gebhart/patrepeval huggingface dataset:
Effects of morphological patterning on endothelial cell migration (2001)

The migration of vascular endothelial cells (ECs) plays an important role in vascular remodeling. Here we studied the effects of cell morphology on the migration of bovine aortic ECs by culturing cells on micropatterned strips of collagen matrix (60-, 30-, and 15-microm wide). The spreading areas of the cells on 15- and 30-microm wide strips were 30% lower than those on 60-microm wide strips and unpatterned collagen. The cells on 15-microm wide strips completely aligned in the direction of the strip, and had significantly lower shape index than those in all other groups. On strips of all widths, ECs tended to migrate in the direction of strips. ECs on 15-microm wide strips had highest speed, particularly in the direction of the strip. Vinculin staining showed that the leading edge of ECs on 15-microm wide strips had focal adhesions that were oriented with their lamellipodial protrusion and the direction of cell migration; this arrangement of the focal adhesions may promote EC migration. The present study provides direct evidence on the role of cell morphology in EC migration, and will help us to understand the mechanisms of EC migration during angiogenesis and wound healing.
Scaling of Si and GaAs trench etch rates with aspect ratio, feature width, and substrate temperature (1995)

The scaling of etch rates with feature dimensions is an important issue in the fabrication of microelectronic and photonic devices. Because etch rates depend on circuit layouts and design rules, considerable effort is spent to modify processes each time changes in design are made. Knowing how etch rates scale with design parameters should accelerate the introduction of new designs into manufacturing while minimizing the cost of doing so. Recently it has been shown that etch rates for a variety of conditions scale with the depth/width or aspect ratio and not on width or depth alone. While various mechanisms might be responsible for such scaling, isolating one mechanism from another is not straight forward. Nonetheless, it is important to understand the underlying mechanisms so that differences in etch chemistry and etch reactor design can be accounted for when scaling plasma processes from one design or reactor to another. To assess the effects of etch chemistry alone, the trench etch rates of Si and GaAs are compared under constant plasma conditions. Substrate temperature is varied to further assess the relative importance of surface vs transport phenomena during the etching process. At higher temperatures, both Si and GaAs trench etch rates scale only with aspect ratio in an Ar/Cl2 electron cyclotron resonance plasma. The results are consistent with an ion-neutral synergy model based on Langmuir adsorption kinetics where the scaling can be explained by the aspect ratio dependence of the neutral reactant transport into the trench: charging effects, ion shadowing, and Knudsen transport are not consistent with the data. At −45 °C, the etch rate no longer scales with aspect ratio alone, but now also depends on trench width. The data at this lower temperature are well described by a model incorporating the deposition of an etch inhibiting layer. While the trench etch rates for GaAs and Si scale in similar ways with aspect ratio and trench width, the dependence on feature dimensions of the Si etch rate is much stronger than that for GaAs at all substrate temperatures because the steady-state surface coverage of Cl is smaller for Si. This results in a greater sensitivity to the incoming, aspect ratio dependent, neutral fluxes. The implications of the models on the goal of aspect ratio independent etching are also discussed.
Activation of Glycosylasparaginase (1996)

The activation mechanism of glycosylasparaginase of Flavobacterium meningosepticum has been analyzed by site-directed mutagenesis and activation of purified precursors in vitro. Mutation of Thr-152 to Ser or Cys leads to gene products that are not activated in vivo but are activated in vitro because processing of the mutant precursors is inhibited by certain amino acids in the cell. Kinetic studies reveal that activation is an intramolecular autoproteolytic process. The involvement of His-150 and Thr/Ser/Cys-152 in activation suggests that autoproteolysis resembles proteolysis by serine/cysteine proteases. Multiple functions of the highly conserved active threonine residue are implicated. The activation mechanism of glycosylasparaginase of Flavobacterium meningosepticum has been analyzed by site-directed mutagenesis and activation of purified precursors in vitro. Mutation of Thr-152 to Ser or Cys leads to gene products that are not activated in vivo but are activated in vitro because processing of the mutant precursors is inhibited by certain amino acids in the cell. Kinetic studies reveal that activation is an intramolecular autoproteolytic process. The involvement of His-150 and Thr/Ser/Cys-152 in activation suggests that autoproteolysis resembles proteolysis by serine/cysteine proteases. Multiple functions of the highly conserved active threonine residue are implicated.
Progenitor cells of the adult human airway involved in submucosal gland development (1995)

A bronchial xenograft model of the human airway was used to identify submucosal gland progenitor cells within the surface airway epithelium. Lineage analysis using recombinant retroviruses has demonstrated considerable diversity in the cellular composition of expanded clones within reconstituted xenograft airway epithelium. These findings provide evidence for the existence of multiple progenitors in the airway with either limited or pluripotent capacity for differentiation. Furthermore, the development of transgene-expressing submucosal glands was associated with a single subset of surface airway epithelial clones. This gland progenitor cell demonstrated two discernible characteristics consistent with the identification of an airway stem cell including: (1) pluripotent capacity for airway differentiation and (2) a two-fold higher proliferative rate than other observed clone types. The number of progenitor cells involved in gland development was also assessed by clonal analysis using alkaline phosphatase and beta-galactosidase transgenes. These studies demonstrated that more than one airway progenitor cell is involved in the initial stages of gland development. A second explanation for the high prevalence of non-clonality in developing glands was suggested from three-dimensional reconstruction of transgene marked glands. These reconstruction experiments demonstrated that 27% of glands contained more than one duct to the surface airway epithelium. This observation suggests a novel mechanism of gland morphogenesis by which independently formed glands interact to join glandular lumens. Such a mechanism of glandular development and morphogenesis may play an important role in normal submucosal gland development and/or the progression of hypersecretory diseases of the adult human airway as seen in cystic fibrosis, chronic bronchitis and asthma. The identification of progenitor cells with the capacity to form submucosal glands has implications on the targets for gene therapy in cystic fibrosis.
Immunostimulatory PyNTTTTGT Oligodeoxynucleotides: Structural Properties and Refinement of the Active Motif (2006)

It is well known that synthetic oligodeoxynucleotides (ODNs) containing unmethylated CpG dinucleotides within a given context stimulate B lymphocytes and plasmacytoid dendritic cells (PDCs) of the vertebrate immune system. We have reported that B lymphocyte and PDC stimulation in humans could also be efficiently achieved by using non-CpG ODNs bearing the immunostimulatory sequence (motif) PyNTTTTGT, wherein Py is C or T and N is any deoxyribonucleotide. We are now reporting a series of studies that gives further precision regarding the composition of this immunostimulatory motif. The analysis of hundreds of ODNs led us to the conclusion that the motif for optimal CpG-independent immune stimulation can be represented by a sequence of the following general formula: PyN(T/A)(T/C/G)(T/C/G)(T/G)GT, wherein Py is C or T and N is any deoxyribonucleotide and wherein at least two of the positions represented within parentheses are Ts. Requirements for optimal ODN activity are as follows: (1) at least one of the versions of the general motif must be located near the central portion of the ODN; and (2) the ODN must be 20 or more nucleotides long. PyN(T/A)(T/C/G)(T/C/G)(T/G)GT ODNs are active in a phosphorothioate or in a phosphodiester backbone. In a phosphodiester backbone a canonical motif is strongly required whereas in a phosphorothioate backbone specificity is, within certain limits, less strict. On the other hand, PyN(T/A)(T/C/G)(T/C/G)(T/G)GT oligonucleotides are inactive as a double chain or as a modified (phosphorothioate or hydroxyl-methyl modified) or unmodified RNA backbone.
Time gated fluorescence spectroscopy in Barrett’s oesophagus (2002)

For the first time it was possible to differentiate low grade dysplasia from non-dysplastic Barrett's mucosa during endoscopy based on delayed laser induced fluorescence endoscopy of PpIX. Furthermore, the method helps to detect specialised intestinal metaplasia in short Barrett's oesophagus.
Rewiring yeast sugar transporter preference through modifying a conserved protein motif (2013)

Utilization of exogenous sugars found in lignocellulosic biomass hydrolysates, such as xylose, must be improved before yeast can serve as an efficient biofuel and biochemical production platform. In particular, the first step in this process, the molecular transport of xylose into the cell, can serve as a significant flux bottleneck and is highly inhibited by other sugars. Here we demonstrate that sugar transport preference and kinetics can be rewired through the programming of a sequence motif of the general form G-G/F-XXX-G found in the first transmembrane span. By evaluating 46 different heterologously expressed transporters, we find that this motif is conserved among functional transporters and highly enriched in transporters that confer growth on xylose. Through saturation mutagenesis and subsequent rational mutagenesis, four transporter mutants unable to confer growth on glucose but able to sustain growth on xylose were engineered. Specifically, Candida intermedia gxs1 Phe(38)Ile(39)Met(40), Scheffersomyces stipitis rgt2 Phe(38) and Met(40), and Saccharomyces cerevisiae hxt7 Ile(39)Met(40)Met(340) all exhibit this phenotype. In these cases, primary hexose transporters were rewired into xylose transporters. These xylose transporters nevertheless remained inhibited by glucose. Furthermore, in the course of identifying this motif, novel wild-type transporters with superior monosaccharide growth profiles were discovered, namely S. stipitis RGT2 and Debaryomyces hansenii 2D01474. These findings build toward the engineering of efficient pentose utilization in yeast and provide a blueprint for reprogramming transporter properties.
Recognition of the high affinity binding site in rev-response element RNA by the Human Immunodeficiency Virus type-1 rev protein (1992)

The Human Immunodeficiency Virus type-1 rev protein binds with high affinity to a bubble structure located within the rev-response element (RRE) RNA in stemloop II. After this initial interaction, additional rev molecules bind to the RRE RNA in an ordered assembly process which requires a functional bubble structure, since mutations in the bubble sequence that reduce rev affinity block multiple complex formation. We have used synthetic chemistry to characterize the interaction between rev protein and its high affinity binding site. A minimal synthetic duplex RNA (RBC6) carrying the bubble and 12 flanking base pairs is able to bind rev with 1 to 1 stoichiometry and with high affinity. When the bubble structure is inserted into synthetic RNA molecules carrying longer stretches of flanking double-stranded RNA, rev forms additional complexes resembling the multimers observed with the RRE RNA. The ability of rev to bind to RBC6 analogues containing functional group modifications on base and sugar moieties of nucleoside residues was also examined. The results provide strong evidence that the bubble structure contains specific configurations of non-Watson--Crick G:G and G:A base pairs and suggest that high affinity recognition of RRE RNA by rev requires hydrogen bonding to functional groups in the major groove of a distorted RNA structure.
A Transforming Growth Factor β Type I Receptor that Signals to Activate Gene Expression (1994)

Transforming growth factor beta (TGF-beta) is a multifunctional factor that regulates many aspects of cellular functions. TGF-beta signals through a heteromeric complex of the type I and type II TGF-beta receptors. However, the molecular mechanism of signal transduction by this receptor complex remains unresolved. The type II receptor belongs to a transmembrane receptor serine-threonine kinase family. A new member of this receptor family (R4) was identified and shown to be a functional TGF-beta type I receptor on the basis of its ability to restore a TGF-beta-induced gene response in mutant cell lines lacking endogenous type I receptor. Both ligand binding and signaling of the R4 protein were dependent on the presence of a functional type II receptor. The type I receptor has an intrinsic serine-threonine kinase activity, which was essential for signal transduction.
Topical fluoroquinolones for eye and ear. (2000)

Topical fluoroquinolones are now available for use in the eye and ear. Their broad spectrum of activity includes the common eye and ear pathogens Staphylococcus aureus and Pseudomonas aeruginosa. For the treatment of acute otitis externa, these agents are as effective as previously available otic preparations. For the treatment of otitis media with tympanic membrane perforation, topical fluoroquinolones are effective and safe. These preparations are approved for use in children, and lack of ototoxicity permits prolonged administration when necessary. Topical fluoroquinolones are not appropriate for the treatment of uncomplicated conjunctivitis where narrower spectrum agents suffice; they represent a simplified regimen for the treatment of bacterial keratitis (corneal ulcers). When administered topically, fluoroquinolones are well tolerated and offer convenient dosing schedules. Currently, bacterial resistance appears limited.
Acceleration Profiles for Minimizing Residual Response (1980)

A pulse-shaping technique based on a short, finite Fourier series expression for the forcing function is shown to attenuate residual dynamic response in elastic systems by several orders of magnitude. The approach is based on selecting the Fourier coefficients to depress the envelope of the residual response spectrum in desired regions. Response spectra comparisons are made for the rectangular, double versine, and shaped pulses.
Where practice makes perfect in texture discrimination: evidence for primary visual cortex plasticity. (1991)

In terms of functional anatomy, where does learning occur when, for a basic visual discrimination task, performance improves with practice (perceptual learning)? We report remarkable long-term learning in a simple texture discrimination task where learning is specific for retinal input. This learning is (i) local (in a retinotopic sense), (ii) orientation specific but asymmetric (it is specific for background but not for target-element orientation), and (iii) strongly monocular (there is little interocular transfer of learning). Our results suggest that learning involves experience-dependent changes at a level of the visual system where monocularity and the retinotopic organization of the visual input are still retained and where different orientations are processed separately. These results can be interpreted in terms of local plasticity induced by retinal input in early visual processing in human adults, presumably at the level of orientation-gradient sensitive cells in primary visual cortex.
Can Two-Photon Correlation of Chaotic Light Be Considered as Correlation of Intensity Fluctuations? (2006)

Two-photon correlation phenomena, including the historical experiment of Hanbury Brown and Twiss, may have to be described quantum mechanically, regardless of whether the source of radiation is classical or quantum. Supporting this point, we present a ghost imaging type of second-order spatial correlation experiment of chaotic light to show that the classical understanding based on the concept of statistical intensity fluctuations does not give a correct interpretation for the observation. From a practical point of view, this experiment demonstrates the possibility of having high contrast lensless two-photon imaging with chaotic light, suggesting imaging applications for radiations for which no effective lens is available.
Identification of linear DNA sequences that specifically bind the adeno-associated virus Rep protein (1994)

We have used baculovirus-expressed Rep68 that has been purified to homogeneity to reexamine the binding properties of the Rep protein. We find that Rep68 is capable of binding to a linear DNA sequence that is contained within a 25-bp sequence of the A stem of the adeno-associated virus (AAV) terminal repeat proximal to the B and C palindromes. This has been shown conclusively by demonstrating that Rep68 could specifically bind to a synthetic oligonucleotide containing the 25-bp region in the absence of the other sequences within the terminal repeat. Rep78 was also capable of binding the A stem recognition element, as demonstrated by the fact that a DNA affinity column containing the 25-bp sequence can be used to purify Rep78. The ability to recognize the linear DNA sequence within the A stem provides a mechanism by which the Rep protein can be oriented on the terminal repeat so that only the correct strand is cut at the terminal resolution site (trs site) during terminal resolution. In addition, computer analysis suggests that sequences similar to the A stem element are present within the three AAV promoter regions. Electrophoretic mobility shift experiments clearly demonstrate that the p5 promoter contains a Rep binding sequence. DNase protection experiments indicate that the Rep binding sequence within the p5 promoter is located between the YY1 initiator sequence and the TATA binding site. This position immediately suggests a mechanism by which the Rep protein could act as a repressor or a transactivator of p5 transcription by interacting with either YY1 or TBP. In addition, gel shift experiments suggest that the p19 promoter also contains a Rep binding site. The presence of Rep binding sites upstream of both promoters suggests that these sites may be involved in coordinate regulation of AAV transcription. In addition, we have identified a heterologous Rep binding sequence within pBR322 DNA. A comparison of the sequences within the A stem, p5, and pBR322 binding sites suggests that a repeating GAGC motif is at least part of the Rep recognition sequence. In the accompanying report (D. M. McCarty, J. H. Ryan, S. Zolutukhin, X. Zhou, and N. Muzyczka, J. Virol. 68:4998-5006, 1994), we examine the relative affinity of Rep to the A stem site and the complete terminal repeat. Finally, we also have reexamined the ability of Rep68 and Rep78 to cut at the trs site in substrates that do not contain the B and C palindromes or any apparent secondary structure.(ABSTRACT TRUNCATED AT 400 WORDS)
Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation. (1989)

Yellow fever (YF) virus is the prototype member of the flavivirus family, a diverse group of human and animal pathogens. A live-attenuated strain of YF virus, called 17D, has been used successfully for human vaccination for more than 50 years. In this report we describe the construction of full-length YF 17D cDNA templates that can be transcribed in vitro to yield infectious YF virus RNA. Because of the instability of full-length YF cDNA clones and their toxic effects on Escherichia coli, we developed a strategy in which full-length templates for transcription were constructed by in vitro ligation of appropriate restriction fragments. The YF virus recovered from cDNA was indistinguishable from the parental virus by several criteria. This system should facilitate the molecular genetic analysis of flavivirus replication and attenuation and may allow YF 17D to be used as a carrier for immunologically important epitopes from other disease agents.
IANA Registration for Enumservice 'XMPP' (2007)

This document requests IANA registration of an Enumservice for XMPP,
the Extensible Messaging and Presence Protocol. This Enumservice
specifically allows the use of 'xmpp' Uniform Resource
Identifiers (URIs) in the context of E.164 Number Mapping (ENUM).
[STANDARDS-TRACK]
Inhibitors of the protease from human immunodeficiency virus: design and modeling of a compound containing a dihydroxyethylene isostere insert with high binding affinity and effective antiviral activity (1991)

The peptidomimetic template and the dihydroxyethylene isostere insert that were applied successfully to the design of renin inhibitors have been extended to the related protease from human immunodeficiency virus (HIV). The present report describes the structure-activity study leading to the identification of an inhibitor with a Ki of less than 1 nM for the HIV type-1 protease (compound II). This compound, containing a diol insert, is highly effective in blocking polyprotein processing in in vitro cell culture assays. Results obtained from kinetic analysis, studies of the stereochemistry of the insert, and modeling have led to insights as to the requisites involved in the active site-inhibitor interaction.
The Chalk River Superconducting Cyclotron (1979)

The Chalk River K=520, 4-sector, superconducting cyclotron1, is designed to accelerate all ions from Li (to 50 MeV/u) to U (to 10 MeV/u) using a 13 MV tandem as injector. Concurrent with the design of the integrated accelerator facility we have been testing major components - specifically the radiofrequency accelerating structure and the cyclotron magnet. The project has now been approved and site preparation is underway. This paper reports on the cyclotron assembly, initial cooldown of the cryostat and first magnetic field measurements.
Improved theory of cyclical electrical field flow fractionation (2006)

Previously reported theories for cyclical electrical field flow fractionation (CyElFFF) are severely limited in that they do not account for diffusion, steric, or electric double layer effects. Experiments have shown that these theories overpredict the retention of particles in CyElFFF. In this work, we present a model for prediction of steric, diffusion, and electrical effects. The electrical double layer effects are treated using a lumped electrical circuit model that accounts for the field shielding by the electrical double layer formed at the electrode-carrier interface. The electrical effects are shown to dominate retention times and outweigh the contributions of diffusion and particle size. Detailed results from the simulations are presented in this work, and a comparison between the theoretical and experimental results obtained from the retentions of polystyrene particle standards is presented in this paper. The models are shown to correctly predict the retention of the polystyrene standards in CyElFFF with a reasonable error, while existing models are shown to have significant failings.