gebhart/patrepeval huggingface dataset:
Deletion of a 9,000-base-pair segment of the vaccinia virus genome that encodes nonessential polypeptides (1981)

Deletions contained within the genomes of unstable and stable variants of vaccinia virus (strain WR) were analyzed. Restriction endonuclease mapping and hybridization to specific 32P-labeled DNA probes indicated that more than 6 X 10(6) daltons of DNA were deleted from the variants. In each case, the deletion occurred on the left side of the genome and started very close to the junction of the inverted terminal repetition and unique sequence. Both variants also contained a new SstI side on the right side of the genome. Hybridization selection and cell-free translation experiments indicated that these variants lost the ability to synthesize at least eight early mRNA's mapping within the deleted region. Although the deleted DNA was not essential for replication of the WR strain of vaccinia virus under laboratory conditions of infection, it presumably has a defined role under other circumstances. This conclusion was based on the conservation within the Elstree strain of vaccinia, the Utrecht strain of rabbitpox, and the Brighton strain of cowpox virus of sequences homologous to the deleted DNA. Moreover, mRNA's that hybridized to the deleted vaccinia virus DNA segment and encoded similar size polypeptides were made in cells infected with rabbitpox and cowpox viruses.
A reconfigurable multifunction computing cache architecture (2001)

A considerable portion of a microprocessor chip is dedicated to cache memory. However, not all applications need all the cache storage all the time, especially the computing bandwidth-limited applications. In addition, some applications have large embedded computations with a regular structure. Such applications may be able to use additional computing resources. If the unused portion of the cache could serve these computation needs, the on-chip resources would be utilized more efficiently. This presents an opportunity to explore the reconfiguration of a part of the cache memory for computing. Thus, we propose adaptive balanced computing (ABC)-dynamic resource configuration on demand from application-between memory and computing resources. In this paper, we present a cache architecture to convert a cache into a computing unit for either of the following two structured computations: finite impulse response and discrete/inverse discrete cosine transform. In order to convert a cache memory to a function unit, we include additional logic to embed multibit output lookup tables into the cache structure. The experimental results show that the reconfigurable module improves the execution time of applications with a large number of data elements by a factor as high as 50 and 60.
Acute-Phase Markers of Inflammation and Glomerular Structure in Patients with Type 2 Diabetes (2005)

Type 2 diabetes is frequently associated with an inflammatory status; the relationships between low-grade inflammation and diabetic nephropathy are still unclear. The aim of this study was to evaluate the relationships between acute-phase markers of inflammation, glomerular structure, and albumin excretion rate (AER) in type 2 diabetes. In 74 patients with type 2 diabetes (23 normoalbuminuric, 30 microalbuminuric, and 21 proteinuric) fibrinogen, serum amyloid A protein (SAA), C-reactive protein (CRP), and IL-6 were determined. AER was measured on three 24-h urine collections; GFR was measured by 51Cr EDTA plasma clearance. A kidney biopsy was performed, and mesangial fractional volume [Vv(mes/glom)] and glomerular basement membrane (GBM) width were estimated by electron microscopic morphometric analysis. CRP, fibrinogen, SAA, and IL-6 differed among groups, with proteinuric patients having the highest levels. SAA and fibrinogen correlated with AER (P < 0.03 and P < 0.001, respectively). GBM width and Vv(mes/glom) increased from normoalbuminuric to proteinuric patients [P < 0.005 normoalbuminuric and microalbuminuric versus proteinuric for GBM, P < 0.01 normoalbuminuric versus proteinuric for Vv(mes/glom)]. In patients with increased GBM width (> 396 nm), CRP, SAA, and IL-6 were higher than in patients with normal GBM width (P < 0.003, P < 0.004, and P < 0.0004, respectively). GBM width was directly correlated with fibrinogen (r = 0.33, P < 0.002) and IL-6 (r = 0.25 P < 0.05). In conclusion, this study demonstrates that acute-phase markers of inflammation are associated with nephropathy status and GBM thickening, suggesting a role for inflammation in the pathogenesis of diabetic glomerulopathy.
A Sensitive Cardiac Troponin T Assay in Stable Coronary Artery Disease (2009)

After adjustment for other independent prognostic indicators, cardiac troponin T concentrations as measured with a highly sensitive assay were significantly associated with the incidence of cardiovascular death and heart failure but not with myocardial infarction in patients with stable coronary artery disease.
Optimization of direct arylation polymerization (DArP) through the identification and control of defects in polymer structure (2014)

ABSTRACT As a newly emerged protocol for the synthesis of conjugated polymers, direct arylation polymerization (DArP) is an environmentally friendly and cost‐effective alternative to traditional methods of polymerization. DArP efficiently yields conjugated polymers with high yield and high molecular weight. However, DArP is also known to produce defects in polymer chemical structure. Together with molecular weight and polydispersity, these defects are considered to be important parameters of polymer structure and they have a strong impact on optical, electronic and thermal properties of conjugated polymers. The four major classes of conjugated polymer defects inherent for DArP have been identified: homocoupling regiodefects, branching defects, end group defects, and residual metal defects. To have a precise control over the polymer properties, it is important to understand what causes the defects to form during the polymerization process and be able to control their content. Here within the scope of current literature, we discuss in detail the definition and origin of all these defects, their influence on polymer properties and effective means to control the defects through fine tuning of the DArP reaction parameters. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53 , 135–147
Cellular and Molecular Mechanisms of Tumor-Induced T-Cell Tolerance (2007)

The spontaneous interaction between tumor cells and the immune system has been shown to result in reciprocal changes leading to a less immunogenic tumor and immune cells less capable or unable to mount an effective response against a growing malignancy. Although several mechanisms have been proposed to account for the ability of tumor cells to render immune cells less efficient, one that has gained particular attention relates to the recognition of tumor antigens by T-cells, a process that unfortunately leads to the induction and establishment of antigen-specific T-cell tolerance rather than T-cell priming. Here, we present the experimental and clinical evidence that help identify this remarkable barrier that the immune system itself and more specifically its mechanisms of tolerance induction has imposed to our efforts to effectively harness the immune system against tumors. In particular, we will discuss the central role of bone marrow-derived antigen-presenting cells (APCs) in the induction of this state of T-cell unresponsiveness and the potential role of the tumor microenvironment in determining the tolerogenic properties of these APCs. Finally, we provide information on receptor-ligands and intracellular signaling pathways that given their role in influencing the inflammatory properties of APCs are being exploited as targets to revert mechanisms of T-cell unresponsiveness in cancer.
An Iterative Receiver for WCDMA Systems with MIMO Transmissions and Hierarchical Constellations (2006)

In this paper we consider the use of M-QAM hierachical constellations (quadrature amplitude modulation) and MIMO (multiple input multiple output) for the transmission of multicast and broadcast services in the downlink connection of a WCDMA (wideband code division multiple access) system. The objective is to increase the efficiency of the transmission by splitting the information in classes with different importance and mapping the bit streams of these classes to more or less protected positions of the modulation symbols. With this strategy, the most important information streams can be received by all users while the less relevant information will only be extracted by users with good propagation conditions. Due to the more demanding channel estimation requirements and the higher sensitivity to interference resulting from the usage of several antennas and hierarchical constellations, an enhanced receiver based on the turbo concept is developed and evaluated. It is shown that high transmission bit rates can be achieved even in high delay spread environments
Circulating microRNA Profile throughout the Menstrual Cycle (2013)

Normal physiological variables, such as age and gender, contribute to alterations in circulating microRNA (miRNA) expression levels. The changes in the female body during the menstrual cycle can also be reflected in plasma miRNA expression levels. Therefore, this study aimed to determine the plasma miRNA profile of healthy women during the menstrual cycle and to assess which circulating miRNAs are derived from blood cells. The plasma miRNA expression profiles in nine healthy women were determined by quantitative real time PCR using Exiqon Human Panel I assays from four time-points of the menstrual cycle. This platform was also used for studying miRNAs from pooled whole blood RNA samples at the same four time-points. Our results indicated that circulating miRNA expression levels in healthy women were not significantly altered by the processes occurring during the menstrual cycle. No significant differences in plasma miRNA expression levels were observed between the menstrual cycle time-points, but the number of detected miRNAs showed considerable variation among the studied individuals. miRNA analysis from whole blood samples revealed that majority of miRNAs in plasma are derived from blood cells. The most abundant miRNA in plasma and blood was hsa-miR-451a, but a number of miRNAs were only detected in one or the other sample type. In conclusion, our data suggest that the changes in the female body during the menstrual cycle do not affect the expression of circulating miRNAs at measurable levels.
Thermoelectric Behavior of Segregated-Network Polymer Nanocomposites (2008)

Segregated-network carbon nanotube (CNT)-polymer composites were prepared, and their thermoelectric properties were measured as a function of CNT concentration at room temperature. This study shows that electrical conductivity can be dramatically increased by creating a network of CNTs in the composite, while the thermal conductivity and thermopower remain relatively insensitive to the filler concentration. This behavior results from thermally disconnected, but electrically connected, junctions in the nanotube network, which makes it feasible to tune the properties in favor of a higher thermoelectric figure of merit. With a CNT concentration of 20 wt %, these composites exhibit an electrical conductivity of 4800 S/m, thermal conductivity of 0.34 W/m x K and a thermoelectric figure of merit (ZT) greater than 0.006 at room temperature. This study suggests that polymeric thermoelectrics are possible and provides the basis for further development of lightweight, low-cost, and nontoxic polymer composites for thermoelectric applications in the future.
Synthesis and Biological Evaluation of 3-Heterocyclyl-7,8,9,10-tetrahydro-(7,10-ethano)-1,2,4-triazolo[3,4-a]phthalazines and Analogues as Subtype-Selective Inverse Agonists for the GABAAα5 Benzodiazepine Binding Site (2004)

The identification of a novel series of 7,8,9,10-tetrahydro-(7,10-ethano)-1,2,4-triazolo[3,4-a]phthalazines as GABA(A)alpha5 inverse agonists, which have both binding and functional (efficacy) selectivity for the benzodiazepine binding site of alpha5- over alpha1-, alpha2-, and alpha3-containing GABA(A) receptor subtypes, is described. Binding selectivity was determined to a large part by the degree of planarity of the fused ring system whereas functional selectivity was dependent on the nature of the heterocycle at the 3-position of the triazolopyridazine ring. 3-Furan and 5-methylisoxazole were shown to be optimal for GABA(A)alpha5 functional selectvity. 3-(5-Methylisoxazol-3-yl)-6-(2-pyridyl)methyloxy-1,2,4-triazolo[3,4-a]phthalazine (43) was identified as a full inverse agonist at the GABA(A)alpha5 subtype with functional selectivity over the other GABA(A) receptor subtypes and good oral bioavailability.
Immunolocalisation of E-cadherin and -catenin in human pterygium (2007)

It is suggested that E-cadherin and beta-catenin are concentrated in pterygium tissue, and are possibly involved with epithelial proliferation and adhesion.
Chaperoning Function of Stress Protein grp170, a Member of the hsp70 Superfamily, Is Responsible for its Immunoadjuvant Activity (2006)

When used as vaccines, tumor-derived stress proteins can elicit antitumor immune responses. For members of the hsp70 superfamily, like grp170, this seems to be due to (a) the chaperoning of antigenic peptide by the stress protein and (b) the binding of the stress protein to receptor(s) on antigen-presenting cells (APC) and subsequent antigen presentation. This suggests that domains exist on the stress protein for each function. In this study, we determine the ability of grp170 and its structural domains to (a) bind to and present melanoma-associated antigen gp100 to the immune system and (b) to bind to receptors on APCs. A direct correlation between chaperone function, binding to APCs in a receptor-like manner, and antitumor immunity was observed. Two mutants that share no common sequence, yet are both effective in their antitumor activities, compete with one another for APC binding. Studies of other members of the hsp70 superfamily, hsp110 and hsp70, or their domain deletion mutants, further confirmed that APC binding segregates with chaperoning function and not sequence. Therefore, these studies suggest that molecular chaperoning is involved in stress protein interactions with APCs, antigen binding, and in eliciting antitumor immunity, thus bridging this ancient function of stress proteins in prokaryotes to their ability to elicit immunity in higher organisms.
Production of Antisera to Synthetic Peptides (2003)

The objective of immunization is to produce polyclonal or monoclonal antibodies that react with a chosen molecule. Immunization may be in vivo by injecting antigen into animals to produce antisera or to provide B-lymphocytes for immortalization as hybridomas, or alternatively, in vitro using splenocytes from untreated animals () for subsequent fusion with myeloma cells to produce monoclonal antibodies (MAbs). The latter approach, despite showing initial promise, is now only rarely used.
BioMoby extensions to the Taverna workflow management and enactment software (2006)

With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.
Off‐resonance saturation as a means of generating contrast with superparamagnetic nanoparticles (2006)

This work demonstrates an alternative approach, termed off-resonance saturation (ORS), for generating contrast that is sensitive to superparamagnetic particles. This method leads to a calculated contrast that increases with superparamagnetic nanoparticle concentration. Experimental data demonstrate that in the presence of superparamagnetic particles, an off-resonance effect exists that is distinct from the magnetization transfer (MT) effect and is highly dependent on diffusion. Data show that the dependence on water diffusion becomes most significant at rates of 0.5 x 10(-9) m(2)/s and slower. We investigated the dependence of the off-resonance effect on off-resonance frequency and particle concentration. The data suggest a useful frequency offset range of 500 Hz < |Deltaomega| < 1500 Hz at 3T. This approach may be especially useful in organs and diseases in which diffusion may be altered by pathologies.
T Cell Activation Determined by T Cell Receptor Number and Tunable Thresholds (1996)

The requirements for T cell activation have been reported to vary widely depending on the state of the T cell, the type of antigen-presenting cell, and the nature of the T cell receptor (TCR) ligand. A unitary requirement for T cell responses was revealed by measurement of the number of triggered TCRs. Irrespective of the nature of the triggering ligand, T cells "counted" the number of triggered TCRs and responded when a threshold of approximately 8000 TCRs was reached. The capacity to reach the activation threshold was severely compromised by a reduction in the number of TCRs. Costimulatory signals lowered the activation threshold to approximately 1500 TCRs, thus making T cells more sensitive to antigenic stimulation.
Microfabricated Device for DNA and RNA Amplification by Continuous-Flow Polymerase Chain Reaction and Reverse Transcription-Polymerase Chain Reaction with Cycle Number Selection (2002)

We have developed a high-throughput microfabricated, reusable glass chip for the functional integration of reverse transcription (RT) and polymerase chain reaction (PCR) in a continuous-flow mode. The chip allows for selection of the number of amplification cycles. A single microchannel network was etched that defines four distinct zones, one for RT and three for PCR (denaturation, annealing, extension). The zone temperatures were controlled by placing the chip over four heating blocks. Samples and reagents for RT and PCR were pumped continuously through appropriate access holes. Outlet channels were etched after cycles 20, 25, 30, 35, and 40 for product collection. The surface-to-volume ratio for the PCR channel is 57 mm-1 and the channel depth is 55 μm, both of which allow very rapid heat transfer. As a result, we were able to collect PCR product after 30 amplification cycles in only 6 min. Products were collected in 0.2-mL tubes and analyzed by agarose gel electrophoresis and ethidium bromide staining. We studied DNA and RNA amplification as a function of cycle number. The effect of the number of the initial DNA and RNA input molecules was studied in the range of 2.5 × 106−1.6 × 108 and 6.2 × 106−2 × 108, respectively. Successful amplification of a single-copy gene (β-globin) from human genomic DNA was carried out. Furthermore, PCR was performed on three samples of DNA of different lengths (each of 2-μL reaction volume) flowing simultaneously in the chip, and the products were collected after various numbers of cycles. Reverse transcription was also carried out on four RNA samples (0.7-μL reaction volume) flowing simultaneously in the chip, followed by PCR amplification. Finally, we have demonstrated the concept of manually pumped injection and transport of the reaction mixture in continuous-flow PCR for the rapid generation of amplification products with minimal instrumentation. To our knowledge, this is the first report of a monolithic microdevice that integrates continuous-flow RT and PCR with cycle number selection.
Retinoids and interferon: a new promising combination? (1991)

The retinoids: all-transretinoic acid (tretinoin), 13-cis retinoic acid (isotretinoin) and the aromatic retinoids etretinate and acitretin have a preventive and therapeutic effect on chemically-induced tumours. Clinically, retinoids have shown variable effectiveness in therapy and/or prevention of oncological diseases of skin, head and neck, lung, bladder, vulva and bone marrow. With a few exceptions, monotherapy with retinoids has not been satisfactory. Similarly, monotherapy with interferon alpha has been used successfully only for some specific indications. Retinoids have a marked differentiation-inducing effect which may contribute to their therapeutic effect. Experiments were carried out in transformed cell lines to test the combination of retinoids with interferon alpha and other cytokines on differentiation. In HL-60 cells, an acute promyelocytic leukaemia cell line, induction of differentiation was determined by induction of an oxidative burst potential. Retinoids showed the following order of activity: tretinoin greater than isotretinoin greater than acitretin. Cytokines had no differentiation-inducing effect by themselves. However, the addition of the following cytokines to retinoids potentiated the retinoid-induced differentiation: IFN alpha, IFN beta, IFN gamma, TNF alpha, G-CSF, IL-1 alpha and IL-4. In experiments with HL-60 or other cell lines, the pattern of differentiation-induction was always dependent on the particular retinoid/cytokine combination. IFN alpha provoked a marked potentiation of retinoid-induced differentiation. The combination of the antiproliferative and differentiation-inducing effect of the retinoids together with the antiproliferative, immunostimulatory and differentiation-potentiating effects of IFN alpha suggests that this combination might be a particularly promising treatment for neoplastic diseases.
Fault Tolerance of Neural Networks (1994)

This effort studied fault tolerance aspects of artificial neural networks, and resulted in the development of neural learning techniques that more effectively utilize the inherent redundancy and excess of resources over the minimum required found in most classically trained networks. Performance evaluation measures were developed and used to quantify network tolerance to faults such as single link failures, multiple node failures, multiple link failures, and also small degradations in multiple links or nodes. Several variations of the basic back-propagation algorithm were designed and implemented, yielding improvements in fault tolerance. An Addition-Deletion algorithm was designed to successively modify the size of a network by deleting nodes that do not contribute to fault tolerance, and to add new nodes in a way that is assured to improve fault tolerance. The techniques designed in this project were compared to those suggested by others, and were found to improve robustness. Also, a Refine algorithm was defined, which takes a robust network which does not satisfy hardware restrictions and transforms it to another network which does.
Two Independent Nuclear Localization Signals Are Present in the DNA-binding High-mobility Group Domains of SRY and SOX9 (1997)

SRY and SOX9, members of the family of high-mobility group (HMG) domain transcription factors, are both essential for testis formation during human embryonic development. The HMG domain is a DNA-binding and DNA-bending motif comprising about 80 amino acid residues. It has been shown that SRY and SOX9 are nuclear proteins. Using normal or mutant SRY-beta-galactosidase and SOX9-beta-galactosidase fusion proteins in transfection studies involving COS-7 cells, we have identified two nuclear localization signals (NLSs) within the HMG domains of both proteins that can independently direct the fusion proteins into the nucleus. Only mutational inactivation of both NLS motifs resulted in complete exclusion of the fusion proteins from the nucleus. The NLS sequences are located at the N and C termini of the HMG domain and are a bipartite NLS motif and a basic cluster NLS motif, respectively. Both NLS motifs are conserved in the HMG domains of other transcription factors. The implications of the present results are discussed regarding (a) the apparent dual function of certain basic amino acid residues in the HMG domain of SRY in both DNA binding and in nuclear localization and (b) the possible control of SOX9 in early gonadal differentiation at the level of nuclear translocation.