gebhart/patrepeval huggingface dataset:
Nanosphere Lithography:  Effect of the External Dielectric Medium on the Surface Plasmon Resonance Spectrum of a Periodic Array of Silver Nanoparticles (1999)

In this paper we examine the effect of solvent on the optical extinction spectrum of periodic arrays of surface-confined silver nanoparticles fabricated by nanosphere lithography (NSL). By use of NSL, it is possible to systematically vary the out-of-plane height of the nanoparticles, and by thermal annealing, we can control the nanoparticle shape. We have studied four separate samples of nanoparticle arrays; three samples have nanoparticles that are truncated tetrahedral in shape but that differ in out-of-plane height and one sample has nanoparticles that are oblate ellipsoidal in shape. By performing UV−vis extinction spectroscopy measurements at 12 μm spatial resolution, we show that the defect sites that occur as a byproduct of the NSL fabrication process play a negligible role in the macroscale extinction spectrum. We find that the extinction spectrum of the nanoparticles that are oblate ellipsoidal in shape is least sensitive to the surrounding dielectric medium, and the extinction spectrum of the nanoparticles that are truncated tetrahedral in shape with the smallest out-of-plane height is most sensitive. A 1 nm shift in the extinction maximum corresponds to a 0.005 change in the refractive index of the external medium. Theoretical calculations based on the discrete dipole approximation (DDA) are presented. The DDA is a coupled finite element method capable of calculating the extinction of light for particles of arbitrary shape and size. The discrepancy between the experimental and theoretical results is small for the oblate ellipsoidal-shaped particle but progressively increases for the truncated tetrahedral-shaped particles as they become more oblate. This discrepancy is lessened by including the effect of substrate−particle interactions in the calculation. The DDA theory predicts a significantly larger red shift in the extinction maximum with increasing solvent refractive index than is observed experimentally.
Effect of protein synthesis inhibitors on growth factor activation of c-fos, c-myc, and actin gene transcription. (1986)

Stimulation of quiescent 3T3 cells with purified growth factors or of the pheochromocytoma cell line PC12 with nerve growth factor results in the rapid transient induction of c-fos, c-myc, and actin gene transcription (M.E. Greenberg and E.B. Ziff, Nature [London] 312:711-716; M.E. Greenberg, L.A. Greene, and E.B. Ziff, J. Biol. Chem. 26:14101-14110). We used protein synthesis inhibitors to investigate whether synthesis of new proteins plays a role in the rapid induction and subsequent repression of the transcription of these genes. Pretreatment of quiescent 3T3 cells with the inhibitor anisomycin before growth factor stimulation caused a superinduction of c-fos and c-myc mRNA levels upon growth factor addition. Nuclear runoff transcription analyses of 3T3 cells indicated that anisomycin potentiated c-fos, c-myc, and also actin expression at the transcriptional level, possibly by inhibiting transcriptional repression. Somewhat different results were obtained when PC12 cells were incubated with either anisomycin or cycloheximide. In PC12 cells protein synthesis inhibitors superinduced nerve growth factor activation of c-fos mRNA production but completely abolished the activation of c-myc. The results suggest that in PC12 cells c-fos transcription is activated by a protein-synthesis-independent mechanism, whereas c-myc stimulation requires new protein synthesis. The difference in the effect of anisomycin on growth factor activation of c-myc expression in 3T3 versus PC12 cells may be due to differential stringency of protein synthesis inhibition in the two cells or could reflect cell type differences in c-myc regulation.
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. (2002)

The increasing availability and maturity of DNA microarray technology has led to an explosion of cancer profiling studies. To extract maximum value from the accumulating mass of publicly available cancer gene expression data, methods are needed to evaluate, integrate, and intervalidate multiple datasets. Here we demonstrate a statistical model for performing meta-analysis of independent microarray datasets. Implementation of this model revealed that four prostate cancer gene expression datasets shared significantly similar results, independent of the method and technology used (i.e., spotted cDNA versus oligonucleotide). This interstudy cross-validation approach generated a cohort of genes that were consistently and significantly dysregulated in prostate cancer. Bioinformatic investigation of these genes revealed a synchronous network of transcriptional regulation in the polyamine and purine biosynthesis pathways. Beyond the specific implications for prostate cancer, this work establishes a much-needed model for the evaluation, cross-validation, and comparison of multiple cancer profiling studies.
Treatment of Blood Hyperviscosity with Calcium Dobesilate in Patients with Diabetic Retinopathy (1985)

This double-blind randomized trial was carried out on 37 patients with diabetic retinopathy and blood hyperviscosity. 19 patients received calcium dobesilate in capsules of 500 mg 3 times daily for 3 months and 18 patients took 3 placebo capsules daily during the same period. Calcium dobesilate was found to reduce whole-blood viscosity in a statistically significant manner which was accompanied by a diminution of the albumin/globulin ratio and a significant reduction of fibrinogen and cholesterol levels. A statistically significant diminution of capillary fragility was also observed in the calcium dobesilate-treated group. These results indicate that calcium dobesilate, by restoring the integrity of the microvessels, and by lowering blood viscosity, could act favorably on the evolution of diabetic retinopathy.
Cytokine Signature Associated with Disease Severity in Dengue (2019)

Dengue is the most rapidly spreading viral disease transmitted by the bite of infected <i>Aedes</i> mosquitos. The pathogenesis of dengue is still unclear; although host immune responses and virus serotypes have been proposed to contribute to disease severity. In this study, we examined the circulating dengue virus (DENV) and measured plasma levels of inflammatory mediators. Ninety-eight patients during a dengue outbreak in eastern India in 2016 were included in the study. The presence of DENV was demonstrated by detecting NS1 antigen; IgM capture ELISA and serotypes were discriminated by type-specific RT-PCR and/or sequencing. Plasma samples were assayed for 41-plex cytokine/chemokines using multiplex Luminex assay. Eighty-five (87%) samples were positive by NS1/IgM capture ELISA/RT-PCR. All four serotypes of DENV were detected in this outbreak, with DENV-2 as the predominant type, seen in 55% of cases. Mixed infections were seen in 39% of subjects. Among the host inflammatory biomarkers, GM-CSF, IFN-γ, IL-10, IL-15, IL-8, MCP-1, IL-6, MIP-1β, and TNF-α levels were significantly increased in dengue with and without warning signs, in severe dengue patients in comparison to healthy controls. Four cytokines IFN-γ, GM-CSF, IL-10, and MIP-1β correlated significantly with disease severity and could serve as potential predictor for disease severity. Information on the host biomarkers and the dengue serotype may help guide in optimizing effective intervention strategies.
Design of CMOS for 60GHz applications (2004)

The viability of digital CMOS as a future mm-wave technology, capable of exploiting the 60GHz band, is explored. Optimal device design and appropriate mm-wave models are presented. From modeling of transistors in 0.13/spl mu/m technology a three cascode-stage amplifier at 1.5 volts would provide 11 dB of gain at 60GHz using 54mW.
Man-made molecular machines: membrane bound (2016)

Nature's molecular machines are a constant source of inspiration to the chemist. Many of these molecular machines function within lipid membranes, allowing them to exploit potential gradients between spatially close, but chemically distinct environments to fuel their work cycle. Indeed, the realisation of such principles in synthetic transmembrane systems remains a tantalising goal. This tutorial review opens by highlighting seminal examples of synthetic molecular machines. We illustrate the importance of surfaces for facilitating the extraction of work from molecular switches and motors. We chart the development of man-made transmembrane systems; from passive to machine-like stimuli-responsive channels, to fully autonomous transmembrane molecular machines. Finally, we highlight higher-order compartmentalised systems that exhibit emergent properties. We suggest that such higher-order architectures could serve as platforms for sophisticated devices that co-ordinate the activity of numerous transmembrane molecular machines.
Hydrophilic Poly(dimethylsiloxane) Stamps for Microcontact Printing (2001)

Poly(dimethylsiloxane) stamps for microcontact printing with polar inks,which no longer need to be reactivated after each printing step, are revealed. The silicone surface is modified by linking a hydrophilic polyethylene glycol chain to SiOH groups created on the surface of the stamp. While stamps that are oxidized conventionally become useless 3 h after their preparation (Figure top), the PEG-modified stamps can still print high-quality patterns after 20 days (Figure bottom).
Vocal activity informed singing voice separation with the iKala dataset (2015)

A new algorithm is proposed for robust principal component analysis with predefined sparsity patterns. The algorithm is then applied to separate the singing voice from the instrumental accompaniment using vocal activity information. To evaluate its performance, we construct a new publicly available iKala dataset that features longer durations and higher quality than the existing MIR-1K dataset for singing voice separation. Part of it will be used in the MIREX Singing Voice Separation task. Experimental results on both the MIR-1K dataset and the new iKala dataset confirmed that the more informed the algorithm is, the better the separation results are.
Correction of Automatic Speech Recognition with Transformer Sequence-To-Sequence Model (2020)

In this work, we introduce a simple yet efficient post-processing model for automatic speech recognition. Our model has Transformer-based encoder-decoder architecture which "translates" acoustic model output into grammatically and semantically correct text. We investigate different strategies for regularizing and optimizing the model and show that extensive data augmentation and the initialization with pretrained weights are required to achieve good performance. On the LibriSpeech benchmark, our method demonstrates significant improvement in word error rate over the baseline acoustic model with greedy decoding, especially on much noisier dev-other and test-other portions of the evaluation dataset. Our model also outperforms baseline with 6-gram language model re-scoring and approaches the performance of re-scoring with Transformer-XL neural language model.
Improving Translation via Targeted Paraphrasing (2010)

Targeted paraphrasing is a new approach to the problem of obtaining cost-effective, reasonable quality translation that makes use of simple and inexpensive human computations by monolin-gual speakers in combination with machine translation. The key insight behind the process is that it is possible to spot likely translation errors with only monolingual knowledge of the target language, and it is possible to generate al-ternative ways to say the same thing (i.e. para-phrases) with only monolingual knowledge of the source language. Evaluations demon-strate that this approach can yield substantial improvements in translation quality. 1
Role of metallothionein in nitric oxide signaling as revealed by a green fluorescent fusion protein (2000)

Although the function of metallothionein (MT), a 6- to 7-kDa cysteine-rich metal binding protein, remains unclear, it has been suggested from in vitro studies that MT is an important component of intracellular redox signaling, including being a target for nitric oxide (NO). To directly study the interaction between MT and NO in live cells, we generated a fusion protein consisting of MT sandwiched between two mutant green fluorescent proteins (GFPs). In vitro studies with this chimera (FRET-MT) demonstrate that fluorescent resonance energy transfer (FRET) can be used to follow conformational changes indicative of metal release from MT. Imaging experiments with live endothelial cells show that agents that increase cytoplasmic Ca(2+) act via endogenously generated NO to rapidly and persistently release metal from MT. A role for this interaction in intact tissue is supported by the finding that the myogenic reflex of mesenteric arteries is absent in MT knockout mice (MT(-/-)) unless endogenous NO synthesis is blocked. These results are the first application of intramolecular green fluorescent protein (GFP)-based FRET in a native protein and demonstrate the utility of FRET-MT as an intracellular surrogate indicator of NO production. In addition, an important role of metal thiolate clusters of MT in NO signaling in vascular tissue is revealed.
Tunnel defects in dentin bridges: their formation following direct pulp capping. (1997)

This study was conducted to observe the formation and nature of tunnel defects in dentin bridges, assess the nature of the associated soft tissue elements, and note the relationship of pulp inflammation and necrosis associated with these defects. A total of 235 teeth with class 5 cavity preparation exposures were randomly distributed throughout the dentitions of 14 adult rhesus monkeys. Each pulp was exposed and left open to the oral microflora at one of four time intervals, flushed with saline, debrided, capped with one of two hard-set calcium hydroxide medicaments [Ca(OH)2 (Dycal or Life)] and restored with a dispersed-phase amalgam alloy. Observation times were 14 days, 5 weeks, and 1 and 2 years. A total of 192 dentin bridges formed against the Ca(OH)2 medicaments Life or Dycal in 235 pulp-capped teeth. Considering all four capping periods, 89% of all dentin bridges contained tunnel defects (172 of 192). Forty-one percent (78) of the 192 dentin bridges were associated with recurring pulp inflammation or necrosis and were always associated with the presence of inflammatory cells and stained bacterial profiles. This study demonstrates that a statistically significant number of dentin bridges contain multiple tunnel defects, most of which appear to remain patent. These patent tunnels fail to provide a hermetic seal to the underlying pulp against recurring infection due to microleakage. Most Ca(OH)2 medicaments have been reported to disintegrate and wash out after 6 months, leaving a void underneath the restoration and thereby a pathway for bacterial infection. This study reemphasizes the need to employ biologically relevant measures that will provide a long-term clinical seal against microleakage following direct pulp capping with Ca(OH)2 medicaments alone.
Molecular and cellular properties of PECAM-1 (endoCAM/CD31): a novel vascular cell-cell adhesion molecule. (1991)

PECAM-1 is a 130-120-kD integral membrane glycoprotein found on the surface of platelets, at endothelial intercellular junctions in culture, and on cells of myeloid lineage. Previous studies have shown that it is a member of the immunoglobulin gene superfamily and that antibodies against the bovine form of this protein (endoCAM) can inhibit endothelial cell-cell interactions. These data suggest that PECAM-1 may function as a vascular cell adhesion molecule. The function of this molecule has been further evaluated by transfecting cells with a full-length PECAM-1 cDNA. Transfected COS-7, mouse 3T3 and L cells expressed a 130-120-kD glycoprotein on their cell surface that reacted with anti-PECAM-1 polyclonal and monoclonal antibodies. COS-7 and 3T3 cell transfectants formed cell-cell junctions that were highly enriched in PECAM-1, reminiscent of its distribution at endothelial cell-cell borders. In contrast, this protein remained diffusely distributed within the plasma membrane of PECAM-1 transfected cells that were in contact with mock transfectants. Mouse L cells stably transfected with PECAM-1 demonstrated calcium-dependent aggregation that was inhibited by anti-PECAM antibodies. These results demonstrate that PECAM-1 mediates cell-cell adhesion and support the idea that it may be involved in some of the interactive events taking place during thrombosis, wound healing, and angiogenesis.
4-Hydroxyisoleucine: A Novel Amino Acid Potentiator of Insulin Secretion (1998)

We report the characterization of a new insulinotropic compound, 4-hydroxyisoleucine. This amino acid has been extracted and purified from fenugreek seeds, which are known in traditional medicine for their antidiabetic properties. 4-Hydroxyisoleucine increases glucose-induced insulin release, in the concentration range of 100 micromol/l to 1 mmol/l, through a direct effect on isolated islets of Langerhans from both rats and humans. The stimulating effect of 4-hydroxyisoleucine was strictly glucose dependent; indeed, ineffective at low (3 mmol/l) or basal (5 mmol/l) glucose concentrations, the amino acid potentiated the insulin secretion induced by supranormal (6.6-16.7 mmol/l) concentrations of glucose. In addition, in the isolated perfused rat pancreas, we could show 1) that the pattern of insulin secretion induced by 4-hydroxyisoleucine was biphasic, 2) that this effect occurred in the absence of any change in pancreatic alpha- and delta-cell activity, and 3) that the more glucose concentration was increased, the more insulin response was amplified. Moreover, 4-hydroxyisoleucine did not interact with other agonists of insulin secretion (leucine, arginine, tolbutamide, glyceraldehyde). Therefore, we conclude that 4-hydroxyisoleucine insulinotropic activity might, at least in part, account for fenugreek seeds' antidiabetic properties. This secretagogue may be considered as a novel drug with potential interest for the treatment of NIDDM.
Fault detection for cloud computing systems with correlation analysis (2015)

The large-scale dynamic cloud computing environment has raised great challenges for fault diagnosis in Web applications. First, fluctuating workloads cause traditional application models to change over time. Moreover, modeling the behaviors of complex applications always requires domain knowledge which is difficult to obtain. Finally, managing large-scale applications manually is impractical for operators. This paper addresses these issues and proposes an automatic fault diagnosis method for Web applications in cloud computing. We propose an online incremental clustering method to recognize access behavior patterns, and uses CCA to model the correlation between workloads and the metrics of application performance/resource utilization in a specific access behavior pattern. Our method detects anomalies by discovering the abrupt change of correlation coefficients with a EWMA control chart, and then locates suspicious metrics using a feature selection method combining ReliefF and SVM-RFE. We validate our method by injecting typical faults in TPC-W an industry-standard benchmark, and the experimental results demonstrate that it can effectively detect typical faults.
Liver transplantation for acute intermittent porphyria: a viable treatment? (2010)

LT can correct the underlying metabolic abnormality in AIP and improves quality of life significantly.
Confined Plasmons in Nanofabricated Single Silver Particle Pairs:  Experimental Observations of Strong Interparticle Interactions (2004)

We report on the optical properties of single isolated silver nanodisks and pairs of disks fabricated by electron beam lithography. By systematically varying the disk size and surface separation and recording elastic scattering spectra in different polarization configurations, we found evidence for extremely strong interparticle interactions. The dipolar surface plasmon resonance for polarization parallel to the dimer axis exhibited a red shift as the interdimer separation was decreased; as expected from previous work, an extremely strong shift was observed. The scattering spectra of single particles and pairs separated by more than one particle radius can be well described by the coupled dipole approximation (CDA), where the particles are approximated as point dipoles using a modified dipole polarizability for oblate spheroids. For smaller particle separations (d < 20 nm), the simple dipole model severely underestimates the particle interaction, indicating the importance of multipolar fields and finite-size effects. The discrete dipole approximation (DDA), which is a finite-element method, describes the experimental results well even at d < 20 nm, including particles that have metallic bridges.
Interruption of nuclear factor kappaB signaling by the androgen receptor facilitates 12-O-tetradecanoylphorbolacetate-induced apoptosis in androgen-sensitive prostate cancer LNCaP cells. (2003)

12-O-tetradecanoylphorbolacetate (TPA) influences proliferation, differentiation, and apoptosis in a variety of cells including prostate cancer cells. Here, we show that androgen treatment potentiates TPA-induced apoptosis in androgen-sensitive prostate cancer LNCaP cells but not in androgen-independent prostate cancer cell lines DU145 and PC-3. The use of the antiandrogen bicalutamide (Casodex) rescued LNCaP cells from 5-alpha-dihydrotestosterone (DHT)/TPA-induced apoptosis, suggesting that DHT/TPA-induced apoptosis is mediated by androgen/androgen receptor (AR). In addition, a caspase-3 inhibitor (Ac-DEVD-CHO) reduced the level of apoptosis, suggesting that DHT/TPA-mediated apoptosis occurs through a caspase-3-dependent pathway. A functional reporter assay using nuclear factor (NF) kappaB-luciferase and an electromobility gel shift assay showed that DHT suppressed NFkappaB activity. In addition, apoptosis mediated by combined DHT/TPA treatment was abrogated by overexpression of the NFkappaB subunit p65 in LNCaP-p65 cells, suggesting that NFkappaB may play an important role in regulating the effects of androgen/AR and TPA on apoptosis. Furthermore, use of the c-Jun N-terminal kinase (JNK) inhibitor SB202190 showed that the combination of DHT/TPA increased JNK activation in LNCaP cells but not in LNCaP-p65 cells, demonstrating that NFkappaB may be able to suppress JNK activity. These results indicate that androgen/AR facilitates TPA-induced apoptosis by interruption of the NFkappaB signaling pathway, leading to activation of JNK in LNCaP cells. These data describe a signaling pathway that could potentially be useful in proposed therapeutic treatment strategies exploiting combinations of different agents that control apoptosis in prostate tumors.