gebhart/patrepeval huggingface dataset:
Biosynthesis of the major brain gangliosides GD1a and GT1b (2012)

Gangliosides-sialylated glycosphingolipids-are the major glycoconjugates of nerve cells. The same four structures-GM1, GD1a, GD1b and GT1b-comprise the great majority of gangliosides in mammalian brains. They share a common tetrasaccharide core (Galβ1-3GalNAcβ1-4Galβ1-4Glcβ1-1'Cer) with one or two sialic acids on the internal galactose and zero (GM1 and GD1b) or one (GD1a and GT1b) α2-3-linked sialic acid on the terminal galactose. Whereas the genes responsible for the sialylation of the internal galactose are known, those responsible for terminal sialylation have not been established in vivo. We report that St3gal2 and St3gal3 are responsible for nearly all the terminal sialylation of brain gangliosides in the mouse. When brain ganglioside expression was analyzed in adult St3gal1-, St3gal2-, St3gal3- and St3gal4-null mice, only St3gal2-null mice differed significantly from wild type, expressing half the normal amount of GD1a and GT1b. St3gal1/2-double-null mice were no different than St3gal2-single-null mice; however, St3gal2/3-double-null mice were >95% depleted in gangliosides GD1a and GT1b. Total ganglioside expression (lipid-bound sialic acid) in the brains of St3gal2/3-double-null mice was equivalent to that in wild-type mice, whereas total protein sialylation was reduced by half. St3gal2/3-double-null mice were small, weak and short lived. They were half the weight of wild-type mice at weaning and displayed early hindlimb dysreflexia. We conclude that the St3gal2 and St3gal3 gene products (ST3Gal-II and ST3Gal-III sialyltransferases) are largely responsible for ganglioside terminal α2-3 sialylation in the brain, synthesizing the major brain gangliosides GD1a and GT1b.
Distributed energy and resource management for full-duplex dense small cells for 5G (2017)

We consider a multi-carrier and densely deployed small cell network, where small cells are powered by renewable energy source and operate in a full-duplex mode. We formulate an energy and traffic aware resource allocation optimization problem, where a joint design of the beamformers, power and sub-carrier allocation, and users scheduling is proposed. The problem minimizes the sum data buffer lengths of each user in the network by using the harvested energy. A practical uplink user rate-dependent decoding energy consumption is included in the total energy consumption at the small cell base stations. Hence, harvested energy is shared with both downlink and uplink users. Owing to the non-convexity of the problem, a faster convergence sub-optimal algorithm based on successive parametric convex approximation framework is proposed. The algorithm is implemented in a distributed fashion, by using the alternating direction method of multipliers, which offers not only the limited information exchange between the base stations, but also fast convergence. Numerical results advocate the redesigning of the resource allocation strategy when the energy at the base station is shared among the downlink and uplink transmissions.
Locational security impact factors for security index constrained economic dispatch problem (2013)

In security constrained economic dispatch, the generation is determined such as to minimize cost to supply the load while fulfilling all of the operational constraints in normal operation and contingency cases. The formulation of a security index provides a quantitative measure for the security in the system and also allows for the determination of the impact of generators on security. Hence, in this paper, first two different security indices are formulated: a violation-based security index and a risk-based security index. These security index formulations are used to introduce locational security impact factors which similarly to the information that locational marginal prices provide for generation economics, give insights into the location dependent impact on system security. These impact factors are then integrated into an iterative approach for the determination of the optimal generation settings given a specific bound on the desired level of system security.
A 3.1&#x2013;9.5 GHz agile UWB pulse radio receiver with discrete-time wideband-IF correlation in 90nm CMOS (2008)

An 8-channel 3.1-9.5 GHz UWB pulse radio receiver is realized using a double-conversion architecture with discrete-time wideband IF correlation. The pulse templates for correlation are pre-stored in memories which allows fast band switching and agile interferer avoidance since no PLL resettling is required. The receiver chip is implemented in a standard 90 nm CMOS process and occupies 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
REBAR: Low-variance, unbiased gradient estimates for discrete latent variable models (2017)

Learning in models with discrete latent variables is challenging due to high variance gradient estimators. Generally, approaches have relied on control variates to reduce the variance of the REINFORCE estimator. Recent work (Jang et al. 2016, Maddison et al. 2016) has taken a different approach, introducing a continuous relaxation of discrete variables to produce low-variance, but biased, gradient estimates. In this work, we combine the two approaches through a novel control variate that produces low-variance, \emph{unbiased} gradient estimates. Then, we introduce a modification to the continuous relaxation and show that the tightness of the relaxation can be adapted online, removing it as a hyperparameter. We show state-of-the-art variance reduction on several benchmark generative modeling tasks, generally leading to faster convergence to a better final log-likelihood.
A versatile-deployable bacterial detection system for food and environmental safety based on LabTube-automated DNA purification, LabReader-integrated amplification, readout and analysis (2014)

Contamination of foods is a public health hazard that episodically causes thousands of deaths and sickens millions worldwide. To ensure food safety and quality, rapid, low-cost and easy-to-use detection methods are desirable. Here, the LabSystem is introduced for integrated, automated DNA purification, amplification and detection. It consists of a disposable, centrifugally driven DNA purification platform (LabTube) and a low-cost UV/vis-reader (LabReader). For demonstration of the LabSystem in the context of food safety, purification of Escherichia coli (non-pathogenic E. coli and pathogenic verotoxin-producing E. coli (VTEC)) in water and milk and the product-spoiler Alicyclobacillus acidoterrestris (A. acidoterrestris) in apple juice was integrated and optimized in the LabTube. Inside the LabReader, the purified DNA was amplified, readout and analyzed using both qualitative isothermal loop-mediated DNA amplification (LAMP) and quantitative real-time PCR. For the LAMP-LabSystem, the combined detection limits for purification and amplification of externally lysed VTEC and A. acidoterrestris are 10(2)-10(3) cell-equivalents. In the PCR-LabSystem for E. coli cells, the quantification limit is 10(2) cell-equivalents including LabTube-integrated lysis. The demonstrated LabSystem only requires a laboratory centrifuge (to operate the disposable, fully closed LabTube) and a low-cost LabReader for DNA amplification, readout and analysis. Compared with commercial DNA amplification devices, the LabReader improves sensitivity and specificity by the simultaneous readout of four wavelengths and the continuous readout during temperature cycling. The use of a detachable eluate tube as an interface affords semi-automation of the LabSystem, which does not require specialized training. It reduces the hands-on time from about 50 to 3 min with only two handling steps: sample input and transfer of the detachable detection tube.
Antibodies to Streptococcal Surface Enolase React with Human α‐Enolase: Implications in Poststreptococcal Sequelae (2000)

The pathogenic mechanisms for developing acute rheumatic fever after group A streptococcal pharyngitis are still poorly understood. The glycolytic enzyme enolase is one of the major proteins on the surface of group A streptococci. Herein, significant cross-reactivity was shown between streptococcal enolase and human enolase. Fluorocytometric analysis revealed that antistreptococcal enolase antibodies react with the enolase expressed on the surface of hematopoietic cells. Furthermore, the enolase on the leukocyte surface was found to be up-regulated by inflammatory stimuli. Evaluation of antibody titers indicated that serum samples from patients with acute rheumatic fever have higher levels of antibodies that react with the human and bacterial enolases than do serum samples from patients with streptococcal pharyngitis or healthy control subjects. These results show that streptococcal enolase is a novel cross-reactive antigen that may play an important role in the initiation of the autoimmune diseases related to streptococcal infection.
Species-Diagnostic Single-Nucleotide Polymorphism and Sequence-Tagged Site Markers for the Parasitic Wasp Genus <I>Nasonia</I> (Hymenoptera: Pteromalidae) (2007)

Wasps of the genus Nasonia are important biological control agents of house flies and related filth flies, which are major vectors of human pathogens. Species of Nasonia (Hymenoptera: Pteromalidae) are not easily differentiated from one another by morphological characters, and molecular markers for their reliable identification have been missing so far. Here, we report eight single-nucleotide polymorphism and three sequence-tagged site markers derived from expressed sequenced tag libraries for the two closely related and regionally sympatric species N. giraulti and N. vitripennis. We studied variation of these markers in natural populations of the two species, and we mapped them in the Nasonia genome. The markers are species-diagnostic and evenly spread over all five chromosomes. They are ideal for rapid species identification and hybrid recognition, and they can be used to map economically relevant quantitative trait loci in the Nasonia genome.
Ca2+-linked upregulation and mitochondrial production of nitric oxide in the mouse preimplantation embryo (2006)

Previous studies have demonstrated a role for the signalling agent nitric oxide in regulating preimplantation embryo development. We have now investigated the biochemical mode of action of nitric oxide in mouse embryos in terms of mitochondrial function and Ca2+ signalling. DETA-NONOate, a nitric oxide donor, decreased day 4 blastocyst cell number and oxygen consumption, consistent with a role for nitric oxide in the inhibition mitochondrial cytochrome c oxidase. Using live cell imaging and the nitric-oxide-sensitive probe DAF-FM diacetate, nitric oxide was detected at all stages of preimplantation development and FRET analysis revealed a proportion of the nitric oxide to be colocalised with mitochondria. This suggests that mitochondria of preimplantation embryos produce nitric oxide to regulate their own oxygen consumption. Inhibiting or uncoupling the electron transport chain induced an increase in nitric oxide and [Ca2+]i as well as disruption of Ca2+ deposits at the plasma membrane, suggesting that mitochondrial disruption can quickly compromise cellular function through Ca2+ -stimulated nitric oxide production. A link between antimycin-A-induced apoptosis and nitric oxide signalling is proposed.
A novel glucosylceramide synthase inhibitor attenuates alpha synuclein pathology and lysosomal dysfunction in preclinical models of synucleinopathy (2021)

Mutations in the lysosomal enzyme glucocerebrosidase (GCase, GBA1 gene) are the most common genetic risk factor for developing Parkinson's disease (PD). GCase metabolizes the glycosphingolipids glucosylceramide (GlcCer) and glucosylsphingosine (GlcSph). Mutations in GBA1 reduce enzyme activity and the resulting accumulation of glycosphingolipids may contribute to the underlying pathology of PD, possibly via altering lysosomal function. While reduction of GCase activity exacerbates α-synuclein (α-syn) aggregation, it has not been determined that this effect is the result of altered glycosphingolipid levels and lysosome function or some other effect of altering GCase. The glycosphingolipid GlcCer is synthesized by a single enzyme, glucosylceramide synthase (GCS), and small molecule inhibitors (GCSi) reduce cellular glycosphingolipid levels. In the present studies, we utilize a preformed fibril (PFF) rodent primary neuron in vitro model of α-syn pathology to investigate the relationship between glycosphingolipid levels, α-syn pathology, and lysosomal function. In primary cultures, pharmacological inhibition of GCase and D409V GBA1 mutation enhanced accumulation of glycosphingolipids and insoluble phosphorylated α-syn. Administration of a novel small molecule GCSi, benzoxazole 1 (BZ1), significantly decreased glycosphingolipid concentrations in rodent primary neurons and reduced α-syn pathology. BZ1 rescued lysosomal deficits associated with the D409V GBA1 mutation and α-syn PFF administration, and attenuated α-syn induced neurodegeneration of dopamine neurons. In vivo studies revealed BZ1 had pharmacological activity and reduced glycosphingolipids in the mouse brain to a similar extent observed in neuronal cultures. These data support the hypothesis that reduction of glycosphingolipids through GCS inhibition may impact progression of synucleinopathy and BZ1 is useful tool to further examine this important biology.
ChemInform Abstract: NITRIERUNG PRIM. AROMATISCHER AMINE (1970)

Abstract N‐Aryl‐benzimidchloride (I) reagieren bei Raumtemperatur mit NaNO 3 /Dimethylformamid zu Benzoyl‐nitroarylaminen (II).
Identification of Cardiovascular Dynamics From Peripheral Circulatory Waveforms Using Laguerre Model Blind System ID (2004)

A new tool has been developed for characterizing both the global and local dynamic behavior exhibited by peripheral circulatory waveforms. The signals representing these waveforms can be derived from a variety of different cardiovascular sensor modalities measuring changes in pressure, flow, or volume. The correlation that exists between two peripheral circulatory waveform measurements taken at different locations allows this new signal-processing algorithm to identify two compact, low order dynamic models in real-time. These models identify the distinct dynamic behavior of the circulatory paths traveled by the pulsatile waveforms using output measurements alone. This new algorithm is based on a multi-channel blind system identification technique that has been reformulated to use a Laguerre basis function series expansion. Additionally, a new deconvolution algorithm has been developed to allow estimation of the unknown common input using the identified Laguerre models, which are generally inversely unstable. This new approach has been shown to provide accurate identification of vascular hemodynamics when applied to experimental data derived from a swine.
Quantitative stress imaging by combining static and dynamic elastography (2015)

There is increasing evidence showing the involvement of mechanical-transduction processes in the interplay between shape-related strains and expressions of the genome in living tissues. However, tools allowing long term control of physiological mechanical stress from the inside the tissues lack the investigation of the impact of such processes in organisms. This work presents the feasibility of obtaining a complete bidimensional (2D) map of the stress applied to an elastic soft tissue according to the Hooke’s law (! = E.&amp;quot;, where! is the stress, E is the Young&amp;apos;s modulus and and &amp;quot; is the strain). By combining the concepts of dynamic (Supersonic Shear Imaging-SSI) and static elastography, both the elastic modulus (E) and the strain (&amp;quot;) can be retrieved respectively. The SSI technique is based on the combination of radiation force induced by an ultrasonic beam and an ultrafast imaging sequence (5000 frames/s) capable of catching in real time the propagation of the resulting shear waves. Then by measuring the shear wave velocity (VS), the complete 2D elasticity map can be retrieved through the well known expression E = 3#VS, where # represents the density of the media. For the static elastography part, the tissue is slightly compressed and an ultrasound image is acquired before and after static compression. The cross-correlation between these two ultrasound images allows the determination of the accurate 2D strain map. Experiments were performed on diverse types of agar-gelatin phantoms mimicking soft tissues which present inclusions with different levels of stiffness. The influence of the boundary conditions on measurements is discussed. The mapping of quasi-static stress applied to biological tissues could play a key role in the understanding of tumor mechanical-transduction processes where mechanical stress may induce changes within the tumor structure. 1
Effects of anisotropy, morphology, and interparticle coupling on the far-infrared optical modes of randomly oriented ZnO nanoparticles (2023)

Polar dielectric nanoparticles (NPs) with uniaxial anisotropy support two-surface phonon polariton modes inside a reststrahlen band. The effective permittivity of a randomly orientated ensemble of NPs is usually assumed to be isotropic due to averaging of the optical response over all orientations. In this work, we demonstrate that this assumption is not valid for ZnO nanoparticles, and the resultant absorption of a nanoparticle film can be tailored by the nanoparticle morphology. We measure distinct features in the absorption spectrum for films or ensembles of interacting polar dielectric NPs, which we attribute to the excitation of SPhP modes due to anisotropy in the dielectric permittivity of the NPs. We identify and characterize these modes in elliptical and rod-like ZnO NPs prepared by solvothermal synthesis and dispersed within an optically transparent matrix. Localized optical modes are identified using Fourier transform infrared absorption spectroscopy and confirmed by finite element simulations. The broadening and maxima of the modes are shown to be governed by the effects of anisotropy, nanoparticle morphology, and interparticle coupling within nanoparticle ensembles.
Molecular characterization of renal calcium channel beta-subunit transcripts (1995)

An apical, hormone-regulated, calcium entry channel in the distal convoluted tubule and/or connecting tubule (DCT/CNT) is thought to play an important role in controlling renal calcium excretion. We previously identified a gene transcript encoding the pore-forming alpha 1-subunit of a calcium channel (alpha 1A, or CaCh4) which may be a candidate for such a molecule. The properties of voltage-dependent calcium channels are known to be modulated by their beta-subunits. To identify the accessory beta-subunit of DCT/CNT calcium channels, degenerate primers based on published beta-subunit sequences were used to amplify rat kidney cDNA by the polymerase chain reaction (PCR), and the products were subcloned and sequenced. Alternatively spliced transcripts of three beta-subunit genes (beta 2, beta 3, and beta 4) were identified. Northern blot analysis indicated that beta 4-subunit is preferentially expressed in kidney cortex. Transcripts of all three beta-subunit genes were detected by PCR in microdissected nephron segments, but only beta 4-subunit was found in DCT/CNT. As the beta 4- and alpha 1A-subunits colocalize to the DCT/CNT, we hypothesize that they may be constituent subunits of a renal calcium channel regulated by a hormone(s).
Online Semantic Knowledge Management for Product Design Based on Product Engineering Ontologies (2011)

This paper formulates an approach to use the semantic web for knowledge management in the product design domain to provide enhanced capabilities of authoring/updating, querying/reasoning, searching, and visualization of information. Engineering has unique challenges, due to the pervasive use of CAD models and underlying interoperability and integration issues. The authors propose a distributed model composed of a host hybrid-data repository, external public linked data sources, a semantic data management engine, and a web-based user interface layer. The hybrid-data repository consists of ontologies to preserve knowledge for the product design domain and a conventional product data base to utilize legacy design data. Near full integration with a web based environment is achieved. The importance of accessing product related CAD data that has been instantiated in ontology models, querying them, and then displaying the data on a web interface in real time with other legacy data, such as hand sketches and notes that have been scanned and relevant information from conventional rational databases public linked data sites, is a useful and transformational capability. The system clearly facilitates design and information management beyond traditional CAD capabilities and creates a foundation for important capability improvements in the domain.
Use of Amulet in behavioral change for geriatric obesity management (2019)

Using a team-science approach, Amulet has the potential, as an open-source mobile health device, to tailor activity interventions to older adults.
Optical nonlinearities in crystalline organic multiple quantum wells (1991)

A study of the linear and nonlinear optical behavior of recently realized crystalline organic semiconductor quantum wells is reported. Using the Davydov Hamiltonian, we find analytical solutions for the optical response function, and we predict the existence of intrinsic optical bistability and two-beam-coupling energy transfer in these materials.
Polycytidine tract deletion from microRNA-detargeted oncolytic Mengovirus optimizes the therapeutic index in a murine multiple myeloma model (2022)

Mengovirus is an oncolytic picornavirus whose broad host range allows for testing in immunocompetent cancer models. Two pathogenicity-ablating approaches, polycytidine (polyC) tract truncation and microRNA (miRNA) targets insertion, eliminated the risk of encephalomyocarditis. To investigate whether a polyC truncated, miRNA-detargeted oncolytic Mengovirus might be boosted, we partially or fully rebuilt the polyC tract into the 5' noncoding region (NCR) of polyC-deleted (MC<sub>0</sub>) oncolytic constructs (NC) carrying miRNA target (miRT) insertions to eliminate cardiac/muscular (miR-133b and miR-208a) and neuronal (miR-124) tropisms. PolyC-reconstituted viruses (MC<sub>24</sub>-NC and MC<sub>37</sub>-NC) replicated <i>in vitro</i> and showed the expected tropism restrictions, but reduced cytotoxicity and miRT deletions were frequently observed. In the MPC-11 immune competent mouse plasmacytoma model, both intratumoral and systemic administration of MC<sub>0</sub>-NC led to faster tumor responses than MC<sub>24</sub>-NC or MC<sub>37</sub>-NC, with combined durable complete response rates of 75%, 0.5%, and 30%, respectively. Secondary viremia was higher following MC<sub>0</sub>-NC versus MC<sub>24</sub>-NC or MC<sub>37</sub>-NC therapy. Sequence analysis of virus progeny from treated mice revealed a high prevalence of miRT sequences loss among MC<sub>24</sub>- and MC<sub>37</sub>- viral genomes, but not in MC<sub>0</sub>-NC. Overall, MC<sub>0</sub>-NC was capable of stably retaining miRT sites and provided a more effective treatment and is therefore our lead Mengovirus candidate for clinical translation.
Quantitative, Spatially Defined Expression of Leukocyte-associated Immunoglobulin-like Receptor in Non–small Cell Lung Cancer (2023)

The spatial, quantitative assessment of LAIR-1 in NSCLC shows positive association of OS with high LAIR-1<sup>+</sup>/CD68<sup>+</sup> cell densities and negative association of OS with high LAIR-1 expression in LUAD tumor subtype.