gebhart/patrepeval huggingface dataset:
RNA-transfected dendritic cells in cancer immunotherapy (2000)

The field of cancer immunotherapy has been recently invigorated by the discovery that vaccination with dendritic cells (DCs) pulsed with tumor antigens is a potent strategy to elicit protective immunity in tumor-bearing animals. The recognition that the cellular arm of the immune response is best equipped to recognize tumor cells as foreign and to lead to their eradication has shifted the emphasis in vaccine development. Vaccines that induce cellular responses, especially by the CD8+ cytotoxic T lymphocyte (CTL) arm of the immune system, are now favored over those that activate humoral immunity. At the same time, DCs have emerged as the most potent antigen-presenting cells (APCs) for eliciting antitumor CTLs. DCs can be generated from cancer patients by culturing adherent PBMCs from the patients for 5–7 days in the presence of cytokines (1).

The major research effort in many labs involves the choice of tumor antigen with which to load these DCs. The issues being addressed are, first, the composition of the antigen, whether a defined tumor antigen or an unfractionated mixture of tumor-derived antigens; and second, the form in which the antigen should be presented, whether as a polypeptide or a nucleic acid. Here, we focus on the use of RNA-transfected DCs in cancer immunotherapy, reviewing current data on the transfection of DCs with RNAs encoding either defined or unfractionated tumor antigens. We also consider the advantages and disadvantages of employing RNA transfection in loading DCs with tumor antigens and the merits of RNA transfection in situations where a low level of transiently expressed protein is sufficient to allow antigen presentation.
Steady‐State and Multiple Cracking of Short Random Fiber Composites (1992)

This paper analyzes the pseudostrain‐hardening phenomenon of brittle matrix composites reinforced with discontinuous flexible and randomly distributed fibers, based on a cohesive crack‐mechanics approach. The first crack strength and strain are derived in terms of fiber, matrix, and interface micromechanical properties. Conditions for steady‐state cracking and multiple cracking are found to depend on two nondimensionalized parameters that embody all relevant material micromechanical parameters. The results are therefore quite general and applicable to a variety of composite‐material systems. Phrased in terms of a failure‐mechanism map, various uniaxial load‐deformation behaviors for discontinuous fiber composites can be predicted. The influence of a snubbing effect due to local fiber/matrix interaction for randomly oriented crack‐bridging fibers on the composite properties is also studied.
Spotting events in continuous speech (2002)

Jeanrenaud et al. (1993) introduced the notion of event spotting and showed that the detection of events could be approached as a word spotting problem. The present authors first concentrate on the problem of spotting complex units such as grammatic events and describe the three issues that have to be addressed. These issues are: 1) hypothesizing-how to detect an event, 2) scoring-how to generate a consistent score for the event, 3) identification-what word sequence constitutes the particular realization of the event. The authors also discuss ways to evaluate the performance of an event spotter and how to characterize the complexity of an event. They then present two approaches to spot events. The first approach is based on posterior probability scoring using sub-grammars, and the second uses a large vocabulary recognizer. They show that both approaches have comparable performance on an event spotting task using the Switchboard corpus. In the posterior probability scoring approach, however, there is the advantage of being able to choose an operating point.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The minimax cache: an energy-efficient framework for media processors (2004)

This work is based on our philosophy of providing interlayer system-level power awareness in computing systems. Here, we couple this approach with our vision of multi-partitioned memory systems, where memory accesses are separated based on their static predictability and memory footprint and managed with various compiler controlled techniques. We show that media applications are mapped more efficiently when scalar memory accesses are redirected to a mini-cache. Our results indicate that a partitioned 8K cache with the scalars being mapped to a 512 byte mini-cache can be more efficient than a 16K monolithic cache from both performance and energy point of view for most applications. In extensive experiments, we report 30% to 60% energy-delay product savings over a range of system configurations and different cache sizes.
In Vivo Feasibility of Real-Time Monitoring of Focused Ultrasound Surgery (FUS) Using Harmonic Motion Imaging (HMI) (2009)

In this study, the Harmonic Motion Imaging for Focused Ultrasound (HMIFU) technique is applied to monitor changes in mechanical properties of tissues during thermal therapy in a transgenic breast cancer mouse model in vivo. An HMIFU system, composed of a 4.5-MHz focused ultrasound (FUS) and a 3.3-MHz phased-array imaging transducer, was mechanically moved to image and ablate the entire tumor. The FUS transducer was driven by an amplitude-modulated (AM) signal at 15 Hz. The acoustic intensity ( I(spta)) was equal to 1050 W/cm(2) at the focus. A digital low-pass filter was used to filter out the spectrum of the FUS beam and its harmonics prior to displacement estimation. The resulting axial displacement was estimated using 1-D cross-correlation on the acquired RF signals. Results from two mice with eight lesions formed in each mouse (16 lesions total) showed that the average peak-to-peak displacement amplitude before and after lesion formation was respectively equal to 17.34 +/- 1.34 microm and 10.98 +/- 1.82 microm ( p << 0.001). Cell death was also confirmed by hematoxylin and eosin histology. HMI displacement can be used to monitor the relative tissue stiffness changes in real time during heating so that the treatment procedure can be performed in a time-efficient manner. The HMIFU system may, therefore, constitute a cost-efficient and reliable alternative for real-time monitoring of thermal ablation.
Is CD133 Expression a Prognostic Biomarker of Non-Small-Cell Lung Cancer? A Systematic Review and Meta-Analysis (2014)

High level of CD133 expression trends to correlate with a worse prognosis and a higher rate of lymph node metastasis in NSCLC patients, revealing CD133 as a potential pathological prognostic marker for NSCLC patients.
Tumor-Associated Antigens for Specific Immunotherapy of Prostate Cancer (2012)

Prostate cancer (PCa) is the most common noncutaneous cancer diagnosis and the second leading cause of cancer-related deaths among men in the United States. Effective treatment modalities for advanced metastatic PCa are limited. Immunotherapeutic strategies based on T cells and antibodies represent interesting approaches to prevent progression from localized to advanced PCa and to improve survival outcomes for patients with advanced disease. CD8+ cytotoxic T lymphocytes (CTLs) efficiently recognize and destroy tumor cells. CD4+ T cells augment the antigen-presenting capacity of dendritic cells and promote the expansion of tumor-reactive CTLs. Antibodies mediate their antitumor effects via antibody-dependent cellular cytotoxicity, activation of the complement system, improving the uptake of coated tumor cells by phagocytes, and the functional interference of biological pathways essential for tumor growth. Consequently, several tumor-associated antigens (TAAs) have been identified that represent promising targets for T cell- or antibody-based immunotherapy. These TAAs comprise proteins preferentially expressed in normal and malignant prostate tissues and molecules which are not predominantly restricted to the prostate, but are overexpressed in various tumor entities including PCa. Clinical trials provide evidence that specific immunotherapeutic strategies using such TAAs represent safe and feasible concepts for the induction of immunological and clinical responses in PCa patients. However, further improvement of the current approaches is required which may be achieved by combining T cell- and/or antibody-based strategies with radio-, hormone-, chemo- or antiangiogenic therapy.
Nucleotide sequence of the herpes simplex virus type 2 thymidine kinase gene (1983)

We have determined the complete nucleotide sequence of the thymidine kinase gene of herpes simplex virus (HSV) type 2 strain 333. The sequence of the thymidine kinase gene exhibits an open translational reading frame of 1,128 nucleotides encoding a protein of 376 amino acids. The DNA sequence was compared with that of the HSV type 1 thymidine kinase gene from strain MP (S. L. McKnight, Nucleic Acids Res. 8:5949-5964, 1980) and from strain CL 101 (M. J. Wagner, J. A. Sharp, and W. C. Summers, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445, 1981) to assess the extent of intra- and intertypic variation for one viral gene. The nucleotides encoding the structural gene varied 1.7% between the two HSV type 1 strains and 19% between HSV type 1 and HSV type 2, which translated to differences in the amino acid sequence of the two proteins of 1.9 and 27%, respectively. The DNA encoding the 5' regulatory sequences appeared to be more conserved than the DNA coding for the structural gene, and the DNA at the 3' end of the gene was the least homologous.
Peptide mapping for detecting variants in protein products. (1992)

The genetic stability of biotechnology production systems is of importance in evaluating the safety and efficacy of protein products. The analysis methods currently available for assessing the genetic stability of such systems are limited by the complexity of the eukaryotic genome and by their inability to predict the effects of post-transcriptional and post-translational events, such as glycosylation or host cell protein level changes, on the protein produced. Therefore, it is important to focus attention on the protein product itself in evaluating product consistency rather than on nucleotide sequence analysis for genetic stability of the production systems involved. Peptide mapping has arisen as the best method for the analysis of proteins as a surrogate measure of genetic stability. This method uses known chemical reactions or enzymes to cleave the protein at specific sites, resulting in discrete peptides whose structure and composition can be readily compared to that of the theoretical protein coded for by the DNA sequence of its gene. Peptide mapping, which is capable of detecting single amino acid changes in a molecule, can also be used for determining glycosylation sites. Peptide mapping requires sophisticated chromatographic techniques and equipment, and is limited to molecules of m.w. of c. 100,000. The method also requires careful validation to limit the potential for misinterpretation of artifactual peaks. Despite its limitations, no better method currently exists to evaluate product consistency and, thereby, the genetic stability of recombinant products.
Paracellular permeability of corneal and conjunctival epithelia. (1989)

The paracellular permeability of normal rabbit cornea and conjunctiva was studied in vivo and in vitro. After intravenous administration, horseradish peroxidase was found to percolate to the intercellular space of conjunctival epithelia and was restricted by the tight junctions of the superficial epithelium. Only minimal tracer was present in the limbus and cornea. The difference between corneal and conjunctival paracellular pathways was further compared in vitro by tissue perfusion studies using various tracers from subepithelial space to apical surface. The intact full-thickness cornea was permeable to mannitol (MW 182) but not to inulin or dextran. The conjunctiva was permeable to mannitol, inulin and FITC-dextran (MW 20,000). The quantitative permeability to 3H-mannitol (X10(-8) cm/sec) of adult rabbit cornea was 0.12 +/- 0.02, which is about 55-fold and 50-fold lower than that of conjunctiva (6.78 +/- 0.21) and peritoneum (6.12 +/- 0.63), respectively. Removal of the corneal epithelium increased the permeability 40-fold; however, removal of the endothelium had little effect on the solute permeation. When both corneal epithelium and endothelium were debrided, the bare stroma became edematous and the permeability increased 70-fold. The permeability of 1-week-old rabbit cornea was 1.32 +/- 0.18, which decreased to 0.46 +/- 0.06 in 2-week-old rabbits, and became similar to the adult level at 4 weeks of age. When Tenon's capsule was included in the perfusion, the conjunctival permeability decreased 2.5-fold. With the apposition of bare corneal stroma to the conjunctiva and Tenon's capsule, the permeability decreased further (4-fold).(ABSTRACT TRUNCATED AT 250 WORDS)
Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)

Abstract Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net
Human furin is a calcium-dependent serine endoprotease that recognizes the sequence Arg-X-X-Arg and efficiently cleaves anthrax toxin protective antigen. (1992)

Previous work demonstrated that human furin is a predominantly Golgi membrane-localized endoprotease that can efficiently process precursor proteins at paired basic residues (-Lys-Arg- or -Arg-Arg-) in transfected cells. Anion-exchange chromatography of culture supernatant from cells expressing a soluble truncated form of human furin resulted in a greatly enriched preparation of the endoprotease (approximately 70% pure as determined by protein staining). Enzymatic studies show that furin is a calcium-dependent (K0.5 = 200 microM) serine endoprotease which has greater than 50% of maximal activity between pH 6.0 and 8.5. The inhibitor sensitivity of furin suggests that it is similar to, yet distinct from, other calcium-dependent proteases. Evidence that furin may require a P4 Arg in fluorogenic peptide substrates suggested that this enzyme might cleave the protective antigen (PA) component of anthrax toxin at the sequence -Arg-Lys-Lys-Arg-. Indeed, PA was cleaved by purified furin at the proposed consensus site (-Arg-X-Lys/Arg-Arg decreases-) at a rate (8 mumol/min/mg total protein) 400-fold higher than that observed with synthetic peptides. In addition, the processing of mutant PA molecules with altered cleavage sites suggests that furin-catalyzed endoproteolysis minimally requires an -Arg-X-X-Arg- recognition sequence for efficient cleavage. Together, these results support the hypothesis that furin processes protein precursors containing this cleavage site motif in the exocytic pathway and in addition, raises the possibility that the enzyme also cleaves extracellular substrates, including PA.
Mannose 6-phosphate receptor-mediated uptake of modified low density lipoprotein results in down regulation of hydroxymethylglutaryl-CoA reductase in normal and familial hypercholesterolemic fibroblasts. (1980)

Monophosphotetramannosyl-1-deoxymannitol-1-yl-low density lipoprotein (Man-6-P-LDL) was prepared by covalent attachment of the pentasaccharide omega-(6-phospho-tetra(alpha 1-3)mannosyl(alpha 1-2)mannose to amino groups on low density lipoprotein. Normal human fibroblasts were shown to specifically bind, internalize, and degrade 125I-labeled Man-6-P-LDL. Specificity for the mannose 6-phosphate (Man-6-P) receptor was demonstrated by competitive displacement with cold Man-6-P-LDL, Man-6-P, or mannose. No displacement was seen with cold LDL. Kd is estimated to be less than or equal to 2 X 10(-9) M. Degradation of 125I-labeled Man-6-P-LDL in familial hypercholesterolemic fibroblasts showed the same time course and specificity as observed in normal fibroblasts. Man-y-P-LDL was also able to deliver cholesterol to the cytosol where down regulation of the enzyme 3-hydroxy-3-methylglutaryl CoA reductase was observed in both normal and familial hypercholesterolemic fibroblasts. Down regulation could be blocked by Man-6-P in both cell lines. The possible uses of agents such as Man-6-P-LDL as research probes and therapeutic tools directed to specific cell types are discussed.
Parallel mixing of photolithographically defined nanoliter volumes using elastomeric microvalve arrays (2005)

Portable microfluidic systems provide simple and effective solutions for low-cost point-of-care diagnostics and high-throughput biomedical assays. Robust flow control and precise fluidic volumes are two critical requirements for these applications. We have developed a monolithic polydimethylsiloxane (PDMS) microdevice that allows for storing and mixing subnanoliter volumes of aqueous solutions at various mixing ratios. Filling and mixing is controlled via two integrated PDMS microvalve arrays. The volumes of the microchambers are entirely defined by photolithography, hence volumes from picoliter to nanoliter can be fabricated with high precision. Because the microvalves do not require an energy input to stay closed, fluid can be stored in a highly portable fashion for several days. We have confirmed the mixing precision and predictability using fluorescence microscopy. We also demonstrate the application of the device for calibrating fluorescent calcium indicators. Due to the biocompatibility of PDMS, the device will have broad applications in miniaturized diagnostic assays as well as basic biological studies.
A Low-Complexity Detector for Large MIMO Systems and Multicarrier CDMA Systems (2008)

We consider large MIMO systems, where by 'large' we mean number of transmit and receive antennas of the order of tens to hundreds. Such large MIMO systems will be of immense interest because of the very high spectral efficiencies possible in such systems. We present a low-complexity detector which achieves uncoded near-exponential diversity performance for hundreds of antennas (i.e., achieves near SISO AWGN performance in a large MIMO fading environment) with an average per-bit complexity of just O(N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> ), where N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> and N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> denote the number of transmit and receive antennas, respectively. With an outer turbo code, the proposed detector achieves good coded bit error performance as well. For example, in a 600 transmit and 600 receive antennas V-BLAST system with a high spectral efficiency of 450 bps/Hz (using BPSK and rate-3/4 turbo code), our simulation results show that the proposed detector performs to within about 7 dB from capacity. This practical feasibility of the proposed high-performance, low-complexity detector could potentially trigger wide interest in the theory and implementation of large MIMO systems. We also illustrate the applicability of the proposed detector in the low-complexity detection of high-rate, non-orthogonal space-time block codes and large multicarrier CDMA (MC-CDMA) systems. In large MC-CDMA systems with hundreds of users, the proposed detector is shown to achieve near single-user performance at an average per-bit complexity linear in number of users, which is quite appealing for its use in practical CDMA systems.
A π-Conjugated System with Flexibility and Rigidity That Shows Environment-Dependent RGB Luminescence (2013)

We have designed and synthesized a π-conjugated system that consists of a flexible and nonplanar π joint and two emissive rigid and planar wings. This molecular system exhibits respectively red, green, and blue (RGB) emission from a single-component luminophore in different environments, namely in polymer matrix, in solution, and in crystals. The flexible unit gives rise to a dynamic conformational change in the excited state from a nonplanar V-shaped structure to a planar structure, leading to a dual fluorescence of blue and green colors. The rigid and planar moieties favor the formation of a two-fold π-stacked array of the V-shaped molecules in the crystalline state, which produces a red excimer-like emission. These RGB emissions are attained without changing the excitation energy.
Propagation of polarized light in turbid media: simulated animation sequences (2000)

A time-resolved Monte Carlo technique was used to simulate the propagation of polarized light in turbid media. Calculated quantities include the reflection Mueller matrices, the transmission Mueller matrices, and the degree of polarization (DOP). The effects of the polarization state of the incident light and of the size of scatterers on the propagation of DOP were studied. Results are shown in animation sequences.
Treatment of Iron Deficiency Anemia in Pregnancy with Intravenous versus Oral Iron: Systematic Review and Meta-Analysis (2018)

In this meta-analysis, IV iron is superior to oral iron for treatment of iron-deficiency anemia in pregnancy. Women receiving IV iron more often achieve desired hemoglobin targets, faster and with fewer side effects.
Construction of human chromosome 21-specific yeast artificial chromosomes. (1989)

Chromosome 21-specific yeast artificial chromosomes (YACs) have been constructed by a method that performs all steps in agarose, allowing size selection by pulsed-field gel electrophoresis and the use of nanogram to microgram quantities of DNA. The DNA sources used were hybrid cell line WAV-17, containing chromosome 21 as the only human chromosome and flow-sorted chromosome 21. The transformation efficiency of ligation products was similar to that obtained in aqueous transformations and yielded YACs with sizes ranging from 100 kilobases (kb) to greater than 1 megabase when polyamines were included in the transformation procedure. Twenty-five YACs containing human DNA have been obtained from a mouse-human hybrid, ranging in size from 200 to greater than 1000 kb, with an average size of 410 kb. Ten of these YACs were localized to subregions of chromosome 21 by hybridization of RNA probes (corresponding to the YAC ends recovered in Escherichia coli) to a panel of somatic cell hybrid DNA. Twenty-one human YACs, ranging in size from 100 to 500 kb, with an average size of 150 kb, were obtained from approximately equal to 50 ng of flow-sorted chromosome 21 DNA. Three were localized to subregions of chromosome 21. YACs will aid the construction of a physical map of human chromosome 21 and the study of disorders associated with chromosome 21 such as Alzheimer disease and Down syndrome.