gebhart/patrepeval huggingface dataset:
An RNA-Based Digital Circulating Tumor Cell Signature Is Predictive of Drug Response and Early Dissemination in Prostate Cancer (2018)

Blood-based biomarkers are critical in metastatic prostate cancer, where characteristic bone metastases are not readily sampled, and they may enable risk stratification in localized disease. We established a sensitive and high-throughput strategy for analyzing prostate circulating tumor cells (CTC) using microfluidic cell enrichment followed by digital quantitation of prostate-derived transcripts. In a prospective study of 27 patients with metastatic castration-resistant prostate cancer treated with first-line abiraterone, pretreatment elevation of the digital CTC<sub>M</sub> score identifies a high-risk population with poor overall survival (HR = 6.0; <i>P</i> = 0.01) and short radiographic progression-free survival (HR = 3.2; <i>P</i> = 0.046). Expression of <i>HOXB13</i> in CTCs identifies 6 of 6 patients with ≤12-month survival, with a subset also expressing the <i>ARV7</i> splice variant. In a second cohort of 34 men with localized prostate cancer, an elevated preoperative CTC<sub>L</sub> score predicts microscopic dissemination to seminal vesicles and/or lymph nodes (<i>P</i> < 0.001). Thus, digital quantitation of CTC-specific transcripts enables noninvasive monitoring that may guide treatment selection in both metastatic and localized prostate cancer.<b>Significance:</b> There is an unmet need for biomarkers to guide prostate cancer therapies, for curative treatment of localized cancer and for application of molecularly targeted agents in metastatic disease. Digital quantitation of prostate CTC-derived transcripts in blood specimens is predictive of abiraterone response in metastatic cancer and of early dissemination in localized cancer. <i>Cancer Discov; 8(3); 288-303. ©2018 AACR.</i><i>See related commentary by Heitzer and Speicher, p. 269</i><i>This article is highlighted in the In This Issue feature, p. 253</i>.
A DRAM system for consistently reducing CPU wait cycles (2003)

This paper describes a DRAM system for consistently reducing CPU wait cycles for an access to DRAMs in a cache-based memory hierarchy. An arithmetical address mapping circuitry and a pseudo dual-port DRAM access protocol provide a DRAM access without a bank conflict and high speed write-back accesses (write for dirty data and read for cache-line filling). Only two adders for the address mapping circuitry and a data-preload register in each DRAM are necessary for the implementation.
ChemInform Abstract: NEW ANTIARRHYTHMIC AGENTS. N‐ARYL‐8‐PYRROLIZIDINEALKANAMIDES (1985)

Abstract Wie im Formelschema angegeben, werden die Pyrrolizidine (IV) und (VII) dargestellt, von denen viele antiarrhythmische Wirkung zeigen.
An accessory gene, lipB, required for the production of active <i>Pseudomonas glumae</i> lipase (1993)

Pseudomonas glumae PG1 is able to secrete lipase into the extracellular medium. The lipase is produced as a precursor protein, with an N-terminal signal sequence. A second open reading frame (ORF) was found immediately downstream of the lipase structural gene, lipA, a situation found for the lipases of some other Pseudomonas species. Inactivation of this ORF resulted in a lipase-negative phenotype, indicating its importance in the production of active extracellular lipase. The ORF, lipB, potentially encodes a protein of 353-amino-acid residues, having a hydrophobic N-terminal (amino acids 1 to 90) and a hydrophilic C-terminal part. As a first step in determining the role of LipB, its subcellular location was determined. The protein was found to fractionate with the inner membranes. The expression of fusions of lipB fragments with phoA revealed an N(in)-C(out) topology for the LipB protein, which was confirmed by protease accessibility studies on EDTA-permeabilized cells and on inverted inner membrane vesicles. These and other results indicate that most of the LipB polypeptide is located in the periplasm and anchored to the inner membrane by an N-terminal transmembrane helix, located between amino acids 19 and 40.
A reconfigurable CMOS neural network (1990)

An analog CMOS neural net with a programmable architecture containing 32 K connections is discussed. The objective of packing as large a network as possible on a chip leads to the choice of an analog approach. Analog signals are used only inside the network. All the input and output data are digital. The reconfigurable network consists of building blocks that can be joined to form various network architectures. The circuit can be programmed to implement single-layer networks or multilayer networks with binary or analog connections.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experimental results with a themoacoustically driven thermoacoustic refrigerator (1997)

The construction of a thermoacoustically (heat) driven, thermoacoustic refrigerator (TADTAR) has been completed. The design utilizes a novel resonator topology and should have a high cooling power density. While the design goal calls for a cooling power level of 500 W over a temperature span of 40 °C, the first refrigeration data recently obtained exhibited only small amounts of cooling. However, as the understanding of the engine improves, so does its performance. Variations in resonator tuning and stack location, gas type and pressure, and stack type and geometry are being explored. Low Prandtl number gas mixtures produce particularly strong improvements in onset conditions and amplitude. [Work supported by Office of Naval Research.]
The CD4 T cell response in acute infection with dengue virus (2017)

Abstract Dengue virus (DENV) is the etiologic agent of dengue fever (DF), the most significant mosquito-borne viral disease in humans. DENV transmission occurs in more than 100 countries and is an increasing public health problem in tropical and sub-tropical regions. Up to 400 million DENV infections occur every year and severity can range from asymptomatic to an acute self-limiting febrile illness (DF) or the more severe hemorrhagic fever (DHF) characterized by severe vascular leakage, thrombocytopenia, and hemorrhagic manifestations. In this study we have investigated the acute CD4+ T cell response in hospitalized patients with different severity of disease manifestations. Samples from patients either diagnosed with DF or DHF have been collected in the acute phase and in the convalescent phase after resolving the infection. Virus specific CD4 T cells were detected based on their ability to produce cytokines in response to stimulation with DENV specific peptide pools in an intracellular cytokine assay. All donors elicited IFNγ in the convalescent phase of infection, regardless of the severity of disease. Interestingly, in the acute phase DF patients elicited IFNγ in response to the peptide pool, while the response in DHF patients was dominated by IL-10. Further characterization revealed that these responding IFNγ and IL 10 producing CD4 T cells differ in memory phenotype as well as activation markers. We are currently establishing specific gene expression signatures, associated with these characteristic phenotypes. Detailed knowledge of phenotype and function of DENV specific T cells will aid in the establishment of correlates of protection against severe disease.
<title>Optical electroabsorption modulators for wideband, linear, low-insertion-loss photonic links</title> (1995)

We describe the characterization and development of semiconductor quantum well electroabsorption modulators (EAMs) for insertion into high-performance photonic links intended for analog applications. Limitations of existing approaches are described, motivating the potential of EAMs for exploiting the flexibility of semiconductor bandgap engineering. Relationships are established between basic modulator device characteristics and the RF system performance measures of link gain (insertion loss), bandwidth, noise figure, and dynamic range; results are then presented that have established the viability of EAMs for wideband, low-loss, linear analog photonic links.
Signaling Extensions for Wavelength Switched Optical Networks (2015)

This document provides extensions to Generalized Multiprotocol Label Switching (GMPLS) signaling for control of Wavelength Switched Optical Networks (WSONs). Such extensions are applicable in WSONs under a number of conditions including: (a) when optional processing, such as regeneration, must be configured to occur at specific nodes along a path, (b) where equipment must be configured to accept an optical signal with specific attributes, or (c) where equipment must be configured to output an optical signal with specific attributes. This document provides mechanisms to support distributed wavelength assignment with a choice of distributed wavelength assignment algorithms.
Abstract 3239: Shp2 inhibitor activity of estramustine phosphate and its triterpenoid analogues (2011)

Abstract Shp2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene. Shp2 mediates proliferative signaling induced by growth factors. Gain-of-function PTPN11 mutations that encode constitutively active Shp2 are leukemic oncogenes. In a continuing effort to identify new Shp2 PTP inhibitors, we screened a small molecule library comprising the National Cancer Institute (NCI) Approved Oncology Drug set and the NIH Clinical Collection. After evaluation of initial hits, estramustine phosphate was verified as a Shp2 PTP inhibitor. A focused structure-activity relationship study indicated that the 17-phosphate group is required for the Shp2 PTP inhibitor activity of estramustine phosphate. A search for estramustine phosphate analogs led to identification of two triperpenoids, enoxolone and celastrol, having Shp2 PTP inhibitor activity. With the previously reported PTP1B inhibitor trodusquemine, our study reveals steroids and triterpenoids with negatively charged phosphate, carboxylate, or sulfonate groups as novel pharmacophores of selective PTP inhibitors. These findings point to a rich natural source for discovery of lead compounds of novel PTP inhibitors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3239. doi:10.1158/1538-7445.AM2011-3239
Microlithography of π-conjugated polymers (1994)

In this work the photochemistry and photoimaging of derivatized polythiophenes will be described. Poly(3-alkylthiophenes) are inherently photolabile. One of the photochemical products leads to cross-linking, which can be utilized in photolithography. During this process, (pi) -conjugation remains virtually intact, and conductivities remain the same as the pristine polymer. The photosensitivity of this polymer to cross-linking, and thereby, insolubilization, can be enhanced by copolymerization with thienyl moieties possessing the methacryoyl functionality. In addition to photoimaging, the stability of the conducting state will be discussed. Strategies for enhancing stabilization will be addressed with a view to assimilating organic wires into integrated circuitry.
The <i>abp</i> locus of <i>Streptococcus uberis</i> encodes a protein homologous to polar amino acid and opine binding proteins of Gram-negative bacteria (1998)

A gene locus abp was identified immediately upstream of the CAMP factor gene cfu in Streptococcus uberis. An open reading frame capable of coding for a 277-residue protein was identified. On the basis of sequence characteristics, the abp gene product is potentially a polar amino acid and opine binding component of an ATP-binding cassette type (ABC-type) transport system similar to those of Gram-negative bacteria. This membrane protein is likely lipid modified at its amino terminus and was present in five S. uberis strains and one Streptococcus parauberis strain examined.Key words: bovine mastitis, Streptococcus uberis, amino acid transport.
Expression, Purification, and Characterization of Ultraviolet DNA Endonuclease from <i>Schizosaccharomyces pombe</i> (1998)

Ultraviolet damage endonuclease (UVDE) is a 68.7 kDa DNA repair enzyme of Schizosaccharomyces pombe that recognizes cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs). UVDE is thought to initiate the first step in an alternative excision repair pathway for removal of UV light-induced DNA damage. We have overexpressed Delta228-UVDE, an active truncated form of UVDE, and have purified this protein to apparent homogeneity. We have characterized purified Delta228-UVDE with respect to its physical properties, divalent cation requirements, and kinetic parameters on oligodeoxynucleotide substrates containing a single CPD. DNA strand cleavage analysis indicates that both full-length UVDE and Delta228-UVDE incise the CPD-containing strand immediately 5' to the lesion. These results provide further insight into the UVDE-mediated alternative excision repair pathway.
Cover Picture: Self‐Organization of Ink‐jet‐Printed Triisopropylsilylethynyl Pentacene via Evaporation‐Induced Flows in a Drying Droplet (Adv. Funct. Mater. 2/2008) (2008)

Abstract Charge carrier transport in organic electronic devices is influenced by the crystalline microstructure and morphology of the organic semiconductor film. Evaporation behavior during drying plays a vital role in controlling the film morphology and the distribution of solute in inkjet‐printed films. On p. 229, Kilwon Cho and co‐workers demonstrate the influence of the evaporation‐induced flow in a single droplet on the crystalline microstructure and film morphology of inkjet‐printed 6,13‐bis((triisopropylsilylethynyl) pentacene. The results provide an excellent method for direct‐write fabrication of high‐performance organic electronics. We have demonstrated the influence of evaporation‐induced flow in a single droplet on the crystalline microstructure and film morphology of an ink‐jet‐printed organic semiconductor, 6,13‐bis((triisopropylsilylethynyl) pentacene (TIPS_PEN), by varying the composition of the solvent mixture. The ringlike deposits induced by outward convective flow in the droplets have a randomly oriented crystalline structure. The addition of dichlorobenzene as an evaporation control agent results in a homogeneous film morphology due to slow evaporation, but the molecular orientation of the film is undesirable in that it is similar to that of the ring‐deposited films. However, self‐aligned TIPS_PEN crystals with highly ordered crystalline structures were successfully produced when dodecane was added. Dodecane has a high boiling point and a low surface tension, and its addition to the solvent results in a recirculation flow in the droplets that is induced by a Marangoni flow (surface‐tension‐driven flow), which arises during the drying processes in the direction opposite to the convective flow. The field‐effect transistors fabricated with these self‐aligned crystals via ink‐jet printing exhibit significantly improved performance with an average effective field‐effect mobility of 0.12 cm 2 V –1 s –1 . These results demonstrate that with the choice of appropriate solvent ink‐jet printing is an excellent method for the production of organic semiconductor films with uniform morphology and desired molecular orientation for the direct‐write fabrication of high‐performance organic electronics.
Correction for field nonuniformity in scintillation cameras through removal of spastial distortion. (1980)

A method to correct for the spatial distortions of gamma cameras has been developed. The method consists of two parts: measuring spatial distortions and repositioning events during accumulation. Distortions are measured using a pattern consisting of parallel slits on 15-mm centers with slit-pattern images obtained in two orthogonal orientations. Slit locations are used to determine X and Y displacements. In repositioning camera events, X and Y event coordinates are digitized and correction displacements added. The procedure is implemented in hardware that replositions each event in real time without introducing additional dead time. Distortion removal offers considerable advantage over other uniformity-improvement schemes, since it correctly compensates for the major cause of nonuniformity, spatial distortion. The method may be used for quantitative studies, because it does not change the number of detected events.
Optical magnetic field sensors with high linearity using Bi-substituted rare earth iron garnets (1995)

Optical magnetic field sensors with high linearity were developed. Bi-substituted rare earth iron garnets were prepared using the liquid phase epitaxy method for use as the Faraday rotators of the sensors. The linearity error of the sensor output was obtained within 1.0% for alternating magnetic fields of up to 300 Oe. The sensor optical system has a new converged beam optical system using ball lenses. The linearity of these sensors is much better than that of sensors using a collimated beam optical system with graded index lenses. Sensors using the collimated beam optical system are nonlinear, since only the zeroth-order beam diffracted by the garnet maze domains is detected. Sensors using the converged beam optical system have high linearity because of the detection of diffracted beams up to the second-order. The experimental results agreed well with the calculated results.
TREATMENT WITH ANTI-CD154 ANTIBODY AND DONOR-SPECIFIC TRANSFUSION PREVENTS ACUTE REJECTION OF MYOBLAST TRANSPLANTATION1 (2002)

In conclusion, the DST + anti-CD154 mAb treatments effectively prolonged myoblast survival, but this treatment could not develop tolerance to complete allogeneic myoblast transplantation.
Nonblocking memory management support for dynamic-sized data structures (2005)

Conventional dynamic memory management methods interact poorly with lock-free synchronization. In this article, we introduce novel techniques that allow lock-free data structures to allocate and free memory dynamically using any thread-safe memory management library. Our mechanisms are lock-free in the sense that they do not allow a thread to be prevented from allocating or freeing memory by the failure or delay of other threads. We demonstrate the utility of these techniques by showing how to modify the lock-free FIFO queue implementation of Michael and Scott to free unneeded memory. We give experimental results that show that the overhead introduced by such modifications is moderate, and is negligible under low contention.
CD163/CD16 Coexpression by Circulating Monocytes/Macrophages in HIV: Potential Biomarkers for HIV Infection and AIDS Progression (2008)

Monocytes and macrophages play a prominent role in the establishment of HIV-1 infection, virus dissemination, and development of viral reservoirs. Like T cells, macrophages display immune polarization that can promote or impair adaptive immunity. We hypothesize that dysregulation of monocyte/macrophage activation and differentiation may promote immune dysfunction and contribute to AIDS pathogenesis. Using flow cytometry, we analyzed the frequency of monocyte subsets in human immunodeficiency virus type 1 (HIV-1) infection relative to seronegative controls, focusing on the CD163(+)/CD16(+) monocyte as a likely precursor of the "alternatively activated" macrophage. Individuals with detectable HIV-1 infection showed an increase in the frequency of CD163(+)/CD16(+) monocytes (CD14(+)) when compared to seronegative or HIV-1-infected persons with undetectable viral loads. A positive correlation between increased CD163(+)/CD16(+) monocyte frequency and viral load was revealed that was not seen between viral load and the number of CD4(+) T cells or frequency of CD16(+) monocytes (without CD163 subtyping). We also found a strong inverse correlations between CD16(+) monocytes (r = -0.71, r(2) = 0.5041, p = 0.0097) or CD163(+)/CD16(+) monocytes (r = -0.86, r(2) = 0.7396, p = 0.0003) and number of CD4(+) T cells below 450 cells/microl. An inverse relationship between CD163(+)/CD16(+) and CD163(+)/CD16() monocytes suggests the expanded CD163(+)/CD16(+) population is derived exclusively from within the "alternatively activated" (MPhi-2) subset. These data suggest a potential role for CD163(+)/CD16(+) monocytes in virus production and disease progression. CD163(+)/CD16(+) monocytes may be a useful biomarker for HIV-1 infection and AIDS progression and a possible target for therapeutic intervention.
Identification and Characterization of an Immunogenic Hybrid Epitope Formed by both HIV gp120 and Human CD4 Proteins (2011)

Certain antibodies from HIV-infected humans bind conserved transition state (CD4 induced [CD4i]) domains on the HIV envelope glycoprotein, gp120, and demonstrate extreme dependence on the formation of a gp120-human CD4 receptor complex. The epitopes recognized by these antibodies remain undefined although recent crystallographic studies of the anti-CD4i monoclonal antibody (MAb) 21c suggest that contacts with CD4 as well as gp120 might occur. Here, we explore the possibility of hybrid epitopes that demand the collaboration of both gp120 and CD4 residues to enable antibody reactivity. Analyses with a panel of human anti-CD4i MAbs and gp120-CD4 antigens with specific mutations in predicted binding domains revealed one putative hybrid epitope, defined by the human anti-CD4i MAb 19e. In virological and immunological tests, MAb 19e did not bind native or constrained gp120 except in the presence of CD4. This contrasted with other anti-CD4i MAbs, including MAb 21c, which bound unliganded, full-length gp120 held in a constrained conformation. Conversely, MAb 19e exhibited no specific reactivity with free human CD4. Computational modeling of MAb 19e interactions with gp120-CD4 complexes suggested a distinct binding profile involving antibody heavy chain interactions with CD4 and light chain interactions with gp120. In accordance, targeted mutations in CD4 based on this model specifically reduced MAb 19e interactions with stable gp120-CD4 complexes that retained reactivity with other anti-CD4i MAbs. These data represent a rare instance of an antibody response that is specific to a pathogen-host cell protein interaction and underscore the diversity of immunogenic CD4i epitope structures that exist during natural infection.
Semiconductor lasers from photoconductive switch filaments (2002)

At the 8/sup th/ Pulsed Power Conference (1991), this group reported the first images of current filaments in high gain photoconductive semiconductor switches (PCSS). Since that time many properties of the current filaments have been reported, including the ability to control the location, shape, and timing of the filaments with an optical trigger. Recently, we have invented a new class of semiconductor laser, using current filaments as the active region. We have fabricated and tested current filament semiconductor lasers (CFSL) producing 75 nJ of 890 nm radiation in 1.5 ns (50 W peak), approximately ten times more energy than conventional (injection-pumped) semiconductor lasers (CSL) in comparable pulse lengths.
Fiber-based platform for synchronous imaging of endogenous and exogenous fluorescence of biological tissue (2019)

Endogenous and exogenous fluorescence emission from biological samples encodes complementary information. Here we report, to the best of our knowledge, the first results from an optical imaging platform with interleaved excitation and detection of exogenous and endogenous fluorescence from tissue samples using a single flexible multimode fiber that delivers the excitation beam and collects the emitted light. A custom-built reflective optical chopper wheel with synchronized rotation temporally multiplexes an autofluorescence lifetime imaging apparatus with an intensity-based fluorescence module tailored to imaging green fluorescent protein. We demonstrate the functionality of such platform imaging dyes of varying fluorescence signatures and resolving cellularized areas on bio-engineered tissue constructs.