gebhart/patrepeval huggingface dataset:
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study (2002)

Molecular dynamics simulation techniques have been used to investigate the effect of 2,2,2-trifluoroethanol (TFE) as a cosolvent on the stability of three different secondary structure-forming peptides: the alpha-helix from Melittin, the three-stranded beta-sheet peptide Betanova, and the beta-hairpin 41-56 from the B1 domain of protein G. The peptides were studied in pure water and 30% (vol/vol) TFE/water mixtures at 300 K. The simulations suggest that the stabilizing effect of TFE is induced by the preferential aggregation of TFE molecules around the peptides. This coating displaces water, thereby removing alternative hydrogen-bonding partners and providing a low dielectric environment that favors the formation of intrapeptide hydrogen bonds. Because TFE interacts only weakly with nonpolar residues, hydrophobic interactions within the peptides are not disrupted. As a consequence, TFE promotes stability rather than inducing denaturation.
Corner Point Geometry in Reservoir Simulation (1989)

Hydrocarbon reservoirs commonly possess a geometry which incorporates both dip and faulting. In order to distinguish depth variations due to these two effects, it is useful to specify a simulation cell through the positions of its eight corner points. The faces of such a cell may be bilinear surfaces, and may form part of a distorted grid. Such a grid may be chosen such that cell boundaries lie along faults, which may be vertical or sloping. Normal and fault connections may be treated on an equivalent basis. A system of ‘coordinate lines’ and corner point depths used to construct such a model is described. An exact analytic expression is obtained for the cell volume. Transmissibility values are calculated in terms of three-vector mutual interface areas, which automatically incorporate corrections for dip and inclined flow. The application of calculated transmissibilities to a simple five point model can lead to an inconsistent finite difference scheme, and to significant errors if the grid is highly distorted. A method of avoiding such errors is presented, which more accurately reflects the interaction between pressures and cell geometry to produce flows. This is derived from basic finite element type principles, and results are presented for test cases, comparing the corrected scheme with a simple five point model.
Induction of Estradiol Metabolism by Dietary Indole-3-carbinol in Humans (1990)

Dietary indoles in cruciferous vegetables induce cytochrome P450 enzymes and have prevented tumors in various animal models. Because estradiol metabolism is also cytochrome P450 mediated and linked to breast cancer risk, indoles may similarly reduce estrogen-responsive tumors in humans. We examined several indoles in female Sprague-Dawley rats for induction of hepatic estradiol 2-hydroxylation. The most potent inducer, indole-3-carbinol, was administered to humans (500 mg daily for 1 wk). It significantly increased the extent (mean +/- SEM) of estradiol 2-hydroxylation from 29.3% +/- 2.1% to 45.6% +/- 2.1% (P less than .001). These results indicate that indole-3-carbinol strongly influences estradiol metabolism in humans and may provide a new chemopreventive approach to estrogen-dependent diseases.
Multimodal Emotion Recognition in Response to Videos (2011)

This paper presents a user-independent emotion recognition method with the goal of recovering affective tags for videos using electroencephalogram (EEG), pupillary response and gaze distance. We first selected 20 video clips with extrinsic emotional content from movies and online resources. Then, EEG responses and eye gaze data were recorded from 24 participants while watching emotional video clips. Ground truth was defined based on the median arousal and valence scores given to clips in a preliminary study using an online questionnaire. Based on the participants' responses, three classes for each dimension were defined. The arousal classes were calm, medium aroused, and activated and the valence classes were unpleasant, neutral, and pleasant. One of the three affective labels of either valence or arousal was determined by classification of bodily responses. A one-participant-out cross validation was employed to investigate the classification performance in a user-independent approach. The best classification accuracies of 68.5 percent for three labels of valence and 76.4 percent for three labels of arousal were obtained using a modality fusion strategy and a support vector machine. The results over a population of 24 participants demonstrate that user-independent emotion recognition can outperform individual self-reports for arousal assessments and do not underperform for valence assessments.
Transcription factor decoy approach to decipher the role of NF-kappa B in oncogenesis. (1996)

Antisense inhibition of the RelA subunit of NF-kappa B transcription factor (but not the NFKB1 subunit) causes pronounced inhibition of tumor cell growth in vitro and in vivo. Inhibition of either subunit, however, results in inhibition of the heterodimeric NF-kappa B complex in antisense-treated cells. Either of the subunits of NF-kappa B can form homo- or heterodimers with other members of the Rel oncogene family. In an effort to decipher the role of homo- vs heterodimeric NNF-kappa B in regulating tumor cell growth, we have used a decoy approach to trap these complexes in vivo. Using double-stranded phosphorothioates as a direct in vivo competitor for homo- vs heterodimeric NF-kappa B, we demonstrate that decoys more specific to RelA inhibit growth tumor cell growth in vitro. We demonstrate that RelA, either as a homodimer or a heterodimer with some other members of the Rel family and not the classical NF-kappa B (RelA/NFKB1), is involved in the differential growth control of tumor cells. Our results indicate that such transcription factor decoys can be a non-antisense tool to study the function of DNA-binding transcription factors.
Affinity and Avidity in Antibody-Based Tumor Targeting (2009)

Many factors contribute to successful tumor targeting by antibodies. Besides properties of the tumor tissue and general antibody pharmacology, a relationship exists between an antibody and its antigen that can shape penetration, catabolism, specificity, and efficacy. The affinity and avidity of the binding interactions play critical roles in these dynamics. In this work, we review the principles that guide models predicting tumor penetration and cellular internalization while providing a critical overview of studies aimed at experimentally determining the specific role of affinity and avidity in these processes. One should gain the perspective that binding affinity can, in part, dictate the localization of antibodies in tumors, leading to high concentrations in the perivascular space or low concentrations diffused throughout the tumor. These patterns can be simply due to the diminution of available dose by binding antigen and are complicated by internalization and degradation stemming from slow rates of dissociation. As opposed to the trend of simply increasing affinity to increase efficacy, novel strategies that increase avidity and broaden specificity have made significant progress in tumor targeting.
Reverse Transcription of 16S rRNA To Monitor Ribosome-Synthesizing Bacterial Populations in the Environment (2009)

Identification and quantification of phylogenetically defined bacterial populations in the environment are often performed using molecular tools targeting 16S rRNA. Fluorescence in situ hybridization has been used to monitor the expression and processing of rRNA by targeting the 3' tail of precursor 16S rRNA. To expand this approach, we employed reverse transcription of total RNA using primer S-D-Bact-0338-a-A-18. Length heterogeneity detected by slab gel analysis, denaturing high-performance liquid chromatography (DHPLC) was used to differentiate the 5' tail of the precursor from mature 16S rRNA, and the relative abundance of the precursor compared to the abundance of mature 16S rRNA was shown to be a sensitive indicator of the physiologic state of Acinetobacter calcoaceticus ATCC 23055(T). Our results demonstrate that this is a sensitive and reliable method with a detection limit of 10 ng of single-stranded DNA. The assay was also used to differentiate among precursor 16S rRNA levels with mixed pure cultures, as well as to examine the response of a mixed activated sludge culture exposed to fresh growth medium and the antibiotic chloramphenicol. The results of this study demonstrate that this assay is a novel reverse transcription assay that simultaneously measures the mature and precursor 16S rRNA pools for mixed bacterial populations in an engineered environment. Furthermore, collection of the reverse transcription products derived from activated sludge samples by the DHPLC approach enabled identification of the active bacterial genera. Comparison of 16S and precursor 16S rRNA clone library results indicated that the precursor 16S rRNA library is a more sensitive indicator for active bacteria in engineered environmental samples.
LXR/RXR ligand activation enhances basolateral efflux of β-sitosterol in CaCo-2 cells (2004)

To examine whether intestinal ABCA1 was responsible for the differences observed between cholesterol and beta-sitosterol absorption, ABCA1-facilitated beta-sitosterol efflux was investigated in CaCo-2 cells following liver X receptor/retinoid X receptor (LXR/RXR) activation. Both the LXR agonist T0901317 and the natural RXR/LXR agonists 22-hydroxycholesterol and 9-cis retinoic acid enhanced the basolateral efflux of beta-sitosterol without altering apical efflux. LXR-mediated enhanced beta-sitosterol efflux occurred between 6 h and 12 h after activation, suggesting that transcription, protein synthesis, and trafficking was likely necessary prior to facilitating efflux. The transcription inhibitor actinomycin D prevented the increase in beta-sitosterol efflux by T0901317. Glybenclamide, an inhibitor of ABCA1 activity, and arachidonic acid, a fatty acid that interferes with LXR activation, also prevented beta-sitosterol efflux in response to the LXR ligand activation. Influx of beta-sitosterol mass did not alter the basolateral or apical efflux of the plant sterol, nor did it alter ABCA1, ABCG1, ABCG5, or ABCG8 gene expression or ABCA1 mass. Similar to results observed with intestinal ABCA1-facilitated cholesterol efflux, LXR/RXR ligand activation enhanced the basolateral efflux of beta-sitosterol without affecting apical efflux. The results suggest that ABCA1 does not differentiate between cholesterol and beta-sitosterol and thus is not responsible for the selectivity of sterol absorption by the intestine. ABCA1, however, may play a role in beta-sitosterol absorption.
Realization of reliable GaN nanowire transistors utilizing dielectrophoretic alignment technique (2006)

We have utilized dielectrophoretic force for assembling long (50μmto200μm) GaN nanowires for device fabrication. These catalyst-free nanowires were grown by direct reaction of NH3 and Ga, which resulted in free-standing nanowires along with GaN microplatelets. GaN nanowires were suspended in a solvent using sonication, and using dielectrophoretic forces nanowires were assembled on prepatterned substrates (SiO2 coated Si and sapphire). With fabrication sequence using batch fabrication processes such as standard photolithography, etching, and oxide deposition we were able to realize stable GaN nanowire devices. The present technique is potentially compatible with complementary metal-oxide semicondoctor technology, and integrating nanodevices with conventional Si microelectronics on the same chip can be made possible with this technique. Utilizing this technique, high mobility (230cm2V−1s−1) GaN nanowire field effect transistors with reliable electrical characteristics have been achieved. These nanowire transistors even after prolonged period of conduction exhibited no deteriorations of their electrical properties. Several key factors in the processing that affect the device yield and reliability have been identified. Simple calculations predicted the effects of nanowire geometry, dispersing solvent, and alignment frequency on the dielectrophoretic force experienced by the nanowires.
A 32-bit CPU with zero standby power and 1.5-clock sleep/2.5-clock wake-up achieved by utilizing a 180-nm C-axis aligned crystalline In-Ga-Zn oxide transistor (2014)

A flip-flop achieving high-speed backup utilizing a Si transistor and long-term retention with zero standby power by means of a transistor of c-axis aligned crystalline (CAAC) In-Ga-Zn oxide, a kind of CAAC oxide semiconductor, featuring extremely low off-state current is proposed. Using the flip-flop, a 32-bit processor has been fabricated with 350-nm Si/180-nm CAAC oxide semiconductor technology, and demonstrated data backup and power shutdown in 1.5 clock cycles at a low power of 1.77 nJ, data recovery in 2.5 clock cycles, and data retention with zero standby power for at least a day. According to simulation results, fast backup and long-term retention can also be achieved with 45-nm Si/180-nm CAAC oxide semiconductor technology.
HgCdTe double heterostructure injection laser grown by molecular beam epitaxy (1991)

While a variety of light-detecting devices have been made with HgCdTe, little has been done to apply this technology to light-emitting devices. We report here the successful fabrication and operation of the first HgCdTe injection laser. This stripe-geometry double-heterostructure laser was operated under pulsed current at temperatures between 40 and 90 K. At 77 K, the emission wavelength was 2.86 μm with a linewidth of 0.3 meV, and the pulsed threshold current density was 625 A/cm2. The double heterostructure, with a 1.4-μm-thick active layer, was grown and in situ doped by molecular beam epitaxy (MBE). The p+ and n+ confinement layers were doped with arsenic and indium, respectively.
Sustained influence of the renal nerves to attenuate sodium retention in angiotensin hypertension (2001)

Recent studies indicate that baroreflex suppression of renal sympathetic nerve activity is sustained for up to 5 days of ANG II infusion; however, steady-state conditions are not associated with ANG II hypertension of this short duration. Thus the major goal of this study was to determine whether neurally induced increments in renal excretory function during chronic intravenous infusion of ANG II are sustained under more chronic conditions when hypertension is stable and sodium balance is achieved. Experiments were conducted in five conscious dogs subjected to unilateral renal denervation and surgical division of the urinary bladder into hemibladders to allow separate 24-h urine collection from denervated (Den) and innervated (Inn) kidneys. ANG II was infused after control measurements for 10 days at a rate of 5 ng. kg(-1). min(-1). Twenty-four-hour control values for mean arterial pressure (MAP) and the ratio for urinary sodium excretion from Den and Inn kidneys (Den/Inn) were 92 +/- 4 mmHg and 0.99 +/- 0.05, respectively. On days 8-10 of ANG II infusion, MAP was stable (+30 +/- 3 mmHg) and sodium balance was achieved. Whereas equal amounts of sodium were excreted from the kidneys during the control period, throughout ANG II infusion there was a greater rate of sodium excretion from Inn vs. Den kidneys (day 10 Den/Inn sodium = 0.56 +/- 0.05), indicating chronic suppression of renal sympathetic nerve activity. The greater rate of sodium excretion in Inn vs. Den kidneys during renal sympathoinhibition also revealed a latent impairment in sodium excretion from Den kidneys. Although the Den/Inn for sodium and the major metabolites of nitric oxide (NO) decreased in parallel during ANG II hypertension, the Den/Inn for cGMP, a second messenger of NO, remained at control levels throughout this study. This disparity fails to support the notion that a deficiency in NO production and action in Den kidneys accounts for the impaired sodium excretion. Most importantly, these results support the contention that baroreflex suppression of renal sympathetic nerve activity is sustained during chronic ANG II hypertension, a response that may play an important role in attenuating the rise in arterial pressure.
Horizontal transmission of deformed wing virus: pathological consequences in adult bees (Apis mellifera) depend on the transmission route (2010)

Recent reports on a steady decline of honeybee colonies in several parts of the world caused great concern. There is a consensus that pathogens are among the key players in this alarming demise of the most important commercial pollinator. One of the pathogens heavily implicated in colony losses is deformed wing virus (DWV). Overt DWV infections manifested as deformed-wing syndrome started to become a threat to honeybees only in the wake of the ectoparasitic mite Varroa destructor, which horizontally transmits DWV. However, a direct causal link between the virus and the symptom 'wing deformity' has not been established yet. To evaluate the impact of different horizontal transmission routes, and especially the role of the mite in the development of overt DWV infections, we performed laboratory infection assays with pupae and adult bees. We could demonstrate that pupae injected with DWV dose-dependently developed overt infections characterized by deformed wings in adult bees, suggesting that DWV, if transmitted to pupae by the mite, is the causative agent of the deformed-wing syndrome. The OID(50) (overt infection dosage) was approximately 2500 genome equivalents. Injecting more than 1×10(7) DWV genome equivalents into adult bees also resulted in overt infections while the same viral dosage fed to adult bees only resulted in covert infections. Therefore, both infection of adult bees through DWV-transmitting phoretic mites and infection of nurse bees through their cannibalizing DWV-infected pupae might represent possible horizontal transmission routes of DWV.
Pulsed laser deposition with a high average power free electron laser: Benefits of subpicosecond pulses with high repetition rate (2003)

We have conducted experiments exploring pulsed laser deposition of thin films using the high average power Thomas Jefferson National Accelerator Facility Free Electron Laser. The combination of parameters of this laser, including subpicosecond pulses, high average power, high repetition rate, and tunability, makes it a unique tool for the study of the effects of laser characteristics on thin-film quality. When compared to ablation and deposition with an ultrafast, high energy per pulse, low repetition rate laser (amplified Ti:sapphire), we find that the lower energy per pulse with high repetition rate of the free electron laser leads to very different plasma emission and produces films with high quality with the potential of very high deposition rates. This is demonstrated in the optical spectroscopy of plasma emission from Ti and the growth of Ni80Fe20 thin films.
Two-Step Differential Expression Analysis Reveals a New Set of Genes Involved in Thyroid Oncocytic Tumors (2005)

Thyroid oncocytic adenomas are a class of tumors characterized by the presence of abundant mitochondria. We performed a differential display RT-PCR analysis on two oncocytic adenomas and their paired controls. We then carried out a microarray analysis using the 460 selected, differentially expressed clones on four other oncocytomas and their paired controls. Thirty genes, 12 encoded by mitochondrial DNA and 18 nuclear-encoded, were overexpressed by a factor of at least 2 in the tumors compared with the controls. Seven of the 18 nuclear-encoded genes are involved in protein metabolism: DKFZP434I116, B3GTL, SNX19, RP42, SENP1, UBE2D3, and the CTSB gene, which is known to be particularly deregulated in most thyroid tumors. Other genes are implicated in signal transduction (ITGAV) or tumorigenesis (AF1q). Immunohistochemistry allowed us to confirm overexpression of the ITGAV and CTSB genes at the protein level and showed a marked relocation of the CTSB protein. We confirmed the overexpression of the AF1q oncogene in 56% of 18 oncocytic tumors by quantitative RT-PCR analysis, which attested to the heterogeneity of these tumors. Our results show an increased expression of genes involved in protein metabolism in oncocytoma, the significance of which requires investigation.
Novel mAbs reveal potent co-stimulatory activity of murine CD27 (1995)

Members of the tumor necrosis factor receptor (TNFR) family are emerging as important molecules implicated in the regulation of proliferation, differentiation and survival of T and B lymphocytes. Among these receptors is CD27, the function of which has thus far only been studied in the human system, where it amplifies the T cell proliferative response induced by TCR triggering. We report here the generation of mAbs to murine CD27, by an efficient method involving the use of transfected Armenian hamster fibroblasts. Previous analysis had already indicated that murine CD27 mRNA is uniquely expressed in lymphoid cells. As determined with one of the newly developed antibodies, murine CD27 is expressed on the great majority of both alpha beta and gamma delta T lymphocytes, on a small population of peripheral B cells, and on a very small subset of B220+ cells in the bone marrow. This distribution largely corresponds to that in the human system. However, unlike human CD27, which is primarily expressed in mature, medullary thymocytes, murine CD27 is found on all thymocytes, except a subset of CD4-CD8- precursors. Upon cross-linking, anti-CD27 mAb amplified the proliferative response of purified T lymphocytes to suboptimal stimulation with concanavalin A at least 4-fold. This indicates that such mAbs can mimick ligand binding and demonstrates that CD27 also acts as a potent co-stimulatory molecule in the murine system.
Reactions of cytidine with 7-bromomethylbenz[a]anthracene, benzyl bromide, and p-methoxybenzyl bromide. Ratio of amino to 3 substitution (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of cytidine with 7-bromomethylbenz[a]anthracene, benzyl bromide, and p-methoxybenzyl bromide. Ratio of amino to 3 substitutionRobert Shapiro and Shian-Jan ShiueyCite this: J. Org. Chem. 1976, 41, 9, 1597–1600Publication Date (Print):April 1, 1976Publication History Published online1 May 2002Published inissue 1 April 1976https://pubs.acs.org/doi/10.1021/jo00871a025https://doi.org/10.1021/jo00871a025research-articleACS PublicationsRequest reuse permissionsArticle Views158Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Modular chemical tools for advanced macromolecular engineering (2007)

Contemporary polymer science requires, more than ever, simple and efficient chemical reactions for constructing complex macromolecular or supramolecular structures. The present feature article highlights our recent efforts to develop modular synthetic platforms in macromolecular synthesis. As examples, the macromolecular engineering possibilities of two “click” reactions (i) the copper-catalyzed cycloaddition of azides and terminal alkynes and (ii) the radical addition of mercaptans onto vinyl double bonds are discussed in detail herein.