gebhart/patrepeval huggingface dataset:
214. Design of Multifunctional Chimeric Antigen Receptors for T Cell Cancer Immunotherapy (2015)

Adoptive therapy with T cells modified with synthetic chimeric antigen receptors (CAR-T cells) is emerging as an important and promising modality for hematologic malignancies, and has the potential for broad applications in cancer therapy. We have worked on novel CAR designs by incorporating strep-tag II in various locations in the extracellular domain of the CAR. We have shown that strep-tag II does not interfere with CAR function, provides an intrinsic marker for identification of CAR expression at the cell surface, and introduces flexibility in tailoring spacer length to optimize CAR function. Moreover, this CAR design can facilitate the application of time-saving and cost-efficient technologies for manufacturing of high-purity CAR T cell products either by using anti-strep-tag II plus anti-CD28 mAb coated microbeads to selectively expand CAR-T cells, or by rapidly enriching CAR-T cells using established Strep-Tactin purification systems. Using NSG mouse/human tumor xenograft models, we show that both strategies readily generate potent CAR T cell products for in vivo therapy. This innovation in CAR design can be universally applied for CARs with different scFv specificity (CD19, CD20, ROR1) and costimulatory domains (CD28, 4-1BB, CD28/4-1BB), and endows CAR-T cells with valuable properties for cGMP manufacturing of therapeutic CAR-T cell product with high efficiency.
Grouping and optimization of XPath expressions in DB2 <sup>®</sup> pureXML (2008)

Several XML DBMSs support XQuery and/or SQL/XML languages, which are based on navigational primitives in the form of XPath expressions. Typically, these systems either model each XPath step as a separate query plan operator, or employ holistic approaches that can evaluate multiple steps of a single XPath expression. There have also been proposals to execute as many XPath expressions as possible within a single FLWOR block simultaneously in a data streaming context.
ChemInform Abstract: Monoclinic LaGa<sub>1‐x</sub>Mn<sub>x</sub>Ge<sub>2</sub>O<sub>7</sub>: A New Blue Chromophore Based on Mn<sup>3+</sup> in the Trigonal Bipyramidal Coordination with Longer Apical Bond Lengths. (2015)

Abstract Blue pigments of LaGa 1‐x Mn x Ge 2 O 7 are prepared by firing La 2 O 3 , Ga 2 O 3 , Mn 2 O 3 , and GeO 2 in stoichiometric amounts using H 3 BO 3 as a flux (Pt crucible, 1100 °C, 6 h).
ChemInform Abstract: Utility of Bifunctional N‐Heterocyclic Phosphine (NHP)‐Thioureas for Metal‐Free Carbon—Phosphorus Bond Construction Toward Regio‐ and Stereoselective Formation of Vinylphosphonates. (2016)

Abstract This novel N‐heterocyclic phosphine‐promoted phospha‐Michael/intramolecular nucleophilic substitution reaction allows for the stereoselective construction of vinyldiazaphosphonates in moderate to excellent yields.
Inhibition of angiogenesis by two-chain high molecular weight kininogen (HKa) and kininogen-derived polypeptides (2002)

We recently reported that the two-chain form of human high molecular weight kininogen (HKa) inhibits angiogenesis by inducing endothelial cell apoptosis (Zhang et al. 2000). This property appears to be primarily conferred by HKa domain 5 (HKa D5). In this manuscript, we further characterize the activity of these polypeptides toward proliferating endothelial cells, as well as their in vivo anti-angiogenic activity in the chick chorioallantoic membrane (CAM). We also demonstrate that short peptides derived from endothelial cell binding regions in HKa domains 3 and 5 inhibit endothelial cell proliferation and induce endothelial cell apoptosis. Like HKa and HKa D5, peptides derived from the latter domain induce endothelial cell apoptosis in a Zn(2+)-dependent manner, while those derived from domain 3 function independently of Zn2+. The implications of these findings to the regulation of angiogenesis and development of anti-angiogenic therapeutics are discussed.
Drug Delivery of Zinc to Barrett‘s Metaplasia By Oral Administration to Barrett‘s Esophagus Patients (2014)

Oral zinc administration can result in effective delivery of zinc to Barrett's epithelia with resulting effects on intracellular signal transduction.
A modular approach to multichannel magnetometry (1991)

A 19-channel SQUID system for biomagnetic measurements has been developed. This system differs from standard instruments in its modular approach. Various gradiometers can be coupled to the SQUIDs, the cryogenic system allows the exchange of single channels and the electronics is based on a cassette system. Problems with thermal insulation, vibrations of the gradiometers and tilted gradiometer geometries are discussed and solutions are presented.
Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls (2016)

Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the...
Conversion of landfill gas to liquid fuels through a TriFTS (tri-reforming and Fischer–Tropsch synthesis) process: a feasibility study (2018)

Biogas produced in landfills contains large amounts of methane (a potent greenhouse gas) and hence requires collection and treatment according to EPA regulations.
pFAR plasmids: New Eukaryotic Expression Vectors for Gene Therapy, devoid of Antibiotic Resistance Markers (2008)

Abstract Efficient production of eukaryotic expression vectors requires the selection of plasmid-containing bacteria. To avoid the risk of dissemination of antibiotic resistance markers, we developed a new system to produce a family of plasmids Free of Antibiotic Resistance genes, called pFARs. The strategy is based on the suppression of a chromosomal nonsense mutation by a plasmid-borne function. The amber mutation was introduced into the Escherichia coli thyA gene that encodes a thymidylate synthase required for dTMP synthesis, resulting in thymidine auxotrophy. In parallel, a small plasmid vector that carries an amber suppressor t-RNA gene was entirely synthesised. The introduction of pFAR plasmids into an optimised thyA mutant restored normal growth to the auxotrophic strain, and led to an efficient production of monomeric supercoiled plasmids, as required for clinical trials. Luciferase activities measured after intramuscular injection and electrotransfer of LUC-encoding pFAR vector were similar to those obtained with a commercial vector containing the same expression cassette. Interestingly, whereas luciferase activities decreased within three weeks after intradermal electrotransfer of conventional expression vectors, sustained levels were observed with the pFAR derivative. Thus, pFAR plasmids represent a novel family of biosafe eukaryotic expression vectors, suitable for gene therapy.
Analysis of a large number of vias and differential signaling in multilayered structures (2003)

A method is presented for full-wave modeling of vertical vias in multilayered circuits. The analysis of the interior problem is based upon the cylindrical wave expansion of the magnetic field Green's function. The multiple interaction among vertical vias is modeled by the Foldy-Lax scattering formula. Multilayered effects are included by using cascaded network of the single-layer components. The exterior problem of the via and the transmission line is analyzed using the method of moments approach. The exterior and interior problems are combined into a system of equations to facilitate the solution of a large number of vias. Using this approach, the scattering matrix of problems of several thousand vias can be calculated with moderate CPU and memory requirement. Numerical results have been obtained for different via configurations and for a large range of frequency. Also illustrated are results for common and differential mode in differential signaling with surrounding idle and shorting vias.
Optimization of system design for 64-slice cone-beam computed tomography (2004)

The technology for x-ray computed tomography (CT) has experienced tremendous growth in recent years. Since the introduction of 4-slice helical scanners in 1998, rapid improvement has been made on CT scanners in terms of the volume coverage, spatial resolution, scan speed, and the number of slices. These advancements not only significantly impact clinical applications, but also bring huge challenges to the CT system design. Because of the complexity of the volumetric CT (VCT) system, various strategies have to be utilized in the design process. These methodologies include theoretical analysis, computer simulation for system performance prediction, bench-top experiments for analysis confirmation, automated image analysis tools for automatically evaluating image performance, and double-blind tests with human observers for parameter optimization. In this paper, we present some of the system design considerations and optimization processes for a 64-slice scanner. These design processes ensure the optimal performance of the cone beam CT scanner. Initial clinical feedback has demonstrated the effectiveness of our approach.
Synthesis and structure-activity relationships of 7.BETA.-(2-(2-aminothiazol-4-yl)acetamido)cephalosporin derivatives. IV. Synthesis of 2-(2-aminothiazol-4-yl)-2-methoxyiminoacetic acid derivatives and related compounds. (1981)

In an effort to improve the antibacterial activity of 7 beta-[2-(2-aminothiazol-4-yl)acetamido]-cephalosporins by introducing a methoxyimino group into the 7-acyl side chain, geometrically isomeric 2-(2-aminothiazol-4-yl)-2-methoxyiminoacetic acids and their derivatives were selectively synthesized. Structurally related acid derivatives were also synthesized. A facile and practical synthesis of an important starting material, 2-(2-chloroacetamidothiazol-4-yl)-(Z)-2-methoxyiminoacetic acid, for the preparation of SCE-1365 which is now under extensive clinical trial was achieved.
Attentive Adversarial Learning for Domain-invariant Training (2019)

Adversarial domain-invariant training (ADIT) proves to be effective in suppressing the effects of domain variability in acoustic modeling and has led to improved performance in automatic speech recognition (ASR). In ADIT, an auxiliary domain classifier takes in equally-weighted deep features from a deep neural network (DNN) acoustic model and is trained to improve their domain-invariance by optimizing an adversarial loss function. In this work, we propose an attentive ADIT (AADIT) in which we advance the domain classifier with an attention mechanism to automatically weight the input deep features according to their importance in domain classification. With this attentive re-weighting, ADDIT can focus on the domain normalization of phonetic components that are more susceptible to domain variability and generates deep features with improved domain-invariance and senone-discriminativity over ADIT. Most importantly, the attention block serves only as an external component to the DNN acoustic model and is not involved in ASR, so AADIT can be used to improve the acoustic modeling with any DNN architectures. More generally, the same methodology can improve any adversarial learning system with an auxiliary discriminator. Evaluated on CHiME-3 dataset, the AADIT achieves 13.6% and 9.3% relative WER improvements, respectively, over a multi-conditional model and a strong ADIT baseline.
<title>DOE in DOIS: a diffractive optic image spectrometer</title> (1996)

One limitation of diffractive optical elements (DOEs) or zone plate lenses is abundant chromatic aberration. A previous report described a novel system that exploits this typically unwanted effect to create an Image Spectrometer [Lyons 1995]. A DOE performs the imaging and provides the dispersion necessary to separate a multispectral target into separate spectral images. A CCD is stepped or scanned along the optical axis recording a series of these spectral images. This paper reports on the DOE that was fabricated, simulated and implemented in a visible DOIS prototype. The data from this prototype can be interpolated to predict the performance of fieldable DOIS systems that can be designed to operate at ultraviolet, visible or infrared [Hinnrichs 1995] wavelengths for multispectral and hyperspectral imaging in medicine, forensics, industrial and environmental monitoring, as well as military applications.
An FM demodulator operating across 2&#x2013;10GHz IF (2013)

An FM demodulator operating across 8GHz IF bandwidth for application in low-power, wideband heterodyne receivers is presented. A 4-stage ring oscillator is frequency modulated by a wideband input. Locking to 1/4th the input frequency, it divides the FM deviation by four, thereby reducing the energy required for wideband demodulation to 0.75nJ/bit. Autocorrelation of the quadrature-phased outputs using a new low-power folded CMOS mixer is capable of detecting FM up to 400Mb/s over 2-10GHz IF. The inductorless 65nm CMOS prototype circuit occupies 0.17mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and dissipates 3mW from 1.2V.
Design of Potent Poxvirus Inhibitors of the Heterodimeric Processivity Factor Required for Viral Replication (2013)

Smallpox constitutes a major bioterrorism threat, which underscores the need to develop antiviral drugs for rapid response in the event of an attack. Viral processivity factors are attractive drug targets in being both specific and essential for their cognate DNA polymerases to synthesize extended strands of DNA. An in silico model of the vacinnia virus processivity factor, comprised of the A20 and D4 heterocomplex, was constructed and used for lead optimization of an indole-based scaffold identified earlier from a high-throughput screening. On the basis of this model, a new class of potent antivirals against vaccinia virus was designed and synthesized, of which two (24a and 24b) exhibited superior improvement over the parent scaffold (IC50 = 42 and 46 vs 82000 nM, respectively). The ability of 24a to suppress vaccinia DNA synthesis is supported by the inhibition of late viral gene expression, as well as by the diminished incorporation of bromodeoxyuridine into viral replication factories.
Biased estimators with adaptive shrinkage targets for orthogonal frequency division multiple access channel estimation (2013)

In orthogonal frequency division multiple access‐based systems where channel frequency response (CFR) estimation has to be carried out using only the user‐specific (localised) pilots within a small time frequency block, the accuracy of the estimates suffer because of the limited number of pilots and imperfect knowledge of the channel statistics. A biased estimator is proposed for the estimation of CFR over the time frequency block. Hypothesis tests are designed to ascertain the time and frequency selectivity of the CFR within the region of interest, and the outcome of these tests are used to determine a vector shrinkage target for the biased estimator. Simulation results indicate that the performance of the proposed estimator is comparable to that of the optimal minimum mean square error estimator, even though it does not have any knowledge of the channel statistics.
Atomic Layer Etching: Benefits and Challenges (2018)

A conceptual framework is introduced to gain insights into performance benefits and challenges of directional and isotropic Atomic Layer Etching (ALE).
Anti-Growth Factor Receptor 3 Antibodies Identify a Sub-Group of Sensory Neuropathy Patients (P3.019) (2014)

OBJECTIVE: To identify antibodies (Abs) toward fibroblast growth factor receptor 3 (FGFR-3) in patients with sensory neuropathy. BACKGROUND: Dorsal root ganglia T cell infiltration suggests immunological mechanisms in paraneoplastic SNN, SNN with autoimmune diseases and some idiopathic cases. Anti-Hu and CRMP5 antibodies (Abs) characterize paraneoplastic SNN but there are no identified biomarkers for non paraneoplastic SNN yet. DESIGN/METHODS: Serum samples were collected from 106 patients with sensory neuropathy (SN) of whom 72 fulfilled the diagnosis criteria of SNN and 211 controls including 41 patients with sensorimotor neuropathies, 46 with systemic autoimmune diseases, 59 with other neurological diseases (ONDs) and 65 healthy blood donors. Sera were analyzed by ELISA with the intracellular domain of FGFR3 and by immunohistochemistry on HEK293 cells transfected with FGFR3 subunits. RESULTS: A protein array with 8000 human proteins identified the intracellular domain of FGFR3 as a target of Abs in 7/16 SNN and 0/30 controls. By ELISA, anti-FGFR3 Abs were detected in 16/106 SN patients and 1/211 controls (p<0.001). Among the 106 SN patients, anti-FGFR3 Abs were found 11/38 with an autoimmune context, 5/46 with idiopathic neuropathy and 0/22 with another origin of the neuropathy (p=0.006). Among the 211 controls, the only patient with anti-FGF3 Abs had systemic autoimmune disease and no known neuropathy. Sensitivity, specificity and positive and negative predictive values of anti-FGFR3 Abs for a diagnosis of idiopathic or dysimmune SN were 19%, 99.6%, 94.1% and 77.3% respectively. The cell based assay confirmed serum reactivity against FGFR3 intracellular domain. The neuropathy was non-length dependent in 87% of patients and fulfilled the criteria of probable SNN in 82%. Trigeminal nerve involvement and pain were frequent features. CONCLUSIONS: Anti-FGFR3 Abs identify a subgroup of sensory neuropathy patients in whom an underlying autoimmune disorder affecting sensory neurons in dorsal root and trigeminal nerve ganglia should be suspected. Study Supported by: the French Ministry of Health (PHRCN 2005-0501104) and la Région Rhône-Alpes (Cluster 11 5-2010-1).
Fast ANN for High-Quality Collaborative Filtering (2014)

Collaborative filtering collects similar patches, jointly filters them, and scatters the output back to input patches; each pixel gets a contribution from each patch that overlaps with it, allowing signal reconstruction from highly corrupted data. Exploiting self-similarity, however, requires finding matching image patches, which is an expensive operation. We propose a GPU-friendly approximated-nearest-neighbor algorithm that produces high-quality results for any type of collaborative filter. We evaluate our ANN search against state-of-the-art ANN algorithms in several application domains. Our method is orders of magnitudes faster, yet provides similar or higher-quality results than the previous work.
Ghrelin Octanoylation Is Completely Stabilized in Biological Samples by Alkyl Fluorophosphonates (2016)

Ghrelin is a peptide hormone involved in multiple physiological processes related to energy homeostasis. This hormone features a unique posttranslational serine octanoylation modification catalyzed by the enzyme ghrelin O-acyltransferase, with serine octanoylation essential for ghrelin to bind and activate its cognate receptor. Ghrelin deacylation rapidly occurs in circulation, with both ghrelin and desacyl ghrelin playing important roles in biological signaling. Understanding the regulation and physiological impact of ghrelin signaling requires the ability to rapidly protect ghrelin from deacylation in biological samples such as blood serum or cell lysates to preserve the relative concentrations of ghrelin and desacyl ghrelin. In in vitro ghrelin O-acyltransferase activity assays using insect microsomal protein fractions and mammalian cell lysate and blood serum, we demonstrate that alkyl fluorophosphonate treatment provides rapid, complete, and long-lasting protection of ghrelin acylation against serine ester hydrolysis without interference in enzyme assay or ELISA analysis. Our results support alkyl fluorophosphonate treatment as a general tool for stabilizing ghrelin and improving measurement of ghrelin and desacyl ghrelin concentrations in biochemical and clinical investigations and suggest current estimates for active ghrelin concentration and the ghrelin to desacyl ghrelin ratio in circulation may underestimate in vivo conditions.
Linearly constrained generalized Lloyd algorithm for reduced codebook vector quantization (2001)

As linearly constrained vector quantization (LCVQ) is efficient for block-based compression of images that require low complexity decompression, it is a "de facto" standard for three-dimensional (3-D) graphics cards that use texture compression. Motivated by the lack of an efficient algorithm for designing LCVQ codebooks, the generalized Lloyd (1982) algorithm (GLA) for vector quantizer (VQ) codebook improvement and codebook design is extended to a new linearly constrained generalized Lloyd algorithm (LCGLA). This LCGLA improves VQ codebooks that are formed as linear combinations of a reduced set of base codewords. As such, it may find application wherever linearly constrained nearest neighbor (NN) techniques are used, that is, in a wide variety of signal compression and pattern recognition applications that require or assume distributions that are locally linearly constrained. In addition, several examples of linearly constrained codebooks that possess desirable properties such as good sphere packing, low-complexity implementation, fine resolution, and guaranteed convergence are presented. Fast NN search algorithms are discussed. A suggested initialization procedure halves iterations to convergence when, to reduce encoding complexity, the encoder considers the improvement of only a single codebook for each block. Experimental results for image compression show that LCGLA iterations significantly improve the PSNR of standard high-quality lossy 6:1 LCVQ compressed images.
Inferring Quantitative Trait Pathways Associated with Bull Fertility from a Genome-Wide Association Study (2013)

Whole-genome association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. As such, the objective of this study was to perform a pathway-based association analysis in Holstein dairy cattle in order to identify relevant pathways involved in bull fertility. The results of a single-marker association analysis, using 1,755 bulls with sire conception rate data and genotypes for 38,650 single nucleotide polymorphisms (SNPs), were used in this study. A total of 16,819 annotated genes, including 2,767 significantly associated with bull fertility, were used to interrogate a total of 662 Gene Ontology (GO) terms and 248 InterPro (IP) entries using a test of proportions based on the cumulative hypergeometric distribution. After multiple-testing correction, 20 GO categories and one IP entry showed significant overrepresentation of genes statistically associated with bull fertility. Several of these functional categories such as small GTPases mediated signal transduction, neurogenesis, calcium ion binding, and cytoskeleton are known to be involved in biological processes closely related to male fertility. These results could provide insight into the genetic architecture of this complex trait in dairy cattle. In addition, this study shows that quantitative trait pathways inferred from single-marker analyses could enhance our interpretations of the results of genome-wide association studies.