gebhart/patrepeval huggingface dataset:
Sphingomonas herbicidovorans MH: a versatile phenoxyalkanoic acid herbicide degrader (1999)

Sphingomonas herbicidovorans MH was isolated from a dichlorprop-degrading soil column. It is able to grow on phenoxyalkanoic acid herbicides, such as mecoprop, dichlorprop, 2,4-D, MCPA, and 2,4-DB. Strain MH utilizes both enantiomers of the chiral herbicides mecoprop and dichlorprop as sole carbon and energy sources. Enantiomer-specific uptake systems are responsible for transporting the acidic substrates across the cell membrane. Catabolism is initiated by two enantiomer-specific alpha-ketoglutarate-dependent dioxygenases that catalyze the cleavage of the ether bond of the respective enantiomer to yield the corresponding phenol and pyruvate. Therefore selective degradation of the enantiomers of mecoprop and dichlorprop by strain MH is not only due to enantioselective catabolism but also to enantioselective transport.
Factors influencing anti-antibody enhancement of tumor targeting with antibodies in hamsters with human colonic tumor xenografts. (1988)

The injection of an antiantibody (second antibody, SA) can enhance the clearance rate of a radiolabeled antitumor antibody (primary antibody, PA) from the blood. We have studied how the dose of the SA and the timing of the SA administration influence the rate of PA clearance and thereby improve tumor/nontumor ratios. Adult hamsters bearing the carcinoembryonic antigen-producing, GW-39 human colonic tumor xenograft were given injections of 131I-labeled, goat anti-carcinoembryonic antigen antibody, and after 6, 24, or 48 h, an injection of donkey anti-goat immunoglobulin was given at SA:PA ratios of 25, 50, 100, or 200:1. In comparison to a control group of animals that were only given 131I-PA, the administration of the SA improved tumor/blood ratios regardless of the SA:PA ratio or time the SA was given. The most important factor in optimizing this procedure was the timing of the SA injection. Significantly improved tumor/nontumor ratios were found when the SA was given between 24 and 48 h after the PA in comparison to 6 h. This was because maximum accretion of radiolabeled PA in the tumor was not achieved until 24 h. At SA:PA ratios of 25:1, only tumor/blood ratios were significantly improved in comparison to the control group. In addition, at SA:PA ratios of 25:1 and 50:1, tumor/spleen and tumor/kidney ratios were lower than the control group, whereas at higher SA:PA ratios, all tumor/nontumor ratios were significantly improved. These studies suggest that for this model, a ratio of SA:PA of 100:1 or higher given at 24 to 48 h after the PA is the best combination for maximizing tumor/nontumor ratios.
Iodinated tomoxetine derivatives as selective ligands for serotonin and norepinephrine uptake sites (1992)

In order to develop selective radioactive ligands for the study of presynaptic monoamine uptake sites, iodinated derivatives of tomoxetine were synthesized and evaluated in radioligand binding assays. Iodotomoxetine derivatives showed high affinity for serotonin (5-HT) uptake sites using a rat cortical membrane preparation. Compound 1R,(R)-(-)-N-methyl-3-(4-iodo-2-methylphenoxy)-3-phenylpropanamine , was the most potent and showed high stereoselectivity for 5-HT uptake sites (Ki, R isomer = 0.65 nM, S isomer = 13.9 nM). Changing the position of the methyl group or eliminating the methyl group at the phenoxy ring resulted in a loss of stereoselectivity. Substitution of the methyl group of tomoxetine with iodine gave the R and S isomers of N-methyl-3-(2-iodophenoxy)-3-phenylpropanamine 4R and 4S. These compounds displayed stereoselectivity for the norepinephrine (NE) (Ki values = 0.24 and 9.35 nM for R and S isomers, respectively). The in vitro binding data suggest that 1R and 4R are potential radioiodinated ligands for pharmacological studies of 5-HT and NE uptake sites, respectively.
Relations of Left Ventricular Mass to Fat-Free and Adipose Body Mass (1998)

LV mass is more strongly related to FFM than to adipose mass, waist/hip ratio, body mass index, or height-based surrogates for lean body weight; LV mass/FFM criteria may increase sensitivity to detect LV hypertrophy.
Molecular Cloning of the Human Kallikrein 15 Gene (KLK15) (2001)

Kallikreins are a subgroup of serine proteases with diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis. By using molecular cloning techniques, we identified a new human kallikrein gene, tentatively named KLK15 (for kallikrein 15 gene). This new gene maps to chromosome 19q13.4 and is located between the KLK1 and KLK3 genes. KLK15 is formed of five coding exons and four introns, and shows structural similarity to other kallikreins and kallikrein-like genes. KLK15 has three alternatively spliced forms and is primarily expressed in the thyroid gland and to a lower extent in the prostate, salivary, and adrenal glands and in the colon testis and kidney. Our preliminary results indicate that the expression of KLK15 is up-regulated by steroid hormones in the LNCaP prostate cancer cell line. The KLK15 gene is also up-regulated, at the mRNA level, in prostate cancer in comparison to normal prostatic tissue. KLK15 up-regulation was found to be associated with more aggressive forms of prostate cancer. This newly discovered gene has the potential of being used as a diagnostic and/or prognostic marker for prostate cancer.
Receptor-mediated cellular entry of nuclear localizing anti-DNA antibodies via myosin 1. (1997)

A unique subset of anti-DNA antibodies enters living cells, interacts with DNase 1, and inhibits endonuclease activity, before their nuclear localization and subsequent attenuation of apoptosis. We now report that endocytosis of these immunoglobulins is mediated by cell surface binding to brush border myosin (myosin 1). Cellular entry and internalization via this unique receptor provides initial contact for entry and sorting these immunoglobulins to translocate to the nuclear pore and enter the nucleus, interact with DNase 1 within the cytoplasm, or recycle back to the cell surface. This internalization pathway provides clues to the translocation of large proteins across cell membranes and the functional effects of intracellular antibodies on cytopathology. This is the first demonstration that brush border myosin functions as a specific cell surface receptor for internalization of large proteins.
Stair ambulation in persons with transtibial amputation: an analysis of the Seattle LightFoot. (1997)

The purpose of this study was to document gait patterns in a group of individuals with transtibial amputations (TTA) during stair ambulation, and to identify the functional limitations associated with this task. Ten persons with TTA fitted with a Seattle LightFoot prosthetic component, and 14 nondisabled subjects participated in this study. Electromyographic activity (EMG) of the vastus lateralis (VL), rectus femoris (RF), gluteus maximus (GMAX), semimembranosus (SMEMB), biceps femoris long head (BFLH), and biceps femoris short head (BFSH) was assessed using indwelling wire electrodes during ascending and descending stairs. Lower limb kinematics (VICON) and stride characteristics (Footswitch Stride Analyzer System) also were collected. Stride characteristics revealed that those with TTA had a significantly slower rate of stair ambulation and demonstrated stance phase asymmetry between limbs compared to the nondisabled. Kinematic analysis determined significant limitations in prosthetic ankle motion, which necessitated compensatory functions at the hip and knee to accomplish stair ascent and descent and resulted in significantly greater muscular effort (increased EMG intensity and duration) compared to nondisabled.
Self-assembled monolayer-enhanced hydrogen sensing with ultrathin palladium films (2005)

Resistive-type palladium structures for hydrogen sensing remains as a research focus for their simplicity in device construction. We demonstrate that a siloxane self-assembled monolayer placed between a substrate and an evaporated ultrathin Pd film promotes the formation of small Pd nanoclusters and reduces the stiction between the palladium and the substrate. The resulting Pd nanocluster film can detect 2%H2 with a rapid response time of ∼70ms and is sensitive to 25 ppm hydrogen, detectable by a 2% increase in conductance due to the hydrogen-induced palladium lattice expansion.
Positive and negative dielectrophoretic collection of colloidal particles using interdigitated castellated microelectrodes (1992)

An interdigitated castellated microelectrode geometry has been found to facilitate particle collection arising from both positive and negative dielectrophoretic effects. These two forms of particle collection differ significantly as functions of the frequency of the applied non-uniform electric field and of the conductivity of the suspending medium. This behaviour is demonstrated for yeast cells and a theoretical explanation is presented in terms of the electric field patterns generated by the electrodes, as well as through consideration of the associated phenomenon of electrorotation.
Blocking artifact reduction in JPEG-coded images (1999)

We proposed the post-processing method to reduce the blocking artifact in low-bit-rate coded JPEG images, which is based on minimum block-boundary-discontinuity criterion. We analyzed the statistical property of block boundary pixel difference, classified all blocks into one of two types using OSLD (overlapped sub-laplacian distribution), and compensated the quantization error depending on the type of block, adaptively. Our postprocessing method can provide better visual quality as well as PSNR than any other method.
Demonstration of Weight-Four Parity Measurements in the Surface Code Architecture (2016)

We present parity measurements on a five-qubit lattice with connectivity amenable to the surface code quantum error correction architecture. Using all-microwave controls of superconducting qubits coupled via resonators, we encode the parities of four data qubit states in either the X or the Z basis. Given the connectivity of the lattice, we perform a full characterization of the static Z interactions within the set of five qubits, as well as dynamical Z interactions brought along by single- and two-qubit microwave drives. The parity measurements are significantly improved by modifying the microwave two-qubit gates to dynamically remove nonideal Z errors.
Conversion of Mouse Epiblast Stem Cells to an Earlier Pluripotency State by Small Molecules (2010)

Epiblast stem cells (EpiSCs) are pluripotent cells derived from post-implantation late epiblasts in vitro. EpiSCs are incapable of contributing to chimerism, indicating that EpiSCs are less pluripotent and represent a later developmental pluripotency state compared with inner cell mass stage murine embryonic stem cells (mESCs). Using a chemical approach, we found that blockage of the TGFβ pathway or inhibition of histone demethylase LSD1 with small molecule inhibitors induced dramatic morphological changes in EpiSCs toward mESC phenotypes with simultaneous activation of inner cell mass-specific gene expression. However, full conversion of EpiSCs to the mESC-like state with chimerism competence could be readily generated only with the combination of LSD1, ALK5, MEK, FGFR, and GSK3 inhibitors. Our results demonstrate that appropriate synergy of epigenetic and signaling modulations could convert cells at the later developmental pluripotency state to the earlier mESC-like pluripotency state, providing new insights into pluripotency regulation.
Enhancement of array gain with stacked parasitic elements (2002)

Microstrip antennas with stacked parasitic elements have been demonstrated to have broad bandwidth and high gain. The broad band characteristics of microstrip antennas with stacked parasitic elements have been studied extensively and are now well understood. Contrarily, enhancing the gain of a microstrip antenna with stacked parasitic elements has been attempted only by a few researchers over the years. An increase in gain of 3 dB has been reported for a stacked concentric ring patch antenna array. In practice, using stacked parasitic elements for gain enhancement is both easy and less costly since no increase in array size is required to provide the additional effective isotropic radiated power (EIRP) for completing the communication link. This paper reports an experimental investigation of gain enhancement of a 2/spl times/2 microstrip array at 29.5 GHz using stacked parasitic antenna elements. The EIRP and radiation patterns as a function of the spacings between the parasitic and driven antenna layers were measured. These results are presented and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Shock-wave induced damage in lipid bilayers: a dissipative particle dynamics simulation study (2011)

The effects of shock-wave impact on the damage of lipid bilayer membranes are investigated with dissipative particle simulations at constant energy (DPDE). A coarse-grained model for the phospholipid bilayer in aqueous environment is employed, which models single lipids as short chains consisting of a hydrophilic head and two hydrophobic tail beads. Water is modeled by mapping four H2O molecules to one water bead. Using the DPDE method enables us to faithfully simulate the non-equilibrium shock-wave process with a coarse-grained model as the correct heat capacity can be recovered. At equilibrium, we obtain self-stabilizing bilayer structures that exhibit bending stiffness and compression modulus comparable to experimental measurements under physiological conditions. We study in detail the damage behavior of the coarse-grained lipid bilayer upon high-speed shock-wave impact as a function of shock impact velocity and bilayer stability. A single damage parameter based on an orientation dependent correlation function is introduced. We observe that mechanical bilayer stability has only small influence on the resulting damage after shock-wave impact, and inertial effects play almost no role. At shock-front velocities below ≲ 3000 ms−1, we observe reversible damage, whereas for speeds ≳ 3900 ms−1 no such recovery, or self-repair of the bilayer, could be observed.
Switching adaptive filters for enhancing noisy and reverberant speech from microphone array recordings (2002)

Switching adaptive filters, suitable for speech beamforming, with no prior knowledge about the speech source are presented. The filters have two sections, of which only one section at any given time is allowed to adapt its coefficients. The switch between both is controlled by a speech detection function. The first section implements an adaptive look direction and cues in on the desired speech. This section only adapts when speech is present. The second section acts as a multichannel adaptive noise canceller. The obtained noise references are typically very bad; hence, adaptation must be restricted to silence-only periods. Several ideas were explored for the first section. The most robust solution, and the one with the best sound quality, was given by the simplest solution, i.e. a delay and sum beamformer that cues in on the direct path only and neglects all multipath contributions. Tests were performed with a four-microphone array in a highly reverberant room with both music and fan type noise as jammers, SNR improvements of 10 dB were typical with no audible distortion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The impact of light and colour on psychological mood: a cross-cultural study of indoor work environments (2006)

The aim of the study was to determine whether indoor lighting and colour would have any systematic impact on the mood of people working indoors. Earlier studies have mostly focused either on light, colour or windows in laboratory settings. The present study was carried out in real work environments at different seasons and in countries with different latitudes. A total of 988 persons completed all parts of the study. In the countries situated far north of the equator there was a significant variation in psychological mood over the year that did not occur in the countries closer to the equator. When all four countries were considered together, it became evident that the light and colour of the workplace itself also had an influence on the mood of persons working there. The workers' mood was at its lowest when the lighting was experienced as much too dark. The mood then improved and reached its highest level when the lighting was experienced as just right, but when it became too bright the mood declined again. On the other hand, the illuminance as measured in objective terms, showed no significant impact on mood at any time of the year. The relationship between mood and the distance to the nearest window was bimodal. The results also indicate that the use of good colour design might contribute to a more positive mood. It is suggested that in future research light and colour should be studied as parts of the more complex system making up a healthy building.
Bacterial adhesion to orthopedic implant polymers (1996)

The degradable polymers poly(orthoester) (POE), poly(L-lactic acid) (PLA), and the nondegradable polymers polysulfone (PSF), polyethylene (PE), and poly(ether ether ketone) (PEEK) were exposed to cultures of Staphylococcus epidermidis, Pseudomonas aeruginosa, or Escherichia coli. Bacteria washed and resuspended in phosphate buffered saline (PBS) adhered to polymers in amounts nearly twice those of bacteria that were left in their growth medium, tryptic soy broth (TSB). In TSB, there was variation in adhesion from species to species, but no significant variation from polymer to polymer within one species. In PBS there were significant differences in the amounts of bacteria adhering to the various polymers with the exception, of S. epidermidis, which had similar adhesion to all polymers. As a whole, P. aeruginosa was the most adherent while S. epidermidis was the least adherent. The estimated values of the free energy of adhesion (delta Fadh) correlated with the amount of adherent P. aeruginosa. When POE, PLA, and PSF were exposed to hyaluronic acid (HA) before exposure to the bacteria, there was 50% more adhesion of E. coli and P. aeruginosa on POE and PLA. With respect to bacterial adhesion, the biodegradable polymers (POE and PLA) in general were not significantly different from the nondegradable polymers.
Pinched flow coupled shear-modulated inertial microfluidics for high-throughput rare blood cell separation (2011)

Blood is a highly complex bio-fluid with cellular components making up >40% of the total volume, thus making its analysis challenging and time-consuming. In this work, we introduce a high-throughput size-based separation method for processing diluted blood using inertial microfluidics. The technique takes advantage of the preferential cell focusing in high aspect-ratio microchannels coupled with pinched flow dynamics for isolating low abundance cells from blood. As an application of the developed technique, we demonstrate the isolation of cancer cells (circulating tumor cells (CTCs)) spiked in blood by exploiting the difference in size between CTCs and hematologic cells. The microchannel dimensions and processing parameters were optimized to enable high throughput and high resolution separation, comparable to existing CTC isolation technologies. Results from experiments conducted with MCF-7 cells spiked into whole blood indicate >80% cell recovery with an impressive 3.25 × 10(5) fold enrichment over red blood cells (RBCs) and 1.2 × 10(4) fold enrichment over peripheral blood leukocytes (PBL). In spite of a 20× sample dilution, the fast operating flow rate allows the processing of ∼10(8) cells min(-1) through a single microfluidic device. The device design can be easily customized for isolating other rare cells from blood including peripheral blood leukocytes and fetal nucleated red blood cells by simply varying the 'pinching' width. The advantage of simple label-free separation, combined with the ability to retrieve viable cells post enrichment and minimal sample pre-processing presents numerous applications for use in clinical diagnosis and conducting fundamental studies.
Structure and dynamics of all of the stereoisomers of europium complexes of tetra(carboxyethyl) derivatives of dota: ring inversion is decoupled from cooperative arm rotation in the RRRR and RRRS isomers (1998)

The absolute configuration of the four stereoisomeric α-substituted derivatives of dota has been defined; in their Eu complexes, 2D-NMR methods have revealed that in solution ring inversion is independent of pendant arm rotation and the (RRRR)-[EuL1a] complex which in the solid state crystallises as a square antiprismatic structure.
Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora (1999)

The "altered Schaedler flora" (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified as Lactobacillus acidophilus (strain ASF 360), Lactobacillus salivarius (strain ASF 361), and Bacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus and Lactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in the Cytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipes phylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes, Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster, Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.
Chirality in bare and passivated gold nanoclusters (2002)

Chiral structures have been found as the lowest-energy isomers of bare $({\mathrm{Au}}_{28}$ and ${\mathrm{Au}}_{55})$ and thiol-passivated $[{\mathrm{Au}}_{28}({\mathrm{SCH}}_{3}{)}_{16}$ and ${\mathrm{Au}}_{38}({\mathrm{SCH}}_{3}{)}_{24}]$ gold nanoclusters. The degree of chirality existing in the chiral clusters was calculated using the Hausdorff chirality measure. We found that the index of chirality is higher in the passivated clusters and decreases with the cluster size. These results are consistent with the observed chiroptical activity recently reported for glutahione-passivated gold nanoclusters, and provide theoretical support for the existence of chirality in these compounds.