gebhart/patrepeval huggingface dataset:
Chemical Vapor Deposition of Aminopropyl Silanes in Microfluidic Channels for Highly Efficient Microchip Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry (2014)

We describe a chemical vapor deposition (CVD) method for the surface modification of glass microfluidic devices designed to perform electrophoretic separations of cationic species. The microfluidic channel surfaces were modified using aminopropyl silane reagents. Coating homogeneity was inferred by precise measurement of the separation efficiency and electroosmotic mobility for multiple microfluidic devices. Devices coated with (3-aminopropyl)di-isopropylethoxysilane (APDIPES) yielded near diffusion-limited separations and exhibited little change in electroosmotic mobility between pH 2.8 and pH 7.5. We further evaluated the temporal stability of both APDIPES and (3-aminopropyl)triethoxysilane (APTES) coatings when stored for a total of 1 week under vacuum at 4 °C or filled with pH 2.8 background electrolyte at room temperature. Measurements of electroosmotic flow (EOF) and separation efficiency during this time confirmed that both coatings were stable under both conditions. Microfluidic devices with a 23 cm long, serpentine electrophoretic separation channel and integrated nanoelectrospray ionization emitter were CVD coated with APDIPES and used for capillary electrophoresis (CE)-electrospray ionization (ESI)-mass spectrometry (MS) of peptides and proteins. Peptide separations were fast and highly efficient, yielding theoretical plate counts over 600,000 and a peak capacity of 64 in less than 90 s. Intact protein separations using these devices yielded Gaussian peak profiles with separation efficiencies between 100,000 and 400,000 theoretical plates.
VIP and PACAP: recent insights into their functions/roles in physiology and disease from molecular and genetic studies (2011)

PACAP/VIP as well as their three classes of receptors are important in many physiological/pathophysiological processes, some of which are identified in these studies using knockout animals. These studies may lead to new novel treatment approaches. Particularly important are their roles in glucose metabolism and on islets leading to possible novel approaches in diabetes; their novel anti-inflammatory, cytoprotective effects, their CNS neuroprotective effects, and their possible roles in diseases such as schizophrenia and chronic depression.
Formation of Porous Polymer Coatings on Complex Substrates Using Vapor Phase Precursors (2016)

In this work, porous poly(methacrylic acid) (PMAA) coatings are formed on complex substrates using vapor phase precursors. The porous coatings are created by partially polymerizing solid monomer deposited onto the substrate. The conformality of the porous PMAA coatings is studied on the external and internal surfaces of cylindrical substrates. Flow effects lead to thickness variations in the θ-direction while thermal gradients and monomer depletion effects lead to thickness variations in the z-direction. These variations can be reduced by modifying the flow rate of the monomer vapor, by reducing the radiative heat on the substrate, or by increasing the dimension size of the substrate. This work shows that vapor phase processing methods can be a viable alternative to solution phase methods and the observed trends can be utilized in a range of vapor phase technologies to optimize porous coatings for use in tissue engineering, sensors, and separations.
Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment (2002)

The majority (>99%) of microorganisms from the environment resist cultivation in the laboratory. Ribosomal RNA analysis suggests that uncultivated organisms are found in nearly every prokaryotic group, and several divisions have no known cultivable representatives. We designed a diffusion chamber that allowed the growth of previously uncultivated microorganisms in a simulated natural environment. Colonies of representative marine organisms were isolated in pure culture. These isolates did not grow on artificial media alone but formed colonies in the presence of other microorganisms. This observation may help explain the nature of microbial uncultivability.
Personal Electronic Notebook with Sharing (2002)

The concept of an electronic or digital engineering design notebook used by designers to capture information for re-use and sharing is becoming reality in many different flavors. Our development of PENS (Personal Electronic Notebook with Sharing) responds to observed designers' needs for a lightweight tool that is facile enough to compete with paper notebooks in functionality. As design information is entered into PENS in real-time, the PENS information web grows. As it grows, selections can be incrementally published for sharing with collaborators over the Internet's World-Wide Web. In an era where both network security concerns and distributed collaboration demands are growing together, PENS has the capability for firewall-independent sharing. To evaluate the utility of the PENS notebook concept, a prototype has been developed and used by 14 mechanical engineering design teams that span local and remote design partnerships.
An implementation of discrete multi-tone over slowly time-varying multiple-input/multiple-output channels (2002)

We have investigated a method for data transmission over slowly time-varying MIMO channels. A low complexity method is introduced that effectively diagonalizes the MIMO channel. This enables the use of discrete multi-tone (DMT) modulation over the MIMO channel to achieve information transmission rates close to the Shannon capacity. DMT requires knowledge of the channel state information at the transmitter which is not always possible in practice. In this case the channel can be only made block diagonal and signal detection requires the solution to a least-squares problem with integer variables. This is a very challenging problem that is theoretically difficult (NP-hard). In this paper, a practically efficient method is proposed to solve this least squares problem.
Light Quality Initiating or Ending the Day Affects Internode Length in Petunia (1995)

`Ultra Rose Star' petunia plants were germinated and grown at 21C. The study was initiated 26 days after seeding and the photoperiod was 15 h of light and 9 h of darkness. During the initial or ending 90 min of the light period, the plants were exposed to a light quality of a higher (≈2.0) or lower (≈0.8) red (R, 660 nm) to far red (FR, 730 nm) ratio than daylight (R: FR, ≈1.1). Flowering occurred within 65 days from seeding for plants in all treatments. Plants receiving a low R: FR during the initial 90 min of the day had similar internode lengths as those plants receiving a high R: FR at the end of the day. The average internode length of the main stem at flowering was 0.6 ± 0.08 cm for plants receiving a low R: FR in the morning or a high R: FR at the end of the day. In addition, the internodes of those plants exposed to a low R: FR in the morning were longer than on plants receiving a low R: FR at night or a high R: FR in the morning. The average internode length at flowering was 0.4 ± 0.08 cm for plants with an ending low R: FR or a beginning high R: FR light quality of the day.
Activin-A binding and biochemical effects in osteoblast-enriched cultures from fetal-rat parietal bone. (1991)

Activin, a disulfide-linked polypeptide dimer first isolated from gonadal tissue extracts, has amino acid sequence and structural homology with transforming growth factor beta (TGF beta). Along with other activities, TGF beta regulates replication and differentiation and interacts with a defined set of binding sites on isolated bone cells. To determine if activin shares these properties, recombinant human activin-A (A-chain homodimer) was examined in osteoblast-enriched cultures obtained from fetal-rat parietal bone. After 23 h of treatment, 60 to 6,000 pM activin-A increased the rate of [3H]thymidine incorporation into DNA 1.5- to 4.0-fold, and at 600 to 6,000 pM, it enhanced the rate of [3H]proline incorporation into collagen and noncollagen protein by up to 1.7-fold. Like earlier studies with TGF beta in primary osteoblast-enriched cultures, the stimulatory effects of activin-A on DNA and protein synthesis were opposed by parathyroid hormone, and the influence of activin-A on collagen synthesis was independent of cell replication. Binding studies with 125I-activin-A indicated approximately 8,000 high-affinity (Kd = 0.4 nM) and 300,000 low-affinity (Kd = 40 to 50 nM) binding sites per cell. Polyacrylamide gel analysis revealed 125I-activin-A-binding complexes of Mr greater than 200,000 and 73,000 which did not appear to correspond to primary TGF beta-binding sites. These results indicate that activin-A produces TGF beta-like effects in bone and that some of these effects may be mediated, at least in part, by distinct activin receptors on bone cells.
Phylogenetic Diversity and the Structural Basis of Substrate Specificity in the β/α-Barrel Fold Basic Amino Acid Decarboxylases (2007)

The beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (ODC) and bacterial and plant enzymes with activity on L-arginine and meso-diaminopimelate. These enzymes catalyze essential steps in polyamine and lysine biosynthesis. Phylogenetic analysis suggests that diverse bacterial species also contain ODC-like enzymes from this fold type. However, in comparison with the eukaryotic ODCs, amino acid differences were identified in the sequence of the 3(10)-helix that forms a key specificity element in the active site, suggesting they might function on novel substrates. Putative decarboxylases from a phylogenetically diverse range of bacteria were characterized to determine their substrate preference. Enzymes from species within Methanosarcina, Pseudomonas, Bartonella, Nitrosomonas, Thermotoga, and Aquifex showed a strong preference for L-ornithine, whereas the enzyme from Vibrio vulnificus (VvL/ODC) had dual specificity functioning well on both L-ornithine and L-lysine. The x-ray structure of VvL/ODC was solved in the presence of the reaction products putrescine and cadaverine to 1.7 and 2.15A, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3(10)-helix enlarging the substrate binding pocket allows L-lysine to be accommodated. The structure of the putrescine-bound enzyme suggests that a bridging water molecule between the shorter L-ornithine and key active site residues provides the structural basis for VvL/ODC to also function on this substrate. Our data demonstrate that there is greater structural and functional diversity in bacterial polyamine biosynthetic decarboxylases than previously suspected.
Standard deviations and standard errors (2005)

The terms “standard error” and “standard deviation” are often confused.1 The contrast between these two terms reflects the important distinction between data description and inference, one that all researchers should appreciate.

The standard deviation (often SD) is a measure of variability. When we calculate the standard deviation of a sample, we are using it as an estimate of the variability of the population from which the sample was drawn. For data with a normal distribution,2 about 95% of individuals will have values within 2 standard deviations of the mean, the other 5% being equally scattered above and below these limits. Contrary to popular misconception, the standard deviation is a valid measure of variability regardless of the distribution. About 95% of observations of any distribution usually fall within the 2 standard …
Sol–Gel Technology (2007)

Abstract Many recent technical developments require materials fabricated by sol–gel technology. This article presents a short review of this huge field, with special accent on the various steps involved in the sol–gel processing technique and the applications of gels. The main definitions and historically scientific roots of sol–gel science are first briefly summarized. Then the specificity of the chemical process involved in the synthesis of a sol and a gel are examined with respect to the various classes of materials: silica, oxides other than silica, complex oxides, ceramics other than oxides and organic–inorganic hybrids. Drying a wet gel is a very critical step. The problems and techniques used to solve this are summarized, in particular the use of chemical additives and supercritical drying. Transformation of dry gels to dense ceramics by thermal treatment is briefly examined. Then the next major part of the article focuses on the interesting properties and applications of sol–gel derived materials, including dry aerogels, ceramic powders, fibers, coatings or monoliths, technical ceramics and materials for bioinorganic and medicinal applications. The last part gives a short account of the tremendous economical development, which the sol–gel technology presently experiences.
Interferon in Nasal Secretions and Sera of Calves After Intranasal Administration of Avirulent Infectious Bovine Rhinotracheitis Virus: Association of Interferon in Nasal Secretions with Early Resistance to Challenge with Virulent Virus (1972)

Calves which had received avirulent infectious bovine rhinotracheitis virus (AV-IBR) by intranasal (IN) administration developed detectable levels of interferon (IF) in nasal secretions as early as 40 hr later. Peak titers (1:640) of IF appeared in secretions 72 to 96 hr after administration of virus, and titers of 1:80 to 1:320 were maintained through the 8th day. Lower titers (1:5 to 1:10) of IF were detected in sera obtained on the 4th to 8th days after administration of virus. Peak titers of IF in respiratory tract secretions were accompanied by a 100- to > 1,000-fold reduction in the levels of AV-IBR present in the secretions. Serum antibody was not detected prior to the 8th day after administration of AV-IBR. Calves which received AV-IBR by the IN route 72 or 96 hr earlier were refractory to challenge with virulent infectious bovine rhinotracheitis virus (IBR), whereas calves receiving AV-IBR 18 or 40 hr earlier became clinically ill following challenge. The temporal association between appearance of IF in respiratory tract secretions and onset of protection against challenge suggests a cause and effect relationship. No IF was detected in either nasal secretions or sera of calves receiving modified IBR virus by intramuscular injection. Following subsequent IN challenge of these calves, IF was detected in nasal secretions as early as 24 hr postchallenge and was maintained at titers of 1:40 to 1:80 for approximately 4 days, even in the absence of virus recovery. Greater ease of local IF induction with IBR virus in calves previously sensitized with that virus is suggested.
THE VITAMIN K–DEPENDENT CARBOXYLASE (2005)

The vitamin K-dependent (VKD) carboxylase uses the oxygenation of vitamin K to convert glutamyl residues (Glus) to carboxylated Glus (Glas) in VKD proteins, rendering them active in a broad range of physiologies that include hemostasis, apoptosis, bone development, arterial calcification, signal transduction, and growth control. The carboxylase has a high-affinity site that selectively binds VKD proteins, usually through their propeptide, and also has a second low-affinity site of VKD protein interaction. Propeptide binding increases carboxylase affinity for the Glu substrate, and the coordinated binding of the VKD propeptide and Glu substrate increases carboxylase affinity for vitamin K and activity, possibly through a mechanism of substrate-assisted catalysis. Tethering of VKD proteins to the carboxylase allows clusters of Glus to be modified to Glas by a processive mechanism that becomes disrupted during warfarin therapy. Warfarin inhibits a vitamin K oxidoreductase that generates the reduced vitamin K cofactor required for continuous carboxylation and causes decreased carboxylase catalysis and increased dissociation of partially carboxylated, inactive VKD proteins. The availability of reduced vitamin K may also control carboxylation in r-VKD protein-expressing cells, where the amounts of reduced vitamin K are sufficient for full carboxylation of low, but not high, expression levels of VKD proteins, and where carboxylation is not improved by overexpression of r-carboxylase. This review discusses these recent advances in understanding the mechanism of carboxylation. Also covered is the identification of functional carboxylase residues, a brief description of the role of VKD proteins in mammalian and lower organisms, and the potential impact of quality control components on carboxylation, which occurs in the endoplasmic reticulum during the secretion of VKD proteins.
Identification of Escherichia coli serotype O157 strains by using a monoclonal antibody (1988)

The O157 antigenic determinant of Escherichia coli serotype O157:H7, an important bacterial pathogen, resides in the polysaccharide portion of its cellular lipopolysaccharide component which, from structural studies, was identified as a linear polymer of a repeating tetrasaccharide unit composed of D-glucose, L-fucose, 2-acetamido-2-deoxy-D-galactose, and 4-acetamido-4,6-dideoxy-D-mannose residues (1:1:1:1). Hybrid cells producing monoclonal antibodies against the E. coli O157 antigen were obtained by fusion of myeloma cells with lymphocytes from BALB/c mice immunized with killed E. coli O157:117 cells. Clones were selected for binding specificity with purified O polysaccharide. One monoclonal antibody used in direct slide agglutinations or in coagglutination reactions with Staphylococcus aureus Cowan 1 cells sensitized with the affinity column-purified antibody accurately detected all strains of E. coli O157 tested. This selected monoclonal antibody did not agglutinate E. coli strains such as E. coli O7 and E. coli O116 or other bacteria which are known to give positive agglutinations with conventional polyclonal E. coli antisera. These results indicate that the monoclonal antibody is a superior specific-typing reagent.
Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects (1993)

Escherichia coli ribonuclease III, purified to homogeneity from an overexpressing bacterial strain, exhibits a high catalytic efficiency and thermostable processing activity in vitro. The RNase III-catalyzed cleavage of a 47 nucleotide substrate (R1.1 RNA), based on the bacteriophage T7 R1.1 processing signal, follows substrate saturation kinetics, with a Km of 0.26 microM, and kcat of 7.7 min.-1 (37 degrees C, in buffer containing 250 mM potassium glutamate and 10 mM MgCl2). Mn2+ and Co2+ can support the enzymatic cleavage of the R1.1 RNA canonical site, and both metal ions exhibit concentration dependences similar to that of Mg2+. Mn2+ and Co2+ in addition promote enzymatic cleavage of a secondary site in R1.1 RNA, which is proposed to result from the altered hydrolytic activity of the metalloenzyme (RNase III 'star' activity), exhibiting a broadened cleavage specificity. Neither Ca2+ nor Zn2+ support RNase III processing, and Zn2+ moreover inhibits the Mg(2+)-dependent enzymatic reaction without blocking substrate binding. RNase III does not require monovalent salt for processing activity; however, the in vitro reactivity pattern is influenced by the monovalent salt concentration, as well as type of anion. First, R1.1 RNA secondary site cleavage increases as the salt concentration is lowered, perhaps reflecting enhanced enzyme binding to substrate. Second, the substitution of glutamate anion for chloride anion extends the salt concentration range within which efficient processing occurs. Third, fluoride anion inhibits RNase III-catalyzed cleavage, by a mechanism which does not involve inhibition of substrate binding.
The Ras Target AF-6 is a Substrate of the Fam Deubiquitinating Enzyme (1998)

The Ras target AF-6 has been shown to serve as one of the peripheral components of cell-cell adhesions, and is thought to participate in cell-cell adhesion regulation downstream of Ras. We here purified an AF-6-interacting protein with a molecular mass of approximately 220 kD (p220) to investigate the function of AF-6 at cell-cell adhesions. The peptide sequences of p220 were identical to the amino acid sequences of mouse Fam. Fam is homologous to a deubiquitinating enzyme in Drosophila, the product of the fat facets gene. Recent genetic analyses indicate that the deubiquitinating activity of the fat facets product plays a critical role in controlling the cell fate. We found that Fam accumulated at the cell-cell contact sites of MDCKII cells, but not at free ends of plasma membranes. Fam was partially colocalized with AF-6 and interacted with AF-6 in vivo and in vitro. We also showed that AF-6 was ubiquitinated in intact cells, and that Fam prevented the ubiquitination of AF-6.
3∶5∶2阵式中前锋队员的训练 (1991)

较长一段时间以来,人们可以看到这样一种趋势:许多球队偏爱以3:5:2阵式来达到战术意图.这一动向很可能是因为几乎没有球队安排三个前锋队员所致。如果说迄今为止以四人组成后卫线,并且面临的是两个对方前锋,那么盯人防守队员中就有一个没有防守对象。
Analysis of RNA phage fr coat protein assembly by insertion, deletion and substitution mutagenesis (1993)

A structure-function analysis of the icosahedral RNA bacteriophage fr coat protein (CP) assembly was undertaken using linker-insertion, deletion and substitution mutagenesis. Mutations were specifically introduced into either pre-existing or artificially created restriction enzyme sites within fr CP gene expressed in Escherichia coli from a recombinant plasmid. This directs synthesis of wild type protein that undergoes self-assembly and forms capsid-like particles indistinguishable morphologically and immunologically from native phage particles. A series of fr CP variants containing sequence alterations in the regions which are (i) exposed on the external surface of capsid or (ii) located on the contacting areas between CP subunits were obtained and their assembly properties investigated. The majority of mutants demonstrated reduction of assembly ability and formed either CP dimers (mutations at residues 2, 10, 63 or 129) or both dimer and capsid structures (residue 2 or 69). The exceptions were variants demonstrating normal assembly and containing insertions at residues 2, 50 or 129 of the fr CP. A third type of assembled structure was formed by a variant with a single amino acid substitution I104T. The alpha A-helix region (residues 97-111) is particularly sensitive to mutation and any alteration in this region decreases accumulation of mutant protein in E. coli. The relative contributions of particular fr CP domains in maintenance of capsid structural integrity as well as the possible capsid assembly mechanism are discussed.