gebhart/patrepeval huggingface dataset:
Redirecting T Cells to Ewing's Sarcoma Family of Tumors by a Chimeric NKG2D Receptor Expressed by Lentiviral Transduction or mRNA Transfection (2012)

We explored the possibility to target Ewing's sarcoma family of tumors (ESFT) by redirecting T cells. To this aim, we considered NKG2D-ligands (NKG2D-Ls) as possible target antigens. Detailed analysis of the expression of MICA, MICB, ULBP-1, -2, and -3 in fourteen ESFT cell lines revealed consistent expression of at least one NKG2D-L. Thus, for redirecting T cells, we fused a CD3ζ/CD28-derived signaling domain to the ectodomain of NKG2D, however, opposite transmembrane orientation of this signaling domain and NKG2D required inverse orientation fusion of either of them. We hypothesized that the particularly located C-terminus of the NKG2D ectodomain should allow reengineering of the membrane anchoring from a native N-terminal to an artificial C-terminal linkage. Indeed, the resulting chimeric NKG2D receptor (chNKG2D) was functional and efficiently mediated ESFT cell death triggered by activated T cells. Notably, ESFT cells with even low NKG2D-L expression were killed by CD8(pos) and also CD4(pos) cells. Both, mRNA transfection and lentiviral transduction resulted in high level surface expression of chNKG2D. However, upon target-cell recognition receptor surface levels were maintained by tranfected RNA only during the first couple of hours after transfection. Later, target-cell contact resulted in strong and irreversible receptor down-modulation, whereas lentivirally mediated expression of chNKG2D remained constant under these conditions. Together, our study defines NKG2D-Ls as targets for a CAR-mediated T cell based immunotherapy of ESFT. A comparison of two different methods of gene transfer reveals strong differences in the susceptibility to ligand-induced receptor down-modulation with possible implications for the applicability of RNA transfection.
Digital transcriptome profiling from attomole-level RNA samples (2010)

Accurate profiling of minute quantities of RNA in a global manner can enable key advances in many scientific and clinical disciplines. Here, we present low-quantity RNA sequencing (LQ-RNAseq), a high-throughput sequencing-based technique allowing whole transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3' polyA tailing of the single-stranded cDNA products and direct single molecule sequencing. We applied LQ-RNAseq to profile S. cerevisiae polyA+ transcripts, demonstrate the reproducibility of the approach across different sample preparations and independent instrument runs, and establish the absolute quantitative power of this method through comparisons with other reported transcript profiling techniques and through utilization of RNA spike-in experiments. We demonstrate the practical application of this approach to define the transcriptional landscape of mouse embryonic and induced pluripotent stem cells, observing transcriptional differences, including over 100 genes exhibiting differential expression between these otherwise very similar stem cell populations. This amplification-independent technology, which utilizes small quantities of nucleic acid and provides quantitative measurements of cellular transcripts, enables global gene expression measurements from minute amounts of materials and offers broad utility in both basic research and translational biology for characterization of rare cells.
The NIST quantitative infrared database (1999)

With the recent developments in Fourier transform infrared (FTIR) spectrometers it is becoming more feasible to place these instruments in field environments. As a result, there has been enormous increase in the use of FTIR techniques for a variety of qualitative and quantitative chemical measurements. These methods offer the possibility of fully automated real-time quantitation of many analytes; therefore FTIR has great potential as an analytical tool. Recently, the U.S. Environmental Protection Agency (U.S.EPA) has developed protocol methods for emissions monitoring using both extractive and open-path FTIR measurements. Depending upon the analyte, the experimental conditions and the analyte matrix, approximately 100 of the hazardous air pollutants (HAPs) listed in the 1990 U.S.EPA Clean Air Act amendment (CAAA) can be measured. The National Institute of Standards and Technology (NIST) has initiated a program to provide quality-assured infrared absorption coefficient data based on NIST prepared primary gas standards. Currently, absorption coefficient data has been acquired for approximately 20 of the HAPs. For each com-pound, the absorption coefficient spectrum was calculated using nine transmittance spectra at 0.12 cm -1 resolution and the Beer's law relationship. The uncertainties in the absorption coefficient data were estimated from the linear regressions of the transmittance data and considerations of other error sources such as the nonlinear detector response. For absorption coefficient values greater than 1 10 -4 mol/mol) -1 m -1 the average relative expanded uncertainty is 2.2 %. This quantitative infrared database is currently an ongoing project at NIST. Additional spectra will be added to the database as they are acquired. Our current plans include continued data acquisition of the compounds listed in the CAAA, as well as the compounds that contribute to global warming and ozone depletion.
Overcoming an Untrusted Computing Base: Detecting and Removing Malicious Hardware Automatically (2010)

The computer systems security arms race between attackers and defenders has largely taken place in the domain of software systems, but as hardware complexity and design processes have evolved, novel and potent hardware-based security threats are now possible. This paper presents a hybrid hardware/software approach to defending against malicious hardware. We propose BlueChip, a defensive strategy that has both a design-time component and a runtime component. During the design verification phase, BlueChip invokes a new technique, unused circuit identification (UCI), to identify suspicious circuitry-those circuits not used or otherwise activated by any of the design verification tests. BlueChip removes the suspicious circuitry and replaces it with exception generation hardware. The exception handler software is responsible for providing forward progress by emulating the effect of the exception generating instruction in software, effectively providing a detour around suspicious hardware. In our experiments, BlueChip is able to prevent all hardware attacks we evaluate while incurring a small runtime overhead.
Treatment with HMGB1 inhibitors diminishes CTL-induced liver disease in HBV transgenic mice (2006)

Using hepatitis B virus (HBV) transgenic mice as recipients of virus-specific cytotoxic T lymphocytes (CTLs), we recently showed that polymorphonuclear neutrophils (PMNs) and the matrix-degrading metalloproteinases (MMPs) they produce are necessary for the intrahepatic recruitment of antigen nonspecific mononuclear cells that amplify the liver damage initiated by the CTLs. We now report that the high-mobility group box 1 protein (HMGB1) is also involved in this process. Transfer of CTLs in HBV transgenic mice induces the translocation of HMGB1 from the nucleus to the cytoplasm of hepatocytes surrounding CTL-containing necroinflammatory liver foci, without significant net synthesis of HMGB1. Treatment of CTL-injected HBV transgenic mice with either recombinant Box-A or glycyrrhizin, two functional inhibitors of extracellular HMGB1, significantly decreases the intrahepatic recruitment of PMNs and all other inflammatory cells, in the face of intact homing of virus-specific CTLs into the liver. The inhibition of PMN chemoattraction explains the mode of action of glycyrrhizin, which has long been used in Japan for the treatment of hepatitis, and suggests that new and more potent inhibitors of HMGB1 may be useful for the treatment of patients chronically infected with HBV.
Applying Genomic and Proteomic Microarray Technology in Drug Discovery (2013)

Microarrays play an increasingly significant role in drug discovery. The commercial landscape has changed dramatically over the past few years and researchers have made great advancements with regard to construction and use. Now in its second edition, Applying Genomic and Proteomic Microarray Technology in Drug Discovery highlights, describes, and
The RING finger/B-Box factor TAM-1 and a retinoblastoma-like protein LIN-35 modulate context-dependent gene silencing in Caenorhabditis elegans (1999)

Context-dependent gene silencing is used by many organisms to stably modulate gene activity for large chromosomal regions. We have used tandem array transgenes as a model substrate in a screen for Caenorhabditis elegans mutants that affect context-dependent gene silencing in somatic tissues. This screen yielded multiple alleles of a previously uncharacterized gene, designated tam-1 (for tandem-array-modifier). Loss-of-function mutations in tam-1 led to a dramatic reduction in the activity of numerous highly repeated transgenes. These effects were apparently context dependent, as nonrepetitive transgenes retained activity in a tam-1 mutant background. In addition to the dramatic alterations in transgene activity, tam-1 mutants showed modest alterations in expression of a subset of endogenous cellular genes. These effects include genetic interactions that place tam-1 into a group called the class B synMuv genes (for a Synthetic Multivulva phenotype); this family plays a negative role in the regulation of RAS pathway activity in C. elegans. Loss-of-function mutants in other members of the class-B synMuv family, including lin-35, which encodes a protein similar to the tumor suppressor Rb, exhibit a hypersilencing in somatic transgenes similar to that of tam-1 mutants. Molecular analysis reveals that tam-1 encodes a broadly expressed nuclear protein with RING finger and B-box motifs.
HIV-1 fusion peptide targets the TCR and inhibits antigen-specific T cell activation (2005)

The fusion peptide (FP) in the N terminus of the HIV envelope glycoprotein, gp41, functions together with other gp41 domains to fuse the virion with the host cell membrane. We now report that FP colocalizes with CD4 and TCR molecules, coprecipitates with the TCR, and inhibits antigen-specific T cell proliferation and proinflammatory cytokine secretion in vitro. These effects are specific: T cell activation by PMA/ionomycin or mitogenic antibodies is not affected by FPs, and FPs do not interfere with antigen-presenting cell function. In vivo, FPs inhibit the activation of arthritogenic T cells in the autoimmune disease model of adjuvant arthritis and reduce the disease-associated IFN-gamma response. Hence, FPs might play 2 roles in HIV infection: mediating membrane fusion while downregulating T cell responses to itself that could block infection. Disassociated from HIV, however, the FP molecule provides a novel reagent for downregulating undesirable immune responses, exemplified here by adjuvant arthritis.
Subpicosecond Electrooptic Sampling (1993)

The electro-optic sampling system developed under AFOSR contract no. F49620-85-0016 has been the workhorse for high speed measurements made in this lab. This report documents the continuing effort to improve this tool and highlights its most recent uses. In addition, we report the development of a time-lens, a new tool that gives us electronic control of the shape of optical pulses. The development of a time-lens has opened tip a new field of research. It is a tool to electronically control the temporal characteristics of optical pulses just like glass lenses control the spatial characteristics. Our results to date include the creation of 7 ps pulses from a CW laser, active focusing (compression) of 55 ps pulses down to 2 ps, and demonstration of the time- reversal properties of time-lenses. A Ph.D. thesis detailing the Stanford time- lens and pulse compression experiments is included as an appendix. Electro-optic sampling, Time-lens, Erbium doped fiber amplifiers
Achieving sufficient spectral bandwidth for volumetric 1H echo‐planar spectroscopic imaging at 4 Tesla (2005)

Complete coverage of the in vivo proton metabolite spectrum, including downfield resonances, requires a spectral bandwidth of approximately 9 ppm. Spectral bandwidth of in vivo echo-planar spectroscopic imaging (EPSI) is primarily limited by gradient strength of the oscillating readout gradient, gradient slew rate, and limits on peripheral nerve stimulation for human subjects. Furthermore, conventional EPSI reconstruction, which utilizes even and odd readout echoes separately, makes use of only half the spectral bandwidth. In order to regain full spectral bandwidth in EPSI, it has previously been suggested to apply an interlaced Fourier transform (iFT), which uses even and odd echoes simultaneously. However, this method has not been thoroughly analyzed regarding its usefulness for in vivo 3D EPSI. In this Note, limitations of the iFT method are discussed and an alternative, cyclic spectral unwrapping, is proposed, which is based on prior knowledge of typical in vivo spectral patterns.
Severe deficiency of switched memory B cells (CD27+IgM−IgD−) in subgroups of patients with common variable immunodeficiency: a new approach to classify a heterogeneous disease (2002)

Hypogammaglobulinemia is the hallmark of common variable immunodeficiency (CVID) syndrome, a heterogeneous disorder predisposing patients to recurrent bacterial infections. In this study, we investigated the peripheral B-cell compartment of 30 well-characterized CVID patients in comparison to 22 healthy controls. Flow cytometric analysis of peripheral blood lymphocytes revealed a reduction of class-switched CD27(+)IgM(-)IgD(-) memory B cells below 0.4% in 77% of our patients (group I), while this B-cell subpopulation exceeded 0.5% in all healthy donors and in 23% of CVID patients (group II). These results correlate well with the capacity of peripheral blood lymphocytes to produce immunoglobulins in vitro upon stimulation with Staphylococcus aureus Cowan I (SAC) plus interleukin-2 because the production of immunoglobulin G in vitro is entirely dependent on the presence of switched memory B cells. The subdivision of group I into patients with an increased proportion of CD21(-) peripheral B cells (> 20%; group Ia) and patients with normal percentages of CD21(-) B cells (< 20%; group Ib) revealed a significant clustering of patients with splenomegaly and autoimmune cytopenias in group Ia. Based on these observations, we propose a fast and reliable new classification for CVID patients by flow cytometric quantification of class-switched memory and immature B cells in the peripheral blood of patients. Our results point toward defects at various stages of B-cell differentiation in CVID subgroups and support the value of a B-cell-oriented classification principle. A consensus on this new classification system will hopefully provide a tool for rapidly defining homogeneous subgroups of CVID for functional studies and genetic linkage analysis.
Targeting the Androgen Receptor in Prostate Cancer — A Resilient Foe (2014)

Personalizing the use of cancer therapeutics is a major focus of current biomedical research. The pioneering work of Huggins and colleagues more than 70 years ago foreshadowed the modern era of precision medicine by treating advanced prostate cancers with approaches designed specifically to impair androgen-receptor signaling.1 The androgen receptor regulates critical cellular growth and survival programs in neoplastic prostate cells (Figure 1) and consequently represents a unique treatment-defining feature of prostate cancer. Reports of dramatic remissions in clinical symptoms resulting from this targeted therapy transformed medical practice conceptually and practically, and today strategies that impair androgen-receptor activity by lowering levels . . .
Salicylic Acid Activates Sigma Factor B by rsbU -Dependent and -Independent Mechanisms (2006)

Salicylic acid (SAL) may impact Staphylococcus aureus virulence by activating the sigB operon (rsbU-V-W-sigB), thus leading to reductions in alpha-toxin production and decreased fibronectin binding (L. I. Kupferwasser et al., J. Clin. Investig. 112:222-233, 2003). As these prior studies were performed in strain RN6390 (an rsbU mutant) and its rsbU-repaired variant, SH1000, the current investigation was designed to determine if the SAL effect occurs via rsbU- and/or rsbV-dependent pathways in an rsbU-intact S. aureus strain (FDA486). We thus quantified the transcription from two sigB-dependent promoters (asp23 and sarA P3) in FDA486 in response to SAL exposure in vitro, using isogenic single-knockout constructs of rsbU, rsbV, or rsbW and a green fluorescent protein reporter system. SAL induced sarA P3 and asp23 promoter activities in a dose-dependent manner in the parental strain. In contrast, sigB activation by SAL was progressively more mitigated in the rsbU and rsbV mutants. As predicted, SAL caused significant reductions in both alpha-toxin production and fibrinogen and fibronectin binding in the parental strain. The extent of these reductions, compared with the parent, was reduced in the rsb mutants (rsbV > rsbU), especially at low SAL concentrations. Since generation of the free SigB protein usually requires a sequential rsbU-V-W-sigB activation cascade, the present phenotypic and genotypic data suggest key roles for both rsbU and rsbV in SAL-mediated activation of sigB in strains with a fully intact sigB operon.
Interleukin-4-dependent proliferation dissociates p44erk-1, p42erk-2, and p21ras activation from cell growth. (1994)

The activation of erk/mitogen-activated protein kinases and p21ras is strongly associated with progression through the cell cycle. Cell growth induced by the cytokine interleukin-4 (IL-4) effectively dissociates the activation of p44erk-1 and p42erk-2 mitogen-activated protein kinases and p21ras from cell proliferation. In two cell lines of T lymphocyte and myeloid origin that were dependent upon IL-4 for continuous growth, IL-4 failed to detectably activate or induce tyrosine phosphorylation of p44erk-1 and p42erk-2. The activation of p21ras was also not detectably affected by IL-4 treatment of these cells. Treatment of the same cells with other growth factors (colony-stimulating factor-1 and Steel factor) or phorbol esters induced the tyrosine phosphorylation and activation of p44erk-1 and p42erk-2 and stimulated p21ras activity. The presence of IL-4 neither diminished nor enhanced the activation of p44erk-1 and p42erk-2 by colony-stimulating factor-1, Steel factor, or 12-O-tetradecanoylphorbol-13-acetate. Furthermore, IL-4 also failed to activate p44erk-1, p42erk-2, and p21ras in normal T lymphocytes and mast cells derived from spleen and bone marrow, respectively. Significantly, these findings demonstrate that IL-4-induced cell growth may be dissociated from the activation of p44erk-1, p42erk-2, and p21ras, suggesting that their activation may not be an absolute requirement for growth factor-stimulated mitogenesis.
Accelerator Mass Spectrometry for Measurement of Long-Lived Radioisotopes (1987)

Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes (10)Be, (14)C,(26)A1, 36Cl, and (129)1 can now be measured in small natural samples having isotopic abundances in the range 10(-12) to 10(- 5) and as few as 10(5) atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of halflives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.
Scalable I/O architecture for buses (2003)

The author discusses current IEEE activities on the P1394 bus standard (1 Mb/s) and the P1596 interconnect (1 Gb/s), which concern the definition of standard control register locations, formats, and functions. This scalable definition, called an I/O architecture, is being considered for use by other bus standards as well (P896.1 Futurebus and the P1014 VME bus standards). The scalable I/O architecture definition is bus-technology-independent, and supports large multiple-bus configurations. Several of the scalable features of the I/O architecture are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intravenous immunoglobulin G reduces MRI activity in relapsing multiple sclerosis (1998)

We wanted to assess whether intravenous immunoglobulin G (IVIG) decreases disease activity on MRI in relapsing MS. Previous trials of IVIG in relapsing-remitting MS demonstrated a reduction of acute relapses, but these studies did not include MRI. We treated 26 patients in a randomized, double-blind, crossover study of IVIG 1 g/kg daily or placebo on 2 consecutive days every month during two 6-month treatment periods. The primary end point was the number of gadolinium-enhancing lesions on monthly serial MRI. Secondary efficacy variables were the occurrence of exacerbations, clinical neurologic ratings, total MS lesion load on T2-weighted MRI, and multimodal evoked potentials. Eighteen patients completed the entire trial; eight patients did not. Twenty-one patients completed the first treatment period and at least two MRI examinations in the second treatment period and were included in the intention-to-treat analysis. On serial MRI, we observed fewer enhancing lesions per patient per scan during IVIG treatment (median, 0.4; range, 0 to 9.3) than during placebo treatment (median, 1.3; range, 0.2 to 25.7; p = 0.03). During IVIG treatment, 15 patients were exacerbation free compared with only 7 on placebo (p = 0.02). The total number of exacerbations in the IVIG period was 11 and in the placebo period, 19 (not significant). None of the remaining secondary efficacy measures were significantly different between the two treatment periods. The number of adverse events, in particular eczema, was significantly higher during IVIG therapy than during placebo treatment. These results suggest that IVIG treatment is beneficial to patients with relapsing MS.
Intraoperative hypothermia during vascular neurosurgical procedures (2009)

Increasing evidence in animal models and clinical trials for stroke, hypoxic encephalopathy for children, and traumatic brain injury have shown that mild hypothermia may attenuate ischemic damage and improve neurological outcome. However, it is less clear if mild intraoperative hypothermia during vascular neurosurgical procedures results in improved outcomes for patients. This review examines the scientific evidence behind hypothermia as a treatment and discusses factors that may be important for the use of this adjuvant technique, including cooling temperature, duration of hypothermia, and rate of rewarming.