gebhart/patrepeval huggingface dataset:
Identification of a T-Cell Receptor from a Therapeutic Murine T-Cell Clone (1997)

Tumor-infiltrating lymphocytes (TIL) have been successfully used for the treatment of metastatic malignancies in clinical trials and in experimental animal models. Tumor-specific reactivity by TIL is mediated via receptors expressed on the surface of T cells (TcRs), which recognize tumor-associated antigens (TAA) presented in the context of MHC molecules on the surface of tumor cells. The current study was performed to identify the TcR alpha and beta chains from a tumor-specific therapeutic TIL clone that can be used to develop a preclinical animal model for genetically modifying lymphocytes and hematopoietic progenitors with TcR genes. TIL 205 was generated from a subcutaneous implant of MCA-205 fibrosarcoma and at 21 days was cloned by limiting dilution. TIL clone 8, obtained from a culture seeded at one cell/well, mediated specific lysis and specific secretion of gamma-interferon to MCA-205 and WP6, a subclone of MCA 205. No reactivity was observed against other syngeneic sarcoma lines. Anchor polymerase chain reaction analysis determined that antigen recognition by clone 8 was mediated by a TcR consisting of V alpha 3/J alpha 27 and V beta 8.2/D beta 2.1/D beta 2.4. Immunofluorescent staining with V beta subfamily specific monoclonal antibodies revealed that > 95% of the T cells in TIL clone 8 expressed V beta 8.2, confirming that TIL clone 8 was indeed a clone. In contrast, approximately 30% of the T cells in the parental TIL 205 expressed V beta 8.2. The transfer of as few as 500,000 TIL clone 8 cells in conjunction with the systemic administration of recombinant human interleukin-2 mediated regression of established 3-day WP6 lung metastases. Thus, clone 8 recognizes a biologically relevant tumor rejection antigen, making the V alpha 3/J alpha 27-V beta 8.2/D beta 2.1/J beta 2.4 TcR isolated from this clone useful as a probe for cloning the tumor-rejection antigen in the WP6 tumor as well as modeling, in mice, the TcR-based gene therapies being developed for humans.
Production and Level of Genetic Stability of an Influenza A Virus Temperature-Sensitive Mutant Containing Two Genes with <i>ts</i> Mutations (1982)

Temperature-sensitive (ts) reassortant vaccine strains derived from the A/Udorn/72 ts-1A2 donor virus were not sufficiently stable genetically in humans. We therefore sought to produce a new, more stable donor virus. We had previously identified a stable ts virus with a ts P3 gene and in the current study identified another relatively stable single-lesion ts virus with a ts mutation in the NP gene. A new ts reassortant virus was constructed by mating these two single mutants and by isolating three reassortant progeny, clones 20, 53, and 55, that contained both a ts P3 and a ts NP gene. These reassortant progeny possessed a 37 to 38 degrees C shutoff temperature and were as restricted in their replication in hamster lungs as the A/Udorn/72 ts-1A2 virus. All isolates from the lungs and nasal turbinates of hamsters were temperature sensitive. An in vitro stress test was used to determine whether the new ts P3 ts NP reassortant virus would undergo loss of its ts phenotype after replication at semipermissive temperature. Clone 20 and 55 reassortants underwent progressive loss of their ts phenotype in vitro, although at a rate slightly less than that of the A/Udorn/72 ts-1A2 virus. The level of genetic stability after replication in vivo was assessed in cyclophosphamide-treated hamsters in which virus replication continued for up to 15 days. Again, both the A/Udorn/72 ts-1A2 and the new ts P3 ts NP reassortant clone 55 manifested a progressive loss of temperature sensitivity after 7 days of replication. Clone 55 virus lost temperature sensitivity significantly less rapidly than the A/Udorn/72 ts-1A2 virus. These results indicated that, although the new ts P3 ts NP reassortant virus was more stable than the A/Udorn/72 ts-1A2 virus, it nevertheless underwent progressive loss of temperature sensitivity after replication in vitro and in vivo. Therefore, it does not appear to be a satisfactory donor virus. This experience plus that gained earlier with other ts mutants of influenza A virus suggest that influenza A virus mutants that rely solely upon their ts phenotype for attenuation are unlikely to exhibit the phenotypic stability required of a vaccine virus. Other genetic techniques are needed to produce more stable influenza A virus strains.
A multi-beam x-ray imaging system based on carbon nanotube field emitters (2006)

In this study, we report a multi-beam x-ray imaging system that can generate a scanning x-ray beam to image an object from multiple projection angles without mechanical motion. The key part of this imaging system is a multi-beam field emission x-ray (MBFEX) source which comprises a linear array of gated electron emitting pixels. The pixels are individually addressable via a MOSFET (metal-oxide-semiconductor field effect transistor) based electronic circuit. The device can provide a tube current of 0.1-1 mA at 40 kVp with less than 300 μm focal spot size from each of the emitting pixels. Multilayer images of different phantoms were reconstructed to demonstrate its potential applications in tomographic imaging. Since no mechanical motion is needed and the electronic switching time is generally negligible the MBFEX system has the potential to simplify the system design and lead to a fast data acquisition for tomographic imaging.
Agents-supported adaptive group awareness: smart distance and WWWaware (2001)

We study how agents can facilitate and mediate interaction, communication, and cooperation among people. We propose the concepts of a smart distance and an awareness network in a distributed collaborative environment. We illustrate the architecture of an agent-mediated collaborative system - the agent-buddy system that can create a sense of group presence and, at the same time, preserve the privacy of each user. Virtual springs systems are used to model the awareness degrees among team members. Each agent makes decisions by considering multiple factors. The goal of the multi-agent team is to minimize the global awareness frustrations with respect to different kinds of tasks. Empirical studies were conducted to analyze the influence of individual behavior on global performance for various kinds of tasks.
Cell-Based Approach for Treatment of Corneal Endothelial Dysfunction (2014)

Decompensation of the corneal endothelium causes severe visual impairments that lead to blindness. Although corneal transplantation is a well-known effective therapy for corneal endothelial dysfunction, many patients are not afforded that therapeutic opportunity owing to the worldwide shortage of donor corneas. Thus, a tissue engineering-based therapy for treating corneal endothelial dysfunction is highly anticipated. Obstacles associated with the development of tissue engineering therapy include in vitro culture of corneal endothelial cells (CECs) and the techniques used to transplant those cells. Limited proliferation ability, cellular senescence, and fibroblastic transformation during culture are all problems associated with the cultivation of CECs. In addition, transplantation of cultured CECs is technically difficult because the corneal endothelium is composed of a fragile monolayer sheet of cells located at the posterior cornea. In this review article, we present our recent findings using a novel cell culture protocol and show that modulation of CEC adhesion properties through a Rho-kinase inhibitor enables transplantation of CECs in the form of a cell suspension without the use of a carrier. Finally, we provide an update on the clinical application status of a cell-based therapy for treating corneal endothelial dysfunction.
Recovery of silica from aqueous silicate solutions via trialkyl or tetraalkylammonium silicomolybdate (1991)

Reaction of aqueous silicate with ammonium molybdate at pH 1.5 affords the β form of silicomolybdic acid. The latter can be precipitated by the addition of a variety of quaternary ammonium salts. The precipitated silicomolybdate can then be decomposed to silica in a two-step combustion process (at 350 and 1000 °C). Recoveries of Si are nearly complete, but the starting silicate solution must be made strongly basic prior to the reaction with molybdate. The overall process can be utilized for the recovery of silicon isotopes and as a method of silica purification. Key words: silica, silicate, silicomolybdate, silicon-29.
Efficient and sustained gene expression in primary T lymphocytes and primary and cultured tumor cells mediated by adeno-associated virus plasmid DNA complexed to cationic liposomes. (1994)

We have used cationic liposomes to facilitate adeno-associated virus (AAV) plasmid transfections of primary and cultured cell types. AAV plasmid DNA complexed with liposomes showed levels of expression several fold higher than those of complexes with standard plasmids. In addition, long-term expression (> 30 days) of the gene, unlike the transient expression demonstrated by typical liposome-mediated transfection with standard plasmids, was observed. Southern analysis of chromosomal DNA further substantiated the hypothesis that the long-term expression was due to the presence of the transgene in the AAV plasmid-transfected group and not in the standard plasmid-transfected group. AAV plasmid-liposome complexes induced levels of transgene expression comparable to those obtained by recombinant AAV transduction. Primary breast, ovarian, and lung tumor cells were transfectable with the AAV plasmid DNA-liposome complexes. Transfected primary and cultured tumor cells were able to express transgene product even after lethal irradiation. High-level gene expression was also observed in freshly isolated CD3+, CD4+, and CD8+ T cells from normal human peripheral blood. Transfection efficiency ranged from 10 to 50% as assessed by intracellular interleukin-2 levels in interleukin-2-transfected cells. The ability to express transgenes in primary tumor and lymphoid cells may be applied toward tumor vaccine studies and protocols which may eventually permit highly specific modulation of the cellular immune response in cancer and AIDS.
A high-performance liquid chromatography based strategy for rapid, sensitive sequencing ofN-linked oligosaccharide modifications to proteins in sodium dodecyl sulphate polyacrylamide electrophoresis gel bands (2001)

The majority of biologically active proteins are glycosylated, therefore any approach to proteomics which fails to address the analysis of oligosaccharides is necessarily incomplete. To appreciate the structure of a glycoprotein fully, to understand the roles for the attached oligosaccharides and to monitor disease associated changes it is necessary to visualise the sugars as well as the protein. To achieve this aim when biological samples are available at the low microgram level or less has involved increasing the sensitivity of the technology for glycan analysis. Since one protein may have many different oligosaccharides attached to it (glycoforms) this is a major technical challenge. CD59, for example, has over 100 different sugars at one N-linked glycosylation site. Applications of recently developed technology suggest that it is now becoming realistic to extend the proteomics analysis of glycoproteins to include details of glycosylation. This is achieved by releasing the N-glycans from the protein in a gel by optimised peptide-N-glycosidase F digestion. The released glycans are then tagged with the fluorophore, 2-amino benzamide. The labelled glycan pools (containing 50-100 femtomoles of glycans) are resolved by predictive normal phase high performance liquid chromatography (HPLC) on an amide based column or by reverse phase HPLC on a C18 column. Preliminary structural assignments are confirmed by exoglycosidase array digestions of the entire glycan pool. Complementary matrix-assisted laser desorption/ionization-mass spectrometry, which requires 10-20 times as much sugar for a single run, can be used where there is sufficient material. This provides a composition analysis but not linkage information.
Conception and fabrication of piezo-resistive ring-shaped AFM probes (2012)

A new concept of Atomic Force Microscope (AFM) oscillating probes using electrostatic excitation and piezoresistive detection is presented. The probe is characterized by electrical methods in vacuum chamber and by mechanical methods in air. The frequency-mixing measurement technique is developed to reduce the parasitic signal level. These probes resonance frequencies are in the 1MHz range and the quality factor is measured about 53,000 in vacuum and 3,000 in air. The force resolution deduced from the measurements is about 8 pN/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sup> .
Quantitative Model-Based Image Analysis of NuMa Distribution Links Nuclear Organization with Cell Phenotype (2001)

Abstract The extracellular matrix (ECM) plays a critical role in directing cell behaviour and morphogenesis by regulating gene expression and nuclear organization. Using non-malignant (S1) human mammary epithelial cells (HMECs), it was previously shown that ECM-induced morphogenesis is accompanied by the redistribution of nuclear mitotic apparatus (NuMA) protein from a diffuse pattern in proliferating cells, to a multi-focal pattern as HMECs growth arrested and completed morphogenesis. A process taking 10 to 14 days. To further investigate the link between NuMA distribution and the growth stage of HMECs, we have investigated the distribution of NuMA in non-malignant S1 cells and their malignant, T4, counter-part using a novel model-based image analysis technique. This technique, based on a multi-scale Gaussian blur analysis (Figure 1), quantifies the size of punctate features in an image. Cells were cultured in the presence and absence of a reconstituted basement membrane (rBM) and imaged in 3D using confocal microscopy, for fluorescently labeled monoclonal antibodies to NuMA (fαNuMA) and fluorescently labeled total DNA.
&#x201C;Cancer Antigen WT1 Protein-Derived Peptide&#x201D;-Based Treatment of Cancer -Toward the Further Development (2008)

Cancer immunotherapy targeting tumor-associated antigens is now being developed. Wilms' tumor gene WT1-encoding protein is one of the promising target antigens for cancer immunotherapy, because the gene has an oncogenic function and is expressed in many kinds of malignancies. Furthermore, a series of investigations indicated that WT1 protein was highly immunogenic in cancer patients. Based on the analysis of anchor residues that were important for the interaction between peptides and HLA class I molecules, WT1 cytotoxic T lymphocyte (CTL) epitopes with the restriction of HLA-A 0201 and HLA-A 2402 were identified, and clinical trials of WT1 peptide vaccination for cancer patients with these HLA class I types were started. The vaccination-driven immunological and/or clinical responses were reported in patients with myeloid malignancies, multiple myeloma, and several solid cancers. Pediatric malignancies also may be target diseases for WT1 peptide vaccination in the future. Addition of HLA class II-restricted WT1 helper epitope peptide, chemotherapy, or molecular-target-based drug to WT1 CTL epitope peptide-based vaccination may enhance the power and usefulness of WT1 peptide vaccine. Other modalities, including gene therapy using genes encoding WT1-specific T cell receptor or DNA vaccination, are also expected to be developed.
Scene Graph Generation with External Knowledge and Image Reconstruction (2019)

Scene graph generation has received growing attention with the advancements in image understanding tasks such as object detection, attributes and relationship prediction,~\etc. However, existing datasets are biased in terms of object and relationship labels, or often come with noisy and missing annotations, which makes the development of a reliable scene graph prediction model very challenging. In this paper, we propose a novel scene graph generation algorithm with external knowledge and image reconstruction loss to overcome these dataset issues. In particular, we extract commonsense knowledge from the external knowledge base to refine object and phrase features for improving generalizability in scene graph generation. To address the bias of noisy object annotations, we introduce an auxiliary image reconstruction path to regularize the scene graph generation network. Extensive experiments show that our framework can generate better scene graphs, achieving the state-of-the-art performance on two benchmark datasets: Visual Relationship Detection and Visual Genome datasets.
Gabor Difference Analysis of Digital Video Quality (2004)

The rapid increase in the development of digital video systems has generated a strong need for objective video quality metrics. Two methods are presented in this work. One is the Gabor difference analysis (GDA) full reference method, and the other is the reverse frame prediction (RFP) no reference video quality method. Both methods are based on the multi-channel properties of the human visual system (HVS). Gabor filtering is used in both methods. In the GDA method, a reference and a degraded digital video sequence are compared by taking into account various psycho-perceptual properties of the HVS. The RFP method does not require a reference video stream and is intended for in-service testing and on-line monitoring. The performances of the proposed methods are evaluated. The methods in this work are shown to be consistent with the data from subjective testing over a wide range of scenes. This work is critical to the evaluation of the effectiveness of compression schemes on HDTV imagery.
Plane magnetic recording medium (1982)

A plane magnetic recording medium comprises a data track traced by a magnetic head wherein said data track is initiallized to have each width smaller than a width of the trace of the magnetic head whereby modulation in its reproducing output can be minimized.
Module packaging for high-speed serial and parallel transmission (2002)

This paper discusses module packaging aspects with regard to high-speed data transmission for both single channel serial and multi channel parallel transmission. The increasing demand for bandwidth and data throughput of opto-electronic modules leads to continuously changing design rules for these modules. These rules are now completely different compared to those of the time of 100 Mbit/s transmission with light emitting diodes. More specifically, one of the key parameters or figure of merit in today's system design is the data throughput per board edge of the printed circuit boards of the corresponding electronic systems, e.g. switches, routers, clustered computers etc. This has a twofold effect on the module design and the module packaging: firstly, the transmission speed of the module has to be continuously increased, and secondly, the size of the module has to be shrunk. The first requirement leads directly to challenges with electromagnetic interference due to the bandwidth increase, the second to challenges in connector technology, precision of fabrication techniques, and, most severe, to challenges in heat dissipation as now at least the same number of watts of power has to be dissipated in a smaller volume. Both requirements together, of course, multiply the requirements on module packaging. In this paper comparisons of pin through hole, lead frame and ball grid array packages are given. Examples like a 2.5 Gbit/s Small Form Factor serial transceiver, a 2.5 Gbit/s OC48 transceiver with parallel electrical connections, first results of a 10 Gbit/s transceiver with opto-electronic components in a TO package, and 12/spl times/2.5 GBd parallel optical transmitter and receiver (Paroli) are presented. Requirements given by standard assembly techniques like pick-and-place ability and reflow solderability are discussed.
Low-cost detection of lasers (2017)

A low-cost method of detecting lasers based on detecting coherence properties of received light is presented. The method uses an unbalanced Mach–Zehnder interferometer with a modulating piezo-mounted mirror in one arm to discriminate against incoherent background light and identify the presence of laser radiation at the nW level against much brighter backgrounds. The wavelength of the coherent input can be determined by comparing the intensities of the modulation frequency harmonics.
3D Framework DNA Origami with Layered Crossovers (2016)

Designer DNA architectures with nanoscale geometric controls provide a programmable molecular toolbox for engineering complex nanodevices. Scaffolded DNA origami has dramatically improved our ability to design and construct DNA nanostructures with finite size and spatial addressability. Here we report a novel design strategy to engineer multilayered wireframe DNA structures by introducing crossover pairs that connect neighboring layers of DNA double helices. These layered crossovers (LX) allow the scaffold or helper strands to travel through different layers and can control the relative orientation of DNA helices in neighboring layers. Using this design strategy, we successfully constructed four versions of two-layer parallelogram structures with well-defined interlayer angles, a three-layer structure with triangular cavities, and a 9- and 15-layer square lattices. This strategy provides a general route to engineer 3D framework DNA nanostructures with controlled cavities and opportunities to design host-guest networks analogs to those produced with metal organic frameworks.
Fiber Raman Amplification Soliton Laser (FRASL) (1986)

We have demonstrated the first Fiber Raman Amplification Soliton Laser (FRASL) by synchronously pumping a loop of fiber with ≈10 psec pulses from a modelocked color center laser. The FRASL output pulses are determined by pulse compression and soliton pulse shaping in the fiber, and have to date been as short as 240 fsec. The lasing wavelength can be time dispersion tuned [1] . The single cavity FRASL is a much simpler configuration than the color center soliton laser [2] , which consists of two coupled cavities and requires feedback stabilization to overcome interferometric instabilities.
Application of Classical Gel Electrophoresis to the Chiral Separation of Milligram Quantities of Terbutaline (1998)

Although the last couple of decades has been tremendous progress in the ability to do chiral separations, the ability to do larger scale chiral separations has lagged somewhat behind the current analytical chiral separation state of the art. The potential of classical gel electrophoresis for chiral separation of milligram quantities of chiral material is examined. A protocol for the chiral separation of milligram quantities of terbutaline using sulfated cyclodextrin as a chiral additive is demonstrated. The possible advantages of the approach are discussed.