gebhart/patrepeval huggingface dataset:
A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures (1997)

A technique is described to identify the rare sequences within an RNA molecule that are available for efficient interaction with complementary DNA probes: the target RNA is digested by RNase H in the presence of a random pool of complementary DNA fragments generated from the same DNA preparation that was used for target RNA synthesis. The DNA region was amplified by PCR, partially digested with DNase and denatured prior to RNA binding. In the presence of single-stranded DNA fragments the RNA was digested with RNase H such that, on average, each molecule was cut once. Cleavage sites were detected by gel electrophoresis either directly with end-labeled RNA or by primer extension. The pattern of accessible sites on c- raf mRNA was determined and compared with the known profile of activity of oligonucleotides found in cells, showing the merit of the method for predicting oligonucleotides which are efficient for in vivo antisense targeting. New susceptible sites in the 3'-untranslated region of c- raf mRNA were identified. Also, four RNAs were probed to ascertain to what extent structure predicts accessibility: the P4-P6 domain of the Tetrahymena group I intron, yeast tRNAAsp, Escherichia coli tmRNA and a part of rat 18S rRNA.
Switch engineering handbook (1993)

Covering virtually all current switching technologies, this comprehensive handbook gives details on specific switch technologies, construction details, selection/specification criteria, and applications. Photographs and drawings provide extensive mechanical and electrical details. It shows readers how to take advantage of the latest developments, select the right switch to reduce cost and enhance performance, assure the correct specification of switches.
Ultrathin Strained-SOI by Stress Balance on Compliant Substrates and FET Performance (2005)

Ultrathin, strained-silicon-on-insulator (s-SOI) structures without a residual silicon-germanium (SiGe) underlayer have been fabricated using stress balance of bi-layer structures on compliant borophosphorosilicate glass (BPSG). The bi-layer structure consisted of SiGe and silicon films, which were initially pseudomorphically grown on a silicon substrate and then transferred onto BPSG by a wafer bonding and SmartCut process. The viscous flow of the BPSG during a high-temperature anneal then allowed the SiGe/Si bi-layer to laterally coherently expand to reach stress balance, creating tensile strain in the silicon film. No dislocations are required for the process, making it a promising approach for achieving high-quality strained-silicon for device applications. To prevent the diffusion of boron and phosphorus into the silicon from the BPSG, a thin nitride film was inserted between the bi-layer and BPSG to act as a diffusion barrier, so that a lightly doped, sub-10-nm s-SOI layer (0.73% strain) was demonstrated. N-channel MOSFETs fabricated in a 25-nm silicon layer with 0.6% strain showed a mobility enhancement of 50%.
Clinical Assessment and Improved Diagnosis of Bocavirus-induced Wheezing in Children, Finland (2009)

Human bocavirus (HBoV) is a widespread respiratory virus. To improve diagnostic methods, we conducted immunoglobulin (Ig) G and IgM enzyme immunoassays with recombinant virus-like particles of HBoV as antigen. Acute-phase and follow-up serum samples from 258 wheezing children and single serum samples from 115 healthy adults in Finland were examined. Our assays had a sensitivity of 97% and a specificity of 99.5%. Of adults, 96% had immunity; none had an acute infection. Of 48 children with serologically diagnosed acute HBoV infections, 45 were viremic and 35 had virus in nasopharyngeal aspirates (NPAs). Of 39 HBoV NPA PCR-positive children co-infected with another virus, 64% had a serologically verified HBoV infection. HBoV caused illness of longer duration than rhinovirus and of equal severity to that of respiratory syncytial virus. Among children with bronchiolitis, >25% had acute HBoV infections. Accurate HBoV diagnosis requires serologic analysis or PCR of serum; PCR of NPAs alone is insufficient.
Therapeutic Perspectives in Alzheimers Disease (2006)

It is now almost a century ago that Alois Alzheimer first presented his results in public. Main characteristics of Alzheimer's disease (AD) are massive cerebral accumulation of amyloid, composed of fibrillary aggregates of the Amyloid beta peptide (Abeta) and intracellular accumulation of abnormally phosphorylated tau protein associated with widespread neurodegeneration. The clinical picture is characterized by progressive and irreversible dementia, which is eventually fatal. To date, there is no cure for this severe disease affecting more than of 30 million individuals worldwide. In the last decades, the treatment of Alzheimer patients was mainly focusing on symptomatical strategies. Based on the augmented knowledge about the mechanisms underlying the pathology of AD, particularly the molecular causes and consequences of AD, different therapeutic approaches arose and recently, treatment with Statins, NSAIDs and Abeta vaccines reached the level of clinical trials, showing some indication of efficacy already. According to actual evaluations, these approaches have realistic chances to become established as therapeutic routine in AD within the next 10 years. We will review here some of the most promising novel approaches to cure and prevent rather than to treat the symptoms of AD.
Identification and characterization of a novel insertion sequence, IS1106, downstream of the porA gene in B15 Neisseria meningitidis (1992)

Examination of Neisseria meningitidis strains associated with endemic meningococcal disease demonstrated differences in the number of copies of a repetitive sequence. Characterization of a copy of this repetitive sequence present in B15 strains has revealed the presence of a novel insertion sequence (IS1106) located within a complex repetitive region downstream of the gene for the major surface antigen (porA). IS1106 has a length of 1137 bp and is flanked by 36bp inverted repeats. Two open reading frames (ORF1 and ORF2) are present in opposite strands in codon-codon register with ORF2 entirely located within ORF1. The predicted protein from ORF1 demonstrates homology with the 5A protein of IS5 (Kroger and Hobom, 1982). Strains from two independent outbreaks of B15 meningococcal disease in the UK were found to contain the same genomic deletion removing a copy of IS1106 downstream of the porA gene.
Privacy-Preserving Quick Authentication in Fast Roaming Networks (2006)

Vehicular networks will become an important component for information accesses in one's daily life. A vehicular network provides a vehicular user not only chances to communicate with peer vehicles but also to use Internet through roadside access points (APs). During a trip a vehicular user could roam across multiple APs either belong to their home wireless domain or to domains owned by different authorities. This poses challenges on privacy and network performance to the current public wireless network access protocols. In this paper we explore an idea that shifts the paradigm of authentication that goes back to home networks to a paradigm of authentication that performs at the APs. We propose three authentication schemes in realizing the idea. These schemes are designed for preserving user's identity and location privacy. They also greatly reduce response time for authentication when roaming. The paper then analyzes the security and privacy properties of these schemes as well as the efficiency of them
Binocular infrared optometer for measuring accommodation in both eyes simultaneously in natural-viewing conditions (1993)

A binocular IR optometer has been developed to measure accommodation continuously and simultaneously in both human eyes in conditions close to natural viewing where a subject gazes at an actual target with binocular vision. Measurement accuracy is ~ 0.24 D with a precision of 0.05 D within a refractive-power range of + 10 to -10 D in model eyes. The dynamic response is over 100 D/s. In addition we measured simultaneously and continuously accommodation, pupil diameter, and eye position of both human eyes in near-reflex conditons using this binocular optometer. Development of the tracking IR binocular optometer is discussed in detail.
Induction of Apoptosis and Necrosis in Cancer Cells by Electric Fields, Electromagnetic Fields, and Photodynamically Active Quinoids (2004)

Bioelectrochemical and electromagnetic methods are widely known to modify or even inhibit biochemical processes. In this respect apoptosis induction and necrosis of cancer cells (e.g. K-562, U-973 or HL-60) are of considerable interest as an adjuvant therapy. The synergistic combination with photodynamic activity is a novel possibility to enhance the efficacy of electromagnetic methods, as shown for quinoid drugs reacting as photodynamic Type 1 radicals. Some of these light reactions were applied to electroporated cancer cells producing the highest percentage of necrosis for cells in suspension. In order to avoid metallic electrodes for such single pulse application a non-invasive treatment it was demonstrated that using pulsating electromagnetic fields (50 Hz) one is able to cause necrosis itself. Moreover this effect is strengthened in the presence of quinoid anthracyclines and actinomycin-C. Additional exposure using visible light yields a maximum lethality. Hence this non-invasive treatment will be of advantage for future development as an adjuvant therapy.
The heterogeneous nucleation of microcellular foams assisted by the survival of microvoids in polymers containing low glass transition particles. Part II: Experimental results and discussion (1994)

Abstract The experimental data obtained for the nucleation of microcellular foams are compared with the theoretical model developed in the first part of this paper. Polystyrene (PS) with rubber particles as nucleation sites is used as an exploratory system. Nitrogen is used as a physical blowing agent to nucleate the bubbles. The influence of process variables, such as saturation pressure, foaming temperature, and concentration and size of rubber particles, is discussed. Results indicate that all these variables play important roles during the nucleation process. A nucleation mechanism based on the survival of microvoids against the resisting surface and elastic forces has been modeled to obtain the cell nucleation density. Increase in saturation pressure increase the cell density to a critical pressure. Beyond this critical pressure, there is no increase in bubble number, indicating that all microvoids are activated. The effect of temperature is more complex than the effect of pressure. Increase in concentration of the rubber particles increase the nucleation cell density. In general, the experimental data are well described by the nucleation model presented in Part I.
Rigorous Modeling for Data Analysis towards Accurate Determination of Shale Gas-Permeability by Multiple-Repeated Pressure-Pulse Transmission Tests on Crushed Samples (2014)

Abstract Determination of the nanodarcy gas permeability and other parameters of shale by pressure-pulse transmission testing of core plugs, drill cuttings, and crushed samples is discussed. The methods available for interpretation of pressure-pulse decay tests are reviewed with emphasis on the difference between the intrinsic and apparent permeability. Improved formulation and analysis which honor the relevant physics of gas transport and interactions of flowing gas with the shale under the pore-proximity and elevated pressure conditions are presented. Modification of the shale and fluid properties under prevailing stress, and pore-size distribution, connectivity, and confinement conditions is shown to be important under any pressure conditions while the gas rarefaction and slippage effects diminish essentially at high pressures but become important at low pressures. The permeability and other parameters of shale samples are determined by numerical modeling and analysis of the pressure tests conducted under different conditions in order to accommodate for temporally and spatially variable conditions. Better design and analysis of experiments for simultaneous determination of several unknown parameters that impact transport calculations, including stress-deformation, adsorption, diffusion, and deviation from Darcy flow are described. The inherent limitations of the earlier methods which rely on the approximate analytical solutions of the simplified diffusivity equation based on the Darcy's law are delineated. It is pointed out that the permeability measured using a Darcy-type equation is the apparent permeability and not the intrinsic permeability. Thus, the primary reason for the contradictory values of permeability measured by application of the analytical models is explained by dependence of the permeability of shale to different testing conditions over which only different average permeability values can be obtained when applying the approximate analytical solutions obtained based on the assumption of a constant permeability value.
Strategy Guideline: Accurate Heating and Cooling Load Calculations (2011)

This guide presents the key criteria required to create accurate heating and cooling load calculations and offers examples of the implications when inaccurate adjustments are applied to the HVAC design process. The guide shows, through realistic examples, how various defaults and arbitrary safety factors can lead to significant increases in the load estimate. Emphasis is placed on the risksincurred from inaccurate adjustments or ignoring critical inputs of the load calculation.
Improving Photosynthetic Efficiency for Greater Yield (2010)

Increasing the yield potential of the major food grain crops has contributed very significantly to a rising food supply over the past 50 years, which has until recently more than kept pace with rising global demand. Whereas improved photosynthetic efficiency has played only a minor role in the remarkable increases in productivity achieved in the last half century, further increases in yield potential will rely in large part on improved photosynthesis. Here we examine inefficiencies in photosynthetic energy transduction in crops from light interception to carbohydrate synthesis, and how classical breeding, systems biology, and synthetic biology are providing new opportunities to develop more productive germplasm. Near-term opportunities include improving the display of leaves in crop canopies to avoid light saturation of individual leaves and further investigation of a photorespiratory bypass that has already improved the productivity of model species. Longer-term opportunities include engineering into plants carboxylases that are better adapted to current and forthcoming CO 2 concentrations, and the use of modeling to guide molecular optimization of resource investment among the components of the photosynthetic apparatus, to maximize carbon gain without increasing crop inputs. Collectively, these changes have the potential to more than double the yield potential of our major crops.
Simulating the Design and Operation of Absorption Trenches for Effluent Disposal (1990)

A computer model was used to optimise the design of an absorption trench system for disposal of sewage effluent. The model predicts how soil water is redistributed in hillslopes by lateral subsurface flows, and the behaviour of areas prone to waterlogging under combined inputs of rainfall and downslope flow from the trenches. The design constraint for the trench layout was the need to avoid surface saturation due to exfiltrating effluent. The model was used to optimise the layout, and to specify the capacity of a holding reservoir necessary to store effluent during prolonged wet periods.
A novel generation of heparan sulfate mimetics for the treatment of prion diseases (2003)

The accumulation of PrP(res), the protease-resistant abnormal form of the host-encoded cellular prion protein, PrP(C), plays a central role in transmissible spongiform encephalopathies. Human contamination by bovine spongiform encephalopathy (BSE) has propelled many scientific teams on a highway for anti-prion drug development. This study reports that heparan sulfate mimetics (HMs), developed originally for their effect on tissue regeneration, abolish prion propagation in scrapie-infected GT1 cells. PrP(res) does not reappear for up to 50 days post-treatment. When tested in vivo, one of these compounds, HM2602, hampered PrP(res) accumulation in scrapie- and BSE-infected mice and prolonged significantly the survival time of 263K scrapie-infected hamsters. Interestingly, HM2602 is an apparently less toxic and more potent inhibitor of PrP(res) accumulation than dextran sulfate 500, a molecule known to exhibit anti-prion properties in vivo. Kinetics of PrP(res) disappearance in vitro and unaffected PrP(C) levels during treatment suggest that HMs are able to block the conversion of PrP(C) into PrP(res). It is speculated that HMs act as competitors of endogenous heparan sulfates known to act as co-receptors for the prion protein. Since these molecules are particularly amenable to drug design, their anti-prion potential could be developed further and optimized for the treatment of prion diseases.
Terahertz pulse propagation in plastic photonic crystal fibers (2005)

Guided-wave single-mode propagation of terahertz pulses in plastic photonic crystal fibers has been experimentally demonstrated for the first time. Low loss propagation has been observed within the experimental bandwidth of 0.1 3 THz.
Glucagon-Like Peptide 1/Glucagon Receptor Dual Agonism Reverses Obesity in Mice (2009)

Sustained GLP1R/GCGR dual agonism reverses obesity in DIO mice and is a novel therapeutic approach to the treatment of obesity.
Hydrogen-Bonded Polymer Capsules Formed by Layer-by-Layer Self-Assembly (2003)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTHydrogen-Bonded Polymer Capsules Formed by Layer-by-Layer Self-AssemblyVeronika Kozlovskaya, Salim Ok, Alioscka Sousa, Matthew Libera, and Svetlana A. SukhishviliView Author Information Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030 Cite this: Macromolecules 2003, 36, 23, 8590–8592Publication Date (Web):October 25, 2003Publication History Received26 July 2003Revised7 October 2003Published online25 October 2003Published inissue 1 November 2003https://pubs.acs.org/doi/10.1021/ma035084lhttps://doi.org/10.1021/ma035084lrapid-communicationACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views2084Altmetric-Citations154LEARN 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 SUBJECTS:Deposition,Layers,Polymer particles,Polymers,Thin films Get e-Alerts
Effects of imipramine and mirtazapine on operant performance in rats (1994)

Abstract The effects of the tricyclic antidepressant imipramine and the atypical antidepressant mirtazapine were compared on the performance of rats in three operant procedures: a differential reinforcement of low rates schedule (DRL), a delayed matching to position (DMTP), and simultaneous visual discrimination tasks. Both compounds improved performance in the DRL task in a similar dose‐related manner. Imipramine, but not mirtazapine, disrupted performance in the visual discrimination task. Imipramine reduced accuracy and increased response latencies and missed trials. Neither compound effected accuracy in the DMTP; both compounds caused some slowness of responding and imipramine caused several animals to fail to respond in a manner similar to that observed in the visual discrimination task. These data suggest that although imipramine and mirtazapine are similarly effective in putative tests of antidepressant activity, imipramine has a greater tendency to disrupt other aspects of cognitive performance, as well as exert generally depressive effects on operant responding.
Expression of the Chemokines IP-10 and Mig in IL-10 Transduced Tumors (2001)

SUMMARY: Several laboratories have reported marked tumor inhibition when the cytokine interleukin-10 (IL-10) is overexpressed as a transgene in a variety of tumor cells. To identify critical effector molecules, we compared the expression of the chemokine crg-2, the murine homolog of human inducible protein 10 (human IP-10) in murine mammary tumors derived from the transplantation of six IL-10 expressing clones of tumor cell line 66.1, parental 66.1, or 66-neo-cells. We observed increased levels of IP-10 mRNA in all IL-10-expressing tumors examined in comparison to 66-neo. IP-10 mRNA was not detected in parental 66.1 tumors. The closely related chemokine Mig (monokine induced by interferon-gamma [IFN-gamma]) was also induced in all IL-10-expressing tumors. Studies of cultured tumor cells in vitro show that mammary epithelial tumor cells, in the absence of host elements, can express IP-10 and Mig in response to induction with either lipopolysaccharide (LPS) or IFN-gamma alone. The combination of LPS plus IFN-gamma resulted in even greater induction of IP-10 RNA. The kinetics of induction differ somewhat for the two chemokines, with IP-10 showing slower induction and less rapid decline. Because both Mig and IP-10 are chemotactic for tumor-infiltrating lymphocytes, we examined the presence of CD4+ and CD8+ lymphocytes in these tumors. Consistent with the upregulation of Mig and IP-10, we saw significantly increased numbers of CD8+ cells and a lesser increase in CD4+ cells in tumors with elevated levels of both chemokines.
Effect of interfacial oxide layers on the current-voltage characteristics of Al-Si contacts (1976)

Aluminum-silicon contacts with very thin interfacial oxide layers and various surface impurity concentrations are studied for both n and p-type silicon. To determine the surface impurity concentrations on p(+)-p and n(+)-n structures, a modified C-V technique was utilized. Effects of interfacial oxide layers and surface impurity concentrations on current-voltage characteristics are discussed based on the energy band diagrams from the conductance-voltage plots. The interfacial oxide and aluminum layer causes image contrasts on X-ray topographs.
Correlated Vibrational Dynamics Revealed by Two-Dimensional Infrared Spectroscopy (2002)

Two-dimensional infrared (2D IR) spectroscopy has been used to monitor the solvent-induced correlated fluctuations in the transition energies of two coupled vibrations. The elongation of diagonal and cross peaks in a 2D IR correlation spectrum reflects the degree of inhomogeneity in the individual transition energies and the correlation between them. Changes in the 2D line shapes as a function of a variable waiting period have been successfully reproduced by a correlated spectral diffusion model.