gebhart/patrepeval huggingface dataset:
Expression of Hairy/enhancer of split genes in neural progenitors and neurogenesis domains of the adult zebrafish brain (2011)

All subdivisions of the adult zebrafish brain maintain niches of constitutive neurogenesis, sustained by quiescent and multipotent progenitor populations. In the telencephalon, the latter potential neural stem cells take the shape of radial glia aligned along the ventricle and are controlled by Notch signalling. With the aim of identifying new markers of this cell type and of comparing the effectors of embryonic and adult neurogenesis, we focused on the family of hairy/enhancer of split [E(spl)] genes. We report the expression of seven hairy/E(spl) (her) genes and the new helt gene in three neurogenic areas of the adult zebrafish brain (telencephalon, hypothalamus, and midbrain) in relation to radial glia, proliferation, and neurogenesis. We show that the expression of most her genes in the adult brain characterizes quiescent radial glia, whereas only few are expressed in progenitor domains engaged in active proliferation or neurogenesis. The low proliferation status of most her-positive progenitors contrasts with the embryonic nervous system, in which her genes are expressed in actively dividing progenitors. Likewise, we demonstrate largely overlapping expression domains of a set of her genes in the adult brain, which is in striking contrast to their distinct embryonic expression profiles. Overall, our data provide a consolidated map of her expression, quiescent glia, proliferation, and neurogenesis in these various subdivisions of the adult brain and suggest distinct regulation and function of Her factors in the embryonic and adult contexts.
Modeling and characterization of transmission energy consumption in Machine-to-Machine networks (2015)

In future, a massive number of devices are expected to communicate for pervasive monitoring and measurement, industrial automation, and home/building energy management. Nevertheless, such Machine-to-Machine (M2M) communications are prone to failure due to depletion of machines energy if the communication system is not designed properly. A key step in building energy-efficient protocols for large-scale M2M communications is to assess, model or characterize a network energy consumption profile. To meet this need, we develop a theoretical and numerical framework to evaluate the cumulative distribution function (CDF) of the total energy consumption by fully exploiting the properties of stochastic geometry. Unlike the other existing approaches, we model the transmission energy as a function of transmission power, packet size, and link affordable capacity that is a logarithmic function of experienced Signal to Interference plus Noise Ratio (SINR). Since it is very difficult, if not impossible, to derive a closed-form expression for the CDF, we derive numerically computable first- and second-order moments of energy consumption. Applying these moments we then propose Log-normal and Log-logistic distributions to approximate the CDF. Our simulation results show that Log-logistic almost precisely approximates the exact CDF.
Electronic structure analysis of threading screw dislocations in 4H–SiC using electron holography (2011)

Off-axis electron holography has been used to map the electrostatic potential distribution of threading screw dislocations in differently n-doped 4H–SiC epitaxial layers. Observed phase contrast indicated the presence of a negatively charged dislocation core. Comparison between experimental and simulated potential profiles indicated that the density of trapped charges increased for a higher doped epilayer. Assuming a single level of the trap at the core, the ionization energy of the trap was calculated to be 0.89±0.22 eV.
Comparative Genome Analysis of Basidiomycete Fungi (2012)

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.
Dynamic susceptibility contrast MRI measures of relative cerebral blood volume continue to show promise as an early response marker in the setting of bevacizumab treatment (2015)

We read with interest Whitney Pope's recent editorial1 in Neuro-Oncology on the paper by Kickingereder et al2 addressing the utility of relative cerebral blood volume (rCBV) derived from susceptibility-contrast perfusion-weighted MRI for determining therapeutic response in bevacizumab-treated recurrent glioblastoma multiforme (GBM). Kickingereder and Pope contend that although pretreatment rCBV may be a predictive marker of overall survival (OS), there is no evidence supporting post-bevacizumab change in rCBV from baseline as an early response marker. We caution against premature dismissal of rCBV change as an early predictor of treatment response.
Non-monotonic effect of growth temperature on carrier collection in SnS solar cells (2015)

We quantify the effects of growth temperature on material and device properties of thermally evaporated SnS thin-films and test structures. Grain size, Hall mobility, and majority-carrier concentration monotonically increase with growth temperature. However, the charge collection as measured by the long-wavelength contribution to short-circuit current exhibits a non-monotonic behavior: the collection decreases with increased growth temperature from 150 °C to 240 °C and then recovers at 285 °C. Fits to the experimental internal quantum efficiency using an opto-electronic model indicate that the non-monotonic behavior of charge-carrier collection can be explained by a transition from drift- to diffusion-assisted components of carrier collection. The results show a promising increase in the extracted minority-carrier diffusion length at the highest growth temperature of 285 °C. These findings illustrate how coupled mechanisms can affect early stage device development, highlighting the critical role of direct materials property measurements and simulation.
Determination of Laminar Flame Speed and Markstein Numbers Deduced From Turbulent Flames Using the Bomb Method (2016)

The flame speed is a central element not only in theoretical combustion and basic research but also a key parameter for several combustion models. Various methods to define and measure laminar flame speed have been applied. One method that is being relevant to determine flame speed and flame stretch (quantified by Markstein numbers) under high pressure and high temperature conditions is the bomb method, where an unsteady spherical expanding flame is investigated in a closed vessel. Especially for higher pressures, instabilities occur in the flame front of spherically expanding flames, due to the decreased flame thickness and diffusion processes. These so called cellular structures increase the flame surface and therefore the laminar flame speed cannot be determined in the usual manner. As high pressures are common under engine conditions, there is a need to be still able to determine the flame speed within these pressure ranges. By exposing the flame to a turbulent flow field, the vortex interactions are mainly responsible for the deformation of the flame surface. This fact can be used to deduce the laminar flame speed from a turbulent flame. In the present work, a turbulent flame speed model to determine unstretched laminar flame speed and Markstein numbers is introduced and validated. For this purpose the flame is exposed to a well-known turbulent flow field that is nearly homogenous and isotropic. By estimating the flame surface, the laminar flame speed can be calculated, using a turbulent stretch model as well as the flamelet assumption in an implicit approach. A high speed 2D laser imaging technique is used to capture the flame propagation. The most significant issue of this method is to correctly identify the surface and the volume of the flame, because solely a cross section of the flame surface can be visualized in the laser sheet. In case of spherical flames, the radius of the cross section corresponds to the flame surface and volume whereas a single radius is not sufficient to quantify a turbulent flame. The idea is to use the circumference of the cross section in a power law approach to quantify the cellular structures as a mean. The implicit model has been validated for methane and hydrogen flame speed at various equivalence ratios at atmospheric and elevated pressure. The results are in a good agreement with laminar determined flame speed and also the Markstein number is obtained qualitatively correct. Although the flame surface and volume cannot be determined directly by 2D measurement techniques, a model has been developed to determine laminar unstretched flame speed and Markstein numbers by investigating unsteady propagating flames in a turbulent flow field.
Noninvasive imaging of the thirteen-lined ground squirrel photoreceptor mosaic (2016)

Ground squirrels are an increasingly important model for studying visual processing, retinal circuitry, and cone photoreceptor function. Here, we demonstrate that the photoreceptor mosaic can be longitudinally imaged noninvasively in the 13-lined ground squirrel (Ictidomys tridecemlineatus) using confocal and nonconfocal split-detection adaptive optics scanning ophthalmoscopy using 790 nm light. Photoreceptor density, spacing, and Voronoi analysis are consistent with that of the human cone mosaic. The high imaging success rate and consistent image quality in this study reinforce the ground squirrel as a practical model to aid drug discovery and testing through longitudinal imaging on the cellular scale.
The Soybean GH2/4 Gene That Encodes a Glutathione S-Transferase Has a Promoter That Is Activated by a Wide Range of Chemical Agents (1995)

Transcriptional activation of the soybean (Glycine max) GH2/4 gene (also referred to as Gmhsp26-A) and increase in abundance of the GH2/4 mRNA (also referred to as pCE54) have been previously shown to occur following treatment of soybean seedlings with auxins, nonauxin analogs, heavy metals, and a variety of other agents. To determine whether the GH2/4 promoter is responsive to an array of different agents, we have analyzed the inducibility of the GH2/4 promoter fused to the beta-glucuronidase reporter gene in transgenic tobacco (Nicotiana tabacum) plants. We have shown that a wide variety of chemical agents induce this promoter in a tissue-specific and concentration-dependent manner. In addition, we have used an affinity-purified antibody raised against recombinant GH2/4 protein to show that the GH2/4 protein increases in response to auxin application and is localized in the cytosol of soybean cells. Recombinant GH2/4 protein can be purified to homogeneity on a glutathione-agarose resin, and the purified protein has glutathione S-transferase activity when assayed with the substrate 1-chloro-2,4-dinitrobenzene.
A new tracking control system with playback RF signal for VCR (2005)

A new tracking control system by mountain climbing method using playback RF signal was developed. In order to use the system without any conventional method, speed compensation control and dynamic mode control were developed. And a new detecting method of rotational phase for cylinder that also uses playback signal was developed.
Conformation of the ATP binding peptide in actin revealed by proton NMR spectroscopy (1987)

The actin peptide 106-124 exists in a completely conserved region of the sequence and binds strongly to both ATP and tripolyphosphate. Binding particularly affects residues 116 and 118 and generally affects the two segments 115-118 and 121-124 [Barden, J. A., & Kemp, B. E. (1987) Biochemistry 26, 1471-1478]. One-dimensional nuclear Overhauser enhancement difference spectroscopy was used to detect molecular interactions between both adjacent and nonadjacent residues. The N-terminal segment 106-112 was found to be largely extended. A sharp bend was detected between Pro-112 and Lys-113. The triphosphate moiety binds to the strongly hydrophilic central segment of the peptide. Evidence was obtained for a reverse turn involving residues 121-124. Amide proton temperature coefficients and coupling constants provide evidence for a type I beta-turn. A model of the ATP binding site is proposed together with its relationship to other parts of the actin structure and to the phalloidin binding site.
Cause of death with bare metal and sirolimus-eluting stents (2006)

At a mean follow-up of 2.6 years in percutaneous coronary intervention patients, the predominant cause of death was non-cardiac. There was no significant difference in either the frequency or the cause of death with implantation of either sirolimus-eluting or bare metal stents.
Altered expression of syndecan‐1 in prostate cancer (2004)

Syndecan-1 is a cell surface heparan sulfate proteoglycan expressed by epithelial cells. It interacts with growth factors, matrix components, and other extracellular proteins, and is thought to be involved in processes such as cell growth, differentiation and adhesion. The expression of syndecan-1 appears generally downregulated in human carcinomas and in experimental cancer models, whereas transfectional expression of syndecan-1 in cultured cancer cells has been shown to inhibit their growth and other aspects of malignant behavior. These findings suggest that analysis of syndecan-1 expression might be of prognostic value in cancer diagnosis, and studies on some carcinomas indeed point to an inverse correlation between syndecan-1 expression and cancer prognosis. So far, little information has been available on the expression of syndecan-1 in human prostate and prostate disease. We have generated and characterized novel antibodies against syndecan-1 and applied them to immunohistochemical staining of specimens representing normal prostate as well as benign and malignant (n=23) prostate disease. The results indicate that syndecan-1 expression is altered but not uniformly absent in prostate cancer, which is in contrast to the expression of high-molecular-weight cytokeratins. The data initially suggest an inverse correlation between syndecan-1 expression and Gleason grade of the tumor, and warrant a larger study to assess the potential prognostic value of analysing syndecan-1 expression in prostate carcinoma.
Bayesian Persuasive Driving (2018)

In the autonomous driving area, interaction between vehicles is still a piece of puzzle which has not been fully resolved. The ability to intelligently and safely interact with other vehicles can not only improve self driving quality but also be beneficial to the global driving environment. In this paper, a Bayesian persuasive driving algorithm based on optimization is proposed, where the ego vehicle is the persuader (information sender) and the surrounding vehicle is the persuadee (information receiver). In the persuasion process, the ego vehicle aims at changing the surrounding vehicle's posterior belief of the world state by providing certain information via signaling in order to achieve a lower cost for both players. The information received by the surrounding vehicle and its belief of the world state are described by Gaussian distributions. Simulation results in several common traffic scenarios are provided to demonstrate the proposed algorithm's capability of handling interaction situations involving surrounding vehicles with different driving characteristics.
Dielectric properties of dysprosium- and scandium-doped hafnium dioxide thin films (2007)

Dysprosium- and scandium-doped HfO2 films have been deposited by atomic-vapor deposition on SiO2∕Si substrates. Glancing-incidence x-ray diffraction demonstrates that Dy0.10Hf0.90Ox and Sc0.10Hf0.90Ox films show a cubic crystal structure, whereas HfO2 films are monoclinic. The dielectric permittivity increases strongly from 16 for HfO2 to 32 for Dy0.10Hf0.90Ox and Sc0.10Hf0.90Ox. This leads to a reduction of the leakage current in the tunneling regime by up to three orders of magnitude for constant effective oxide thickness. For thick films (≳6nm), it is shown that leakage occurs via the Poole-Frenkel mechanism and that doping HfO2 increases leakage for constant physical oxide thickness.
Synthesis and Properties of Dodecyl Trehaloside Detergents for Membrane Protein Studies (2012)

Sugar-based detergents, mostly derived from maltose or glucose, prevail in the extraction, solubilization, stabilization, and crystallization of membrane proteins. Inspired by the broad use of trehalose for protecting biological macromolecules and lipid bilayer structures, we synthesized new trehaloside detergents for potential applications in membrane protein research. We devised an efficient synthesis of four dodecyl trehalosides, each with the 12-carbon alkyl chain attached to different hydroxyl groups of trehalose, thus presenting a structurally diverse but related family of detergents. The detergent physical properties, including solubility, hydrophobicity, critical micelle concentration (CMC), and size of micelles, were evaluated and compared with the most popular maltoside analogue, β-D-dodecyl maltoside (DDM), which varied from each other due to distinct molecular geometries and possible polar group interactions in resulting micelles. Crystals of 2-dodecyl trehaloside (2-DDTre) were also obtained in methanol, and the crystal packing revealed multiple H-bonded interactions among adjacent trehalose groups. The few trehaloside detergents were tested for the solubilization and stabilization of the nociceptin/orphanin FQ peptide receptor (ORL1) and MsbA, which belong to the G-protein coupled receptor (GPCR) and ATP-binding cassette transporter families, respectively. Our results demonstrated the utility of trehaloside detergents as membrane protein solubilization reagents with the optimal detergents being protein dependent. Continuing development and investigations of trehaloside detergents are attractive, given their interesting and unique chemical-physical properties and potential interactions with membrane lipids.
SK channels and calmodulin (2015)

Calcium ions are Nature's most widely used signaling mechanism, mediating communication between pathways at virtually every physiological level. Ion channels are no exception, as the activities of a wide range of ion channels are intricately shaped by fluctuations in intracellular Ca(2+) levels. Mirroring the importance and the breadth of Ca(2+) signaling, free Ca(2+) levels are tightly controlled, and a myriad of Ca(2+) binding proteins transduce Ca(2+) signals, each with its own nuance, comprising a constantly changing symphony of metabolic activity. The founding member of Ca(2+) binding proteins is calmodulin (CaM), a small, acidic, modular protein endowed with gymnastic-like flexibility and E-F hand motifs that chelate Ca(2+) ions. In this review, I will trace the history that led to the realization that CaM serves as the Ca(2+)-gating cue for SK channels, the experiments that revealed that CaM is an intrinsic subunit of SK channels, and itself a target of regulation.
A fully functional 1 K ECL RAM on a bounded SOI wafer (2003)

A fully functional 1 K ECL RAM (emitter-coupled logic random-access memory) with a Schottky-clamped cell has been fabricated on a bounded silicon-on-insulator (SOI) wafer. The complete isolation made possible by both the SOI technique and the trench structure has made it possible to reduce the number of soft errors induced by alpha -particles. The cell was completely isolated by using U-grooves deep enough to reach the thick oxide layer (1 mu m). The SOI RAM's performance was improved by reducing the parasitic capacitance. It is shown that the rate of soft-error occurrence for the SOI RAM is three-hundred times smaller than that for the conventional RAM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hemodynamically important right ventricular infarction: follow-up evaluation of right ventricular systolic function at rest and during exercise with radionuclide ventriculography and respiratory gas exchange. (1987)

The prognosis and recovery of right ventricular systolic function in patients with hemodynamically documented right ventricular myocardial infarction (RVMI) is unclear. Therefore 27 patients who met hemodynamic criteria for RVMI were followed for at least 1 year. Four patients died within 1 year and 23 survived. Postmortem examination performed in three of the four patients showed extensive infarction of the right and left ventricles. Survivors underwent early and late follow-up resting radionuclide ventriculograms and late exercise studies. During long-term follow-up (1 to 4 years) resting radionuclide ventriculography demonstrated a significant improvement in right ventricular ejection fraction (30 +/- 7% to 43 +/- 8%; p less than .001) and right ventricular wall motion index (2.2 +/- 0.4 to 1.5 +/- 0.5; p less than .001) in 18 patients who survived longer than 1 year. Fourteen of these patients underwent upright bicycle exercise while off beta-blocking drugs and peak radionuclide ejection fraction was acquired after anaerobic threshold was achieved. Right ventricular ejection fraction increased significantly from 41 +/- 10% to 47 +/- 12% (p less than .001), as did the left ventricular ejection fraction (55 +/- 15% to 60 +/- 12%; p less than .05). The direction and magnitude of change of the right ventricular ejection fraction correlated significantly with the left ventricular ejection fraction (r = .82, p less than .02). Deviations from this correlation occurred in patients who had a decreased forced expiratory volume in 1 sec and an abnormal ventilatory reserve during exercise.(ABSTRACT TRUNCATED AT 250 WORDS)
A "paradoxical" solution to the signature problem (2019)

research-article Share on A "paradoxical" solution to the signature problem Authors: Shafi Goldwasser MIT Laboratory for Computer Science MIT Laboratory for Computer ScienceView Profile , Silvio Micali MIT Laboratory for Computer Science MIT Laboratory for Computer ScienceView Profile , Ronald L. Rivest MIT Laboratory for Computer Science MIT Laboratory for Computer ScienceView Profile Authors Info & Claims Providing Sound Foundations for Cryptography: On the Work of Shafi Goldwasser and Silvio MicaliOctober 2019 Pages 265–284https://doi.org/10.1145/3335741.3335753Published:04 October 2019Publication History 1citation158DownloadsMetricsTotal Citations1Total Downloads158Last 12 Months8Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access