gebhart/patrepeval huggingface dataset:
Opposing Roles of WNT-5A and WNT-11 in Interleukin-1β Regulation of Type II Collagen Expression in Articular Chondrocytes (2006)

Interleukin (IL)-1beta is a major catabolic cytokine that plays a pivotal role in cartilage destruction. This study examined the possible involvement and regulatory mechanisms of Wnt signaling in IL-1beta-induced inhibition of type II collagen expression in chondrocytes. Treatment of chondrocytes with IL-1beta up-regulated Wnt-5a and down-regulated Wnt-11 expression. Conditioned medium from Wnt-5a-expressing cells inhibited type II collagen expression, whereas knockdown of Wnt-5a by siRNA blocked the inhibitory effects of IL-1beta on type II collagen expression. In contrast to the inhibitory effects of Wnt-5a, Wnt-11 stimulated type II collagen expression. Wnt-5a and Wnt-11 did not cause accumulation of beta-catenin or activation of the beta-catenin-Tcf/Lef transcriptional complex. Instead, we found that Wnt-5a activated c-Jun N-terminal kinase and that an inhibitor of this kinase blocked Wnt-5a inhibition of type II collagen expression. In contrast, Wnt-11 activated protein kinase C and an inhibitor of this kinase blocked Wnt-11 stimulation of type II collagen expression. Collectively, these results indicate that Wnt-5a and Wnt-11 signaling through distinct non-canonical Wnt pathways have opposing effects on type II collagen expression by chondrocytes.
FPGA-accelerated Information Retrieval: High-efficiency document filtering (2009)

Power consumption in data centres is a growing issue as the cost of the power for computation and cooling has become dominant. An emerging challenge is the development of ldquoenvironmentally friendlyrdquo systems. In this paper we present a novel application of FPGAs for the acceleration of information retrieval algorithms, specifically, filtering streams/collections of documents against topic profiles. Our results show that FPGA acceleration can result in speed-ups of up to a factor 20 for large profiles.
Extremely low frequency electromagnetic field enhances human keratinocyte cell growth and decreases proinflammatory chemokine production (2008)

Background Proliferation and differentiation of keratinocytes are central processes in tissue regeneration after injury. Chemokines, produced by a wide range of cell types including keratinocytes, play a regulatory role in inflammatory skin diseases. Several studies have shown that an electromagnetic field (EMF) can influence both inflammatory processes and repair mechanisms including wound healing on different tissue models. Objectives To elucidate the effect of extremely low frequency EMF (ELF-EMF) on keratinocyte proliferation and production of chemokines [RANTES, monocyte chemoattractant protein (MCP)-1, macrophage inflammatory protein (MIP)-1α and interleukin (IL)-8] in order to evaluate a potential therapeutic use of magnetic fields. Methods The human keratinocyte cell line HaCaT was exposed at 1 mT, 50 Hz for different lengths of time and compared with unexposed control cells. Cell growth and viability were evaluated at different exposure times by cell count and trypan blue exclusion. Chemokine production and expression were analysed by enzyme-linked immunosorbent assay (ELISA) and by real-time polymerase chain reaction. Total NF-κB p65 was quantified by ELISA. Results Significantly increased growth rates were observed after 48 h of EMF exposure as compared with control cells, while no difference in cell viabilities were detected. Gene expression and release of RANTES, MCP-1, MIP-1α and IL-8 were significantly reduced after 72 h of exposure. NF-κB levels became almost undetectable after only 1 h of EMF exposure, and were inversely correlated with cell density. Conclusions Our results show that ELF-EMF modulates chemokine production and keratinocyte growth through inhibition of the NF-κB signalling pathway and thus may inhibit inflammatory processes. ELF-EMF could represent an additional therapeutic approach in the treatment of skin injury.
Global analysis of cellular transcription following infection with an hiv-based vector (2003)

We have examined the changes in cellular transcription resulting from infection with HIV-based vectors. Previous work suggested that the incoming viral genome may under some circumstances be detected as DNA damage, so to explore this possibility, we compared the transcriptional response to infection with an HIV-based vector to the response to treatment with the DNA-damaging agent etoposide. Expression levels of about 12,000 cellular RNA transcripts were determined in a human B-cell line at different times after either treatment. Statistical analysis revealed that the infection with the lentivirus vector resulted in quite modest changes in gene expression. Treatment with etoposide, in contrast, caused drastic changes in expression of genes known or inferred to be involved in apoptosis. Statistically significant though subtle parallels in the cellular transcriptional responses to etoposide treatment and HIV-vector infection could be detected. Several further data sets analyzing infections with HIV-based vectors or wild-type HIV-1 showed similar modest effects on cellular transcription and very modest parallels among different data sets. These findings establish that HIV-vector or HIV-1 infection has remarkably little effect on cellular transcription. The statistical methods described here may be of wide use in mining microarray data sets. Our observations support the idea that gene therapy with HIV-based vectors should not be particularly toxic to cells due to disruption of cellular transcription.
Etiology of Community‐Acquired Pneumonia: Increased Microbiological Yield with New Diagnostic Methods (2009)

By supplementing traditional diagnostic methods with new PCR-based methods, a high microbial yield was achieved. This was especially evident for patients with complete sampling. Mixed infections were frequent (most commonly S. pneumoniae together with a respiratory virus).
Functional diversity of T lymphocytes due to secretion of different cytokine patterns (1991)

Different helper T cell subsets secrete different patterns of cytokines when stimulated by antigen. The TH1 and TH2 subsets differ in the secretion of at least eight cytokines, and three or more other cytokine secretion patterns also exist among both mouse and human T cell clones. Several properties of strong immune responses suggest that at least the TH1 and TH2 phenotypes can be present in vivo. As cytokines are major determinants of the functions of the T cells that produce them, these patterns lead to different properties of the T cell subsets. TH1 cells mediate several functions connected with cytotoxicity and local inflammatory reactions, and so these T cells are particularly effective at combating viruses and intracellular bacteria and parasites. TH2 cells are much more effective at stimulating B cells to produce antibody, and so should be more effective against free-living bacteria, and in inducing protective humoral immunity. Antibody and delayed inflammatory reactions are often mutually exclusive during immune responses, and this can be at least partially explained by cross-inhibition of TH1 and TH2 cells. A newly discovered cytokine, IL10, has been implicated as one of the cross-regulatory cytokines, as this TH2 product inhibits cytokine synthesis by TH1 cells.
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". (1990)

The four-base loops that cap many double-helical structures in rRNA (the so-called "tetra-loops") exhibit highly invariant to highly variable sequences depending upon their location in the molecule. However, in the vast majority of these cases the sequence of a tetra-loop is independent of its location and conforms to one of three general motifs, GNRA, UNCG, and (more rarely) CUUG. For the most frequently varying of the 16S rRNA tetra-loops, that at position 83 (Escherichia coli numbering), the three sequences CUUG, UUCG, and GCAA account for almost all examples encountered, and each of them has independently arisen at least a dozen times. The closing base pair of tetra-loop hairpins reflects the loop sequence, tending to be C.G for UUCG loops and G.C for CUUG loops.
Diabetic nephropathy &ndash; complications and treatment (2014)

Diabetic nephropathy is a significant cause of chronic kidney disease and end-stage renal failure globally. Much research has been conducted in both basic science and clinical therapeutics, which has enhanced understanding of the pathophysiology of diabetic nephropathy and expanded the potential therapies available. This review will examine the current concepts of diabetic nephropathy management in the context of some of the basic science and pathophysiology aspects relevant to the approaches taken in novel, investigative treatment strategies.
The Ca signal from fura‐2 loaded mast cells depends strongly on the method of dye‐loading (1985)

The Ca concentration ([Ca2+]i) in single rat peritoneal mast cells was measured by means of the new fluorescent Ca-indicator dye fura-2. Dye-loaded cells were made to degranulate with either antigen or compound 48/80. In cells loaded with extracellularly applied, membrane-permeant fura-2 ester, degranulation was accompanied by a permanent loss of 40-60% of the fluorescence, but comparison of fluorescence at different wavelengths indicated no or only small changes in [Ca2+]i. When cells were loaded by microinjection of the impermeant potassium salt of the dye, degranulation resulted in no permanent loss of fluorescence, but instead was preceded by transient fluorescence changes that indicate a rapid, large and transient increase in [Ca2+]i. We suggest that ester-loaded fura-2 accumulates to a significant degree in the secretory granules and is lost from the cell during exocytosis.
Solution structure of γ‐bungarotoxin: The functional significance of amino acid residues flanking the RGD motif in integrin binding (2004)

Gamma-bungarotoxin, a snake venom protein isolated from Bungarus multicinctus, contains 68 amino acids, including 10 cysteine residues and a TAVRGDGP sequence at positions 30-37. The solution structure of gamma-bungarotoxin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The structure is similar to that of the short-chain neurotoxins that contain three loops extending from a disulfide-bridged core. The tripeptide Arg-Gly-Asp (RGD) sequence is located at the apex of the flexible loop and is similar to that of other RGD-containing proteins. However, gamma-bungarotoxin only inhibits platelet aggregations with an IC50 of 34 microM. To understand its weak activity in inhibiting platelet aggregation, we mutated the RGD loop sequences of rhodostomin, a potent platelet aggregation inhibitor, from RIPRGDMP to TAVRGDGP, resulting in a 196-fold decrease in activity. In addition, the average Calpha-to-Calpha distance between R33 and G36 of gamma-bungarotoxin is 6.02 A, i.e., shorter than that of other RGD-containing proteins that range from 6.55 to 7.46 A. These results suggested that the amino acid residues flanking the RGD motif might control the width of the RGD loop. This structural difference may be responsible for its decrease in platelet aggregation inhibition compared with other RGD-containing proteins.
N-terminal and cDNA characterization of murine lymphocyte antigen Ly-6C.2. (1988)

The Ly-6C.2 molecule was purified from K36 tumor cells by affinity chromatography and gel filtration. The electrophoretically homogeneous preparation, with m.w. 15,000, was tested with a panel of antibodies that confirmed the presence of the LY-6C.2 epitope. An N-terminal sequence of 39 amino acids was obtained showing 59% homology with the corresponding portion of the Ly-6A.2 polypeptide. Based on the least homologous (29%) 14 amino acid segment, an oligonucleotide probe was constructed, and Ly-6C.2 cDNA was cloned from a BW5147 cDNA library. A 794-base pair cDNA containing the entire coding region had 82% homology with Ly-6A.2 cDNA. The encoded polypeptide sequence of 131 amino acids containing a perfect correlation with the N-terminal sequence data was 63% homologous with that of Ly-6A.2. The greatest homology was in the leader, first 16 N-terminal and last 39 C-terminal amino acids. The latter are likely to be important in determining the attachment of glycophosphatidylinositol. Despite results indicating fewer disulfide constraints in the Ly-6C molecule, the predicted sequence contains 10 cysteine residues nearly perfectly matched with those predicted in Ly-6A.
Statistical Methods for Evaluating DNA Methylation as a Marker for Early Detection or Prognosis (2007)

We summarize standard and novel statistical methods for evaluating the classification accuracy of DNA methylation markers. The choice of method will depend on the type of marker studied (qualitative/quantitative), the number of markers, and the type of outcome (time-invariant/time-varying). A minimum of two error rates are needed for assessing marker accuracy: the true-positive fraction and the false-positive fraction. Measures of association that are computed from the combination of these error rates, such as the odds ratio or relative risk, are not informative about classification accuracy. We provide an example of a DNA methylation marker that is strongly associated with time to death (logrank p=0.0003) that is not a good classifier as evaluated by the true-positive and false-positive fractions. Finally, we would like to emphasize the importance of study design. Markers can behave differently in different groups of individuals. It is important to know what factors may affect the accuracy of a marker and in which subpopulations the marker may be more accurate. Such an understanding is extremely important when comparing marker accuracy in two groups of subjects.
Advanced illumination techniques for GPU volume raycasting (2008)

Volume raycasting techniques are important for both visual arts and visualization. They allow an efficient generation of visual effects and the visualization of scientific data obtained by tomography or numerical simulation. Thanks to their flexibility, experts agree that GPU-based raycasting is the state-of-the art technique for interactive volume rendering. It will most likely replace existing slice-based techniques in the near future. Volume rendering techniques are also effective for the direct rendering of implicit surfaces used for soft body animation and constructive solid geometry.
Caspases: Enemies Within (1998)

Apoptosis, an evolutionarily conserved form of cell suicide, requires specialized machinery. The central component of this machinery is a proteolytic system involving a family of proteases called caspases. These enzymes participate in a cascade that is triggered in response to proapoptotic signals and culminates in cleavage of a set of proteins, resulting in disassembly of the cell. Understanding caspase regulation is intimately linked to the ability to rationally manipulate apoptosis for therapeutic gain.
Activation of latent TGF‐β1 by low‐power laser in vitro correlates with increased TGF‐β1 levels in laser‐enhanced oral wound healing (2007)

The term Laser "Photobiomodulation" was coined to encompass the pleiotropic effects of low-power lasers on biological processes. The purpose of this study was to investigate whether transforming growth factor (TGF)-beta had a role in mediating the biological effects of low-power far-infrared laser irradiation. We assayed for in vitro activation using various biological forms of cell-secreted, recombinant, and serum latent TGF-beta using the p3TP reporter and enzyme-linked immunosorbent assays. We demonstrate here that low-power lasers are capable of activating latent TGF-beta1 and -beta3 in vitro and, further, that it is capable of "priming" these complexes, making them more amenable to physiological activation present in the healing milieu. Using an in vivo oral tooth extraction-healing model, we observed an increased TGF-beta1, but not beta3, expression by immunohistochemistry immediately following laser irradiation while TGF-beta3 expression was increased after 14 days, concomitant with an increased inflammatory infiltrate. All comparisons were performed between laser-irradiated wounds and nonirradiated wounds in each subject essentially using them as their own control (paired T-test p<0.05). Low-power laser irradiation is capable of activating the latent TGF-beta1 complex in vitro and its expression pattern in vivo suggests that TGF-beta play a central role in mediating the accelerated healing response.
Surface Functionalization of Electrodes with Molecular Reagents (1986)

The use of molecular reagents to manipulate the properties of electrode surfaces has broad application in areas such as electrochemical synthesis, energy conversion and storage, displays, sensors, and new kinds of microelectronic devices. Surface modification of electrodes has contributed to a revival of interest in basic and applied research in electrochemistry and electrochemical devices. This article is focused on specific examples of systems modified electrodes where basic developments provide promising opportunities for applications stemming from the properties of molecules attached to an electrode surface.
High Temperature Requirement A3 (HtrA3) Promotes Etoposide- and Cisplatin-induced Cytotoxicity in Lung Cancer Cell Lines (2010)

Lung cancer is the leading cause of cancer-related deaths worldwide. Here we show for the first time that HtrA3 is a mitochondrial stress-response factor that promotes cytotoxicity to etoposide and cisplatin in lung cancer cell lines. Exogenous expression of wild type HtrA3 domain variants significantly attenuated cell survival with etoposide and cisplatin treatment in lung cancer cell lines H157 and A549 compared with expression of protease inactive mutants (S305A) or vector control. Conversely, HtrA3 suppression promoted cell survival with etoposide and cisplatin treatment in lung cancer cell lines Hop62 and HCC827. Survival was attenuated by re-expression of wild type HtrA3 variants during treatment but not by protease inactive mutants or vector control. HtrA3 also co-fractionated and co-localized with mitochondrial markers with both endogenous and exogenous expression in normal lung and lung cancer cell lines but was translocated from mitochondria following etoposide treatment. Moreover, HtrA3 translocation from mitochondria correlated with an increase in cell death that was attenuated by either HtrA3 suppression or Bcl-2 overexpression. Taken together, these results suggest that HtrA3 may be a previously uncharacterized mitochondrial cell death effector whose serine protease function may be crucial to modulating etoposide- and cisplatin-induced cytotoxicity in lung cancer cell lines.
Somatic mutations of adenomatous polyposis coli gene and nuclear b‐catenin accumulation have prognostic significance in invasive urothelial carcinomas: Evidence for Wnt pathway implication (2008)

Wnt pathway signaling is crucial in many cancers and data indicate crosstalk with other key cancer pathways, however in urothelial carcinogenesis it has not been extensively studied. We searched for mutations in adenomatous polyposis coli (APC), a key regulator of the pathway, and studied b-catenin expression and interactions with the expression of other markers of apoptosis, angiogenesis, and proliferation in patients with invasive urothelial cancer. The mutation cluster region of APC was directly sequenced in 70 patients with muscle invasive disease who were treated with surgery and adjuvant chemotherapy. COX-2, p53, Ki67, and b-catenin were studied immunohistochemically and micro vessel density was quantified by CD105 expression. Single somatic amino-acid substitutions (missense) were found in 9 (13%) and frameshift deletions in 2 (3%) tumors, all located in regions adjacent to b-catenin binding sites. Patients having either APC missense mutations or b-catenin nuclear accumulation had less frequent COX-2 overexpression (24% vs. 76%, p = 0.043) and more frequent lymph node involvement (75% vs. 38%, p = 0.023). Patients with either APC mutations or b-catenin accumulation had shorter disease-free interval (13.4 vs. 28 months, p = 0.07), whereas in multivariate analysis they had shorter disease-specific survival (60.5 vs. 20.6 months, p = 0.048). Somatic APC missense mutations are not rare in advanced urothelial neoplasms. Either APC mutations and/or aberrant expression of b-catenin are associated with worse outcome. Further study of the role of the Wnt pathway, potential crosstalk with other pathways and potential candidate therapeutic targets in urothelial cancer is needed.
Altered srf Expression in Bacillus subtilis Resulting from Changes in Culture pH Is Dependent on the Spo0K Oligopeptide Permease and the ComQX System of Extracellular Control (1998)

The expression of the srf operon of Bacillus subtilis, encoding surfactin synthetase and the competence regulatory protein ComS, was observed to be reduced when cells were grown in a rich glucose- and glutamine-containing medium in which late-growth culture pH was 5.0 or lower. The production of the surfactin synthetase subunits and of surfactin itself was also reduced. Raising the pH to near neutrality resulted in dramatic increases in srf expression and surfactin production. This apparent pH-dependent induction of srf expression required spo0K, which encodes the oligopeptide permease that functions in cell-density-dependent control of sporulation and competence, but not CSF, the competence-inducing pheromone that regulates srf expression in a Spo0K-dependent manner. Both ComP and ComA, the two-component regulatory pair that stimulates cell-density-dependent srf transcription, were required for optimal expression of srf at low and high pHs, but ComP was not required for pH-dependent srf induction. The known negative regulators of srf, RapC and CodY, were found not to function significantly in pH-dependent srf expression. Late-growth culture supernatants at low pH were not active in inducing srf expression in cells of low-density cultures but were rendered active when their pH was raised to near neutrality. ComQ (and very likely the srf-inducing pheromone ComX) and Spo0K were found to be required for the extracellular induction of srf-lacZ at neutral pH. The results suggest that srf expression, in response to changes in culture pH, requires Spo0K and another, as yet unidentified, extracellular factor. The study also provides evidence consistent with the hypothesis that ComP acts both positively and negatively in the regulation of ComA and that both activities are controlled by the ComX pheromone.
Frequency-warping and speaker-normalization (2002)

We have proposed the use of scale-cepstral coefficients as features in speech recognition. We have developed a corresponding frequency-warping function, such that, in the warped domain the formant envelopes of different speakers are approximately translated versions of one and another for any given vowel. These methods were motivated by a desire to achieve speaker-normalization. In this paper, we point out very interesting parallels of the various steps in computing the scale-cepstrum, with those observed in computing features based on physiological models of the auditory system or psychoacoustic experiments. It may therefore be useful to have a better understanding of the need for the various signal-processing steps which may result in the development of more robust recognizers.