gebhart/patrepeval huggingface dataset:
Thymoquinone regulates gene expression levels in the estrogen metabolic and interferon pathways in MCF7 breast cancer cells (2013)

New drugs are continuously being developed for the treatment of patients with estrogen receptor-positive breast cancer. Thymoquinone is one of the drugs that exhibits anticancer characteristics based on in vivo and in vitro models. This study further investigates the effects of thymoquinone on human gene expression using cDNA microarray technology. The quantification of RNA samples was carried out using an Agilent 2100 Bioanalyser to determine the RNA integrity number (RIN). The Agilent Low Input Quick Amplification Labelling kit was used to generate cRNA in two-color microarray analysis. Samples with RIN >9.0 were used in this study. The universal human reference RNA was used as the common reference. The samples were labelled with cyanine-3 (cye-3) CTP dye and the universal human reference was labelled with cyanine-5 (cye-5) CTP dye. cRNA was purified with the RNeasy Plus Mini kit and quantified using a NanoDrop 2000c spectrophotometer. The arrays were scanned data analysed using Feature Extraction and GeneSpring software. Two-step qRT-PCR was selected to determine the relative gene expression using the High Capacity RNA-to-cDNA kit. The results from Gene Ontology (GO) analysis, indicated that 8 GO terms were related to biological processes (84%) and molecular functions (16%). A total of 577 entities showed >2-fold change in expression. Of these entities, 45.2% showed an upregulation and 54.7% showed a downregulation in expression. The interpretation of single experiment analysis (SEA) revealed that the cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) and UDP glucuronosyltransferase 1 family, polypeptide A8 (UGT1A8) genes in the estrogen metabolic pathway were downregulated significantly by 43- and 11‑fold, respectively. The solute carrier family 7 (anionic amino acid transporter light chain, xc-system), member 11 (SLC7A11) gene in the interferon pathway, reported to be involved in the development of chemoresistance, was downregulated by 15‑fold. The interferon-induced protein with tetratricopeptide repeats (IFIT)1, IFIT2, IFIT3, interferon, α-inducible protein (IFI)6 (also known as G1P3), interferon regulatory factor 9 (IRF9, ISGF3), 2'-5'-oligoadenylate synthetase 1, 40/46 kDa (OAS1) and signal transducer and activator of transcription 1 (STAT1) genes all showed changes in expression following treatment with thymoquinone. The caspase 10, apoptosis-related cysteine peptidase (CASP10) gene was activated and the protein tyrosine phosphatase, receptor type, R (PTPRR) and myocyte enhancer factor 2C (MEF2C) genes were upregulated in the classical MAPK and p38 MAPK pathways. These findings indicate that thymquinone targets specific genes in the estrogen metabolic and interferon pathways.
The Multimedia Video Processor (MVP): a chip architecture for advanced DSP applications (2002)

The Texas Instruments Multimedia Video Processor (MVP), a single-chip multi-processing DSP for performing a variety of functions, provides unprecedented computing power and programmability. The MVP is particularly well suited for image and video applications. Utilizing a flexible parallel architecture, the chip can satisfy many video, audio, imaging and graphics functions, such as those required for desktop multimedia.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Establishment and characterization of human laryngeal squamous cell carcinoma cell lines (1999)

These newly established and characterized laryngeal squamous cell carcinoma cell lines will be useful for investigating the biologic characteristics of laryngeal cancer.
CANCER CONTROL WITH RADICAL PROSTATECTOMY ALONE IN 1,000 CONSECUTIVE PATIENTS (2002)

Radical retropubic prostatectomy provided long-term cancer control in 75% of patients with clinically localized prostate cancer and was effective in the majority of those with high risk cancer, including T2c or biopsy Gleason sum 8 to 10, or PSA greater than 20 ng./ml. Further research should address identifying patients who can safely avoid aggressive therapy.
Molecular Mechanisms of Sweet Receptor Function (2005)

The T1R taste receptors, like other type 3 G-protein-coupled recep-tors (GPCRs), have a large amino terminal extracellular domain.Type 3 GPCRs typically function as dimers, but each monomer canindependently bind ligand. Based on studies with the metabotropicglutamate receptors (mGluRs) the site for ligand binding in type 3GPCRs is thought to be in a shell-like cleft formed by two lobeswithin the extracellular domain. Occupation of the binding cleft andbinding to both of the lobes allows the ‘shells’ to close and stabilizesthe active conformation of the receptor (Kunishima
Functional association of retinoic acid and hedgehog signaling in Xenopus primary neurogenesis (1999)

Previous work has shown that the posteriorising agent retinoic acid can accelerate anterior neuronal differentiation in Xenopus laevis embryos (Papalopulu, N. and Kintner, C. (1996) Development 122, 3409-3418). To elucidate the role of retinoic acid in the primary neurogenesis cascade, we investigated whether retinoic acid treatment of whole embryos could change the spatial expression of a set of genes known to be involved in neurogenesis. We show that retinoic acid expands the N-tubulin, X-ngnr-1, X-MyT1, X-&Dgr;-1 and Gli3 domains and inhibits the expression of Zic2 and sonic hedgehog in the neural ectoderm, whereas a retinoid antagonist produces opposite changes. In contrast, sonic and banded hedgehog overexpression reduced the N-tubulin stripes, enlarged the neural plate at the expense of the neural crest, downregulated Gli3 and upregulated Zic2. Thus, retinoic acid and hedgehog signaling have opposite effects on the prepattern genes Gli3 and Zic2 and on other genes acting downstream in the neurogenesis cascade. In addition, retinoic acid cannot rescue the inhibitory effect of Notch(ICD), Zic2 or sonic hedgehog on primary neurogenesis. Our results suggest that retinoic acid acts very early, upstream of sonic hedgehog, and we propose a model for regulation of differentiation and proliferation in the neural plate, showing that retinoic acid might be activating primary neurogenesis by repressing sonic hedgehog expression.
Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region (2001)

The HIV-1 gp41 envelope glycoprotein promotes fusion of the virus and cell membranes through the formation of a trimer-of-hairpins structure, in which the amino- and carboxyl-terminal regions of the gp41 ectodomain are brought together. Synthetic peptides derived from these two regions (called N and C peptides, respectively) inhibit HIV-1 entry. In contrast to C peptides, which inhibit in the nanomolar range, N peptides are weak inhibitors with IC(50) values in the micromolar range. To test the hypothesis that the weak inhibition of N peptides results from their tendency to aggregate, we have constructed chimeric variants of the N-peptide region of gp41 in which soluble trimeric coiled coils are fused to portions of the gp41 N peptide. These molecules, which present the N peptide in a trimeric coiled-coil conformation, are remarkably more potent inhibitors than the N peptides themselves and likely target the carboxyl-terminal region of the gp41 ectodomain. The best inhibitors described here inhibit HIV-1 entry at nanomolar concentrations.
A compact wireless gas sensor using a carbon nanotube/PMMA thin film chemiresistor (2004)

The design and development of a compact wireless gas sensor with a surface modified multiwalled carbon nanotube (f-CNT) chemiresistor as the sensing element is presented in this paper. f-CNT/polymer composite sensing film is patterned on a printed circuit board and is integrated to the wireless system. The change in resistance of the CNT/polymer composite film due to exposure of different gases is utilized as the principle of this gas sensor. The response for different organic vapors are evaluated and it is observed that the f-CNT/PMMA composite film shows fast response and change in resistance of the order of 102–103 due to its surface modification.
Inhibition of immunoglobulin E synthesis through FcγRII (CD32) by a mechanism independent of B‐cell receptor co‐cross‐linking (2005)

The inhibitory effect on antibody production by immune complexes has been shown to depend on co-ligation of the B-cell antigen receptor (BCR) with the low-affinity receptor for immunoglobulin G (IgG) (Fc gammaRIIb, CD32). Here we report that immunoglobulin E (IgE) synthesis, induced in a BCR-independent manner by interleukin-4 (IL-4) and anti-CD40 antibody, was inhibited by CD32 ligation. The observed effect was specific for CD32 as, first, antibodies directed against other B-cell surface structures had no inhibitory effect, and, second, treatment with anti-CD32 of cells that had been in culture for 2 days was ineffective owing to the down-regulation of CD32 expression. IgE inhibition was also observed in cells stimulated by IL-4/CD40 F(ab')(2) or IL-4 plus soluble CD40 ligand, demonstrating that co-cross-linking of CD32 and CD40 was not necessary to induce inhibition. Mechanistic studies into the IgE class switch process demonstrated that IL-4/anti-CD40-induced IgE germline gene transcription and B-cell proliferation were not affected by CD32 ligation. The data demonstrate that the negative regulatory role of the CD32 molecule is not restricted to BCR-induced B-cell activation, but is also functional on other B-cell activation pathways mediated by CD40 and IL-4.
Slow shock interactions in the heliosphere using an adaptive grid MHD model (2005)

Abstract. A one-dimensional (1-D), time-dependent, adaptive-grid MHD model with solar wind structure has been used in the past to study the interaction of shocks. In the present study, we wish to study some fundamental processes that may be associated with slow shock genesis and their possible interactions with other discontinuities. This adaptive-grid model, suitable for appropriate spatial and temporal numerical simulations, is used for this purpose because its finer grid sizes in the vicinity of the steep gradients at shocks make it possible to delineate the physical parameters on both sides of the shocks. We found that a perturbation with deceleration of solar wind will generate an ensemble consisting of a forward slow shock, a fast forward wave and a reverse slow shock. On the other hand, a perturbation with an increase in acceleration of solar wind will generate both a slow shock and a fast shock. These two perturbations, although not unique, may be representative of momentum and pressure changes at the solar surface. During the transition of a fast shock overtaking a slow shock from behind, the slow shock might disappear temporarily. Also, during the process of the merging of two slow shocks, a slow shock-like structure is formed first; later, the slow shock-like structure evolves into an intermediate shock-like structure. This intermediate shock-like structure then evolves into an intermediate wave and a slow shock-like structure. Finally, the slow shock-like structure evolves into a slow shock, but the intermediate wave disappears by interacting with the non-uniform solar wind. This complex behavior demonstrates the non-unique nature of the formation of slow shocks, intermediate shocks and their derivative structures. We emphasize the main aim of this work to be both: (a) non-unique input physical parameters to explain the paucity of observed slow shocks, as well as (b) the impossibility of backward tracing to the history of input boundary conditions in view of the present inability to describe unambiguous inputs at the Sun.
Modeling of Infrared Gas Sensors Using a Ray Tracing Approach (2010)

Many gas molecules absorb electromagnetic radiation at characteristic wavelengths in the infrared region. This absorption can be used to identify defined substances like CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , ammoniac, and so forth. A lot of different types of gas sensors are based on the principle of infrared absorption like photoacoustic sensors (e.g., Golay cells), dispersive infrared instruments (e.g., utilizing a diffraction grating), or Fourier transform infrared (FTIR) spectrometers. However, the most commonly used types of infrared absorbing gas sensors are nondispersive infrared (NDIR) sensors. Such a NDIR gas sensor consists of some basic function blocks, i.e., an IR-source, the sensor cell or optical path containing the sample gas, a gas specific filter, and an IR-detector. One of the central issues in the design of this kind of sensors is the geometry of the sensor cell. In this paper we investigate the use of statistic ray tracing to predict the efficiency of 3-D cell geometries for NDIR gas sensors. We demonstrate the feasibility of the method and show examples on how to apply it on given 3-D sensor models where we illustrate the agreement between simulated and measured gas response data.
Selectivity of Piezoelectric-Excited Millimeter-Sized Cantilever (PEMC) Sensors to Bacillus anthracis Spores in the Presence of Bacillus thuringiensis and Bacillus cereus Spores in a Flow Cell (2006)

We report a highly sensitive, rapid and reliable method for the detection of Bacillus Anthracis spores at 300/mL using a piezoelectric-excited millimeter-sized cantilever (PEMC) sensor. Antibody specific to Bacillus anthracis (BA, Sterne strain 7702) spores was immobilized on PEMC sensors, and exposed to spores (300 to 3x106 spores/mL). The resonant frequency decreased at a rate proportional to the spore concentration and reached a steady state frequency change of 5 plus/minus 5 (n=3), 92 plus/minus 7 (n=3), 500 plus/minus 10 (n=3), 1030 plus/minus 10 (n=2), and 2696 plus/minus 6 (n=2) Hz corresponding to 0, 3x10(^2), 3x10(^3), 3x10(^4), and 3x10(^6) spores/mL, respectively. Selectivity of the antibody functionalized sensor was determined with samples containing BA (3 x 10(^6)/mL) mixed with Bacillus thuringiensis (BT; 1.5x10(^9)/mL) in various volume ratios that yielded BA:BT ratios of 1:0, 1:0.008, 1:0.004, 1:0.002 and 0:1. The corresponding resonance frequency decreases were, 2345, 1980, 1310, 704 and 10 Hz. Sample containing 100% BT spores (1.5 x 10(^9)/mL and no BA) gave a steady state frequency decrease of 10 Hz, which is within noise level of the sensor, indicating excellent selectivity. These results show that detection of Bacillus anthracis spore at a very low concentration (300 spores/mL) and with high selectivity in presence of another Bacillus spore (BT) can be accomplished using piezoelectric-excited millimeter-sized cantilever sensors.
Web page design (1998)

Much is known about depth and breadth tradeoff issues in graphical user interface menu design. We describe an experiment to see if large breadth and decreased depth is preferable, both subjectively and via performance data, while attempting to design for optimal scent throughout different structures of a website. A study is reported which modified previous procedures for investigating depth/breadth tradeoffs in content design for the web. Results showed that, while increased depth did harm search performance on the web, a medium condition of depth and breadth outperformed the broadesf shallow web structure overall.
Critical Issues in Gene Therapy for Neurologic Disease (2002)

Gene therapy for the nervous system is a newly emerging field with special issues related to modes of delivery, potential toxicity, and realistic expectations for treatment of this vital and highly complex tissue. This review focuses on the potential for gene delivery to the brain, as well as possible risks and benefits of these procedures. This includes discussion of appropriate vectors, such as adeno-associated virus, lentivirus, gutless adenovirus, and herpes simplex virus hybrid amplicons, and cell vehicles, such as neuroprogenitor cells. Routes of delivery for focal and global diseases are enumerated, including use of migratory cells, facilitation of vascular delivery across the blood-brain barrier, cerebrospinal fluid delivery, and convection injection. Attention is given to examples of diseases falling into different etiologic types: metabolic deficiency states, including Canavan disease and lysosomal storage disorders; and degenerative conditions, including Parkinson's disease and other neurodegenerative conditions.
Comparative pharmacokinetics of testosterone enanthate and testosterone cyclohexanecarboxylate as assessed by serum and salivary testosterone levels in normal men (1984)

The pharmacokinetics of 2 testosterone esters, testosterone enanthate and testosterone cyclohexanecarboxylate, were compared in a single blind crossover study in healthy young men. Their effects on serum and salivary levels of testosterone, as well as on the serum levels of LH, FSH and prolactin were measured after the injection of doses equivalent to 140 mg free testosterone. Both preparations yielded supraphysiological testosterone levels in serum and saliva as early as 2 h following injection, reaching peak levels 4 to 5 times above basal between 8 and 24 h. LH and FSH levels were suppressed as long as serum testosterone levels were elevated. Nine days after injecting testosterone enanthate and 7 days after giving testosterone cyclohexanecarboxylate, serum and salivary levels of testosterone had returned to basal. The longer activity of testosterone enanthate was also evidenced from more extended suppression of gonadotrophin levels. Although neither preparation is ideal because of the initial supraphysiological peaks, testosterone enanthate appears preferable for clinical use because of its slightly longer duration of action.
B lymphocytes from patients with chronic lymphocytic leukemia contain signal transducer and activator of transcription (STAT) 1 and STAT3 constitutively phosphorylated on serine residues. (1997)

To explore the pathogenesis of chronic lymphocytic leukemia (CLL), we examined whether phosphorylation of one or more signal transducer and activator of transcription (STAT) factors was abnormal in cells from CLL patients. No constitutive tyrosine phosphorylation was detected on any STAT in CLL cells. To assess the phosphorylation of serine residues of STAT1 and STAT3 in CLL cells, we raised antibodies that specifically recognize the form of STAT1 phosphorylated on ser-727 and the form of STAT3 phosphorylated on ser-727. We found that in 100% of patients with CLL (n = 32), STAT1 and STAT3 were constitutively phosphorylated on serine. This was in contrast to normal peripheral blood B lymphocytes or CD5+) B cells isolated from tonsils, in which this phosphorylation was absent. Serine phosphorylation of STAT1 and STAT3 was seen occasionally in other leukemias, but it was a universal finding only in CLL. The serine phosphorylation of these STATs was a continuous process, as incubation of CLL cells with the kinase inhibitor H7 led to the dephosphorylation of these serine residues. The STAT serine kinase in CLL cells has not been identified, and appears to be neither mitogen-activated protein kinase nor pp70(s6k). In summary, the constitutive serine phosphorylation of STAT1 and STAT3 is present in all CLL samples tested to date, although the physiologic significance of this modification remains to be determined.
15-Deoxy-Δ12,14-prostaglandin J2Inhibition of NF-κB-DNA Binding through Covalent Modification of the p50 Subunit (2001)

Cyclopentenone prostaglandins display anti-inflammatory activities and interfere with the signaling pathway that leads to activation of transcription factor NF-kappaB. Here we explore the possibility that the NF-kappaB subunit p50 may be a target for the cyclopentenone 15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)). This prostaglandin inhibited the DNA binding ability of recombinant p50 in a dose-dependent manner. The inhibition required the cyclopentenone moiety and could be prevented but not reverted by glutathione and dithiothreitol. Moreover, a p50 mutant with a C62S mutation was resistant to inhibition, indicating that the effect of 15d-PGJ(2) was probably due to its interaction with cysteine 62 in p50. The covalent modification of p50 by 15d-PGJ(2) was demonstrated by reverse-phase high pressure liquid chromatography and mass spectrometry analysis that showed an increase in retention time and in the molecular mass of 15d-PGJ(2)-treated p50, respectively. The interaction between p50 and 15d-PGJ(2) was relevant in intact cells. 15d-PGJ(2) effectively inhibited cytokine-elicited NF-kappaB activity in HeLa without reducing IkappaBalpha degradation or nuclear translocation of NF-kappaB subunits. 15d-PGJ(2) reduced NF-kappaB DNA binding activity in isolated nuclear extracts, suggesting a direct effect on NF-kappaB proteins. Finally, treatment of HeLa with biotinylated-15d-PGJ(2) resulted in the formation of a 15d-PGJ(2)-p50 adduct as demonstrated by neutravidin binding and immunoprecipitation. These results clearly show that p50 is a target for covalent modification by 15d-PGJ(2) that results in inhibition of DNA binding.
Prostatic carcinoma cell migration via alpha(v)beta3 integrin is modulated by a focal adhesion kinase pathway. (1999)

The highly invasive human prostate cancer PC3 cell line was found to express the alpha(v)beta3 integrin; in contrast, the noninvasive LNCaP prostate cancer cell line did not express alpha(v)beta3. PC3 cells adhered to and migrated on vitronectin (VN), an alpha(v)beta3 ligand expressed in mature bone where prostate cancer cells preferentially metastasize. In contrast, LNCaP cells did not adhere to or migrate on VN. Analysis of primary human prostate cancer cells isolated from 16 surgical specimens, showed that these cells expressed alpha(v)beta3, whereas normal prostate epithelial cells did not. In addition, only primary prostate cancer cells adhered to and migrated on VN. The role of alpha(v)beta3 in mediating prostate epithelial cell migration was confirmed using LNCaP cell transfectants expressing beta3 (beta3-LNCaP). Exogenous expression of alpha(v)beta3 induced LNCaP cells to adhere to and migrate on VN. In response to alpha(v)beta3 engagement, increased tyrosine phosphorylation of focal adhesion kinase (FAK), a signaling molecule activated by integrins and able to modulate cell migration, was detected. Transfection of FAK-related nonkinase, known to compete with FAK for its correct localization and phosphorylation, caused inhibition of beta3-LNCaP cell migration, specifically on VN. These data indicate that de novo expression of alpha(v)beta3 integrin in prostate cancer cells generates a migratory phenotype that is modulated by a FAK signaling pathway. This study points to alpha(v)beta3 as potential target in prostate cancer cell invasion and metastasis.
Abstraction mechanisms for pictorial slicing (2002)

Big programs tend to have big slices, so reverse engineering tools based on slicing must apply additional abstractions to make slices intelligible. We have built a tool that displays slices as diagrams. By confining the slice to the statements of a single procedure, by eluding all primitive statements, and by merging different calls of the same procedure, we eliminate local information that is easily seen in the code without the help of tools. And by labelling edges with the variables responsible for flows between procedure calls, global information about called procedures is represented locally. The resulting diagram gives a compact but rich summary of the role of called procedures in the slice.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>