gebhart/patrepeval huggingface dataset:
Spatially Selective Deposition of a Reactive Polysaccharide Layer onto a Patterned Template (2003)

The amine-containing polysaccharide chitosan was selectively deposited onto patterned gold surfaces in response to an applied voltage. Standard microfabrication techniques were used to pattern gold onto silicon wafers, and these gold patterns served as templates for the electric field directed deposition of chitosan. Experiments conducted with a fluorescently labeled chitosan derivative demonstrated the spatially selective deposition of chitosan onto gold surfaces that were polarized to serve as negative electrodes. Studies with unlabeled chitosan demonstrated that a “templated” chitosan, deposited by voltage programming of electrodes, can subsequently react with standard amine-selective functional groups. This indicates that common coupling chemistries can be exploited to assemble a variety of compounds onto the deposited chitosan pattern. Thus, chitosan appears to be a unique interface material that can be “templated” onto patterned inorganic surfaces and is reactive for the subsequent assembly of organic and biological molecules.
Efficient killing of inhaled bacteria in ΔF508 mice: role of airway surface liquid composition (1999)

Cystic fibrosis mice have been generated by gene targeting but show little lung disease without repeated exposure to bacteria. We asked if murine mucosal defenses and airway surface liquid (ASL) Cl(-) were altered by the DeltaF508 cystic fibrosis transmembrane conductance regulator mutation. Naive DeltaF508 -/- and +/- mice showed no pulmonary inflammation and after inhaled Pseudomonas aeruginosa had similar inflammatory responses and bacterial clearance rates. We therefore investigated components of the innate immune system. Bronchoalveolar lavage fluid from mice killed Escherichia coli, and the microbicidal activity was inhibited by NaCl. Because beta-defensins are salt-sensitive epithelial products, we looked for pulmonary beta-defensin expression. A mouse homolog of human beta-defensin-1 (termed "MBD-1") was identified; the mRNA was expressed in the lung. Using a radiotracer technique, ASL volume and Cl(-) concentration ([Cl(-)]) were measured in cultured tracheal epithelia from normal and DeltaF508 -/- mice. The estimated ASL volume was similar for both groups. There were no differences in ASL [Cl(-)] in DeltaF508 -/- and normal mice (13.8 +/- 2.6 vs. 17.8 +/- 5.6 meq/l). Because ASL [Cl(-)] is low in normal and mutant mice, salt-sensitive antimicrobial factors, including MBD-1, may be normally active.
Tn5401, a new class II transposable element from Bacillus thuringiensis (1994)

A new class II (Tn3-like) transposable element, designated Tn5401, was recovered from a sporulation-deficient variant of Bacillus thuringiensis subsp. morrisoni EG2158 following its insertion into a recombinant plasmid. Sequence analysis of the insert revealed a 4,837-bp transposon with two large open reading frames, in the same orientation, encoding proteins of 36 kDa (306 residues) and 116 kDa (1,005 residues) and 53-bp terminal inverted repeats. The deduced amino acid sequence for the 36-kDa protein shows 24% sequence identity with the TnpI recombinase of the B. thuringiensis transposon Tn4430, a member of the phage integrase family of site-specific recombinases. The deduced amino acid sequence for the 116-kDa protein shows 42% sequence identity with the transposase of Tn3 but only 28% identity with the TnpA transposase of Tn4430. Two small open reading frames of unknown function, designated orf1 (85 residues) and orf2 (74 residues), were also identified. Southern blot analysis indicated that Tn5401, in contrast to Tn4430, is not commonly found among different subspecies of B. thuringiensis and is not typically associated with known insecticidal crystal protein genes. Transposition was studied with B. thuringiensis by using plasmid pEG922, a temperature-sensitive shuttle vector containing Tn5401. Tn5401 transposed to both chromosomal and plasmid target sites but displayed an apparent preference for plasmid sites. Transposition was replicative and resulted in the generation of a 5-bp duplication at the target site. Transcriptional start sites within Tn5401 were mapped by primer extension analysis. Two promoters, designated PL and PR, direct the transcription of orf1-orf2 and tnpI-tnpA, respectively, and are negatively regulated by TnpI. Sequence comparison of the promoter regions of Tn5401 and Tn4430 suggests that the conserved sequence element ATGTCCRCTAAY mediates TnpI binding and cointegrate resolution. The same element is contained within the 53-bp terminal inverted repeats, thus accounting for their unusual lengths and suggesting an additional role for TnpI in regulating Tn5401 transposition.
Enhanced mode locking of color-center lasers (1989)

A significant enhancement in the mode locking of a KCl:Tl color-center laser has been observed when a length of optical fiber having positive group-velocity dispersion was incorporated within an external control cavity. Pulse durations of ~260 fsec were obtained by this method, representing a compression factor ~60x that with the colorcenter laser alone. Similar results have also been observed with an InGaAsP semiconductor diode amplifier as the nonlinear element within the control cavity.
Absorption-Induced Image Resolution Enhancement in Scattering Media (2016)

Highly scattering media pose significant challenges for many optical imaging applications due to the loss of information inherent to the scattering process. Absorption can also result in significant degradation of image quality. However, absorption can actually improve the resolution of images transmitted through scattering media in certain cases. Here we study how the presence of absorption can enhance the quality of an image transmitted through a scattering medium, by investigating the dependence of this enhancement on the medium’s scattering properties. We find that absorption-induced image resolution enhancement is substantially larger for media consisting of isotropic scatterers (e.g., dielectric nanoparticles) than for strongly forward-scattering media (e.g., biological tissue). This work leads to a broader understanding, and ultimately control, of the optical properties of strongly absorbing, scattering media.
A Comprehensive Comparison of Routing Protocols for Large-Scale Wireless MANETs (2006)

Efficient routing protocols can provide significant benefits to mobile ad hoc networks, in terms of both performance and reliability. Many routing protocols for such networks have been proposed so far. Amongst the most popular ones are dynamic source routing (DSR), ad hoc on-demand distance vector (AODV), temporally-ordered routing algorithm (TORA) and location-aided routing (LAR). Despite the popularity of those protocols, research efforts have not focused in evaluating their performance when applied to large-scale wireless networks. Such networks are comprised of hundreds of nodes, connected via long routes. This greatly affects the network efficiency, since it necessitates frequent exchange of routing information. In this paper we present our observations regarding the behavior of the above protocols, in large-scale mobile ad hoc networks (MANETs). We consider wireless mobile terminals spread over a large geographical area, and we perform extensive simulations, using the QualNet and NS-2 simulators. The results of the simulations yield some interesting conclusions: AODV suffers in terms of packet delivery fraction (PDF) but scales very well in terms of end-to-end delay. DSR on the other hand scales well in terms of packet delivery fraction but suffers an important increase of end-to-end delay, as compared to its performance achieved in small-scale topologies. Also, the effect of maximum connections is severe on TORA, which seems unable to route large amounts of traffic. LAR, seems to scale very well, in terms of all metrics employed
Multivariate endpoint detection of plasma etching processes (2002)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2002.
Hepatic steatosis in total parenteral nutrition: failure of fatty infiltration to correlate with abnormal serum hepatic enzyme levels. (1986)

Total parenteral nutrition (TPN) is associated with hepatic biochemical and morphologic changes. Suggested causes include excessive glucose calories, fatty acid deficiency, and enterically derived hepatotoxins escaping atrophied bowel. Male Sprague-Dawley rats were cannulated or sham operated with internal jugular ligation. The cannulated groups received TPN with a 25% dextrose base, or TPN 12.5% dextrose and given nothing by mouth, or saline solution and allowed to eat ad lib. Sham animals ate ad lib. After 6 days the animals were killed and portal blood was assayed for endotoxin and cultured. Cultures were also taken of the liver. Serum hepatic enzyme concentration and hepatic fat were determined. All cultures and endotoxin assays were negative. Microscopy revealed nonlipid vacuolization in both TPN groups, a finding reproduced by direct portal infusion of endotoxin. There was significant hepatic steatosis in the 25% dextrose base TPN versus all other groups (28.6% liver weight versus 6.3% liver weight; p less than 0.05). This was correlated with caloric intake (28.7 calories/100 gm/day versus 21.2 calories/100 gm/day; p less than 0.05). Liver enzymes were not significantly different among groups. We conclude that hepatic steatosis in TPN is a result of overfeeding a glucose only substrate and that fatty infiltration is independent of changes in blood hepatic enzyme concentrations. Although other morphologic changes of hepatotoxin-induced injury were seen in the TPN group, portal endotoxemia to the level of 1 ng/ml could not be documented.
Anomalous behavior of electrical conductivity and thermal noise in carbon black‐containing polymers at Tg and Tm (1975)

Abstract Pronounced maxima in resistivity–temperature curves have been found at or above T g for a number of amorphous polymers (PS, PMMA, PVC) containing a small percentage of carbon black. The maxima appeared only after a certain period of storage at T &lt; T g or at heating rates substantially higher than those used in cooling the samples prior to the measurement. For this reason, no maxima were observed during cooling. In crystalline polymers (PE, PP), maxima at T m appeared both on heating and cooling. Marked relaxation effects (time‐dependent resistivity) were recorded in the T g and T m regions. Good agreement was found between resistivity and thermal noise data.
Combination of in situ hybridization and immunocytochemistry to detect messenger RNAs in identified CNS neurons and glia in tissue culture. (1991)

We have developed a technique in which immunofluorescence is combined with in situ hybridization using cDNA and RNA probes to assess the expression and distribution of messenger RNAs (mRNA) by neurons and neuroglia in tissue cultures of the rat dentate gyrus. The probes used in this study include a cDNA probe for ribosomal RNA (rRNA) and an RNA probe (cRNA) for glial fibrillary acidic protein (GEAP), an intermediate filament protein subunit expressed by astrocytes in the central nervous system. Both ubiquitous (tubulin) and cell type-specific (MAP-2 and GEAP) antibodies were used to identify neurons and neuroglia in culture. Using this procedure, the mRNA for rRNA was found in the cell bodies and large processes of MAP-2-positive neurons and throughout the cytoplasm of GEAP-positive flat astrocytes. In process-bearing astrocytes, GEAP mRNA is concentrated in the cell body, although some hybridization also occurred in astrocyte cell processes. With this combined in situ hybridization-immunofluorescence technique, the expression and distribution of an mRNA can be examined in different immunocytochemically identified cell types under identical culture and hybridization conditions. It is also possible to determine if there is a differential subcellular distribution of an mRNA in a single cell and if the distribution of the mRNA reflects the distribution of the protein itself. Finally, this technique can be utilized to verify the specificity of probes for cell type-specific mRNAs and to determine appropriate hybridization conditions to produce a specific signal.
Receptor-Mediated Endocytosis of Hormones in Cultured Cells (1981)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Improving snow cover mapping in forests through the use of a canopy reflectance model (1998)

MODIS, the moderate resolution imaging spectroradiometer, will be launched in 1998 as part of the first earth observing system (EOS) platform. Global maps of land surface properties, including snow cover, will be created from MODIS imagery. The MODIS snow-cover mapping algorithm that will be used to produce daily maps of global snow cover extent at 500 m resolution is currently under development. With the exception of cloud cover, the largest limitation to producing a global daily snow cover product using MODIS is the presence of a forest canopy. A Landsat Thematic Mapper (TM) time-series of the southern Boreal Ecosystem–Atmosphere Study (BOREAS) study area in Prince Albert National Park, Saskatchewan, was used to evaluate the performance of the current MODIS snow-cover mapping algorithm in varying forest types. A snow reflectance model was used in conjunction with a canopy reflectance model (GeoSAIL) to model the reflectance of a snow-covered forest stand. Using these coupled models, the effects of varying forest type, canopy density, snow grain size and solar illumination geometry on the performance of the MODIS snow-cover mapping algorithm were investigated. Using both the TM images and the reflectance models, two changes to the current MODIS snow-cover mapping algorithm are proposed that will improve the algorithm's classification accuracy in forested areas. The improvements include using the normalized difference snow index and normalized difference vegetation index in combination to discriminate better between snow-covered and snow-free forests. A minimum albedo threshold of 10% in the visible wavelengths is also proposed. This will prevent dense forests with very low visible albedos from being classified incorrectly as snow. These two changes increase the amount of snow mapped in forests on snow-covered TM scenes, and decrease the area incorrectly identified as snow on non-snow-covered TM scenes. © 1998 John Wiley & Sons, Ltd.
Inhibitory effects of anti‐tumor platinum compounds on DNA, RNA and protein syntheses in mammalian cells in vitro (1970)

Abstract The inhibitory effects of anti‐tumor, bacterial filament forming platinum compounds, Cis‐Pt(II) (NH 3 ) 2 Cl 2 (A), Cis‐Pt(IV) (NH 3 ) 2 Cl 4 (B), and Pt(II) (NH 2 ) 2 (CH 2 ) 2 Cl 2 (C) on DNA, RNA and protein syntheses was measured by the incorporation of 3 H‐thymidine, 3 H‐uridine, and 3 H‐L‐leucine, respectively, into an acid‐insoluble polymer in human amnion AV 3 cells. Compound A, the most effective tumor‐inhibiting platinum compound, was shown to selectively inhibit DNA synthesis below 5μM and to inhibit 3 H‐thymidine incorporation more rapidly than 3 H‐uridine or 3 H‐leucine incorporation at 25μM. Like A, compounds B and C were also shown to inhibit all three processes after a 24‐hour period of treatment at 25μM. A correlation was established between the relative anti‐tumor effectiveness of compounds A, B, and C and the extent of their inhibitory effects. On the other hand, two non‐tumor‐inhibiting platinum compounds, [Pt(II) (NH 3 ) 4 ]Cl 2 (D) and Trans‐Pt(IV) (NH 3 ) 2 Cl 4 (E) had no inhibitory effects, except compound E, which exhibited a rapid initial inhibition of 3 H‐L‐leucine incorporation at 100μM. The inhibition of 3 H‐thymidine incorporation into cells pretreated 4 h with 5μM of compounds A, B, and C was shown to be irreversible. Finally the inhibition of the incorporation of 3 H‐thymidine into DNA by A was shown not to be caused by the inhibition of the uptake of the tracer into the acid‐soluble pool. A number of possible explanations for the greater sensitivity of DNA synthesis and the sequential inhibition of DNA, RNA and protein synthesis at higher concentrations are suggested.
Treatment of Photoaging (2004)

A 45-year-old fair-skinned woman has noted increasing sallowness, roughness, fine wrinkles, and mottled hyperpigmentation on her face. She is bothered by these changes and is worried about the development of nonmelanoma skin cancer. What treatments may minimize skin aging and lower the risk of skin cancer?
Mechanical studies of the bone bioglass interfacial bond (1975)

A series of squirrel monkeys received segmental femoral replacements in a study of the strength of the interface developed between the implant and bone. Implants were either made completely of bioglass-ceramic, or 316L stainless steel with a flame-sprayed coating of bioglass. Fracture torque, energy at fracture, and shear stress at failure were compared to values obtained from a control group of pairs of tibias. Femurs containing bulk bioglass-ceramic implants showed about a 25% difference in strength compared to the opposite bone, while femurs containing flame-sprayed implants exhibited extremely low structural strength. While the strength of the metal-glass bond was very low (less than 500 kgf/cm2), the bone-bioglass bond was found to be at least as strong as the bioglass-ceramic, and at least 3/4 as strong as the host bone.
A survey ofCampylobacterspecies shed in faeces of beef cattle using polymerase chain reaction (2003)

A polymerase chain reaction (PCR)-based survey of campylobacters associated with faeces collected from 382 beef cattle was undertaken. To ensure the removal of PCR inhibitors present in faeces and determine if adequate extraction was achieved, faeces were seeded with internal control DNA (i.e., DNA designed to amplify with the Campylobacter genus primer set, but provide a smaller amplicon) before the extraction procedure. In only two samples (0.5%) were the internal control or Campylobacter genus amplicons not detected. In the remaining 380 faecal samples, Campylobacter DNA was detected in 83% of the faecal samples (80% of the faecal samples were positive for Campylobacter genus DNA, and 3% of the samples were negative for Campylobacter genus DNA but positive for DNA of individual species). The most frequently detected species was Campylobacter lanienae (49%), a species only recently connected to livestock hosts. Campylobacter jejuni DNA was detected in 38% of the faecal samples, and Campylobacter hyointestinalis and Campylobacter coli DNA were detected in 8% and 0.5% of the samples, respectively. Campylobacter fetus DNA was not detected. Twenty-four percent of the faecal samples contained DNA of at least two species of Campylobacter. Of these samples, the majority (81%) contained DNA of C. jejuni and C. lanienae. The results of this study indicate that beef cattle commonly release a variety of Campylobacter species into the environment and may contribute to the high prevalence of campylobacteriosis in humans inhabiting areas of intensive cattle production, such as southern Alberta. Furthermore, this study demonstrates the utility of using PCR as a rapid and accurate method for simultaneously detecting the DNA of a diverse number of Campylobacter species associated with bovine faeces.
Role of a Mitogen-activated Protein Kinase Pathway in the Induction of Phase II Detoxifying Enzymes by Chemicals (1999)

Mitogen-activated protein kinase (MAPK) cascades are activated by diverse extracellular signals and participate in the regulation of an array of cellular programs. In this study, we investigated the roles of MAPKs in the induction of phase II detoxifying enzymes by chemicals. Treatment of human hepatoma (HepG2) and murine hepatoma (Hepa1c1c7) cells with tert-butylhydroquinone (tBHQ) or sulforaphane (SUL), two potent phase II enzyme inducers, stimulated the activity of extracellular signal-regulated protein kinase 2 (ERK2) but not c-Jun N-terminal kinase 1. tBHQ and SUL also activated MAPK kinase. Inhibition of MAPK kinase with its inhibitor, PD98059, abolished ERK2 activation and impaired the induction of quinone reductase, a phase II detoxifying enzyme, and antioxidant response element (ARE)-linked reporter gene by tBHQ and SUL. Overexpression of a dominant-negative mutant of ERK2 also attenuated tBHQ and SUL induction of ARE reporter gene activity. Interestingly, although expression of Ras and its mutant forms showed distinct effects on basal ARE reporter gene activity, they did not affect the activation of reporter gene by the inducers. Furthermore, a dominant-negative mutant of Ras had little effect on ERK2 activation by tBHQ and SUL, implicating a Ras-independent mechanism. Indeed, both tBHQ and SUL were able to stimulate Raf-1 kinase activity in vivo as well as in vitro. Thus, our results indicate that the induction of ARE-dependent phase II detoxifying enzymes is mediated by a MAPK pathway, which may involve direct activation of Raf-1 by the inducers.
PinA Inhibits ATP Hydrolysis and Energy-dependent Protein Degradation by Lon Protease (1998)

The bacteriophage T4 PinA protein inhibited degradation of [3H]alpha-methyl casein by purified Lon protease from Escherichia coli, but inhibition was noncompetitive with respect to casein. PinA did not inhibit cleavage of the fluorogenic peptide, N-glutaryl-alanylalanylphenylalanyl-3-methoxynaphthylamide and, moreover, did not block the ability of protein substrates, such as casein, to activate cleavage of fluorogenic peptides by Lon. Thus, PinA does not block the proteolytic active site or the allosteric protein-binding site on Lon. Inhibition of basal ATPase activity was variable (50-90%), whereas inhibition of protein-activated ATPase activity was usually 80-95%. Inhibition was noncompetitive with respect to ATP. PinA did not block activation of peptide cleavage by nonhydrolyzable analogs of ATP. These data suggest that PinA does not bind at the ATPase active site of Lon and does not interfere with nucleotide binding to the enzyme. PinA inhibited cleavage of the 72-amino acid protein, CcdA, degradation of which requires ATP hydrolysis, but did not inhibit cleavage of the carboxyl-terminal 41-amino acid fragment of CcdA, degradation of which does not require ATP hydrolysis. PinA thus appears to interact at a novel regulatory or enzymatic site involved in the coupling between ATP hydrolysis and proteolysis, possibly blocking the protein unfolding or remodeling step essential for degradation of high molecular weight protein substrates by Lon.
A Data Partitioning Approach for Parallelizing Rule Based Inferencing for Materialized OWL Knowledge Bases. (2008)

Materialized knowledge bases perform inferencing when data is loaded into them, so that answering queries is reduced to simple lookup and thus are faster. A major bottleneck of such a system is the inferencing process, which is slow and memory intensive. In this work we examine the problem of speeding up as well as scaling the inferencing process for OWL Knowledge Bases, that employ rule based reasoners. We propose a data partitioning approach for this problem, in which the input data is partitioned into smaller chunks that are then processed independently. We propose a parallel reasoning algorithm and show the correctness of our technique for the class of rule-sets obtained from OWL ontologies. We present two optimizations of this algorithm to further improve the performance. Finally, we present an implementation based on a popular open source tool. In our experiments using a standard OWL benchmark we have observed speedups of upto 18x, on a parallel cluster of 16 processors.