gebhart/patrepeval huggingface dataset:
von Hippel-Lindau syndrome: cloning and identification of the plasma membrane Ca(++)-transporting ATPase isoform 2 gene that resides in the von Hippel-Lindau gene region. (1993)

We have isolated and analyzed full-length complementary DNA clones encoded by a 200-kilobase gene encompassing the D3S601 locus that resides in the von Hippel-Lindau (VHL) gene region. The deduced amino acid sequence shows 99% identity with the published sequence of the rat plasma membrane Ca(++)-transporting ATPase isoform 2 complementary DNA, implying that we have cloned and positioned the human plasma membrane Ca(++)-transporting ATPase isoform 2 gene within the VHL critical region. The gene is expressed in VHL target tissues and should be considered a potential candidate gene for the VHL disease.
New classes and applications of hash functions (1979)

In this paper we exhibit several new classes of hash functions with certain desirable properties, and introduce two novel applications for hashing which make use of these functions. One class of functions is small, yet is almost universal2. If the functions hash n-bit long names into m-bit indices, then specifying a member of the class requires only O((m + log2log2(n)) log2(n)) bits as compared to O(n) bits for earlier techniques. For long names, this is about a factor of m larger than the lower bound of m+log2n-log2m bits. An application of this class is a provably secure authentication techniques for sending messages over insecure lines. A second class of functions satisfies a much stronger property than universal2. We present the application of testing sets for equality. The authentication technique allows the receiver to be certain that a message is genuine. An 'enemy' - even one with infinite computer resources - cannot forge or modify a message without detection. The set equality technique allows the the operations 'add member to set', 'delete member from set' and 'test two sets for equality' to be performed in expected constant time and with less than a specified probability of error.
High-performance nanostructured MR contrast probes (2010)

Magnetic resonance imaging (MRI) has become a powerful technique in biological molecular imaging and clinical diagnosis. With the rapid progress in nanoscale science and technology, nanostructure-based MR contrast agents are undergoing rapid development. This is in part due to the tuneable magnetic and cellular uptake properties, large surface area for conjugation and favourable biodistribution. In this review, we describe our recent progress in the development of high-performance nanostructured MR contrast agents. Specifically, we report on Gd-enriched nanostructured probes that exhibit T(1) MR contrast and superparamagnetic Fe(3)O(4) and CoFe(2)O(4) nanostructures that display T(2) MR contrast enhancement. The effects of nanostructure size, shape, assembly and surface modification on relaxivity are described. The potential of these contrast agents for in vitro and in vivo MR imaging with respect to colloidal stability under physiological conditions, biocompatibility, and surface functionality are also evaluated.
Natural Language Processing for Online Applications (2007)

This text covers the technologies of document retrieval, information extraction, and text categorization in a way which highlights commonalities in terms of both general principles and practical concerns. It assumes some mathematical background on the part of the reader, but the chapters typically begin with a non-mathematical account of the key issues. Current research topics are covered only to the extent that they are informing current applications; detailed coverage of longer term research and more theoretical treatments should be sought elsewhere. There are many pointers at the ends of the chapters that the reader can follow to explore the literature. However, the book does maintain a strong emphasis on evaluation in every chapter both in terms of methodology and the results of controlled experimentation.
Supplementary Figure S5 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression (2023)

&lt;p&gt;Supplementary Figure S5. Mena isoform expression does not affect Integrin alphav, beta1 or FAK levels.&lt;/p&gt;
Autonome Entdeckung in den chemischen Wissenschaften, Teil II: Ausblick (2019)

Abstract In dem zweiteiligen Aufsatz wird der Beitrag von Automation zu verschiedenen Aspekten der chemischen Entdeckung untersucht. In Teil 2 betrachten wir ausgewählte Beispiele. Eine Diskussion der Rolle von Automation und Rechnung im wissenschaftlichen Prozess und deren Einfluss auf die Beschleunigung von Entdeckungsaufgaben wird immer wichtiger. Selbst wenn automatisierte Systeme die Laborarbeit immens unterstützen können, kann man argumentieren, dass auch die besten Roboter noch nicht wirklich etwas “entdecken”. Zur effektiven Entwicklung autonomer Plattformen müssen wir ihren bisherigen Einsatz evaluieren und herausfinden, wie sie sich auf künftige Probleme anwenden lassen. Den Hauptteil dieses Aufsatzes nimmt die Definition von weiterführenden Forschungsrichtungen ein: Verarbeitung komplexer Daten, Erstellung empirischer Modelle, Automation experimenteller und rechnerischer Validierung, Versuchsauswahl und Evaluation des Fortschritts auf dem Weg zur autonomen Entdeckung.
The Effect of Activating Fibroblast Growth Factor Receptor 3 Mutations on Osteogenic Differentiation and Ectopic Bone Formation by Human Periosteal Derived Cells (2012)

Activating mutations in Fibroblast Growth Factor Receptor 3 (FGFR3) have previously been shown to cause\nskeletal dysplasias through their effect on growth plate chondrocytes. However, the effect of FGFR3 mutations on\nbone progenitor cells may differ. The objective of this study was to investigate the effect of specific activating FGFR3\nmutations on ectopic in vivo bone formation by periosteal derived cells (PDCs) seeded on calcium phosphate/\ncollagen scaffolds.\n\nPDCs were isolated from hypochondroplasic (N540K mutation) and achondroplasic (G380R mutation)\npatients, along with age/sex matched controls. These cells were characterised in vitro for proliferation, osteogenic\ndifferentiation, FGFR3 signalling and in vivo bone formation. Subsequently, empirical modelling was used to find\ncorrelations between in vivo formed bone and in vitro cell behaviour. These data showed that in contrast to the G380R\nmutation, which produced no bone, the N540K mutation induced significant ectopic bone formation on specific\ncarriers. This allowed correlation between percentage of induced bone formation to elevated in vitro proliferation\nand differentiation. Correlating osteogenic markers included Collagen type 1, alkaline phosphatase and osteocalcin.\nEnhanced proliferation was attributed to increased phosphorylation of Erk-1/2.\n\nThis study highlights the importance of FGFR3 in periosteal cell differentiation and also indicates it potential for\ntargeted tissue engineering strategies.
European Cities (2002)

European cities are on the rise, and are taking advantage of the opportunities of the European integration and globalization processes. But they also face economic changes, social inequalities, poverty, and a new set of constraints. Taking examples through the European Union, this book explores the impact of the transformation of the nation states on cities and the change of local societies and local governments. It argues that new modes of urban governance are emerging, and that cities are becoming collective actors within European governance. It shows why and how the bulk of European cities still appear to be original forms of compromise, aggregation, representation of diverse interests, and culture. Different modes of governance are gradually being structured in most middle-sized European cities despite processes of social exclusion segregation accompanied by the increased mobility of some citizens. Are Europeans going to invent a new form of institutionalized and territorialized capitalism, of which medium-sized European cities will be one of the pillars and one of the actors? Failing that, the effects of changing scales could be expressed as profound transformations of the European urban model.
Quantum Cerenkov Radiation from Electron Vortex Beams (2014)

Using quantum field theory, we calculate Cherenkov radiation from an electron with vortex-shape wavefunction. When such an electron travels through a photonic waveguide, it emits a single photon with specific frequency, angle, and angular momentum.
Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans (2021)

Summary The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside ascr#8 mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal-ventral and left-right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least two-fold higher expression in a specific CEM neuron type versus both other CEM neurons and adult males. These included two G protein coupled receptor (GPCR) genes, srw-97 and dmsr-12 , that were specifically expressed in non-overlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act non-redundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.
On the nature of phase transitions in the tetragonal tungsten bronze GdK2Nb5O15 ceramics (2014)

Phase transitions in gadolinium potassium niobate GdK2Nb5O15 (GKN) ceramics have been investigated by x-ray diffraction, dielectric susceptibility, differential scanning calorimetry, and Raman scattering. The results of our complementary studies show that GKN exhibits two phase transitions at Tc1 = 238 °C and Tc2 = 375 °C attributed to the ferroelectric-antiferroelectric-paraelectric (FE-AFE-PE) phase transitions. According to the x-ray diffraction analysis, the FE and PE phases were refined in the polar P4bm and centrosymmetric P4/mbm space groups. For the intermediate phase, the structure is refined in the space group P4nc with doubling of the c unit cell parameter, which is compatible with an AFE phase. This result was confirmed by Raman spectroscopy since new low-frequency lines are activated in the AFE phase due to the Brillouin zone-folding effect, typical for the modulated phases. The presence of the AFE phase between the FE and PE phases and the complex nature of tetragonal tungsten bronze crystal structure can explain the large thermal hysteresis observed at the FE-AFE transition between heating and cooling cycle and the strong depression of the Curie-Weiss temperature T0. The semi-phenomenological Ising-like model based on the obtained experimental data is proposed to account for the observed FE-AFE-PE transition sequence.
Gene Cloning, Purification, and Characterization of a Novel Peptidoglutaminase-Asparaginase from Aspergillus sojae (2012)

Glutaminase is an enzyme that catalyzes the hydrolysis of l-glutamine to l-glutamate, and it plays an important role in the production of fermented foods by enhancing the umami taste. By using the genome sequence and expressed sequence tag data available for Aspergillus oryzae RIB40, we cloned a novel glutaminase gene (AsgahA) from Aspergillus sojae, which was similar to a previously described gene encoding a salt-tolerant, thermostable glutaminase of Cryptococcus nodaensis (CnGahA). The structural gene was 1,929 bp in length without introns and encoded a glutaminase, AsGahA, which shared 36% identity with CnGahA. The introduction of multiple copies of AsgahA into A. oryzae RIB40 resulted in the overexpression of glutaminase activity. AsGahA was subsequently purified from the overexpressing transformant and characterized. While AsGahA was located at the cell surface in submerged culture, it was secreted extracellularly in solid-state culture. The molecular mass of AsGahA was estimated to be 67 kDa and 135 kDa by SDS-PAGE and gel filtration chromatography, respectively, indicating that the native form of AsGahA was a dimer. The optimal pH of the enzyme was 9.5, and its optimal temperature was 50°C in sodium phosphate buffer (pH 7.0). Analysis of substrate specificity revealed that AsGahA deamidated not only free l-glutamine and l-asparagine but also C-terminal glutaminyl or asparaginyl residues in peptides. Collectively, our results indicate that AsGahA is a novel peptidoglutaminase-asparaginase. Moreover, this is the first report to describe the gene cloning and purification of a peptidoglutaminase-asparaginase.
Effect of cell cycle position on the survival of 9L cells treated with nitrosoureas that alkylate, cross-link, and carbamoylate. (1986)

The relationship between cell cycle position and cytotoxicity was studied in 9L rat brain tumor cells treated with nitrosoureas that, depending on their structures, can alkylate or alkylate and cross-link DNA and/or carbamoylate biomolecules. Because pure populations of G1-, S-, and G2-M-phase cells could not be obtained with the centrifugal elutriation methods used, drug sensitivity of cells in each phase of the cell cycle was estimated using a mathematical model that accounts for variation in enrichment of elutriated fractions. 1,3-Bis(2-chloroethyl)-1-nitrosourea, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea, 1-(2-chloroethyl)-3-(trans-4-methylcyclohexyl)-1-nitrosourea, 1-(2-chloroethyl)-3-(2,6-dioxo-3-piperidyl)-1-nitrosourea, which alkylate and cross-link DNA and carbamoylate biomolecules, and 2-[3-(2-chloroethyl)-3-nitrosoureido]-D-glucopyranose (chlorozotocin), which alkylates and cross-links DNA but cannot carbamoylate biomolecules, killed more cells in G1 and G2-M phases than in S phase. N-Ethylnitrosourea, which alkylates and carbamoylates but does not form DNA interstrand cross-links, was more toxic to cells in S phase than in other phases. Cell kill caused by N,N'-bis(trans-4-hydroxycyclohexyl)-N-nitrosourea, a compound that carbamoylates only, increased progressively through the cell cycle from G1 to M. Nitrosoureas that cross-link DNA were more cytotoxic than nitrosoureas that do not cross-link DNA, although the latter had phase specificity. The results suggest that the increased sensitivity of G1- and G2-M-phase cells to chloroethylnitrosoureas is related to the formation of DNA interstrand cross-links.
An Expanding Role for Environmental Microbes in Shaping the Immune Response to Infection with Mycobacterium tuberculosis (2017)

identify aberrancy of coagulation in patients with bleeding or thrombotic events on ECMO.Northrop and colleagues demonstrated that ECMO patients experienced fewer bleeding events, less exposure to blood products, and increased circuit life after implementation of a comprehensive anticoagulation laboratory protocol that included thromboelastography, stratified in accordance with patient stability and heparin dose (11).This excellent prospective study by Dalton and colleagues adds to our understanding of the frequency and timing of bleeding and thrombotic complications and their associations with clinically important outcomes from ECMO in pediatric patients.With the establishment of a study group, the stage is now set for investigating whether bleeding and thrombotic-associated outcomes are alterable with standardized anticoagulation and patient care practices.Future studies must address the innumerable challenges around coagulation, anticoagulation, and blood-circuit interface in a diverse and increasingly complex population of ECMO patients (12).
Autonomous wideband mechanical energy harvester (2012)

The aim of this work is to demonstrate, by theory and experiment, the feasibility of a mechanical energy harvester able to operate with a high efficiency over a wide vibration frequency band. Herein this work we propose a new method for adjusting the resonant frequency of a mechanical harvester, based on piezoelectric material. The idea is to use the dependence that exists between piezoelectric material stiffness and the electric load coupled with. Hence, piezoelectric stiffness can be controlled by controlling the electric load. We present the model of our system and then the main experimental results that validate the principle for resonant frequency tuning. Finally, we present the low power consumption electronic developed to automatically adjust the vibration frequency in order to maximize, in real time, the output power.
Fluid dynamics and mass transport in organic vapor jet printing (2012)

Organic vapor jet printing (OVJP) is a high-resolution mask and solvent-free organic thin film deposition and patterning technique. In this work, we analyze factors that affect the material deposition rate and the dynamics of gas flow through an OVJP print head consisting of an array of micron-sized nozzles. Scaling laws governing carrier gas flow dynamics through a system of microchannels and nozzles are developed. From these laws, we predict the deposition rate and doping ratio of organic material as a function of carrier gas flow. The analysis is applied to an experimental print head, and is compared to results obtained via a more complex, direct simulation Monte Carlo model. The print head is used to grow efficient green phosphorescent organic light emitting diodes having an external quantum efficiency and luminance comparable to analogous devices grown by vacuum thermal evaporation.
Chemical Constituents from Croton insularis. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
A Novel Delay Fault Testing Methodology Using On-Chip Low-Overhead Delay Measurement Hardware at Strategic Probe Points (2005)

We propose a delay fault testing methodology using on-chip delay measurement hardware. We have designed a process-tolerant, low-overhead delay measurement hardware and developed an algorithm to judiciously insert the hardware at internal nodes of logic blocks. Experimental results for a set of ISCAS89 benchmarks show up to 16.9% improvement in transition fault coverage and up to 10.5% increase in the number of detected faults for segment delay fault model, with fixed test length. The reduction in test length is up to 59% for transition fault, with fixed target coverage. The delay and area overhead due to additional DFT logic is limited to 2% and 4% respectively.
Near-field Photochemical Imaging of Noble Metal Nanoobjects using an azodye polymer (2005)

International audience
Realizing the Heteromorphic Superlattice: Repeated Heterolayers of Amorphous Insulator and Polycrystalline Semiconductor with Minimal Interface Defects (2023)

An unconventional "heteromorphic" superlattice (HSL) is realized, comprised of repeated layers of different materials with differing morphologies: semiconducting pc-In<sub>2</sub> O<sub>3</sub> layers interleaved with insulating a-MoO<sub>3</sub> layers. Originally proposed by Tsu in 1989, yet never fully realized, the high quality of the HSL heterostructure demonstrated here validates the intuition of Tsu, whereby the flexibility of the bond angle in the amorphous phase and the passivation effect of the oxide at interfacial bonds serve to create smooth, high-mobility interfaces. The alternating amorphous layers prevent strain accumulation in the polycrystalline layers while suppressing defect propagation across the HSL. For the HSL with 7:7 nm layer thickness, the observed electron mobility of 71 cm<sup>2</sup> Vs<sup>-1</sup> , matches that of the highest quality In<sub>2</sub> O<sub>3</sub> thin films. The atomic structure and electronic properties of crystalline In<sub>2</sub> O<sub>3</sub> /amorphous MoO<sub>3</sub> interfaces are verified using ab-initio molecular dynamics simulations and hybrid functional calculations. This work generalizes the superlattice concept to an entirely new paradigm of morphological combinations.
Chemical Modification of the M1Agonist VU0364572 Reveals Molecular Switches in Pharmacology and a Bitopic Binding Mode (2012)

We previously reported the discovery of VU0364572 and VU0357017 as M(1)-selective agonists that appear to activate M(1) through actions at an allosteric site. Previous studies have revealed that chemical scaffolds for many allosteric modulators contain molecular switches that allow discovery of allosteric antagonists and allosteric agonists or positive allosteric modulators (PAMs) based on a single chemical scaffold. Based on this, we initiated a series of studies to develop selective M(1) allosteric antagonists based on the VU0364572 scaffold. Interestingly, two lead antagonists identified in this series, VU0409774 and VU0409775, inhibited ACh-induced Ca(2+) responses at rat M(1-5) receptor subtypes, suggesting they are nonselective muscarinic antagonists. VU0409774 and VU0409775 also completely displaced binding of the nonselective radioligand [(3)H]-NMS at M(1) and M(3) mAChRs with affinities similar to their functional IC(50) values. Finally, Schild analysis revealed that these compounds inhibit M(1) responses through a fully competitive interaction at the orthosteric binding site. This surprising finding prompted further studies to determine whether agonist activity of VU0364572 and VU0357017 may also engage in previously unappreciated actions at the orthosteric site on M(1). Surprisingly, both VU0364572 and VU0357017 completely displaced [(3)H]-NMS binding to the orthosteric site of M(1)-M(5) receptors at high concentrations. Furthermore, evaluation of agonist activity in systems with varying levels of receptor reserve and Furchgott analysis using a cell line expressing M(1) under control of an inducible promotor was consistent with an action of these compounds as weak orthosteric partial agonists of M(1). However, consistent with previous studies suggesting actions at a site that is distinct from the orthosteric binding site, VU0364572 or VU0357017 slowed the rate of [(3)H]-NMS dissociation from CHO-rM(1) membranes. Together, these results suggest that VU0364572 and VU0357017 act as bitopic ligands and that novel antagonists in this series act as competitive orthosteric site antagonists.
Abstract 14623: "Estrogen Prevents Aortic Calcification by inducing MGP Expression and Inhibiting BMP Expression in an Estrogen Receptor alpha Dependent Way (2010)

Background: Unopposed RANKL (receptor activator of NFkB ligand) activation causes osteoporosis and vascular calcification in mice, and both phenotypes coincide in women with estrogen deficiency. RA...
Characterization of the biochemical and structural phenotypes of four CYP1B1 mutations observed in individuals with primary congenital glaucoma (2008)

Consistent with the hypothesis, these PCG-related mutations cause identifiable structural changes negatively impacting CYP1B1 biochemistry and stability.
Computational optical sensing and imaging: introduction to the feature issue (2008)

This Applied Optics feature issue on Computational Optical Sensing and Imaging (COSI) highlights papers presented at the COSI 2007 Topical Meeting sponsored by the Optical Society of America. © 2008 Optical Society of America.