gebhart/patrepeval huggingface dataset:
Glutathione conjugation of aflatoxin B1 exo- and endo-epoxides by rat and human glutathione S-transferases (1992)

Much evidence supports the view that the rate of conjugation of glutathione (GSH) with aflatoxin B1 (AFB1) exo-epoxide is an important factor in determining the species variation in risk to aflatoxins and that induction of GSH S-transferases can yield a significant protective effect. An assay has been developed in which the enzymatic formation of the conjugates of GSH and AFB1 exo-epoxide and the recently described AFB1 endo-epoxide is measured directly. 1H NMR spectra are reported for both the AFB1 exo- and endo-epoxide-GSH conjugates. Structural assignments were made by comparison with AFB1 exo- and endo-epoxide-ethanethiol conjugates, for which nuclear Overhauser effects were measured to establish relative configurations. The endo-epoxide was found to be a good substrate for GSH conjugate formation in rat liver cytosol while mouse liver cytosol conjugated the exo-epoxide almost exclusively. Human liver cytosol conjugated both epoxide isomers to much lower extents than did cytosols prepared from rats or mice. Purified rat GSH S-transferases catalyzed the formation of the AFB1 exo-epoxide-GSH conjugate in the order 1-1 approximately 4-4 approximately 3-3 greater than 2-2 greater than 4-6 (7-7 and 8-8 did not form the exo-epoxide-GSH conjugate at levels above the nonenzymatic rate). The only rat GSH S-transferases that conjugated the endo-epoxide were 4-4 and 4-6, with 4-4 being the more active.(ABSTRACT TRUNCATED AT 250 WORDS)
LTR retroelements in the genome of Daphnia pulex (2010)

Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.
Digital Thermo-Optic Switch Formed Using Silicone Resin (1997)

A digital thermo-optic switch formed using silicone resin exhibits an insertion loss of &lt;2.5 dB, an extinction ratio of &gt;30 dB at 1.55 μm, and operates even at 80 °C.
GFN-xTB Based Computations Provide Comprehensive Insights into Emulsion Radiation-Induced Graft Polymerization (2023)

In this article, a deep insight into emulsion radiartion-induced graft polymerization (RIGP) was obtained by computing explicit solvation free energies, conformational entropy, monomer radius and dipole moments with the state-of-the-art Conformer-Rotamer Ensemble Sampling Tool (CREST) package primalily at semiempirical GFN-xTB level. By leveraging the robustness of the CREST package, above parameters provided dynamic nature of methacrylate monoers with the consideration of realistic emulsion conditions. With the chemical and physical importance of the above results, CREST-determined explanatory variables sufficiently led to the building of the prediction models for the RIGP of methacrylate monomers. The machine learning model building resulted in effective reactivity predictions and unveiled important factors for the radiation-induced graft polymerization in a chemically interpretable fashion.
Classification of Edible Oils and Uncovering Adulteration of Virgin Olive Oil Using FTIR with the Aid of Chemometrics (2009)

3 Abstract: olive o il adulteration adulteration wi th l ess expensive ed ible o ils is a m ajor i ssue f or t he olive oil industry. In this study we have used fourier transform i nfrared (FTIR) spectroscopy to classify different edible oils including the virgin olive oil. We also h ave identified adulteration of virgin o live oil with different volume ratios (2 5, 50 and 75 %) o f b oth c orn and sunflower o ils quantitatively. The total spectral data in region of (4000 -400) cm for all oil samples was recorded -1 and then analyzed using different chemometric t ools such as principal component analysis (PCA), clustering and partial l east sq uare discriminant an alysis (PLSDA).
Genome Sequence of Pseudomonas sp. Strain So3.2b, Isolated from a Soil Sample from Robert Island (Antarctic Specially Protected Area 112), Antarctic (2023)

Strain So3.2b of the genus Pseudomonas was isolated from a soil sample from Robert Island (Antarctic Specially Protected Area 112), Antarctic. We report the complete genome sequence of this isolate, with a length of 6.17 Mbp and a GC content of 60.5%.
Physical-Layer Modeling and System-Level Design of Chip-Scale Photonic Interconnection Networks (2011)

Photonic technology is becoming an increasingly attractive solution to the problems facing today's electronic chip-scale interconnection networks. Recent progress in silicon photonics research has enabled the demonstration of all the necessary optical building blocks for creating extremely high-bandwidth density and energy-efficient links for on-chip and off-chip communications. From the feasibility and architecture perspective however, photonics represents a dramatic paradigm shift from traditional electronic network designs due to fundamental differences in how electronics and photonics function and behave. As a result of these differences, new modeling and analysis methods must be employed in order to properly realize a functional photonic chip-scale interconnect design. In this paper, we present a methodology for characterizing and modeling fundamental photonic building blocks which can subsequently be combined to form full photonic network architectures. We also describe a set of tools which can be utilized to assess the physical-layer and system-level performance properties of a photonic network. The models and tools are integrated in a novel open-source design and simulation environment. We present a case study of two different photonic networks-on-chip to demonstrate how our improved understanding and modeling of the physical-layer details of photonic communications can be used to better understand the system-level performance impact.
Progress in the Design of Optical Fiber Sensors for the Measurement of Pulsed Electric Currents (1986)

The state of the art in the design of fiber sensors for pulsed electric currents is reviewed. Some of the more useful configurations are described and compared. Transfer functions are computed and used to illustrate the effect of linear birefringence and twisting on the characteristics of the sensors. The technique of annealing bend-induced birefringence is described and its present capabilities indicated. An analysis of the ultimate limits to noise equivalent current is given, indicating that several orders of magnitude improvement should be obtainable.
Pgc1α Related Coactivator (prc) Promotes Mitochondrial Biogenesis And Substrate Utilization In C2c12 Myotubes (2010)

The transcriptional co-activator PGC1α is a potent regulator of skeletal muscle metabolism. Less is known about the role of the other PGC family members PGC1β, and PRC. We have recently reported a potential role for PRC in the maintenance of mitochondrial function in C2C12 myotubes during glycolytic substrate overload when PGC1α is suppressed. PURPOSE: The present study was designed to investigate the role of PRC in the development and maintenance of the metabolic profile of C2C12 myotubes. METHODS: To achieve this purpose, moderate over-expression studies were performed using a plasmid containing the full-length cDNA of PRC in the mammalian expression vector pSV-SPORT. C2C12 myoblasts were transfected overnight using lipofectamine 2000 and 2μg plasmid DNA prior to 5 days differentiation. We measured oxygen consumption using a Seahorse XF metabolic flux analyzer, glucose and palmitate uptake/oxidation using 2DG glucose and 14C palmitate respectively, and protein and mRNA levels of mitochondrial targets using western blotting and qPCR. siRNA knockdown was performed in myocytes and myotubes using custom designed PRC duplex siRNA or a scrambled siRNA control (Dharmacon). RESULTS: Transient over-expression increased PRC mRNA and PRC protein content within physiological levels, 163% and 22%, respectively. The rise in cellular PRC resulted in an increase in mitochondrial components at both the mRNA [citrate synthase (1.9-fold), COX4 (2.6-fold), COX5 (2.7-fold) and cytochrome-c (5.6-fold)] and protein level [SDH (15%), COX4 (12%) and cytochrome-c (27%)]. PRC over-expression also increased cell respiration (142%). In addition, PRC over-expression increased GLUT4 mRNA (4.4 fold) and protein (13%) resulting in a 197% increase in basal and 253% increase in insulin (100nM) stimulated 2DG uptake. Finally, PRC over-expression increased CPT1 (26%) resulting in increased palmitate uptake (28%) and oxidation (31%). CONCLUSIONS: Collectively, our data suggest that PRC has an important regulatory role in skeletal muscle in vitro. Similar to PGC1α, PRC increases proteins in the mitochondrial respiratory chain, increases glucose and lipid uptake/oxidation, and stimulates respiration. This suggests that PRC plays an active role in regulating skeletal muscle metabolism and further investigation into the role of PRC in the response to exercise and diabetes is warranted.
Determining the impact of psychosis on rates of false‐positive and false‐negative diagnosis in Alzheimer's disease (2017)

Patients with psychosis were five times more likely to be misdiagnosed as dementia with Lewy bodies, whereas patients without psychosis were more likely to be falsely diagnosed with AD when vascular pathology is the underlying neuropathologic cause of dementia.
Action of Disinfectant Quaternary Ammonium Compounds againstStaphylococcus aureus (2006)

Mode-of-action studies concluded that alkyldimethylbenzylammonium chloride (ADBAC) (a blend of C(12), C(14) and C(16) alkyl homologues) and didecyldimethylammonium chloride (DDAC) are both membrane-active agents, possessing subtly different modes of action reflecting early cell interactions against Staphylococcus aureus. ADBAC and DDAC exhibited similar MIC behaviors from 0.4 ppm to 1.8 ppm over an inoculum range of 1 x 10(5) to 1 x 10(9) CFU/ml at 35 degrees C. For ADBAC and DDAC, an increased rapidity of killing against S. aureus (final concentration, 2 x 10(9) CFU/ml) was observed at 35 degrees C compared to 25 degrees C. Concentration exponents (eta) for killing were <2.5 for both agents, and temperature influenced the eta value. Examination of leakage and kill data suggested that a single leakage marker was not indicative of cell death. ADBAC and DDAC possessed Langmuir (L4) and high-affinity (H3/4) uptake isotherms, respectively. ADBAC molecules formed a single monolayer of coverage of cells at the end of primary uptake, and DDAC formed a double monolayer. Rapid cell leakage occurred at bactericidal concentrations, with total depletion of the intracellular potassium and 260-nm-absorbing pools released in this strict order. Autolysis was observed for ADBAC and DDAC at concentrations of 9 mug/ml (0.0278 mM and 0.0276 mM, respectively) and above, together with the depletion of approximately 30% of the internal potassium pool. Autolysis contributed to ADBAC and DDAC lethality, although high biocide concentrations may have inhibited autolytic enzyme activity.
Déploiement de service multicast dans des environnements hétérogènes (2002)

The first part of this dissertation focuses on bandwidth sharing among unicast and multicast flows. We first propose MFQ (Multicast Fair Queuing), a simple and scalable active queue management mechanism that aims to share the bandwidth fairly between competing multicast flows using a pre-defined inter-multicast fairness function. Then, we describe SBQ (Service Based Queuing), a simple scheduler which uses only two queues in order to enhance the network resource sharing between unicast and multicast flows. A novel method for re-marking multicast packets in DiffServ networks based on the number of downstream members is designed and analyzed. The performance of all these schemes is evaluated under a variety of realistic configurations and traffic patterns. Results indicate that MFQ achieves the expected bandwidth sharing between multicast competing flows, while SBQ guarantees a fair allocation of the bandwidth between unicast and multicast flows. Finally, we describe an extension to the multicast service model that enables the counting of group members at the senders as well as at the intermediate routers in the multicast delivery tree. The second part of this dissertation addresses the issue of supporting IP multicast in networks including heterogeneous transmission media. In a first step, we consider the GEO transparent satellites and we determine the adaptations that should be added to the different routing protocols in order to take into account the inherent characteristics of these systems and those of the multicast applications that will profit from them. In a second step, we focus on the deployment of IP multicast over the next-generation of GEO satellites supporting multiple spot-beams and on-board switching technologies. We propose a new encapsulation scheme optimized for IP multicast and we develop two alternative approaches that could be used to enable switching in the on-board satellite processor: the self-routing approach and the label switching. We present SMRP (Satellite Multicast Routing Protocol) that process the PIM-SM messages received by the system entities from terrestrial nodes. At the end of this dissertation, we present and demonstrate the advantages of a novel switching mechanism between the two modes of PIM-SM protocol. This mechanism uses a coordination between the members concerned by the switching to decide whether it is better to switch or not. Furthermore, it could take into account the network and members constraints.
Design Challenges for HIV-1 Vaccines Based on Humoral Immunity (2014)

OPINION article Front. Immunol., 16 July 2014Sec. HIV and AIDS Volume 5 - 2014 | https://doi.org/10.3389/fimmu.2014.00335
The ErbB4 extracellular region retains a tethered‐like conformation in the absence of the tether (2011)

The epidermal growth factor receptor (EGFR) and its homologs ErbB3 and ErbB4 adopt a tethered conformation in the absence of ligand in which an extended hairpin loop from domain II contacts the juxtamembrane region of domain IV and tethers the domain I/II pair to the domain III/IV pair. By burying the hairpin loop, which is required for formation of active receptor dimers, the tether contact was thought to prevent constitutive activation of EGFR and its homologs. Amino-acid substitutions at key sites within the tether contact region fail to result in constitutively active receptors however. We report here the 2.5 Å crystal structure of the N-terminal three extracellular domains of ErbB4, which bind ligand but lack domain IV and thus the tether contact. This ErbB4 fragment nonetheless adopts a domain arrangement very similar to the arrangement adopted in the presence of the tether suggesting that regions in addition to the tether contribute to maintaining this conformation and inactivity in the absence of the tether contact. We suggest that the tether conformation may have evolved to prevent crosstalk between different EGFR homologs and thus allow diversification of EGFR and its homologs.
Coarse-to-fine Optimization for Speech Enhancement (2019)

In this paper, we propose the coarse-to-fine optimization for the task of speech enhancement. Cosine similarity loss [1] has proven to be an effective metric to measure similarity of speech signals. However, due to the large variance of the enhanced speech with even the same cosine similarity loss in high dimensional space, a deep neural network learnt with this loss might not be able to predict enhanced speech with good quality. Our coarse-to-fine strategy optimizes the cosine similarity loss for different granularities so that more constraints are added to the prediction from high dimension to relatively low dimension. In this way, the enhanced speech will better resemble the clean speech. Experimental results show the effectiveness of our proposed coarse-to-fine optimization in both discriminative models and generative models. Moreover, we apply the coarse-to-fine strategy to the adversarial loss in generative adversarial network (GAN) and propose dynamic perceptual loss, which dynamically computes the adversarial loss from coarse resolution to fine resolution. Dynamic perceptual loss further improves the accuracy and achieves state-of-the-art results compared with other generative models.
Algorithms for Improving Speed and Accuracy of Automated Three-Dimensional Reconstruction With a Depth Camera Mounted on An Industrial Robot (2021)

Abstract Three-dimensional reconstruction technology is used in a wide variety of applications. Automatically creating accurate pointclouds for large parts with complex geometries usually requires expensive metrology instruments. We are interested in using low-cost depth cameras mounted on commonly available industrial robots to create accurate pointclouds for large parts automatically. Manufacturing applications require fast cycle times. Therefore, we are interested in speeding up the 3D reconstruction process. We present algorithmic advances in 3D reconstruction that achieve a sub-millimeter accuracy using a low-cost depth camera. Our system can be used to determine a pointcloud model of large and complex parts. Advances in camera calibration, cycle time reduction for pointcloud capturing, and uncertainty estimation are made in this work. We continuously capture pointclouds at an optimal camera location with respect to part distance during robot motion execution. The redundancy in pointclouds achieved by the moving camera significantly reduces errors in measurements without increasing cycle time. Our system produces sub-millimeter accuracy.
Melanosomal Tyrosine Transport in Normal and Pink‐eyed Dilution Murine Melanocytes (1995)

Tyrosine is the endogenous substrate for melanin production within melanosomes, but the method of tyrosine transport into the melanosome has not been investigated. In the mouse, melanogenesis is disrupted by mutations in the p gene resulting in the pink-eyed dilution phenotype; it has been suggested that the p gene codes for a tyrosine transport protein. We determined that normal (melan-a) melanosome-rich granular fractions take up 10 microns [3H]tyrosine at 21.1 +/- 6.1 (SEM, standard error of the mean) pmol/min/mg protein (N = 7) compared with 21.3 +/- 5.8 SEM pmol/min/mg protein (N = 5) for pink-eyed dilution, whose plasma membrane tyrosine transport was also normal (Km 89 microM; Vmax 302 pmol/min/mg cell protein). We also demonstrated that pink-eyed dilution melanosomes are immature by virtue of their low density, high hexosaminidase activity, and lack of pigment. These data indicate that a tyrosine transport system exists in the melanosomal membrane and that the p gene does not encode a tyrosine transporter of critical importance.
Effect of various irrigating fluids on the ultrastructure of articular cartilage (1990)

The effect of five different irrigating fluids on the ultrastructure of articular cartilage was studied utilizing the scanning electron microscope. Gross histologic studies have shown no significant difference amongst commonly used irrigating fluids on the surface or matrix composition of articular cartilage. Recent in vivo and in vitro biochemical studies, in addition, have shown no significant deleterious effects of irrigating fluids on articular cartilage composition. This study was prospectively undertaken to assess the effect of irrigating fluids on the ultrastructure of articular cartilage. When comparing five irrigating solutions utilizing the scanning electron microscope, specimens irrigated with 1.5% glycine seemed to show a more consistently smooth appearance. Ultrastructural changes were noted with the other four irrigating solutions tested.
Small conductance potassium channels drive ATP-activated chloride secretion in the oviduct (2011)

The molecular mechanisms controlling fluid secretion within the oviduct have yet to be determined. As in other epithelia, both secretory and absorptive pathways are likely to work in tandem to drive appropriate ionic movement to support fluid movement across the oviduct epithelium. This study explored the role of potassium channels in basolateral extracellular ATP (ATP(e))-stimulated ion transport in bovine oviduct epithelium using the Ussing chamber short-circuit current (I(SC)) technique. Basal I(SC) in bovine oviduct epithelium comprises both chloride secretion and sodium absorption and was inhibited by treatment with basolateral K(+) channel inhibitors tetrapentlyammonium chloride (TPeA) or BaCl(2). Similarly, ATP-stimulated chloride secretion was significantly attenuated by pretreatment with BaCl(2,) tetraethylammonium (TEA), tolbutamide, and TPeA. Basolateral K(+) current, isolated using nystatin-perforation technique, was rapidly activated by ATP(e), and pretreatment of monolayers with thapsigargin or TPeA abolished this ATP-stimulated K(+) current. To further investigate the type of K(+) channel involved in the ATP response in the bovine oviduct, a number of specific Ca(2+)-activated K(+) channel inhibitors were tested on the ATP-induced ΔI(SC) in intact monolayers. Charbydotoxin, (high conductance and intermediate conductance inhibitor), or paxilline, (high conductance inhibitor) did not significantly alter the ATP(e) response. However, pretreatment with the small conductance inhibitor apamin resulted in a 60% reduction in the response to ATP(e). The presence of small conductance family member KCNN3 was confirmed by RT-PCR and immunohistochemistry. Measurements of intracellular calcium using Fura-2 spectrofluorescence imaging revealed the ability of ATP(e) to increase intracellular calcium in a phospholipase C-inositol 1,4,5-trisphosphate pathway-sensitive manner. In conclusion, these results provide strong evidence that purinergic activation of a calcium-dependent, apamin-sensitive potassium conductance is essential to promote chloride secretion and thus fluid formation in the oviduct.
Factors in Corn Steep Water Promoting Growth of Plant Tissues. (1959)

Recently, we have been trying to maintain sterile cultures of tissues taken from plants which are especially responsive to the length of the daily photoperiod. We expect that in the process of establishing the cultures, particular requirements for growth substances by the various species will become evident; correlations between these requirements and sensitivities to the light and dark regimes will be sought. We also hope to learn whether or not the influence of inductive photoperiodic treatments given to intact plants can be maintained in cultures of tissues derived from such plants. If the influence is maintained, a good method for studying the nature of the influence will be available. In addition, proper control of the growing conditions may cause formation of small, sterile