gebhart/patrepeval huggingface dataset:
NAT Constraints Management in Tree-Based P2P Live Streaming Systems (2016)

In this paper we present an approach for organizing peers in a centralized tree-based P2P live streaming system in order to minimize peer connectivity failures due to network address translation (NAT) constraints. The centralized coordinator in our system optimizes peers position according to their upload bandwidth to reach maximum P2P contribution and optimizes the position of each single peer to avoid incompatible NAT connectivity between peers which can cause a decrease in the system's performance. A network optimization technique is used to reach the optimal peer placement in the tree to satisfy the download demands of as many peers as possible.
Why Acquiring Excitation Data Improves the Quality of Reconstructed Fluorescence Images for Highly Heterogeneous Diffusive Media (2008)

Diffuse optical fluorescence tomography often relies on the assumption that samples are homogeneous. This degrades the correspondence between tomography data sets and model predictions. We provide evidence that data normalization significantly improve on this situation. Article not available.
Mutations in <i>mmpL</i> and in the Cell Wall Stress Stimulon Contribute to Resistance to Oxadiazole Antibiotics in Methicillin-Resistant Staphylococcus aureus (2014)

Staphylococcus aureus is a leading cause of hospital- and community-acquired infections, which exhibit broad resistance to various antibiotics. We recently disclosed the discovery of the oxadiazole class of antibiotics, which has in vitro and in vivo activities against methicillin-resistant S. aureus (MRSA). We report herein that MmpL, a putative member of the resistance, nodulation, and cell division (RND) family of proteins, contributes to oxadiazole resistance in the S. aureus strain COL. Through serial passages, we generated two S. aureus COL variants that showed diminished susceptibilities to an oxadiazole antibiotic. The MICs for the oxadiazole against one strain (designated S. aureus COL(I)) increased reproducibly 2-fold (to 4 μg/ml), while against the other strain (S. aureus COL(R)), they increased >4-fold (to >8 μg/ml, the limit of solubility). The COL(R) strain was derived from the COL(I) strain. Whole-genome sequencing revealed 31 mutations in S. aureus COL(R), of which 29 were shared with COL(I). Consistent with our previous finding that oxadiazole antibiotics inhibit cell wall biosynthesis, we found 13 mutations that occurred either in structural genes or in promoters of the genes of the cell wall stress stimulon. Two unique mutations in S. aureus COL(R) were substitutions in two genes that encode the putative thioredoxin (SACOL1794) and MmpL (SACOL2566). A role for mmpL in resistance to oxadiazoles was discerned from gene deletion and complementation experiments. To our knowledge, this is the first report that a cell wall-acting antibiotic selects for mutations in the cell wall stress stimulon and the first to implicate MmpL in resistance to antibiotics in S. aureus.
Co-abstraction of shape collections (2012)

We present a co-abstraction method that takes as input a collection of 3D objects, and produces a mutually consistent and individually identity-preserving abstraction of each object. In general, an abstraction is a simpler version of a shape that preserves its main characteristics. We hypothesize, however, that there is no single abstraction of an object. Instead, there is a variety of possible abstractions, and an admissible one can only be chosen conjointly with other objects' abstractions. To this end, we introduce a new approach that hierarchically generates a spectrum of abstractions for each model in a shape collection. Given the spectra, we compute the appropriate abstraction level for each model such that shape simplification and inter-set consistency are collectively maximized, while individual shape identities are preserved.
Preclinical evaluation of CD38 chimeric antigen receptor engineered T cells for the treatment of multiple myeloma (2015)

Meeting abstracts Adoptive transfer of T cells transduced with tumor-reactive Chimeric Antigen Receptors (CARs) is a promising strategy for cancer immunotherapy. The CD38 molecule, with its high and homogenous expression on Multiple Myeloma (MM) cells, appears a suitable target for antibody therapy
<title>IR detection at room temperature using semiconducting YBaCuO</title> (1996)

Semiconducting YBaCuO thin films are a candidate for infrared bolometers operating at room temperature without the need for temperature control. Semiconducting YBaCuO thin films were fabricated by rf magnetron sputtering onto silicon substrates at room temperature. Room temperature deposition provides compatibility with CMOS technology to allow for the fabrication of low cost infrared imaging arrays with focal plane signal processing. The temperature coefficient of resistance (TCR) of the thin films was measured to be as high as 4% K<SUP>-1</SUP> over a wide temperature range near 300 K. In this respect, amorphous YBaCuO thin films provided a higher TCR than epitaxial, tetragonal YBa<SUB>2</SUB>Cu<SUB>3</SUB>O<SUB>6+x</SUB> films. The noise voltage at 30 Hz was measured to be typically less than 1 (mu) V/Hz<SUP>1/2</SUP>. If the thin films are integrated into a typical air-gap thermal isolation structure, the projected responsivity R<SUB>v</SUB> would be as high as 3.8 multiplied by 10<SUP>5</SUP> V/W with 1 (mu) A of current bias providing an estimated detectivity D<SUP>*</SUP> of 1.6 multiplied by 10<SUP>9</SUP> cm Hz<SUP>1/2</SUP>/W at a frame frequency of 30 Hz.
The objective measurement of individual earplug field performance (2009)

This paper presents a field-microphone-in-real-ear (MIRE) method for the objective measurement of individual earplug field attenuation. This development was made possible by using a recently designed instrumented expandable custom earplug. From the measurement of the noise reduction (NR) through the earplug, this method predicts the attenuation that would be experienced by the wearer and that would be measured using the real-ear attenuation at threshold (REAT) method. Formulations presented include establishing the relationship between NR, insertion loss, and REAT, as well as defining the laboratory and field calibration procedures required to determine the correction factors to be applied to the measured NR. This method was validated experimentally by comparing the predicted field-MIRE attenuation values to the REAT values measured on a group of test-subjects. This method offers fast and accurate measurement of earplug field performance on an individual basis and could lead to further developments for effective hearing protection practices as well as for hearing protection device rating and labeling.
Advances in Tensiometry for Long-term Monitoring of Soil Water Pressures (2002)

Soil water pressures, measured over space and time, are needed to predict the direction of water flow and chemical transport in the vadose zone. Advanced tensiometers (ATs), which utilize a water-filled porous cup connected directly to a pressure transducer, can be installed at almost any location and depth using standard drilling techniques such as auger drilling, but these methods can significantly disturb the site. For sites where minimal disturbance is desired, alternate approaches for tensiometer placement have been sought. To test installation techniques and performance longevity, advanced tensiometers were placed into the ground at a test site near Richland, WA using two different installation methods, auger drilling and a drive-cone push technique. The tensiometers were subsequently monitored for nearly 2 yr without refilling or recalibration. The data indicated that tensiometers placed by the auger technique took several months to equilibrate, while the cone push units came to equilibrium within 24 h following their installation. Soil water pressures always remained above −90 cm pressure head (−90 mbar) at depths >90 cm. At the greatest depth (730 cm), positive then negative pressures were observed as the water table was lowered and the soil drained. The results suggest that for our test conditions (coarse sandy soil, no vegetation), soil water pressures stay well within the tensiometer range and unit gradient conditions persist, indicating a draining profile. Advanced tensiometers, placed either by auger or cone penetrometer, provide a robust and reliable method for long-term monitoring of soil water pressure profiles.
Gradient-Based Colorimetric Array Sensor for Continuous Monitoring of Multiple Gas Analytes (2020)

Colorimetry is widely used in chemical sensing due to its high sensitivity and high selectivity. However, most colorimetric sensors are one-time use because the color-producing reactions or bindings are usually irreversible. In addition, traditional colorimetric sensors like the detection tubes are bulky and packed individually, making parallel sensing of multiple analytes difficult. Here, we demonstrate a gradient-based colorimetric array sensor (GCAS) to overcome these limitations. Different colorimetric sensing elements are inkjet-printed as parallel straight lines on a porous substrate. Lateral transport of analytes across the substrate creates color gradients on the sensing elements. The color gradients shift along the transport direction over time, and GCAS tracks the gradient shifts and converts them into analyte concentrations in real time. Using a low-cost complementary metal-oxide semiconductor imager, we show detection of three air pollutants using a single GCAS chip and 24 h continuous monitoring of ambient ozone.
Synthesis of Cubic Boron Nitride by Al-Mg Solvents (1997)

The aluminum-magnesium (Al-Mg) alloys have been proved to be an effective solvent for synthesis of cubic-phase boron nitride (cBN) from hexagonal-phase boron nitride (hBN) at the conditions of high pressures and high temperatures (HP/HT). Various kinds of hBN powders having different crystallinity have been tested for cBN synthesis with Al-Mg solvents. The conversion ratio from hBN to cBN and the shape of synthesized cBN crystals appeared to be affected strongly by chemical composition and added amount of Al-Mg solvents as well as crystallinity of BN powders. As the magnesium content increased in the Al-Mg solvents, the conversion ratio increased and the size of cBN crystals became larger. The crystal facets developed well in the specimens with solvents having high Mg content. It was observed that a hBN→cBN transformation occurred more easily in the specimens having well crystallized hBN powders. Amorphous BN having much B₂O₃, impurity exhibited a low threshold temperature for transformation to cBN, which was attributed to crystallization of amorphous BN to well crystallized hBN prior to transformation into cBN with help of B₂O₃.
Identification of Harpins in <i>Pseudomonas syringae</i> pv. tomato DC3000, Which Are Functionally Similar to HrpK1 in Promoting Translocation of Type III Secretion System Effectors (2007)

Harpins are a subset of type III secretion system (T3SS) substrates found in all phytopathogenic bacteria that utilize a T3SS. Pseudomonas syringae pv. tomato DC3000 was previously reported to produce two harpins, HrpZ1 and HrpW1. DC3000 was shown here to deploy two additional proteins, HopAK1 and HopP1, which have the harpin-like properties of lacking cysteine, eliciting the hypersensitive response (HR) when partially purified and infiltrated into tobacco leaves, and possessing a two-domain structure similar to that of the HrpW1 class of harpins. Unlike the single-domain harpin HrpZ1, the two-domain harpins have C-terminal enzyme-like domains: pectate lyase for HopAK1 and lytic transglycosylase for HopP1. Genetic techniques to recycle antibiotic markers were applied to DC3000 to generate a quadruple harpin gene polymutant. The polymutant was moderately reduced in the elicitation of the HR and translocation of the T3SS effector AvrPto1 fused to a Cya translocation reporter, but the mutant was unaffected in the secretion of AvrPto1-Cya. The DC3000 hrpK1 gene encodes a putative translocator in the HrpF/NopX family and was deleted in combination with the four harpin genes. The hrpK1 quadruple harpin gene polymutant was strongly reduced in HR elicitation, virulence, and translocation of AvrPto1-Cya into plant cells but not in the secretion of representative T3SS substrates in culture. HrpK1, HrpZ1, HrpW1, and HopAK1, but not HopP1, were independently capable of restoring some HR elicitation to the hrpK1 quadruple harpin gene polymutant, which suggests that a consortium of semiredundant translocators from three protein classes cooperate to form the P. syringae T3SS translocon.
Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by <i>Rhodopseudomonas palustris</i> (2015)

Lignocellulosic biomass hydrolysates hold great potential as a feedstock for microbial biofuel production, due to their high concentration of fermentable sugars. Present at lower concentrations are a suite of aromatic compounds that can inhibit fermentation by biofuel-producing microbes. We have developed a microbial-mediated strategy for removing these aromatic compounds, using the purple nonsulfur bacterium Rhodopseudomonas palustris. When grown photoheterotrophically in an anaerobic environment, R. palustris removes most of the aromatics from ammonia fiber expansion (AFEX) treated corn stover hydrolysate (ACSH), while leaving the sugars mostly intact. We show that R. palustris can metabolize a host of aromatic substrates in ACSH that have either been previously described as unable to support growth, such as methoxylated aromatics, and those that have not yet been tested, such as aromatic amides. Removing the aromatics from ACSH with R. palustris, allowed growth of a second microbe that could not grow in the untreated ACSH. By using defined mutants, we show that most of these aromatic compounds are metabolized by the benzoyl-CoA pathway. We also show that loss of enzymes in the benzoyl-CoA pathway prevents total degradation of the aromatics in the hydrolysate, and instead allows for biological transformation of this suite of aromatics into selected aromatic compounds potentially recoverable as an additional bioproduct.
Pinene-Derived Iminodiacetic Acid (PIDA): A Powerful Ligand for Stereoselective Synthesis and Iterative Cross-Coupling of C(sp<sup>3</sup>) Boronate Building Blocks (2011)

Efficient access to chiral C(sp(3)) boronates in stereochemically pure form is critical for realizing the substantial potential of such building blocks in complex-molecule synthesis. We herein report that a pinene-derived iminodiacetic acid (PIDA) ligand enables the highly diastereoselective synthesis of a wide range of oxiranyl C(sp(3)) boronates from the corresponding olefins. These oxiranyl PIDA boronates, in turn, can be readily transformed into unprecedented stable α-boryl aldehydes via a novel 1,2-migration of the boronate group that proceeds with complete maintenance of stereochemical purity. B-Protected haloboronic acids containing dual sp(3)-hybridized C centers are readily accessible via this platform, and the herein demonstrated capacity for stereocontrolled iterative C(sp(3)) cross-coupling with this novel type of bifunctional reagent to access a medicinally important chiral small-molecule target in highly enantioenriched form represents a substantial advance for the building-block-based approach to synthesis.
A Major Advance in the Synthesis of Fluoroalkyl Pyrazoles: Tuneable Regioselectivity and Broad Substitution Patterns (2016)

A novel approach towards highly functionalized fluoroalkyl pyrazoles was developed by using fluoroalkyl amino reagents in combination with a variety of fluorinated ketimines. Tuneable introduction of fluoroalkyl groups in the 3- and 5-positions was possible by using vinamidinium intermediates or the corresponding enamino ketones after hydrolysis. These high-value building blocks can give rise to a large number of analogues for bioactivity screening and discovering new heterocyclic bioactive ingredients in various life science fields.
Engineering Biodegradable and Biocompatible Bio-ionic Liquid Conjugated Hydrogels with Tunable Conductivity and Mechanical Properties (2017)

Conventional methods to engineer electroconductive hydrogels (ECHs) through the incorporation of conductive nanomaterials and polymers exhibit major technical limitations. These are mainly associated with the cytotoxicity, as well as poor solubility, processability, and biodegradability of their components. Here, we describe the engineering of a new class of ECHs through the functionalization of non-conductive polymers with a conductive choline-based bio-ionic liquid (Bio-IL). Bio-IL conjugated hydrogels exhibited a wide range of highly tunable physical properties, remarkable in vitro and in vivo biocompatibility, and high electrical conductivity without the need for additional conductive components. The engineered hydrogels could support the growth and function of primary cardiomyocytes in both two dimentinal (2D) and three dimensional (3D) cultures in vitro. Furthermore, they were shown to be efficiently biodegraded and possess low immunogenicity when implanted subcutaneously in rats. Taken together, our results suggest that Bio-IL conjugated hydrogels could be implemented and readily tailored to different biomedical and tissue engineering applications.
Noninvasive detection of expiratory flow limitation in COPD patients during nasal CPAP (2006)

The difference between mean inspiratory and expiratory respiratory reactance (delta(rs)) measured with forced oscillation technique (FOT) at 5 Hz allows the detection of expiratory flow limitation (EFL) in chronic obstructive pulmonary disease (COPD) patients breathing spontaneously. This aim of this study was to evaluate whether this approach can be applied to COPD patients during noninvasive pressure support. Delta(rs) was measured in seven COPD patients subjected to nasal continuous positive airway pressure (CPAP) at 0, 4, 8 and 12 cmH2O in sitting and supine positions. Simultaneous recording of oesophageal pressure and the Mead and Whittenberger (M-W) method provided a reference for scoring each breath as flow-limited (FL), non-flow-limited (NFL) or indeterminate (I). For each patient, six consecutive breaths were analysed for each posture and CPAP level. According to M-W scoring, 47 breaths were FL, 166 NFL and 51 I. EFL scoring using FOT coincided with M-W in 94.8% of the breaths. In the four patients who were FL in at least one condition, delta(rs) was reduced with increasing CPAP. These data suggest that the forced oscillation technique may be useful in chronic obstructive pulmonary disease patients on nasal pressure support by identifying continuous positive airway pressure levels that support breathing without increasing lung volume, which in turn increase the work of breathing and reduce muscle effectiveness and efficiency.
Pharmacology of Airway Goblet Cell Mucin Release (2003)

Airway mucus hypersecretion is one of the major clinical manifestations of patients suffering from various pulmonary diseases. However, no drugs are yet available to control airway mucus hypersecretion. For the past 15 years, a plethora of information has amassed with regard to the pharmacology of airway goblet cell mucin secretion using various primary cell culture systems. The recent discovery of various MUC genes has also greatly stimulated research in this field. Nevertheless, the heterogeneity of the oligosaccharide structure of mucin molecules makes it extremely difficult to assess the significance of the information derived from the pharmacological studies. Therefore, it seems crucially important to understand the roles of individual mucins in conjunction with normal airway physiology and pathology, which should be the future research directions necessary for studying airway goblet cell mucin pharmacology.
Electroencephalographic and behavioral convulsant effects of hydrobromide and hydrochloride salts of bupropion in conscious rodents (2009)

A novel bromide salt of the antidepressant bupropion (bupropion HBr) has recently been developed and approved for use in the United States. Given previous use of bromides to treat seizures, and that the existing chloride salt of bupropion (HCl) can cause seizures, it is important to determine if the HBr salt may be less likely to cause seizures than the HCl salt. In the present animal studies this was evaluated by means of quantified electroencephalogram (EEG), observation, and the rotarod test in mice and rats. Both bupropion salts were tested at increasing equimolar doses administered intraperitoneally. The results in mice showed that bupropion HCl 125 mg/kg induced a significantly higher ten-fold increase in the mean number of cortical EEG seizures compared to bupropion HBr (7.50 +/- 2.56 vs 0.75 +/- 0.96; p = 0.045), but neither drug caused any brain injuries. In rats bupropion HBr 100 mg/kg induced single EEG seizure activity in the cortical and hippocampal (depth) electrodes and in significantly (p < 0.05) fewer rats (44%) compared to bupropion HCl, which induced 1 to 4 convulsions per rat in all rats (100%) dosed. The total duration of cortical seizures in bupropion HCl-treated rats was significantly longer than the corresponding values obtained in bupropion HBr-treated rats (424.6 seconds vs 124.5 seconds respectively, p < 0.05). Bupropion HCl consistently induced more severe convulsions at each dose level compared to bupropion HBr. Both treatments demonstrated a similar dose-dependent impairment of rotarod performance in mice. In conclusion, these findings suggest that bupropion HBr may have a significantly lower potential to induce seizures in mice and rats, particularly at higher doses, compared to bupropion HCl. Determination of this potential clinical advantage will require human studies. If confirmed by such studies, it is likely that this potential beneficial clinical benefit would be due to the presence of the bromide salt given the long history of the use of bromide to treat seizure disorders.
Single chain des-(B30) insulin. Intramolecular crosslinking of insulin by trypsin catalyzed transpeptidation. (1985)

Single chain des-(B30) insulin (SCI) has been synthesized from porcine insulin by trypsin in a medium with a low content of water. Trypsin catalyzes an intramolecular transpeptidation reaction in which the glycineA1 residue substitutes the alanineB30 residue, rendering a LysB29 -GlyA1 peptide link between the A- and B-chains of insulin. The insulin derivative has been purified by column chromatography and appears to be homogeneous in HPLC and disc electrophoresis. The structure was proven to be B(1-29)-A(1-21) insulin by proteolysis with Armilliaria mellea protease followed by a few steps of Edman degradation. The electrophoretic mobility indicates that SCI has a more condensed structure than that of insulin. Perfect rhombohedral crystals were obtained under conditions resembling those under which insulin crystallizes in the same form. SCI was devoid of effect in the blood sugar lowering assay in mice, the estimated potency being less than 0.1% of that of insulin.