gebhart/patrepeval huggingface dataset:
Bandpass engineering of lithographically scribed channel-waveguide Bragg gratings (2004)

We propose and demonstrate a powerful approach to spectral bandpass engineering (apodization) of one-dimensional channel-waveguide Bragg reflectors. Bandpass engineering is accomplished by precise photolithographic control of the length and the longitudinal placement of individual grating lines, which provides unique line-by-line diffractive amplitude and phase control. Channel-waveguide gratings that exhibit complex filtering functions have been fabricated and modeled. When a second-order apodization effect that comprises effective waveguide refractive-index variation with grating-line length is included in the simulation, extraordinary agreement between predicted and observed spectral passband profiles is obtained.
A History of Play in Print Board Games from the Renaissance to Milton Bradley (2018)

This essay considers how a historical legacy of printed games dating back to the sixteenth century in Italy laid the foundation for modern board games like those produced by Milton Bradley. The technology of print and the broad publics it reached enabled the spread of a common gaming culture- one built upon shared visual structures in game boards. Modern board games, of course, relied upon similar rules and replicated the ludic functions of their Renaissance progenitors. But perhaps more importantly, they built upon and perpetuated entrenched narratives about how fortune and morality contributed to lived experiences, presenting their viewers and players with a familiar printed imagination of the game of life.
Prospects for antisense nucleic acid therapy of cancer and AIDS (1991)

Biologic and Therapeutic Implications of Antisense Inhibition of Gene Expression Oligonucleotide Base Hybridization as a Modulator of Genetic Message Readout Novel Antisense Derivatives: Antisense DNA Intercalators, Cleavers and Alkylators Antisense DNA Treatment of HL-60 Promyelocytic Leukemia Cells.
What does chronic electrical stimulation teach us about muscle plasticity? (1999)

The model of chronic low-frequency stimulation for the study of muscle plasticity was developed over 30 years ago. This protocol leads to a transformation of fast, fatigable muscles toward slower, fatigue-resistant ones. It involves qualitative and quantitative changes of all elements of the muscle fiber studied so far. The multitude of stimulation-induced changes makes it possible to establish the full adaptive potential of skeletal muscle. Both functional and structural alterations are caused by orchestrated exchanges of fast protein isoforms with their slow counterparts, as well as by altered levels of expression. This remodeling of the muscle fiber encompasses the major, myofibrillar proteins, membrane-bound and soluble proteins involved in Ca2+ dynamics, and mitochondrial and cytosolic enzymes of energy metabolism. Most transitions occur in a coordinated, time-dependent manner and result from altered gene expression, including transcriptional and posttranscriptional processes. This review summarizes the advantages of chronic low-frequency stimulation for studying activity-induced changes in phenotype, and its potential for investigating regulatory mechanisms of gene expression. The potential clinical relevance or utility of the technique is also considered.
Modulation of Oligodendrocyte Differentiation by Mechanotransduction (2016)

Oligodendrocytes (OLs) are responsible for the myelination of axons in the central nervous system (CNS). The differentiation of OLs encompasses several stages, through which cells undergo dramatic biochemical and morphological changes. OL differentiation is modulated by soluble factors (SFs)-such as growth factors and hormones-, known to be essential for each maturation stage. Besides SFs, insoluble factors such as extracellular matrix (ECM) proteins and other microenvironmental elements also play a pivotal role during OL differentiation. Recently, a growing number of studies were published concerning the effect of biophysical properties of the extracellular milieu on OL differentiation and myelination, showing the importance of ECM stiffness and topography, strain forces and spatial constraints. For instance, it was shown <i>in vitro</i> that OL differentiation and maturation is enhanced by substrates within the reported range of stiffness of the brain and that this effect is potentiated by the presence of merosin, whereas the myelination process is influenced by the diameter of axonal-like fibers. In this mini review article, we will discuss the effect of mechanical cues during OL differentiation and the possible molecular mechanisms involved in such regulation.
Effects of fluoxetine at antidepressant doses on short-term outcome of detoxified alcoholics (1996)

Compulsivity in alcohol-dependent patients is a frequent cause of early relapse in the post-detoxification period. The present study is a 2-month trial on detoxified alcoholics undergoing a double-blind placebo-controlled treatment with fluoxetine (20 mg/day). The rating instruments were the Hamilton Depression and Anxiety Scales, a visual analogue scale for alcohol craving and an original scale for evaluating alcohol withdrawal. The abstinence rate for fluoxetine-treated patients was significantly higher than in the placebo group, whereas no difference between treatments was found on the rating scales. Medical problems, additional psychiatric diagnoses, and family alcoholism were negatively correlated with abstinence. Two subgroups of patients having significantly different characteristics were identified as to the outcome, by means of cluster analysis. They are likely to represent two different stages in the evolution of alcoholism. Our results show that, independently from craving, fluoxetine at antidepressant doses is able to prevent relapses in weaned alcoholics. The anticompulsive therapy can positively influence the short-term outcome, while other factors are negatively associated with abstinence.
The Helicobacter pylori Vacuolating Toxin Inhibits T Cell Activation by Two Independent Mechanisms (2003)

Helicobacter pylori toxin, VacA, damages the gastric epithelium by erosion and loosening of tight junctions. Here we report that VacA also interferes with T cell activation by two different mechanisms. Formation of anion-specific channels by VacA prevents calcium influx from the extracellular milieu. The transcription factor NF-AT thus fails to translocate to the nucleus and activate key cytokine genes. A second, channel-independent mechanism involves activation of intracellular signaling through the mitogen-activated protein kinases MKK3/6 and p38 and the Rac-specific nucleotide exchange factor, Vav. As a consequence of aberrant Rac activation, disordered actin polymerization is stimulated. The resulting defects in T cell activation may help H. pylori to prevent an effective immune response leading to chronic colonization of its gastric niche.
A Single Internal Ribosome Entry Site Containing a G Quartet RNA Structure Drives Fibroblast Growth Factor 2 Gene Expression at Four Alternative Translation Initiation Codons (2003)

The 484-nucleotide (nt) alternatively translated region (ATR) of the human fibroblast growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. Although the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation codons are initiated by a mechanism of internal entry of ribosomes. We undertook here a detailed analysis of the cis-acting elements defining the FGF-2 internal ribosome entry site (IRES). A thorough deletion analysis study within the 5'-ATR led us to define a 176-nt region as being necessary and sufficient for IRES function at four codons present in a downstream 308-nt RNA segment. Unexpectedly, a single IRES module is therefore responsible for translation initiation at four distantly localized codons. The determination of the FGF-2 5'-ATR RNA secondary structure by enzymatic and chemical probing experiments showed that the FGF-2 IRES contained two stem-loop regions and a G quartet motif that constitute novel structural determinants of IRES function.
ChemInform Abstract: Classical Trajectory Studies of the Molecular Dissociation Dynamics of Formaldehyde: H2CO → H2 + CO (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Preserved irradiated homolgous cartilage for orbital reconstruction. (1980)

Human costal cartilage is an excellent implant material for orbital and periorbital reconstruction because of its light weight, strength, homogeneous consistency and the ease with which it can be carved. Its use has been limited by the necessity of a separate surgical procedure to obtain the material. Preserved irradiated homologous cartilage has been shown to have almost all the autogenous cartilage and is concenient to use. Preserved irradiated homologous cartilage transplants do not elicit rejection reactions, resist infection and rarely undergo absorption.
Evaluation of Butanol–Gasoline Blends in a Port Fuel-injection, Spark-Ignition Engine (2009)

This paper assesses different butanol–gasoline blends used in a port fuel-injection, spark-ignition engine to quantify the influence of butanol addition on the emission of unburned hydrocarbons, carbon monoxide, and nitrogen oxide. Furthermore, in-cylinder pressure was measured to quantify combustion stability and to compare the ignition delay and fully developed turbulent combustion phases as given by 0%–10% and 10%–90% Mass Fraction Burned (MFB). The main findings are: 1) a 40% butanol/60% gasoline blend by volume (B40) minimizes HC emissions; 2) no significant change in NOx emissions were observed, with the exception of the 80% butanol/20% gasoline blend; 3) the addition of butanol improves combustion stability as measured by the COV of IMEP; 4) butanol added to gasoline reduces ignition delay (0%–10% MFB); and 5) the specific fuel consumption of B40 blend is within 10% of that of pure gasoline for stoichiometric mixture.
Resonant stretching of cells and other elastic objects from transient cavitation (2013)

The phenomenon of stretched cells in the vicinity of an oscillating bubble is investigated in this work. Experiments reveal that a red blood cell can be stretched up to five times its initial size towards the end of the collapse of a laser-induced cavitation bubble. We hypothesize that the cell elasticity is crucial for the elongation. In order to get insight in the physics involved, numerical simulations based on potential flow theory (with the boundary element method) are performed. A simple membrane tension model for the elongating cell is employed. We observe that the stretching can only occur if the cell exhibits some elastic properties within a certain threshold. The maximum elongation occurs when the oscillations of the bubble and cell are out of phase, that is, the bubble oscillates at half the oscillation time of the cell.
Quantitation of SPECT performance: Report of Task Group 4, Nuclear Medicine Committee (1995)

A comprehensive performance testing program is an essential ingredient of high-quality single-photon emission computed tomography (SPECT). Many of the procedures previously published are complicated, time consuming, or require a special testing environment. This Task Group developed a protocol for evaluating SPECT imaging systems that was simple, practical, required minimal test equipment, and could be performed in a few hours using processing software available on all nuclear medicine computers. It was designed to test rotational stability of uniformity and sensitivity, tomographic spatial resolution, uniformity and contrast, and the accuracy of attenuation correction. It can be performed in less than three hours and requires only a Co-57 flood source, a line source, and a tomographic cylindrical phantom. The protocol was used 51 times on 42 different cameras (seven vendors) by four different individuals. The results were used to establish acceptable ranges for the measured parameters. The variation between vendors was relatively small and appeared to reflect slight differences in basic camera performance, collimation, and reconstruction software. Individuals can use the tabulated values to evaluate the performance of individual systems.
Permeation-driven flow in poly(dimethylsiloxane) microfluidic devices (2005)

Poly(dimethylsiloxane) is currently the material of choice for rapidly fabricating microfluidic devices. As the size of these devices decreases, a significant hydrodynamic flow is generated due to permeation of fluid through the channel walls. We develop a theoretical model verified by single bead tracking experiments, which demonstrates that large flow rates (>10 microm/s) can be passively generated in a straight microchannel filled with water. Realizing that this flow may be unwanted in some applications, we present a method to eliminate it by inhibiting mass transfer of water into the poly(dimethylsiloxane) walls. Furthermore, we explore applications to harness this passively generated flow inside a microfluidic device such as bead stacking, chemical concentration, and passive pumping.
Intracytoplasmic delivery of anionic proteins (2004)

Protein delivery is emerging as an interesting alternative to gene delivery. We have used our experience with transfection to develop a technique for efficient delivery of anionic proteins such as antibodies into the cytoplasm of cells. As for DNA, when complexed with cationic lipids, large amounts of proteins are shown to enter adherent cells via ubiquitously expressed syndecans. However, protein surface area rather than electric charge ratio governs the delivery characteristics. Delivery of anti-beta-actin and anti-alpha-tubulin IgG's leads to fiber depolymerization. Intracellular delivery of an antibody could thus be regarded as another method for interfering with gene activity.
Real-time attack on single Escherichia coli cells by the human antimicrobial peptide LL-37 (2011)

Natural antimicrobial peptides (AMPs) provide prototypes for the design of unconventional antimicrobial agents. Existing bulk assays measure AMP activity but do not provide details of the growth-halting mechanism. We use fluorescence microscopy to directly observe the attack of the human antimicrobial peptide LL-37 on single Escherichia coli cells in real time. Our findings strongly suggest that disruption of the cytoplasmic membrane is not the growth-halting mechanism. At 8 μM, LL-37 binding saturates the outer membrane (OM) within 1 min. Translocation across the OM and access to the periplasmic space (5-25 min later) correlates in time with the halting of growth. Septating cells are attacked more readily than nonseptating cells. The halting of growth may occur because of LL-37 interference with cell wall biogenesis. Only well after growth halts does the peptide permeabilize the cytoplasmic membrane to GFP and the small dye Sytox Green. The assay enables dissection of antimicrobial design criteria into two parts: translocation across the OM and the subsequent halting of growth.
Production of viral vectors using recombinase-mediated cassette exchange (2005)

DNA viruses are often used as vectors for foreign gene expression, but large DNA region from cloned or authentic viral genomes must usually be handled to generate viral vectors. Here, we present a unique system for generating adenoviral vectors by directly substituting a gene of interest in a small transfected plasmid with a replaced gene in a replicating viral genome in Cre-expressing 293 cells using the recombinase-mediated cassette exchange (RMCE) reaction. In combination with a positive selection of the viral cis-acting packaging signal connected with the gene of interest, the purpose vector was enriched to 97.5 and 99.8% after three and four cycles of infection, respectively. Our results also showed that the mutant loxP V (previously called loxP 2272), a variant target of Cre used in the RMCE reaction, was useful as a non-compatible mutant to wild-type loxP. This method could be useful for generating not only a large number of adenovirus vectors simultaneously, but also other DNA virus vectors including helper-dependent adenovirus vector.
Control of DC/DC converters for solar energy system with maximum power tracking (2002)

Solar power converters were used to convert the electrical energy from solar arrays to a stable and reliable power source. The object of this paper is to analyze and design DC/DC power converters of different types in a PV power system to investigate the performance of such converters. A simple method which combines discrete time control and a PI compensator is used to track the maximum power points (MPPs) of the solar array. The system is kept to operate close to the MPPs, thus the maximum possible power transfer from the solar array is achieved. The implementation of the proposed power converter system was based on a digital signal processor. Experimental tests were carried out for buck, boost and buck-boost power converters using a simple maximum power point tracking algorithm. The efficiencies for the system with different power converters are compared and presented.
Dynamics of T-Cell Responses and Memory T Cells during Primary Simian Immunodeficiency Virus Infection in Cynomolgus Macaques (2007)

Cellular immune responses make an important contribution to both the control of human immunodeficiency virus (HIV) replication and disease progression. We used a pathogenic model of SIVmac251 infection of cynomolgus macaques to longitudinally evaluate cellular immune responses in association with various rates of disease progression. We found an inverse relationship between plasma viral load and the simian immunodeficiency virus (SIV)-specific T cells responses in peripheral blood and lymph nodes. SIV-specific T-cell responses in peripheral blood were transient during primary infection, with the highest responses detected around 3 months after infection. There was also a transient increase of central memory CD8(+) T cells in peripheral blood during primary infection, and effector memory T-cell counts in peripheral lymph nodes were increased. This study emphasizes the importance of the early virus-specific immune responses in the outcome of HIV/SIV disease and provides details about the changes of virus-specific immune responses over time.
Squalene-hopene cyclase from Bradyrhizobium japonicum: cloning, expression, sequence analysis and comparison to other triterpenoid cyclases (1997)

With the help of a PCR-based screening method, the gene encoding squalenehopene cyclase (SHC) of Bradyrhizobium japonicum USDA 110 was isolated from a cosmid library. The SHC catalyses the cyclization of squalene to hopanoids, a class of triterpenoid lipids recently discovered in nitrogen-fixing, root-nodule-forming Bradyrhizobium bacteria. Hybridization experiments showed that the gene is present in bacteria of all Bradyrhizobium strains tested and in photosynthetic bacteria forming stem nodules on tropical legumes of the genus Aeschynomene. The Bradyrhizobium shc gene is 1983 bp in length and encodes a protein of 660 amino acid residues with a calculated molecular mass of 73671 Da. Comparison of the deduced amino acid sequence with the sequences of other SHCs revealed highest similarity (70%) to the SHC from the Gram-negative Zymomonas mobilis and lower similarity (48%) to the SHCs from the Gram-positive Alicyclobacillus acidocaldarius and Alicyclobacillus acidoterrestris. Bradyrhizobium SHC also showed similarity (38-43%) to eukaryotic oxidosqualene cyclases. The B. japonicum shc gene was expressed in Escherichia coli. The recombinant SHC catalysed the cyclization of squalene to the hopanoids hopene and diplopterol in vitro. However, the formation of the gammacerane derivative tetrahymanol, which is produced in addition to hopanoids in B. japonicum strains in vivo, could not be detected in vitro. Therefore, the presence of a second squalene cyclase in B. japonicum can be assumed. Sequence analysis of 0.5 kb upstream from the shc gene identified a partial ORF with significant similarity to the C-terminus of an ORF located immediately upstream from the shc gene in Z. mobilis. Both ORFs also showed similarity to phytoene desaturases from cyanobacteria and plants. The 3'-end of this ORF from B. japonicum overlaps with 13 bp at the 5'-end of shc. The close proximity of this ORF to shc suggests that shc and this ORF may be part of an operon.
4-Toluene sulfonate methyl-monooxygenase from Comamonas testosteroni T-2: purification and some properties of the oxygenase component (1991)

Comamonas testosteroni T-2 synthesizes an inducible enzyme system that oxygenates 4-toluene sulfontate (TS) to 4-sulfobenzyl alcohol when grown in TS-salts medium. We purified this TS methyl-monooxygenase system (TSMOS) and found it to consist of two components. A monomeric, iron-sulfur flavoprotein (component B), which has been shown to act as a reductase in the 4-sulfobenzoate dioxygenase system of this organism (H. H. Locher, T. Leisinger, and A. M. Cook, Biochem. J. 274:833-842, 1991), carried electrons from NADH to component M, an oxygenase. This oxygenase had the UV-visible spectral characteristics of an iron-sulfur protein. Mrs of about 152,000 for the native oxygenase and of 43,000 under denaturing conditions indicated a homotri- or homotetrameric enzyme, whose N-terminal amino acids and amino acid composition were determined. The activity of the purified enzyme was enhanced about fivefold by the addition of Fe2+. In the presence of O2 and NADH, components B and M together catalyzed the stoichiometric transformation of TS or p-toluate to the corresponding alcohol. The reaction was confirmed as oxygenation of the methyl group by observation of an oxygen atom from 18O2 in carboxybenzyl alcohol. The substrate range of TSMOS included carboxylated analogs of TS (p- and m-toluates and 4-ethylbenzoate), whereas p-xylene, toluene, and p-cresol were not substrates. TSMOS also catalyzed demethylation; 4-methoxybenzoate was transformed to 4-hydroxybenzoate and formaldehyde.
Effects of Increased Glucokinase Gene Copy Number on Glucose Homeostasis and Hepatic Glucose Metabolism (1997)

The relationship between glucokinase (GK) gene copy number and glucose homeostasis was studied in transgenic mice with additional copies of the entire GK gene locus (Niswender, K. D., Postic, C., Jetton, T. L., Bennett, B. D., Piston, D. W., Efrat, S., and Magnuson, M. A. (1997) J. Biol. Chem. 272, 22564-22569). The plasma glucose concentration was reduced by 25 +/- 3% and 37 +/- 4% in mice with one or two extra copies of the gene locus, respectively. The basis for the hypoglycemic phenotype was determined using metabolic tracer techniques in chronically cannulated, conscious mice with one extra GK gene copy. Under basal conditions (6-h fasted) transgenic mice had a lower blood glucose concentration (-12 +/- 1%) and a slightly higher glucose turnover rate (+8 +/- 3%), resulting in a significantly higher glucose clearance rate (+21 +/- 2%). Plasma insulin levels were not different, suggesting that increased glucose clearance was due to augmented hepatic, not islet, GK gene expression. Under hyperglycemic clamp conditions the transgenic mice had glucose turnover and clearance rates similar to the controls, but showed a lower plasma insulin response (-48 +/- 5%). Net hepatic glycogen synthesis was markedly elevated (+360%), whereas skeletal muscle glycogen synthesis was decreased (-40%). These results indicate that increased GK gene dosage leads to increased hepatic glucose metabolism and, consequently, a lower plasma glucose concentration. Increased insulin secretion was not observed, even though the transgene is expressed in islets, because hypoglycemia causes a down-regulation in islet GK content (Niswender, K. D., Postic, C., Jetton, T. L., Bennett, B. D., Piston, D. W., Efrat, S., and Magnuson, M. A. (1997) J. Biol. Chem. 272, in press).