gebhart/patrepeval huggingface dataset:
Diffusion and Binding of Monoclonal Antibody TNT-1 in Multicellular Tumor Spheroids (1991)

Tumor spheroids of HT-29 human colon adenocarcinoma and A375 melanoma were established to investigate the uptake and clearance kinetics of TNT-1, a monoclonal antibody that targets necrotic cells of tumors. Our data reveal that there was rapid uptake of TNT-1 and its F(ab')2 fragment in both spheroid models, whereas an antibody of irrelevant specificity, Lym-1, and its F(ab')2 fragment bound poorly to the spheroids. Unlike previously reported monoclonal antibodies to tumor cell-surface antigens, TNT-1 showed 1) a linear uptake that increased over time without saturation in tumor spheroids and 2) an unexpected uptake by a subpopulation of cells in the viable outer rim of the spheroids. These preclinical studies provide important information concerning the therapeutic potential of TNT monoclonal antibodies for the treatment of cancer and micrometastases.
ANALYSIS AND BENCHMARKING OF PENTRAN CODE USING THE OECD-NEA BENCHMARK PROBLEMS (2009)

It is our pleasure to be able to contribute this paper to a special session honoring Dr. Enrico Sartori, whose effort and devotion have resulted in significant international collaborations, enhancement in particle transport methods and various reactor physics problems through benchmarking, and ease of access to latest nuclear data and nuclear codes. In this paper, we overview our past efforts in benchmarking the PENTRAN code using different OECD-NEA benchmark problems. PENTRAN has been benchmarked based on the VENUS-3 critical facility, the Kobayashi benchmark problems, and C7G5 MOX eigenvalue problem. The paper presents the results obtained, and discusses the lessons learned. This paper reviews our efforts in benchmarking the PENTRAN (Parallel Environment Neutralparticle TRANsport) 3-D, Sn parallel code [1, 2] using the OECD-NEA benchmark problems. PENTRAN has been used for solving several real-world problems for different applications; however, in this paper, we will focus on the use of NEA benchmarks to evaluate different features of the PENTRAN code. We will present the results of the VENUS-3 benchmark facility [3], the Kobayashi 3-D void duct benchmark problems [4], and the C5G7 MOX criticality problem [5]. Besides evaluating the accuracy of the results, we will discuss the code performance, specifically in a parallel environment, as well as the impact of its unique features, and any limitations we have observed in solving these problems. . This paper is organized as follows. In Section II, we briefly discuss the important features of PENTRAN. In Section III, we present important features of each problem, and examine PENTRAN’s solution accuracy and parallel performance, and discuss the lessons learned. Section IV concludes this paper. 2. PENTRAN’S UNIQUE FEATURES AND ITS SUPPORTING CODES
<title>Optimum optical and electrical filter characteristics in optically preamplified direct detection (N)RZ receivers</title> (2001)

We give optimum values for the bandwidths of realistic optical and electrical filters (optical Fabry-Perot filters and fiber Bragg gratings, electrical Bessel filters and first order RC low pass filters), as well as for realistic NRZ and (33% duty cycle) RZ input pulses for a free space laser communication system employing an optical booster and a direct detection receiver with optical preamplification. Different extinction ratios, the presence of background radiation, and the influence of the booster amplifier's amplified spontaneous emission (ASE) are emphasized. Our results show that the optimum optical filter bandwidth (both for NRZ and RZ) has to be sought in the range of 1.5 to 3 times the data rate. Using the optimum filter bandwidths, RZ coding yields a sensitivity improvement of up to 1.5 dB compared to NRZ transmission. For typical system parameters and link distances higher than several thousand kilometers the booster ASE becomes less important than strong background radiation, while it causes severe sensitivity degradations for shorter distances.© (2001) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Analysis of Early-Phase Insulin Responses in Nonobese Subjects With Mild Glucose Intolerance (1992)

Impaired early-phase insulin response to glucose was associated with mild glucose intolerance, suggesting the importance of impaired insulin secretion in the development of glucose intolerance in nonobese subjects.
Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations (1994)

Multiple copy sampling and the bond scaling-relaxation technique are combined to generate 3-dimensional conformations of protein loop segments. The computational efficiency and sensitivity to initial loop copy dispersion are analyzed. The multicopy loop modeling method requires approximately 20-50% of the computational time required by the single-copy method for the various protein segments tested. An analytical formula is proposed to estimate the computational gain prior to carrying out a multicopy simulation. When 7-residue loops within flexible proteins are modeled, each multicopy simulation can sample a set of loop conformations with initial dispersions up to +/- 15 degrees for backbone and +/- 30 degrees for side-chain rotatable dihedral angles. The dispersions are larger for shorter and smaller for longer and/or surface loops. The degree of convergence of loop copies during a simulation can be used to complement commonly used target functions (such as potential energy) for distinguishing between native and misfolded conformations. Furthermore, this convergence also reflects the conformational flexibility of the modeled protein segment. Application to simultaneously building all 6 hypervariable loops of an antibody is discussed.
Few-Shot Learning With Embedded Class Models and Shot-Free Meta Training (2019)

We propose a method for learning embeddings for few-shot learning that is suitable for use with any number of shots (shot-free). Rather than fixing the class prototypes to be the Euclidean average of sample embeddings, we allow them to live in a higher-dimensional space (embedded class models) and learn the prototypes along with the model parameters. The class representation function is defined implicitly, which allows us to deal with a variable number of shots per class with a simple constant-size architecture. The class embedding encompasses metric learning, that facilitates adding new classes without crowding the class representation space. Despite being general and not tuned to the benchmark, our approach achieves state-of-the-art performance on the standard few-shot benchmark datasets.
Analysis and measurement of the modulation transfer function of harmonic shear wave induced phase encoding imaging (2013)

B-scan imaging relies on geometric focusing of ultrasound echoes. In contrast, the method of Shear Wave Induced Phase Encoding imaging achieves lateral resolution of an elastic target by using traveling shear waves to encode the position of scatters in the phase of the received echo. A Fourier series description of the phase modulated echo signal is developed, demonstrating that echo harmonics at multiples of the shear wave frequency reveal target k-space data at identical multiples of the shear wavenumber. Modulation transfer functions (MTFs) are calculated for maximum shear wave acceleration and maximum shear constraints, and compared with a conventionally focused aperture. The relative SNR of this method versus a conventionally focused aperture is determined from these MTFs. Reconstructions of wire targets in a gelatin phantom using a cylindrical shear wave source are presented, including Images generated from the fundamental and second harmonic of the shear wave modulation frequency. Comparison of images generated at 1 and 3.5 MHz demonstrate the weak dependence of lateral resolution on ultrasound frequency with this method.
High efficiency blue fluorescent organic light-emitting diodes using a conventional blue fluorescent emitter (2015)

High efficiency blue fluorescent organic light-emitting diodes were developed by using a blue delayed fluorescent emitter as a sensitizer.
Rate of Penetration Prediction in Shale Formation Using Fuzzy Logic (2019)

Abstract Rate of Penetration (ROP) means how fast the drilling bit is drilling through the formations. It is known that in the oil and gas industry, most of the well cost is taken by the drilling operations. So, it is very crucial to drill carefully and improve the drilling processes. Nevertheless, it is hard to know the influence of every single parameter because most of the drilling parameters depend on each other, and altering an individual parameter will have an impact on the other. Due to the difficulty of the drilling operations, up to the present time, there is no dependable model that can estimate the ROP correctly. Consequently, using the artificial intelligence (AI) in the drilling is becoming more and more applicable because it can consider all the unknown parameters in building the model. In this work, a real filed data that contain the real time surface drilling parameters and the drilling fluid properties were utilized by fuzzy logic (FL) to estimate the rate of penetration. The achieved results proved that fuzzy logic technique can be applied effectively to estimate the rate of penetration accurately with R = 0.97 and AAPE = 7.3%, which outperformed the other ROP models. The developed AI models also have the advantage of using less input parameters than the previous ROP models.
Interferon and Ribavirin Combination Treatment Synergistically Inhibit HCV Internal Ribosome Entry Site Mediated Translation at the Level of Polyribosome Formation (2013)

We demonstrated both IFN-α and RBV inhibit HCV IRES through prevention of polyribosome formation. The combination of IFN-α and RBV treatment synergistically inhibits HCV IRES translation via using two different mechanisms involving PKR activation and depletion of intracellular guanosine pool through inhibition of IMPDH.
Supplementary Materials and Methods from Aurora A–Selective Inhibitor LY3295668 Leads to Dominant Mitotic Arrest, Apoptosis in Cancer Cells, and Shows Potent Preclinical Antitumor Efficacy (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
KIR Genetics Modifies Susceptibility to Inflammatory Disorder by Reprogramming Human Natural Killer Cell Function (2012)

Abstract Abstract 3282 Innate lymphocytes can play both protective and pathogenic roles in chronic inflammatory disorders. Recently, killer-cell immunoglobulin-like receptors (KIRs) and its cognitive ligands - human leukocyte antigen (HLA) class I molecules - were identified as genetic risk factors for Crohn's Disease (CD), a common inflammation symptom. Natural killer (NK) cells, the major KIR-expressing cell type, can be educated through KIR-HLA ligation. To uncover the cellular mechanism that determines CD susceptibility, we utilize a novel single-cell functional proteomics microchip and other highly-multiplexed assays (Ma, C. et al. Nature Medicine, 2011, 17, 738–743). We show that, in genetically pertinent individuals, natural killer (NK) cells are functionally reprogrammed to modulate the activation threshold of CD4+ T cells, a major cellular mediator of chronic inflammation. Genetic study of 455 CD patients bearing the AA haplotype identifies that the HLA-C1/C1 allotype, ligand of the KIR2DL3 receptor, is significantly enriched (p&lt;0.0001). Moreover, when evaluating the secretion of 20 cytokines from single purified NK cells that are retrieved from the peripheral blood, we observe that NK cells expressing KIR2DL3 were strongly polarized to robustly produce a myriad of pro-inflammatory cytokines and chemoattractants in copious amounts. Comparing to those from other subjects, NK cells from HLA-C1/C1 subjects produce significantly increased level (p&lt;0.05) of 11 soluble mediators, including TNF, INF-g, ILs, and CCLs. Furthermore, among all NK cells within the HLA-C1/C1 subjects, NK cells expressing KIR2DL3 receptors are the most potent to produce cytokines (2-log higher) and exhibit the highest polyfunctionality. These observations are also confirmed by intracellular staining and ELISA assay of NK cell culture media. Most importantly, the KIR-educated NK cells can strongly augment the activation and proliferation of CD4+ T cells. As shown in autologous NK and CD4+ T cell co-culture assay, CD4+ T cells proliferate aggressively in the presence of NK cells in a dose-dependent fashion (R2=0.99). NK surface costimulatory molecules blockage and NK-CD4+ T cells transwell-separation experiments indicate that this augmentation is not contact-dependent. On the other hand, NK cytokine depletion and ELISA essay of the co-culture media confirmed that soluble factors, such as ILs, IFN-g and TNF, activate CD4+ T cells. KIR2DL3 signaling-mediated education licenses NK cells the capacity to secrete large amounts of pro-inflammatory cytokines and chemokines, which in turn lowers activation threshold of CD4+ T cells and increases susceptibility to chronic inflammation disorders. Our study establishes, for the first time, an immunologic cellular mechanism that explains the KIR genetics-based susceptibility to CD and other chronic inflammatory syndromes. Disclosures: No relevant conflicts of interest to declare.
Supplementary Figure 1 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC (2023)

&lt;p&gt;Supplementary Figure 1 - PDF file 596K, Covalent binding of the EGFR L858R/T790M protein by CO-1686&lt;/p&gt;
PR_b-targeted delivery of tumor necrosis factor-α by polymersomes for the treatment of prostate cancer (2009)

Targeted delivery of therapeutics is an active area of research with cancer being an important target because of the necessity for new and better cancer therapies. In this study we design and assess peptide functionalized polymer vesicles, or polymersomes, self assembled from poly(ethylene oxide)-b-poly(butadiene) (PEO-PBD) diblock copolymers for the treatment of prostate cancer. PR_b, a highly effective α5β1 targeting peptide that mimics the cell adhesion binding site in fibronectin, was recently developed in our group, and is here conjugated onto the surface of our polymer vesicles with controlled orientation, ensuring proper and uniform orientation of the targeting peptide at the interface. Polymer vesicles, although often proposed as highly advantageous drug delivery agents, have so far seen limited use as targeted delivery carriers with this study focusing on targeting the polymer vesicles to prostate cancer cells and delivering a therapeutic payload. PR_b-functionalized polymer vesicles are found to effectively internalize within prostate cancer cells after adhering specifically to α5β1 integrins expressed on the surface of prostate cancer cells. Internalization of polymer vesicles was found to be dependent on the surface concentration of PR_b. In addition polymer vesicles encapsulating a model protein therapeutic, tumor necrosis factor-α (TNFα), were delivered to LNCaP human prostate cancer cellsin vitro. Dramatic improvements in the cytotoxic potential of the delivered TNFα were achieved for PR_b-functionalized polymer vesicles, while polymer vesicles functionalized with the peptide GRGDSP were found to perform no better than non-functionalized polymer vesicles. The potency and specificity of these PR_b-targeted polymersomes show great promise for the targeted delivery of therapeutics.
Supplementary Table S1 from Direct Detection and Quantification of Neoantigens (2023)

&lt;p&gt;Sequences used for plasmid construction.&lt;/p&gt;
Triarylphosphines : Molecular Geometry, Anodic Behavior and ESR Study of the Radical Cations (1993)

Abstract A large series of triarylphosphines has been prepared and their geometry was studied by force field calculations. A very good agreement was found between the calculated and experimental (X Ray) geometries. The oxidation potentials were determined by electrochemical techniques and the corresponding cations were studied by ESR. Both the oxidation potentials and the ESR features were shown to depend strongly on the molecular geometry.
Keratin-14 (KRT14) Positive Leader Cells Mediate Mesothelial Clearance and Invasion by Ovarian Cancer Cells (2019)

Epithelial ovarian cancer metastasis is driven by spheroids, which are heterogeneous cancer cell aggregates released from the primary tumour mass that passively disseminate throughout the peritoneal cavity to promote tumour spread, disease recurrence, and acquired chemoresistance. Despite their clinical importance, the molecular events that control spheroid attachment and invasion into underlying healthy tissues remain poorly understood. We examined a novel in vitro invasion model using imaging mass spectrometry to establish a "snapshot" of the spheroid/mesothelial interface. Amongst numerous adhesion-related proteins, we identified a sub-population of highly motile, invasive cells that expressed the basal epithelial marker KRT14 as an absolute determinant of invasive potential. The loss of KRT14 completely abrogated the invasive capacity, but had no impact on cell viability or proliferation, suggesting an invasion-specific role. Our data demonstrate KRT14 cells as an ovarian cancer "leader cell" phenotype underlying tumor invasion, and suggest their importance as a clinically relevant target in directed anti-tumour therapies.
Feasibility Conditions of Interference Alignment via Two Orthogonal Subcarriers (2013)

Conditions are derived on line-of-sight channels to ensure the feasibility of interference alignment. The conditions involve choosing only the spacing between two subcarriers of an orthogonal frequency division multiplexing (OFDM) scheme. The maximal degrees-of-freedom are achieved and even an upper bound on the sum-rate of interference alignment is approached arbitrarily closely.
Point Mutation Detection by Surface Plasmon Resonance Imaging Coupled with a Temperature Scan Method in a Model System (2008)

The detection of point mutations in genes presents clear biological and medical interest. Various methods have been considered. In this paper, we take advantage of surface plasmon resonance imaging, a technique allowing detection of unlabeled DNA hybridization. Coupled with a temperature scan, this approach allows us to determine the presence of single-point mutations in oligonucleotide samples from the analysis of DNA's melting curves in either the homozygous or heterozygous case. Moreover, these experimental data are confirmed in good agreement with numerical calculations.
Distributed Resource Allocation Based on Queue Balancing in Multihop Cognitive Radio Networks (2011)

Cognitive radio (CR) allows unlicensed users to access the licensed spectrum opportunistically (i.e., when the spectrum is left unused by the licensed users) to enhance the spectrum utilization efficiency. In this paper, the problem of allocating resources (channels and transmission power) in multihop CR networks is modeled as a multicommodity flow problem with the dynamic link capacity resulting from dynamic resource allocation, which is in sharp contrast with existing flow-control approaches that assume fixed link capacity. Based on queue-balancing network flow control that is ideally suited for handling dynamically changing spectrum availability in CR networks, we propose a distributed scheme (installed and operational in each node) for optimal resource allocation without exchanging spectrum dynamics information between remote nodes. Considering the power masks, each node makes resource-allocation decisions based on current or past local information from neighboring nodes to satisfy the throughput requirement of each flow. Parameters of these proposed schemes are configured to maintain the network stability. The performance of the proposed scheme for both asynchronous and synchronous scenarios is analyzed comparatively. Both cases of sufficient and insufficient network capacity are considered.
Thermally stable and efficient polymer solar cells based on a novel donor-acceptor copolymer (2016)

We report high photovoltaic performance of a novel donor-acceptor (D-A) conjugated polymer poly[2,6[4,8-bis(2-ethyl-hexyl)benzo[1,2-b;4,5-b']dithiophene-co-2,5-thiophene-co-4,7[5,6-bis-octyloxy-benzo[1,2,5]thiadiazole]-co-2,5-thiophene] (PBDTTBTZT) in bulk heterojunctions with [6,6]-phenyl-C71-butyric acid methyl ester (PC70BM). A power conversion efficiency (PCE) of more than 7% is obtained for optimized charge-extracting electrodes. Upon application of thermal stress via annealing, a superior thermal stability is demonstrated as compared to poly[N-9″-hepta-decanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT).
Single molecule detection in single living cells (2000)

The ability to detect a single analyte molecule represents the ultimate in sensitivity. Single molecule detection has emerged as a powerful tool to characterize heterogeneous systems, in which traditional bulk sampling methods provide a signal averaged over a large number of analytes. Traditionally, single molecule measurements have required highly controlled experimental conditions using ultrapure solvents to create a minimum level of interference. These constraints have primarily limited this technique to examination of systems in vitro. In this report we present the first instance of real-time single molecule detection in living cells. Our experimental approach allows dynamic monitoring of individual fluorophores in vivo, despite the highly complex cellular environment.
In Vitro Comparison of Prototype Magnetic Tool with Conventional Nitinol Basket for Ureteroscopic Retrieval of Stone Fragments Rendered Paramagnetic with Iron Oxide Microparticles (2012)

The prototype magnetic tool improved the efficiency of retrieving stone particles rendered paramagnetic that were less than 2 mm but showed no advantage for larger fragments. This system has the potential to decrease the number of small retained fragments after ureteroscopic lithotripsy.
A Defective Stimulus-Secretion Coupling Rather Than Glucotoxicity Mediates the Impaired Insulin Secretion in the Mildly Diabetic F1 Hybrids of GK-Wistar Rats (1995)

Adult F1 hybrids of male GK and female Wistar control rats exhibit mild, spontaneous non-insulin-dependent diabetes mellitus characterized by impaired glucose-induced insulin secretion. Using isolated pancreatic islets of hybrid rats, we first studied whether impaired glucose-induced insulin response is present not only in adult but also in neonatal rats. Furthermore, we investigated whether the impaired glucose-induced insulin response can be restored by long-term normalization of glycemia. Both 1-week- and 2- to 3-month-old hybrid rats had similar body weights but increased fed blood glucose levels (P < 0.05) compared with age-matched control rats. At 5.5 mmol/l glucose, insulin release was two- to threefold lower in isolated islets of hybrid than in control rats of both age groups (P < 0.05). At 16.7 mmol/l glucose, insulin secretion from hybrid islets was approximately 25% of that from control islets of both 1-week- and 2- to 3-month-old rats. For the second objective, batches of 250 islets from hybrid or control rats were transplanted under the kidney capsule of athymic, normoglycemic nude mice and maintained there for 4 weeks. Perfusion of kidneys demonstrated that glucose-induced (16.7 mmol/l) insulin secretion was impaired markedly in hybrid grafts compared with that in control grafts (0.66 +/- 0.23 vs. 1.8 +/- 0.38 pmol/20 min; P < 0.01), whereas stimulation by 20 mmol/l arginine resulted in similar insulin responses in both groups. The volumes of the grafted islets were similar in kidneys bearing either control or hybrid islets.(ABSTRACT TRUNCATED AT 250 WORDS)