gebhart/patrepeval huggingface dataset:
Oligonucleotides Tethering Hoechst 33258 Derivatives:  Effect of the Conjugation Site on Duplex Stabilization and Fluorescence Properties (1997)

A series of DNA conjugates have been prepared in which two different derivatives of Hoechst 33258 have been tethered to a sequence containing a 5'-GAATTC-3' target site. The two derivatives differ only in the length of the tether between the DNA and the Hoechst fluorophore. By using a DNA backbone labeling protocol, one in which the Hoechst dye is tethered to an internucleotide phosphoramidate residue, it was possible to easily vary the site of attachment with respect to the A-T rich binding site. When tethered outside the GAATTC sequence, little if any helix stabilization results upon hybridization of the conjugate to its complementary sequence. As the site of conjugation is moved to one end of the target sequence and finally within the AATT sequence, more effective helix stabilization results. When tethered between the two A residues, or between the A and T residue, a delta Tm of at least +20 degrees C is observed. Upon hybridization and formation of the B-form DNA, binding by the tethered Hoechst dye results, and the bound dye becomes brightly fluorescent. Upon a simple titration of the single-stranded conjugate with the complementary target sequence the quantum yield enhancement for hybridization only appears to be 5-7-fold at best. These fluorescence effects, generally less dramatic than those observed with other sequences, result from an increase in quantum yield for the single-stranded conjugate relative to the free Hoechst 33258. Heating the single-stranded conjugate reduces the inherent fluorescence of the single-stranded conjugate to a level comparable with that of the free Hoechst dye. In experiments monitoring absorbance vs temperature, a cooperative transition is observed for the single-stranded conjugate. Both the high quantum yield observed for the single-stranded conjugate and the observed thermally induced transition suggest that the single-stranded conjugate can dimerize (at the GAATTC site), mediated by the groove-binding fluorophore.
Characterization of the Promoter Region of the Human Transforming Growth Factor-β Type II Receptor Gene (1995)

Diminished cellular responsiveness to transforming growth factor-beta (TGF-beta) is frequently correlated with decreased transcription of the type II receptor for TGF-beta (TGF-beta RII). We have cloned and characterized the human TGF-beta RII promoter and, using S1 nuclease mapping and 5' rapid amplification of cDNA ends polymerase chain reaction, have identified five alternative transcription start sites within the region -33 to +57. DNA transfection experiments and electrophoretic mobility shift assays have revealed the existence of five distinct regulatory regions including two positive regulatory elements and two negative regulatory elements in addition to the core promoter region. The first positive regulatory element (-219 to -172) interacts with two distinct nuclear protein complexes, at least one of which appears to be a previously unidentified transcription factor. The second positive regulatory element (+1 to +35) also interacts with two separate protein complexes, both of which appear to be novel transcription factors. Deletion of either positive regulatory element markedly decreased expression of the target gene, suggesting that both positive regulatory elements are necessary for basal expression levels of TGF-beta RII.
New weight transform schemes for delayless subband adaptive filtering (2002)

Very long adaptive filters are used for controlling the acoustic echo due to the acoustic echo of the loudspeaker and microphone. Subband adaptive filters have been proposed to save computations as well as speed up convergence. Delayless subband adaptive filters remove the additional signal path delay due to the analysis-synthesis system in their conventional counterpart by transforming the subband filters to a corresponding fullband one and cancelling the echo using the fullband filter. The weight transform from subband to fullband plays a crucial role in the delayless subband adaptive filters. In this paper, a defect of the FFT-stacking weight transform is identified, and new transform schemes are proposed. Simulation results show that significant performance improvements can be achieved by employing the proposed weight transform schemes.
Pocket PhotoMesa (2004)

Small devices such as Palm and Pocket PC have gained wide popularity with the advance and affordability of mobile technologies. Image browsers are among popular software applications on small devices. The limitations introduced by these devices such as screen resolution, processing power and storage impose a challenge for multimedia applications designed for larger displays to adapt to small screens. For an image browser, layout of images and navigation between them are critical factors of the users' experience.Motivated by these challenges, we developed Pocket PhotoMesa: an image browser for the pocket pc that employs quantum strip Treemaps for laying out images and Zoomable User Interfaces for navigation. In this paper, we discuss the development of Pocket PhotoMesa and we describe a usability study comparing the performance and users' experience using Pocket PhotoMesa and ACDSee image browser (a current commercial offering) for the Pocket PC.
TGFβ receptor internalization into EEA1-enriched early endosomes (2002)

Transforming growth factor (TGF)beta is an important physiological regulator of cellular growth and differentiation. It activates a receptor threonine/serine kinase that phosphorylates the transcription factor Smad2, which then translocates into the nucleus to trigger specific transcriptional events. Here we show that activated type I and II TGF beta receptors internalize into endosomes containing the early endosomal protein EEA1. The extent of TGF beta-stimulated Smad2 phosphorylation, Smad2 nuclear translocation, and TGF beta-stimulated transcription correlated closely with the extent of internalization of the receptor. TGF beta signaling also requires SARA (Smad anchor for receptor activation), a 135-kD polypeptide that contains a FYVE Zn(++) finger motif. Here we show that SARA localizes to endosomes containing EEA1, and that disruption of this localization inhibits TGF beta-induced Smad2 nuclear translocation. These results indicate that traffic of the TGF beta receptor into the endosome enables TGF beta signaling, revealing a novel function for the endosome as a compartment specialized for the amplification of certain extracellular signals.
Self-Assembly of Stiff, Adhesive and Self-Healing Gels from Common Polyelectrolytes (2014)

Underwater adhesion has numerous potential medical, household, and industrial applications. It is typically achieved through covalent polymerization and cross-linking reactions and/or the use of highly specialized biological or biomimetic polymers. As a simpler alternative to these covalent and biomimetic strategies, this article shows that stiff, gel-like complexes that adhere to various substrates under water can also be prepared through the ionic cross-linking of common, commercial polyelectrolytes. The gels form spontaneously when synthetic polycations, such as poly(allylamine) (PAH), are mixed with strongly binding multivalent anions, pyrophosphate (PPi) and tripolyphosphate (TPP). The PAH/PPi and PAH/TPP gels exhibit very high storage moduli (G∞′ ≈ 400 kPa), self-heal when torn, and adhere to both hydrophilic and hydrophobic substrates under water (with short-term tensile adhesion strengths of 350–450 kPa). Furthermore, these gels can be dissolved on demand (if adhesion needs to be reversed) by changing the ambient pH, which controls the ionization state of the polyelectrolyte and ionic cross-linker. These properties suggest that synthetic polycations cross-linked with PPi and TPP ions could provide a simple, inexpensive, and scalable platform for underwater adhesion.
Utilization of glutathione (l‐γ‐glutamyl‐l‐cysteinylglycine) by Fusobacterium nucleatum subspecies nucleatum (1994)

Although fusobacteria use amino acids and peptides as energy source, it is not known whether they are able to actively transport peptides into the cell. In the present study the tripeptide glutathione was used as a model substance to investigate peptide uptake in Fusobacterium nucleatum subsp. nucleatum. Cells harvested after 2 days of growth on blood agar or in their exponential growth phase in broth were suspended in buffer with glutathione, L-cysteinylglycine and L-cysteine. As a measure of cell uptake, the formation of hydrogen sulfide was followed. Cells from blood agar had a low capacity to form hydrogen sulfide from the tripeptide glutathione and the dipeptide L-cysteinylglycine. However, hydrogen sulfide was formed from L-cysteinylglycine, but not from glutathione or from L-cysteine, by cells grown in broth in such a way that it strongly indicated an active transport of L-cysteinylglycine with a Km of 18 microM. Hydrogen sulfide was efficiently formed from glutathione by cells grown in broth in the presence 1 mM glutathione. In these cells a glycylglycine-dependent L-gamma-glutamyl peptidase activity was induced. It is probable that the efficient utilization of glutathione for hydrogen sulfide formation mirrored the uptake of L-cysteinylglycine after an L-gamma-glutamyl peptidase had split L-glutamate off from glutathione.
Spleen cell cytokine secretion in Mycobacterium bovis BCG-infected mice (1992)

Three susceptible mouse strains, i.e., BALB/c (H-2d), C57BL/6 (H-2b), and major histocompatibility complex-congenic BALB.B10 (H-2b), were infected intravenously with 4 x 10(6) CFU of live Mycobacterium bovis BCG and analyzed 4 weeks later for in vitro spleen cell cytokine secretion in response to purified protein derivative (PPD), BCG culture filtrate (CF), BCG cellular extract, total BCG, the purified extracellular 30-32-kDa antigen (the fibronectin-binding antigen 85), or the intracellular 65-kDa heat shock protein. C57BL/6 and BALB.B10 mice produced 5- to 10-fold more gamma interferon and interleukin-2 (IL-2) when stimulated with CF, PPD, and antigen 85 than BALB/c mice did. When stimulated with BCG extract and whole BCG, gamma interferon and IL-2 levels were generally lower and comparable in the three strains. IL-4 was detected in spleen cell culture supernatants from infected BALB/c mice but not from C57BL/6 or BALB.B10 mice. IL-5 could not be detected. C57BL/6 and BALB.B10 spleen cells also produced more tumor necrosis factor alpha and IL-6 after stimulation with PPD and CF than BALB/c cells did. Finally, BCG vaccination generated efficient protective immunity in C57BL/6 and BALB.B10 mice but not in BALB/c mice. These data suggest that secreted mycobacterial CF antigens selectively induce a strong TH1 response in BCG-infected C57BL/6 and BALB.B10 mice, whereas in BALB/c mice this response is partly counterbalanced by TH2 cells.
Cutting Edge: Predetermined Avidity of Human CD8 T Cells Expanded on Calibrated MHC/Anti-CD28-Coated Microspheres (2003)

Cytotoxic CD8 T cells are key effectors in the immunotherapy of malignant and viral diseases. However, the lack of efficient methods for their in vitro priming and expansion has become a bottleneck to the development of vaccines and adoptive transfer strategies. Synthetic artificial APCs (aAPCs) are now emerging as an attractive tool for eliciting and expanding CTL responses. We show that, by controlling the MHC density on aAPCs, high- or low-avidity tumor-directed human CTL lines can be raised effectively in vitro if costimulation via CD28 and IL-12 is provided. Compared with low-avidity CTL lines, high-avidity CTLs need 100- to 1000-fold less peptide for activation, bind more MHC tetramers, and, as expected, are superior in recognizing tumor cell lines expressing Ag. We believe that the possibility to raise Ag-specific T cells with predetermined avidity will be crucial for the future use of aAPCs in immunotherapeutical settings.
Host groups: A multicast extension to the Internet Protocol (1985)

This RFC defines a model of service for Internet multicasting and
proposes an extension to the Internet Protocol (IP) to support such a
multicast service. Discussion and suggestions for improvements are
requested. See RFC-988.
Computer telephony integration and its applications (2000)

Computer telephony integration (CTI) enhances the capability and flexibility of the switches or the network end equipment by computer technology. This article introduces the components of CTI such as switch-to-host interfaces, application programming interfaces, and resource architectures. Then we describe two CTI configurations: first-party call control and third-party call control. CTI-based telecommunication services such as unified messaging and call center are described. We also illustrate the Integrated Office Telephony System (IOTS), a CTI system developed at Computer Communication Research Laboratories, which integrates the switch and CTI server on a personal computer platform.
Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov. (1999)

Three strains of Eubacterium aerofacien, JCM 10188T, JCM 7790 and JCM 7791, and 178 freshly isolated strains of the Eubacterium aerofaciens group from human faeces were characterized by biochemical tests, cell wall peptidoglycan type and 16S rRNA analysis. The Eubacterium aerofaciens group was divided into four groups by fermentation patterns of sucrose and cellobiose, and were further divided into 16 sub-groups by fermentation patterns of aesculin, salicin and amygdalin. All of the strains of the Eubacterium aerofaciens group were shown to be phylogenetically distantly related to Eubacterium limosum, which is the type species of genus Eubacterium. Eubacterium aerofaciens was shown to have a specific phylogenetic association with Coriobacterium glomerans. All the strains belonging to Eubacterium aerofaciens resembled Coriobacterium glomerans in possessing a high G + C content (60 mol%). Cell wall analysis, however, revealed the presence of different A4 beta (L-Ala)-D-Glu-L-Orn-L-Asp peptidoglycan types. Based on a 16S rRNA sequence divergence of greater than 9% with Coriobacterium glomerans and the presence of a unique peptidoglycan type, a new genus, Collinsella, is proposed for Eubacterium aerofaciens, with one species, Collinsella aerofaciens. The type strain of Collinsella aerofaciens is JCM 10188T.
Immunization of Mice Against West Nile Virus with Recombinant Envelope Protein (2001)

West Nile (WN) virus is a mosquito-borne flavivirus that emerged in the United States in 1999 and can cause fatal encephalitis. Envelope (E) protein cDNA from a WN virus isolate recovered from Culex pipiens in Connecticut was expressed in Escherichia coli. The recombinant E protein was purified and used as Ag in immunoblot assays and immunization experiments. Patients with WN virus infection had Abs that recognized the recombinant E protein. C3H/HeN mice immunized with E protein developed E protein Abs and were protected from infection with WN virus. Passive administration of E protein antisera was also sufficient to afford immunity. E protein is a candidate vaccine to prevent WN virus infection.
<title>Sagnac interferometers for accurate measurements of true nonreciprocal effects</title> (1994)

We use a polarization maintaining fiber optic gyroscope as a sensor for highly stable and sensitive measurements of fluid flow rates and magnetic fields.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
A Review of Mixture Preparation and Combustion Control Strategies for Spark-Ignited Direct-Injection Gasoline Engines (1997)

&lt;div class="htmlview paragraph"&gt;The current extensive revisitation of the application of gasoline direct-injection to automotive, four-stroke, spark-ignition engines has been prompted by the availability of technological capabilities that did not exist in the late 1970s, and that can now be utilized in the engine development process. The availability of new engine hardware that permits an enhanced level of computer control and dynamic optimization has alleviated many of the system limitations that were encountered in the time period from 1976 to 1984, when the capabilities of direct-injection, stratified-charge, spark-ignition engines were thoroughly researched. This paper incorporates a critical review of the current worldwide research and development activities in the gasoline direct-injection field, and provides insight into new areas of technology that are being applied to the development of both production and prototype engines.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The advantages and disadvantages of the emerging technologies that are being utilized to develop gasoline direct-injection combustion systems, such as electronic common-rail injection, variable swirl and tumble control, computational fluid dynamics, and laser diagnostics of fuel sprays and combustion are discussed in detail within the context of the total industry effort to enhance the attainable brake specific fuel consumption and emissions. Significant emphasis is placed upon extracting the key findings of each investigation and discussing the relative potential of the technique for meeting the major requirements of the gasoline direct-injection engine. Areas of general consensus that are evident among the hundreds of researchers who are currently investigating this field are noted, as are apparent conflicts that must be resolved in the near future by obtaining additional data. Also noted and discussed are a number of critical research areas for which it is obvious that insufficient effort and resources are being devoted. One example of such an area is the development of a proven laboratory test for quantifying the deposit formation tendencies of direct-injection gasoline injectors.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Based upon the review of all available technical publications, the trends and directions of the current effort on gasoline direct-injection engine are noted, and the remaining difficult developmental areas are discussed. For planning purposes, the totality of the literature is used to formulate likely engine scenarios regarding the development of specific engine configurations, and to outline technological path options and trends that may be expected in the displacement of the port fuel injection engine by the gasoline direct-injection engine.&lt;/div&gt;
Heterogeneous Nuclear Ribonucleoprotein L Interacts with the 3′ Border of the Internal Ribosomal Entry Site of Hepatitis C Virus (1998)

Translation initiation of hepatitis C virus (HCV) RNA occurs by internal entry of a ribosome into the 5' nontranslated region in a cap-independent manner. The HCV RNA sequence from about nucleotide 40 up to the N terminus of the coding sequence of the core protein is required for efficient internal initiation of translation, though the precise border of the HCV internal ribosomal entry site (IRES) has yet to be determined. Several cellular proteins have been proposed to direct HCV IRES-dependent translation by binding to the HCV IRES. Here we report on a novel cellular protein that specifically interacts with the 3' border of the HCV IRES in the core-coding sequence. This protein with an apparent molecular mass of 68 kDa turned out to be heterogeneous nuclear ribonucleoprotein L (hnRNP L). The binding of hnRNP L to the HCV IRES correlates with the translational efficiencies of corresponding mRNAs. This finding suggests that hnRNP L may play an important role in the translation of HCV mRNA through the IRES element.
Silicon Liquid Phase Epitaxy: A Review (1986)

The development of a process for the growth of epitaxial layers of silicon from the liquid phase by using tin as a solvent is reviewed. This technology has been found to have the following unique attributes: (i) low growth temperatures, (ii) complete conservation of silicon, (iii) complete suppression of autodoping, (iv) high minority carrier lifetime in the epitaxial layers and the substrates, and (v) the ability to obtain selective epitaxial growth with total absence of nucleation on oxide‐coated surfaces. The process has been applied towards the fabrication of power field‐controlled devices which utilize buried grids and solar cell structures which utilize the selective epitaxial growth for refilling grooves etched in substrates.
On the cytotoxicity of vitamin C and metal ions (1983)

The toxicity of ascorbate towards phage lambda and the phages T2-T7 has been investigated. At room temperature the T-odd and lambda bacteriophages are highly susceptible to ascorbate-induced damage, whereas the T-even phages are practically resistant. The toxicity of ascorbate is dependent on the presence of copper (or iron) and oxygen, although oxygen is not required in the presence of H2O2. Hydrogen peroxide is essential for the ascorbate-induced phage inactivation and the damage is prevented by catalase. At the concentrations used, most of the copper ions are bound to the phage particles. Chelating agents such as EDTA or histidine fully protect the phages, whereas salicylate only reduces the rate of phage inactivation. OH scavengers such as sucrose, formate, mannitol, tert-butyl alcohol or poly(ethylene glycol) have no protective effect. Experiments with DNA labeled phages indicate that both phage adsorption and DNA injection are impaired as a result of the exposure to ascorbate and copper. The failure to express the viral genetic information as a result of single and double-strand breaks in the DNA, probably also contribute to the loss of the plaque-forming ability of the phages. The results are interpreted in terms of a 'site-specific' Fenton mechanism according to which the binding of the transition metal ions to the biological target is a prerequisite for the production of damage. The bound metal ion is reduced either by O(2), ascorbate or other reductants and is subsequently reoxidized by H2O2 yielding OH. radicals. This cyclic redox reaction of the metal generates OH. radicals which react with vital macromolecules with a high probability of causing 'multi-hit' damage. This 'site-specific' formation of OH. radicals, which takes place near the target molecules, accounts both for the high damaging efficiency and for the failure of OH. scavengers to protect against it.
Vascular tumors of the retina and choroid: Diagnosis and treatment (2010)

The vascular tumors of the retina and choroid comprise a diverse group of congenital and acquired lesions. The major vascular tumors of the retina include retinal capillary hemangioma, cavernous hemangioma of the retina, retinal vasoproliferative tumor, and racemose hemangiomatosis of the retina or Wyburn-Mason syndrome. Choroidal vascular tumors include circumscribed choroidal hemangioma and diffuse choroidal hemangioma. While classified as benign, visual symptoms secondary to exudative retinal detachment and a variety of other mechanisms are common and are a major source of long-term visual disability. While many therapeutic modalities exist, treatment of symptomatic cases can be challenging. Of particular importance, many of the vascular tumors of the retina and choroid have significant associations with systemic disease. As ocular symptoms are often the most common presenting disease manifestation, the ophthalmologist plays an important role in accurate and early diagnosis. The ability to initiate prompt screening and treatment in appropriate cases is critical. In the following article, the key clinical and diagnostic features of the major retinal and choroidal vascular tumors, their systemic associations, and the literature pertaining to the most currently available treatment strategies are reviewed.