gebhart/patrepeval huggingface dataset:
Data from A PSMA-Targeting CD3 Bispecific Antibody Induces Antitumor Responses that Are Enhanced by 4-1BB Costimulation (2023)

<div>Abstract<p>Patients with hematologic cancers have improved outcomes after treatment with bispecific antibodies that bind to CD3 on T cells and that redirect T cells toward cancer cells. However, clinical benefit against solid tumors remains to be shown. We made a bispecific antibody that targets both the common prostate tumor–specific antigen PSMA and CD3 (PMSAxCD3) and provide evidence for tumor inhibition in several preclinical solid tumor models. Mice expressing the human extracellular regions of CD3 and PSMA were generated to examine antitumor efficacy in the presence of an intact immune system and PSMA expression in normal tissues. PSMAxCD3 accumulated in PSMA-expressing tissues and tumors as detected by immuno-PET imaging. Although PSMAxCD3 induced T-cell activation and showed antitumor efficacy in mice with low tumor burden, PSMAxCD3 lost efficacy against larger solid tumors, mirroring the difficulty of treating solid tumors in the clinic. Costimulatory receptors can enhance T-cell responses. We show here that costimulation can enhance the antitumor efficacy of PSMAxCD3. In particular, 4-1BB stimulation in combination with PSMAxCD3 enhanced T-cell activation and proliferation, boosted efficacy against larger tumors, and induced T-cell memory, leading to durable antitumor responses. The combination of CD3 bispecific antibodies and anti-4-1BB costimulation represents a therapeutic approach for the treatment of solid tumors.</p></div>
Butylated Hydroxytoluene Inactivated Lipid-Containing Viruses (1975)

Butylated hydroxytoluene (BHT) is widely used as a food preservative for its antioxidizing property. This small, hydrophobic molecule has been found to be a potent inactivator of lipid-containing mammalian and bacterial viruses.
Hierarchical fast mode decision algorithm for intra prediction in HEVC (2015)

This paper proposes a fast intra prediction algorithm for the High Efficiency Video Coding (HEVC). HEVC has 35 modes, such as DC mode, Planar mode, and 33 angular modes for the intra-prediction. To reduce the complexity and to support fast decision for intra prediction, this paper proposes a hierarchical mode decision method (HMD). The proposed HMD mainly focuses on how to reduce the number of prediction modes. The experimental results show that the proposed HMD can reduce the encoding time about 39.17% with little BDBR loss. On average, the proposed HMD can achieve the encoding time saving e about 14.13 ~ 19.37% compared to that of the existing algorithms with slightly increasing 0.01 ~ 0.42% BDBR.
Carbonic anhydrase enzymes regulate mast cell–mediated inflammation (2016)

Type 2 cytokine responses are necessary for the development of protective immunity to helminth parasites but also cause the inflammation associated with allergies and asthma. Recent studies have found that peripheral hematopoietic progenitor cells contribute to type 2 cytokine-mediated inflammation through their enhanced ability to develop into mast cells. In this study, we show that carbonic anhydrase (Car) enzymes are up-regulated in type 2-associated progenitor cells and demonstrate that Car enzyme inhibition is sufficient to prevent mouse mast cell responses and inflammation after Trichinella spiralis infection or the induction of food allergy-like disease. Further, we used CRISPR/Cas9 technology and illustrate that genetically editing Car1 is sufficient to selectively reduce mast cell development. Finally, we demonstrate that Car enzymes can be targeted to prevent human mast cell development. Collectively, these experiments identify a previously unrecognized role for Car enzymes in regulating mast cell lineage commitment and suggest that Car enzyme inhibitors may possess therapeutic potential that can be used to treat mast cell-mediated inflammation.
System Level User Behavior Biometrics using Fisher Features and Gaussian Mixture Models (2013)

We propose a machine learning-based method for biometric identification of user behavior, for the purpose of masquerade and insider threat detection. We designed a sensor that captures system-level events such as process creation, registry key changes, and file system actions. These measurements are used to represent a user's unique behavior profile, and are refined through the process of Fisher feature selection to optimize their discriminative significance. Finally, a Gaussian mixture model is trained for each user using these features. We show that this system achieves promising results for user behavior modeling and identification, and surpasses previous works in this area.
An Automatic, Unstructured Grid-Generation System for Geologically Complex Reservoirs (1995)

Summary This paper presents an automatic, 3D, locally unstructured hybridgrid-generation system for sloping faults. This gridding system replaces a portion of an existing finite-difference grid around sloping faults with a finite-element grid made of tetrahedrons. This innovative approach retains the finite-difference character of the grid and minimizes the decrease in computational efficiency. This paper discusses the details of the gridding techniques used and provides several example grids that demonstrate that locally unstructured grids can accurately represent geologically complex reservoirs.
DEGASSING OF ALUMINUM A356 ALLOY USING ULTRASONIC VIBRATIONS (2007)

In order to investigate the effects of ultrasonic vibration on degassing of aluminum alloys, three experimental systems have been designed and built: one for ultrasonic degassing in open air, one for ultrasonic degassing under reduced pressure, and one for ultrasonic degassing with a purging gas. Experiments were first carried out in air to test degassing using ultrasonic vibration alone. The limitations with ultrasonic degassing were outlined. Further experiments were then performed under reduced pressures and in combination with purging argon gas. Experimental results suggest that ultrasonic vibration alone is efficient for degassing a small volume of melt. Ultrasonic vibration can be used for assisting vacuum degassing, making vacuum degassing much faster than that without using ultrasonic vibration. Ultrasonically assisted argon degassing is the fastest method for degassing among the three methods tested in this research. More importantly, dross formation during ultrasonically assisted argon degassing is much less than that during argon degassing. The mechanisms of ultrasonic degassing are discussed.
AUTOLOGOUS ENGINEERED CARTILAGE RODS FOR PENILE RECONSTRUCTION (1999)

Conditions such as inadequate and ambiguous genitalia that are caused by rudimentary penis, severe hypospadias or traumatic injury require surgical intervention. Although silicone penile prostheses are an accepted treatment modality, biocompatibility issues may be a problem in select cases. We previously demonstrated that rods composed of cartilage could be created using chondrocytes seeded on biodegradable polymer scaffolds. We showed that the cartilage rods engineered ex situ were readily elastic and withstood high degrees of pressure. We investigated the feasibility of applying the engineered cartilage rods in situ in an animal model.Autologous chondrocytes harvested from rabbit ears were grown and expanded in culture. Cells were seeded onto biodegradable poly-L-lactic acid coated polyglycolic acid polymer rods at a concentration of 50 x 10(6) chondrocytes per cm3. A total of 18 chondrocyte polymer scaffolds were implanted into the corporal spaces in 10 rabbits. As controls, 1 corpus in each of 2 rabbits was not implanted. The animals were sacrificed 1, 2, 3 or 6 months after implantation. Histological analysis was performed using hematoxylin and eosin, aldehyde fuschin-alcian blue and toluidine blue staining.All animals tolerated the implants for the duration of the study without any complications. Gross examination after retrieval at 1 month showed well formed, milky white cartilage structures within the corpora. All polymers were fully degraded by 2 months. There was no evidence of erosion or infection at any of the implant sites. Histological analysis using alcian blue and toluidine blue staining revealed mature and well formed chondrocytes in the retrieved implants.Autologous chondrocytes seeded on preformed biodegradable polymer structures form cartilage structures within the rabbit corpus cavernosum. This technology appears to be useful for creating autologous penile prostheses.
Rothmund-Thomson syndrome due toRECQ4 helicase mutations: Report and clinical and molecular comparisons with Bloom syndrome and Werner syndrome (2000)

Rothmund-Thomson syndrome (RTS), an autosomal recessive disorder, comprises poikiloderma, growth deficiency, some aspects of premature aging, and a predisposition to malignancy, especially osteogenic sarcomas. Two kindreds with RTS were recently shown to segregate for mutations in the human RECQL4 helicase gene. We report identification of a new RTS kindred in which both brothers developed osteosarcomas. Mutation analysis of the RECQL4 gene was performed on both brothers and both parents. The brothers were shown to be compound heterozygotes for mutations in the RECQL4 gene, including a single basepair deletion in exon 9 resulting in a frameshift and early termination codon and a base substitution in the 3-prime splice site in the intron-exon boundary of exon 8, which would be predicted to cause a deletion of at least part of a consensus helicase domain. Each parent was shown to be a heterozygote carrier for one mutation. This report strengthens the association between mutations in RECQL4 helicase gene and RTS. Two other recessive disorders, Bloom syndrome and Werner syndrome, are known to be due to other human RECQ helicase gene mutations. These three disorders all manifest abnormal growth, premature aging, and predisposition to site-specific malignancies. The clinical and molecular aspects of RTS, Bloom syndrome, and Werner syndrome are compared and contrasted.
Hydrophobic Variations of <i>N</i>‐Oxide Amphiphiles for Membrane Protein Manipulation: Importance of Non‐hydrocarbon Groups in the Hydrophobic Portion (2013)

Amphipathic agents called detergents serve as membrane-mimetic systems to maintain the native structures of membrane proteins during their manipulation. However, membrane proteins solubilized in conventional detergents tend to undergo denaturation and aggregation, necessitating the development of novel amphipathic agents with enhanced properties. Here we describe several new amphiphiles that contain an N-oxide group as the hydrophilic portion. The new amphiphiles have been evaluated for the ability to solubilize and stabilize a fragile multi-subunit assembly from biological membranes. We found that cholate-based agents were promising in supporting retention of the native protein quaternary structure, while deoxycholate-based amphiphiles were highly efficient in extracting/solubilizing the intact superassembly from the native membrane. Monitoring superassembly solubilization and stabilization as a function of variation in amphiphile structure led us to propose that a non-hydrocarbon moiety such as an amide, ether, or a hydroxy group present in the lipophilic regions can manifest distinctive effects in the context of membrane protein manipulation.
Immunological studies of acetylcholine receptors (1976)

Immunochemical techniques for the study of acetylcholine receptors are described. Immunization of rabbits, rats, guinea pigs, and goats with acetylcholine receptor protein purified from Electrophorus electric organ tissue results in muscular weakness and death due to impaired neuromuscular transmission. Serum from immunized animals contains high concentrations of antibodies directed at receptors from the electric organ and low concentrations of antibodies directed at receptors from skeletal muscle. The detailed similarities between the disease of receptor-immunized animals "experimental autoimmune myasthenia gravis" (EAMG), and myasthenia gravis are compared. Reactions of antisera from animals with EAMG with receptor from Electrophorus and Torpedo are studied. Antireceptor antibodies in these antisera are directed predominantly and determinants other than the acetylcholine-binding site.
Protocol: Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening (2016)

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial immune system CRISPR (clustered regularly interspaced short palindromic repeats) has been adapted for genome-scale screening by combining Cas9 with guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom-or ready-made guide RNA libraries are constructed and packaged into lentivirus for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified from the screen, we further describe strategies for confirming the screening phenotype as well as genetic perturbation through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 6-10 weeks followed by 3-4 weeks of validation.
Beta (β) tungsten thin films: Structure, electron transport, and giant spin Hall effect (2015)

We use a simple magnetron sputtering process to fabricate beta (β) tungsten thin films, which are capable of generating giant spin Hall effect. As-deposited thin films are always in the metastable β-W phase from 3.0 to 26.7 nm. The β-W phase remains intact below a critical thickness of 22.1 nm even after magnetic thermal annealing at 280 °C, which is required to induce perpendicular magnetic anisotropy (PMA) in a layered structure of β-W/Co40Fe40B20/MgO. Intensive annealing transforms the thicker films (&gt;22.1 nm) into the stable α-W phase. We analyze the structure and grain size of both β- and α-W thin films. Electron transport in terms of resistivity and normal Hall effect is studied over a broad temperature range of 10 K to at least 300 K on all samples. Very low switching current densities are achieved in β-W/Co40Fe40B20/MgO with PMA. These basic properties reveal useful behaviors in β-W thin films, making them technologically promising for spintronic magnetic random access memories and spin-logic devices.
Modulation of aromatase expression in the breast tissue by ERR alpha-1 orphan receptor. (1998)

We have previously identified a silencer element (S1) that is situated between promoters I.3 and II of the human aromatase gene and that down-regulates the action of these promoters. We recently applied the yeast one-hybrid approach to screen a human breast tissue hybrid cDNA expression library for genes encoding the proteins binding to the silencer region. Most proteins identified from this approach belong to the nuclear receptor superfamily. Fifty % of the positive clones encode for ERR alpha-1, and other positive clones include EAR-2, EAR-3 (COUP-TF1), RAR gamma, and p120E4F. Because ERR alpha-1 was found to be the major protein interacting with S1, we decided to examine the regulatory action of ERR alpha-1 on promoter I.3 of the human aromatase gene. Using a reporter plasmid that includes the aromatase genomic fragment containing promoter I.3 and S1, ERR alpha-1 was found to have a positive regulatory function in breast cancer SK-BR-3 cells. Gel mobility shift assays have confirmed that ERR alpha-1 binds to S1 in a dose-dependent manner, and DNase I footprinting analysis has revealed that ERR alpha-1 binds to a region, 5'-AAGGTCAGAAAT-3', which is within S1 and between 96 and 107 bp relative to the transcriptional start site of promoter I.3. In addition, despite the fact that the nuclear receptor SF1 was shown previously to bind to the same site and to mediate a cAMP response in ovary, our yeast one-hybrid screening did not find any SF-1 clones. Gel mobility shift assays further revealed that SF-1 can bind to the silencer element with an affinity comparable with ERR alpha-1. Because our reverse transcription-PCR analysis was not able to detect SF1 mRNA in breast cancer tissue or in SK-BR-3 cells, it is thought that SF1 protein is not expressed in breast cancer tissue. Two ERR alpha-1 RNA variants with differences at the 5'-end have been reported. Our reverse transcription-PCR analysis identified the shorter variant in 28 of 32 breast tumor specimens and the longer variant in only 1 specimen. In addition, the shorter variant was detected in breast cancer SK-BR-3 cells as well as in a breast tumor fibroblast line WS3TF. The results suggest that ERR alpha-1 is one of the nuclear proteins interacting with S1 in breast cancer tissue. It is thought that the silencer element in the human aromatase gene may function differently in different tissues because of distinct expression patterns of transcription factors.
Nanoliposome C6‐Ceramide in combination with anti‐CTLA4 antibody improves anti‐tumor immunity in hepatocellular cancer (2022)

Combination therapy represents an effective therapeutic approach to overcome hepatocellular cancer (HCC) resistance to immune checkpoint blockade (ICB). Based upon previous work demonstrating that nanoliposome C6-ceramide (LipC6) not only induces HCC apoptosis but also prevents HCC-induced immune tolerance, we now investigate the potential of LipC6 in combination with ICB in HCC treatment. We generated orthotopic HCC-bearing mice, which have typical features in common with human patients, and then treated them with LipC6 in combination with the antibodies (Abs) for programmed cell death protein 1 (PD-1) or cytotoxic T-lymphocyte antigen 4 (CTLA4). The tumor growth was monitored by magnetic resonance imaging (MRI) and the intrahepatic immune profiles were checked by flow cytometry in response to the treatments. Realtime PCR (qPCR) was used to detect the expression of target genes. The results show that LipC6 in combination with anti-CTLA4 Ab, but not anti-PD-1 Ab, significantly slowed tumor growth, enhanced tumor-infiltrating CD8<sup>+</sup> T cells, and suppressed tumor-resident CD4<sup>+</sup> CD25<sup>+</sup> FoxP3<sup>+</sup> Tregs. Further molecular investigation indicates that the combinational treatment suppressed transcriptional factor Krüppel-like Factor 2 (KLF2), forkhead box protein P3 (FoxP3), and CTLA4. Our studies suggest that LipC6 in combination with anti-CTLA4 Ab represents a novel therapeutic approach with significant potential in activating anti-HCC immune response and suppressing HCC growth.
Comparison of Yield and Composition of Oil Extracted from Corn Fiber and Corn Bran (1999)

ABSTRACT We recently reported that corn fiber oil contains high levels of three potential cholesterol‐lowering phytosterol components: ferulate‐phytosterol esters (FPE) (3–6 wt%), free phytosterols (1–2 wt%), and phytosterol‐fatty acyl esters (7–9 wt%). A previous study also indicated that corn bran oil contained less phytosterol components than corn fiber oil. The current study was undertaken to attempt to confirm this preliminary observation using more defined conditions. Accordingly, oil was extracted from corn fiber and corn bran prepared under controlled laboratory conditions, using the same sample of corn hybrid kernels for each, and using recognized bench‐scale wet‐milling, and dry‐milling procedures, respectively. After extraction, the chemical composition of the phytosterol components in the oil were measured. This study confirmed our previous observation—that FPE levels were higher in corn fiber oil than in corn bran oil. During industrial wet‐milling, almost all of the FPE are recovered in the fiber fraction (which contains both fine and coarse fiber). During laboratory‐scale wet‐milling, ≈60–70% of the FPE are recovered in the coarse fiber (pericarp) and 30–40% are recovered in the fine fiber. During laboratory‐scale dry‐milling, <20% of the FPE are recovered in the bran (pericarp), and the rest in the grits. The recoveries of the other two phytosterol components (free phytosterols and phytosterol‐fatty acyl esters) revealed a more complex distribution, with significant levels found in several of the dry‐ and wet‐milled products.
Visible Continuum Generation Using a Femtosecond Erbium-Doped Fiber Laser and a Hybrid HNLF-PCF Nonlinear Fiber (2008)

Visible supercontinuum in the fundamental mode is generated in a silica hybrid nonlinear fiber using a femtosecond, erbium-doped fiber laser pump. The nonlinear fiber consists of highly nonlinear, germano-silicate fiber (HNLF) fusion spliced to a photonic crystal fiber (PCF).
(Pentamethylcyclopentadienyl)ruthenium π‐Complexes of Metalloporphyrins: Platforms with Novel Photo‐ and Electrochemical Properties (2008)

Unusually accepting: A series of metalloporphyrin–ruthenocene complexes, synthesized by direct coordination of a [Ru(Cp*)]+ fragment to the π-electron “face” of several metallooctaethylporphyrins (see graphic), undergo efficient photoinduced electron transfer from the ruthenocene unit (acting as the electron donor) to the singlet excited state of the metalloporphyrin unit (acting as the electron acceptor) to give a charge-separated state.
Smart play-out (2003)

We describe "smart play-out", a new method for executing and analyzing scenario based behavior, which is part of the Play-In/Play-Out methodology and the Play-Engine tool. Behavior is "played in" directly from the system's GUI, and as this is being done the Play-Engine continuously constructs Live Sequence Charts (LSCs), a powerful extension of sequence diagrams. Later, behavior can be "played out" freely from the GUI, and the tool executes the LSCs directly, thus driving the system's behavior. An inherent difficulty in constructing a ``play-out" mechanism is how to resolve the nondeterminism allowed by the LSC specification in order to obtain an executable model. Smart play-out, is a recent strengthening of the play-out mechanism, which addresses this problem by using powerful verification methods, mainly model-checking, to execute and analyze the LSCs, helping the execution to avoid deadlocks and violations. Thus, smart play-out utilizes verification techniques to run programs, rather than to verify a program with respect to given requirements, as in traditional verification approaches. The ideas appear to be relevant in various stages of system development, including requirements specification and analysis, implementation and testing.
A Thermally Actuated Microelectromechanical (MEMS) Device For Measuring Viscosity (2011)

A thermally actuated non-cantilever-beam microelectromechanical viscosity sensor is presented. The proposed device is based on thermally induced vibrations of a simple silicon diaphragm and its damping due to the surrounding fluid. This vibration viscometer device utilizes thermal actuation through an in situ resistive heater and piezoresistive sensing, both of which utilize CMOS compatible materials leading to an inexpensive and reliable system. Thermal analysis was performed utilizing temperature diodes in the silicon diaphragm to determine the minimum heater voltage pulse amplitude and time in order to prevent heat loss to the oil under test that would lead to local viscosity changes. Viscosity measurements were performed and compared to motor oil measured on a commercial cone-and-plate viscometer. <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hfill$</tex></formula> [2010-0130]