna terminal at 0.93 GHz, where a folded monopole at one chassis edge excites the chassis' fundamental electric dipole mode and a coupled loop at the other chassis edge excites its own fundamental magnetic dipole mode. Since the two radiation modes are nearly orthogonal to each other, an isolation of over 30 dB is achieved. Moreover, we show that the antenna system can be conveniently modified for multiband operation, such as in the 900/1800/2600 MHz bands. Furthermore, by controlling the phase of the feed current on the folded monopole, the two antennas can be co-located on the same chassis edge with an isolation of over 20 dB. The co-located dual-antenna prototype was fabricated and verified in the measurements.
A Novel Heterocyclic Magenta Dye-forming Coupler for Color Photographic Use:Synthesis of 1H-Pyrazolo(1,5-b)(1,2,4)triazole. (1991)

1, 2, 4] triazole (1) is a novel 5, 5 fused ring system with a bridgehead nitrogen atom and a new type of magenta dye-forming coupler skeleton for color photographic use. The synthesis of 1 was achieved by two methods (A and B) In the method A, the 5, 5 fused ring was constructed by the reaction between an acid anhydride and a N-aminotriazolium compound ( 5 ) which was prepared by N-amination of 4-benzyl-3, 5-dimethyltriazole ( 4 ). The reaction of 5 with various acid anhydrides was studied to clarify the cyclization mechanism. In the method B, the 5, 5 fused ring was constructed by the dehydrating N-N bond formation of amidoximes ( The method B was applied to manufacturing magenta dye-forming couplers practically used in color photographs. This paper describes these synthetic methods in detail.
Microbending Fiber Optic Sensors For Smart Structures (1990)

Fiber optic smart structures can be used to perform a variety of functions ranging from monitoring the manufacturing process, performing nondestructive evaluation of components once the parts have been made, providing means to implement vehicle health monitoring and maintenance systems, and enabling systems such as actively damped structures and performance monitoring of aircraft engines. This paper describes a low cost approach to mirobending sensing and its application to feasibility studies for manufacturing and health maintenance.
Discovery and Validation of a Six-Marker Serum Protein Signature for the Diagnosis of Active Pulmonary Tuberculosis (2017)

New non-sputum biomarker tests for active tuberculosis (TB) diagnostics are of the highest priority for global TB control. We performed in-depth proteomic analysis using the 4,000-plex SOMAscan assay on 1,470 serum samples from seven countries where TB is endemic. All samples were from patients with symptoms and signs suggestive of active pulmonary TB that were systematically confirmed or ruled out for TB by culture and clinical follow-up. HIV coinfection was present in 34% of samples, and 25% were sputum smear negative. Serum protein biomarkers were identified by stability selection using L1-regularized logistic regression and by Kolmogorov-Smirnov (KS) statistics. A naive Bayes classifier using six host response markers (HR6 model), including SYWC, kallistatin, complement C9, gelsolin, testican-2, and aldolase C, performed well in a training set (area under the sensitivity-specificity curve [AUC] of 0.94) and in a blinded verification set (AUC of 0.92) to distinguish TB and non-TB samples. Differential expression was also highly significant (<i>P</i> < 10<sup>-20</sup>) for previously described TB markers, such as IP-10, LBP, FCG3B, and TSP4, and for many novel proteins not previously associated with TB. Proteins with the largest median fold changes were SAA (serum amyloid protein A), NPS-PLA2 (secreted phospholipase A2), and CA6 (carbonic anhydrase 6). Target product profiles (TPPs) for a non-sputum biomarker test to diagnose active TB for treatment initiation (TPP#1) and for a community-based triage or referral test (TPP#2) have been published by the WHO. With 90% sensitivity and 80% specificity, the HR6 model fell short of TPP#1 but reached TPP#2 performance criteria. In conclusion, we identified and validated a six-marker signature for active TB that warrants diagnostic development on a patient-near platform.
Digital tomosynthesis mammography: comparison of mass classification using 3D slices and 2D projection views (2008)

We are developing computer-aided diagnosis (CADx) methods for classification of masses on digital breast tomosynthesis mammograms (DBTs). A DBT data set containing 107 masses (56 malignant and 51 benign) collected at the Massachusetts General Hospital was used. The DBTs were obtained with a GE prototype system which acquired 11 projection views (PVs) over a 50-degree arc. We reconstructed the DBTs at 1-mm slice interval using a simultaneous algebraic reconstruction technique. The regions of interest (ROIs) containing the masses in the DBT volume and the corresponding ROIs on the PVs were identified. The mass on each slice or each PV was segmented by an active contour model. Spiculation measures, texture features, and morphological features were extracted from the segmented mass. Four feature spaces were formed: (1) features from the central DBT slice, (2) average features from 5 DBT slices centered at the central slice, (3) features from the central PV, and (4) average features from all 11 PVs. In each feature space, a linear discriminant analysis classifier with stepwise feature selection was trained and tested using a two loop leave-one-case-out procedure. The test Az of 0.91±0.03 from the 5-DBT-slice feature space was significantly (p=0.003) higher than that of 0.84±0.04 from the 1-DBT-slice feature space. The test Az of 0.83±0.04 from the 11-PV feature space was not significantly different (p=0.18) from that of 0.79±0.04 from the 1-PV feature space. The classification accuracy in the 5-DBT-slice feature space was significantly better (p=0.006) than that in the 11-PV feature space. The results demonstrate that the features of breast lesions extracted from the DBT slices may provide higher classification accuracy than those from the PV images.
Antiobesity Efficacy of a Novel Cannabinoid-1 Receptor Inverse Agonist, N-((1S,2S)-3-(4-Chlorophenyl)-2- (3-cyanophenyl)-1-methylpropyl)-2-methyl-2-{(5- (2007)

The cannabinoid-1 receptor (CB1R) has been implicated in the control of energy balance. To explore the pharmacological utility of CB1R inhibition for the treatment of obesity, we evaluated the efficacy of N-[(1S,2S)-3-(4-chlorophenyl)-2-(3cyanophenyl)-1-methylpropyl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide (MK-0364) and determined the relationship between efficacy and brain CB1R occupancy in rodents. MK-0364 was shown to be a highly potent CB1R inverse agonist that inhibited the binding and functional activity of various agonists with a binding Ki of 0.13 nM for the human CB1R in vitro. MK-0364 dose-dependently inhibited food intake and weight gain, with an acute minimum effective dose of 1 mg/kg in diet-induced obese (DIO) rats. CB1R mechanism-based effect was demonstrated for MK-0364 by its lack of efficacy in CB1R-deficient mice. Chronic treatment of DIO rats with MK-0364 dose-dependently led to significant weight loss with a minimum effective dose of 0.3 mg/kg (p.o.), or a plasma Cmax of 87 nM. Weight loss was accompanied by the loss of fat mass. Partial occupancy (30–40%) of brain CB1R by MK-0364 was sufficient to reduce body weight. The magnitude of weight loss was correlated with brain CB1R occupancy. The partial receptor occupancy requirement for efficacy was also consistent with the reduced food intake of the heterozygous mice carrying one disrupted allele of CB1R gene compared with the wild-type mice. These studies demonstrated that MK-0364 is a highly potent and selective CB1R inverse agonist and that it is orally active in rodent models of obesity.
Heap data allocation to scratch-pad memory in embedded systems (2005)

This paper presents the first-ever compile-time method for allocating a portion of the heap data to scratch-pad memory. A scratch-pad is a fast directly addressed compiler-managed SRAM memory that replaces the hardware-managed cache. It is motivated by its better real-time guarantees vs cache and by its significantly lower overheads in access time, energy consumption, area and overall runtime. Existing compiler methods for allocating data to scratch-pad are able to place only global and stack data in scratch-pad memory; heap data is allocated entirely in DRAM, resulting in poor performance. Runtime methods based on software caching can place heap data in scratch-pad, but because of their high overheads from software address translation, they have not been successful, especially for heap data. In this paper we present a dynamic yet compiler-directed allocation method for heap data that for the first time, (i) is able to place a portion of the heap data in scratch-pad; (ii) has no software-caching tags; (iii) requires no run-time per-access extra address translation; and (iv) is able to move heap data back and forth between scratch-pad and DRAM to better track the program's locality characteristics. With our method, global, stack and heap variables can share the same scratch-pad. When compared to placing all heap variables in DRAM and only global and stack data in scratch-pad, our results show that our method reduces the average runtime of our benchmarks by 34.6%, and the average power consumption by 39.9%, for the same size of scratch-pad fixed at 5% of total data size.
ChemInform Abstract: A NEW, EFFECTIVE CATALYTIC SYSTEM FOR EPOXIDATION OF OLEFINS BY HYDROGEN PEROXIDE UNDER PHASE‐TRANSFER CONDITIONS (1984)

Abstract In Gegenwart von Phasentransfer‐Katalysatoren (II) erhält man aus Olefinen wie (I) mit Wasserstoffperoxid, Wolframat und Phosphat Epoxide wie (III).
Comparison of type 2 and type 6 fimbriae of Bordetella pertussis by using agglutinating monoclonal antibodies (1988)

Two types of fimbriae have been identified on the pathogenic gram-negative organism Bordetella pertussis. Monoclonal antibodies to these fimbriae were produced to better understand the role of fimbriae as serotype-specific agglutinogens and to investigate the antigenic relationship between these fimbriae. Three monoclonal antibodies were identified that specifically agglutinated B. pertussis cells containing the U.S. Reference Factor 2 agglutinogen, and six monoclonal antibodies were produced that agglutinated only those strains containing the U.S. Reference Factor 6 agglutinogen. Indirect immunofluorescence studies and immunogold electron microscopy demonstrated that these monoclonal antibodies bind to an outer membrane component on serotype-specific strains of B. pertussis. All of the monoclonal antibodies reacted with native or partially assembled type-specific fimbriae but not with monomeric fimbrial subunits as indicated by Western blot (immunoblot) analysis. The fimbrial agglutinogens recognized by the monoclonal antibodies were also uniquely reactive with either U.S. Reference Factor 2 or 6 antiserum (Eldering agglutinogen 2 or 6 polyclonal antiserum) in an indirect ELISA. No cross-reactivity of the monoclonal antibodies with the unrelated fimbriae was observed in any of the comparative immunological studies. Some of the monoclonal antibodies agglutinated certain strains of B. bronchiseptica, suggesting that this closely related species can contain antigenically similar fimbriae. These monoclonal antibodies should prove useful for further structural and functional analysis of Bordetella fimbriae and for studies on the role that these antigens play in prevention of infection and disease.
Enhanced Ridge Preservation by Bone Mineral Bound With Collagen‐Binding Synthetic Oligopeptide: A Clinical and Histologic Study in Humans (2010)

The ridge-preservation approach using synthetic oligopeptide-coated bone mineral with collagen membrane effectively prevented the resorption of hard tissue with higher bone-to-graft contact, and the oligopeptide-coated bone may be a choice for ridge-preservation procedures while assuring new bone formation.
Intelligent Diagnosis and Learning in Centrifugal Pumps (2006)

This paper addresses the problem of on-line diagnosis of cavitation in centrifugal pumps. The paper introduces an application of the Open Prediction System (OPS) to cavitation diagnosis. The application of OPS results in an algorithmic framework for diagnosis of cavitation in centrifugal pumps. The diagnosis is based on repeated evaluation of a data scan providing full record of input signals which are observed for a fixed short period of time. Experimental verification of the algorithmic framework and the proposed methodology proved that a condition monitoring system built upon them is capable of diagnosing a wide range of cavitation conditions that can occur in a centrifugal pump, including the very early incipient cavitation.
Biological monitoring of exposure to botulinum neurotoxins (2008)

Biological monitoring is an important method of assessing human exposure to toxic chemicals and biological toxins. To provide a means of assessing exposure, we have developed methods to measure protein toxins in human clinical samples. These methods include the Endopep-MS method, which can detect and differentiate botulinum neurotoxins (BoNTs) in food and clinical samples. The Endopep-MS method has three levels of selectivity that include extracting the toxin with high-affinity antibodies that are selective for only one of the BoNT serotypes; cleavage of synthetic peptides according to the specific enzymatic activity for each of the BoNT serotypes; and selectively detecting the toxin-dependent peptides by using high resolution matrix-assisted laser-desorption ionization time-of-flight mass spectrometry. The Endopep-MS method is specific for detecting each of the BoNT serotypes. Since botulism in humans is generally caused by BoNT A, B, E, or F, these serotypes are the focus of this report. The method is very sensitive, detecting less than 0.5 mouse LD50 of BoNT A in serum and 0.1 mouse LD50 of BoNT B, E, and F in human serum samples. The method has been applied to selected food matrices and serum and stool samples from individuals diagnosed with botulism.
Feasibility of centralized PON monitoring using PON-tuned OTDR (2012)

The increasing deployment of passive optical networks (PON) implies in an equally increasing need for automatic monitoring systems. Cost-effective solutions employing an optical time domain reflectometry (OTDR) system in the optical line terminal (OLT) have already been proposed, and “PON-tuned” OTDRs are already commercially available. Despite the claims from manufacturers and previous proposals in the literature, precise and reliable fault detection and localization are still unsolved problems for the telecom operators. In this paper, we evaluate the feasibility of obtaining reliable information on fault position and loss by direct inspection of the OTDR trace and via measurements of end-fiber reflectivity devices. Detailed calculations considering usually neglected parameters such as non-uniformity of splitters, fiber bending losses as well as different Rayleigh backscattering factors and fiber attenuation coefficients will be provided and experimentally verified. The limits and reliability of automated solutions for OTDR PON monitoring will be discussed.
Measurement of gluconeogenesis and pyruvate recycling in the rat liver: a simple analysis of glucose and glutamate isotopomers during metabolism of [1,2,3‐<sup>13</sup>C<sub>3</sub>]propionate (1997)

Simple equations that relate glucose and glutamate 13C-NMR multiplet areas to gluconeogenesis and pyruvate recycling during metabolism of [1,2,3-(13)C3]propionate are presented. In isolated rat livers, gluconeogenic flux was 1.2 times TCA cycle flux and about 40% of the oxaloacetate pool underwent recycling to pyruvate prior to formation of glucose. The 13C spectra of glucose collected from rats after gastric versus intravenous administration of [1,2,3-(13)C3]propionate indicated that pyruvate recycling was slightly higher in vivo (49%) while glucose production was unchanged. This indicates that a direct measure of gluconeogenesis and pyruvate recycling may be obtained from a single 13C-NMR spectrum of blood collected after oral administration of enriched propionate.
Strontium nitrate suppresses chemically‐induced sensory irritation in humans (2000)

Skin care products are complex formulations that may cause sensory irritation symptoms, characterized by stinging, burning, and itching. Substances capable of counteracting sensory irritation are of great practical interest. Strontium salts have been demonstrated to inhibit sensory irritation and inflammation when applied topically. In this double-blind study, we evaluated the efficacy of strontium nitrate in reducing chemically-induced skin sensory irritation in 8 subjects. In a random order, 20% strontium nitrate in 70% glycolic acid (pH=0.6) (mixture) was applied to the volar aspect of the forearm and a positive control (70% glycolic acid, pH=0.6) to the contralateral forearm. The irritation sensation was evaluated each min for the first 20 min after topical application using a scale from 0-4. The duration of the irritation sensation in min was also recorded. Strontium nitrate mixed with glycolic acid, in comparison with glycolic acid alone, markedly (p<0.01) shortened the duration of the irritation sensation from 24.4+/-4.1 (mean+/-SEM) min to 8.9+/-3.7 (mean+/-SEM) min, and significantly (p<0.05) reduced the mean magnitude of the irritation sensation at all time points (overall). The study demonstrated that strontium nitrate potently suppresses the sensation of chemically-induced irritation.