gebhart/patrepeval huggingface dataset:
ValidNESs: a database of validated leucine-rich nuclear export signals (2012)

ValidNESs (http://validness.ym.edu.tw/) is a new database for experimentally validated leucine-rich nuclear export signal (NES)-containing proteins. The therapeutic potential of the chromosomal region maintenance 1 (CRM1)-mediated nuclear export pathway and disease relevance of its cargo proteins has gained recognition in recent years. Unfortunately, only about one-third of known CRM1 cargo proteins are accessible in a single database since the last compilation in 2003. CRM1 cargo proteins are often recognized by a classical NES (leucine-rich NES), but this signal is notoriously difficult to predict from sequence alone. Fortunately, a recently developed prediction method, NESsential, is able to identify good candidates in some cases, enabling valuable hints to be gained by in silico prediction, but until now it has not been available through a web interface. We present ValidNESs, an integrated, up-to-date database holding 221 NES-containing proteins, combined with a web interface to prediction by NESsential.
Structural features that make oligopeptides susceptible substrates for hydrolysis by recombinant thimet oligopeptidase (1997)

A systematic analysis of the peptide sequences and lengths of several homologues of bioactive peptides and of a number of quenched-fluorescence (qf) opioid- and bradykinin-related peptides was performed to determine the main features leading the oligopeptides to hydrolysis by the recombinant rat testis thimet oligopeptidase (EC 3.4.24.15). The results indicate that a minimum substrate length of six amino acids is required and that among the oligopeptides six to thirteen amino acid residues long, their susceptibility as substrates is highly variable. Thimet oligopeptidase was able to hydrolyse, with similar catalytic efficiency, peptide bonds having hydrophobic or hydrophilic amino acids as well as proline in the P1 position of peptides, ranging from a minimum of six to a maximum of approximately thirteen amino acid residues. An intriguing observation was the shift of the cleavage site, at a Leu-Arg bond in qf dynorphin-(2-8) [qf-Dyn2-8; Abz-GGFLRRV-EDDnp, where Abz stands for o-aminobenzoyl and EDDnp for N-(2,4-dinitrophenyl)ethylenediamine], to Arg-Arg in qf-Dyn2-8Q, in which Gln was substituted for Val at its C-terminus. Similarly, a cleavage site displacement was also observed with the hydrolysis of the internally quenched-fluorescence bradykinin analogues containing Gln at the C-terminal position, namely Abz-RPPGFSPFR-EDDnp and Abz-GFSPFR-EDDnp are cleaved at the Phe-Ser bond, but Abz-RPPGFSPFRQ-EDDnp and Abz-GFSPFRQ-EDDnp are cleaved at the Pro-Phe bond.
UAV Base Station Location Optimization for Next Generation Wireless Networks: Overview and Future Research Directions (2019)

Unmanned aerial vehicles mounted base stations (UAV-BSs) are expected to become one of the significant components of the Next Generation Wireless Networks (NGWNs). Rapid deployment, mobility, higher chances of unobstructed propagation path, and flexibility features of UAV-BSs have attracted significant attention. Despite, potentially, high gains brought by UAV-BSs in NGWNs, many challenges are also introduced by them. Optimal location assignment to UAV-BSs, arguably, is the most widely investigated problem in the literature on UAV-BSs in NGWNs. This paper presents a comprehensive survey of the literature on the location optimization of UAV-BSs in NGWNs. A generic optimization framework through a universal Mixed Integer Non-Linear Programming (MINLP) formulation is constructed and the specifications of its constituents are elaborated. The generic problem is classified into a novel taxonomy. Due to the highly challenging nature of the optimization problem a range of solutions are adopted in the literature which are also covered under the aforementioned classification. Furthermore, future research directions on UAV-BS location optimization in 5G and beyond non-terrestrial aerial communication systems are discussed.
COMBINATION THERAPY WITH B7-H4 AND CTLA-4.IG PROLONGS ISLET ALLOGRAFT SURVIVAL (2010)

Transplantation is published monthly and is the most cited and influential journal in the field, with more than 25,000 citations per year. The journal celebrated its 50th year in 2016. Transplantation has been the trusted source for extensive and timely coverage of the most important advances in transplantation. The Editors and Editorial Board are an international group of research and clinical leaders that includes many pioneers of the field, representing a diverse range of areas of expertise. This capable editorial team provides thoughtful and thorough peer review, and delivers rapid, careful and insightful editorial evaluation of all manuscripts submitted to the journal.
Mutational analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase reveals essential contributions of the N-terminal peptide that closes over the active site (2008)

RNA guanine-N7 methyltransferase catalyzes the third step of eukaryal mRNA capping, the transfer of a methyl group from AdoMet to GpppRNA to form m(7)GpppRNA. Mutational and crystallographic analyses of cellular and poxvirus cap methyltransferases have yielded a coherent picture of a conserved active site and determinants of substrate specificity. Models of the Michaelis complex suggest a direct in-line mechanism of methyl transfer. Because no protein contacts to the guanine-N7 nucleophile, the AdoMet methyl carbon (Cepsilon) or the AdoHcy sulfur (Sdelta) leaving group were observed in ligand-bound structures of cellular cap methyltransferase, it was initially thought that the enzyme facilitates catalysis by optimizing proximity and geometry of the donor and acceptor. However, the structure of AdoHcy-bound vaccinia virus cap methyltransferase revealed the presence of an N-terminal "lid peptide" that closes over the active site and makes multiple contacts with the substrates, including the AdoMet sulfonium. This segment is disordered in the vaccinia apoenzyme and is not visible in the available structures of cellular cap methyltransferase. Here, we conducted a mutational analysis of the vaccinia virus lid peptide ((545)DKFRLNPEVSYFTNKRTRG(563)) entailing in vivo and in vitro readouts of the effects of alanine and conservative substitutions. We thereby identified essential functional groups that interact with the AdoMet sulfonium (Tyr555, Phe556), the AdoMet adenine (Asn550), and the cap triphosphate bridge (Arg560, Arg562). The results suggest that van der Waals contacts of Tyr555 and Phe556 to the AdoMet Sdelta and C epsilon atoms, and the electron-rich environment around the sulfonium, serve to stabilize the transition state of the transmethylation reaction.
Highlighting the potential of aptamer-based strategy to treat EGFRvIII-positive glioblastoma (2016)

Epidermal growth factor receptor variant III (EGFRvIII) is the most common EGFR mutant found in glioblastoma (GBM). Due to a truncation of large portion of the extracellular region, EGFRvIII  is unable to bind any ligand and constitutively signals to downstream effector molecules. It is tumor-specific, highly oncogenic and usually co-expressed with EGFR wild type (EGFRwt). EGFR tyrosine kinase inhibitors (TKIs) have proven ineffective in GBM and different mechanisms account for the occurrence of resistance to such inhibitors. Among these, EGFR TKIs induce a  switch to platelet-derived growth factor receptor β (PDGFRβ) expression and signaling, thus rendering the tumors addicted to such receptor for continued growth and resistance to treatment. In our recent investigation, we showed the ability of a nuclease-resistant RNA aptamer, named CL4, to bind and inhibit EGFRvIII thus hampering proliferation, migration and invasion of EGFRvIII-positive GBM cells. Importantly, both CL4 and EGFR TKIs cooperate with a previously validated anti-PDGFRβ aptamer in inhibiting cell growth. Here, we highlight the potential of the EGFRvIII aptamer to hamper the EGFRvIII functional interplay with other receptor tyrosine kinases (RTKs) and cell surface proteins responsible for GBM development and progression. The utility of CL4 as targeting ligand for drug-delivery approaches is also discussed. Overall, aptamer-based molecules have significant implications for managing GBM in the near future.
Contents, Vol. 83, 1987 (1987)

dosage and for added warnings and precau tions.This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Building semiconductor structures in optical fiber (2006)

Fabrication of semiconductor devices inside microstructured optical fiber may lead to all-fiber optoelectronics. In addition, the pervasive nature of electronics and optoelectronics technology based on silicon, GaAs and other crystalline semiconductors is familiar to almost all scientists and engineers...\n&amp;amp;more...
Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points? (2007)

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.
Gate Sizing for Constrained Delay/Power/Area (1997)

Gate sizing has a significant impact on the delay, power dissipation, and area of the final circuit. It consists of choosing for each node of a mapped circuit a gate implementation in the library so that a cost function is optimized under some constraints. For instance, one wants to minimize the power consumption and/or the area of a circuit under some user-defined delay constraints, or to obtain the fastest circuit within a given power budget. Although this technology-dependent optimization has been investigated for years, the proposed approaches some- times rely on assumptions, cost models, or algorithms that make them unrealistic or impossible to apply on real-life large circuits. We discusse here a gate sizing algorithm (GS), and show how it is used to achieve constrained optimization. It can be applied on large circuits within a reasonable CPU time, e.g., minimizing the power of a 10 000 gates circuit under some delay constraint in 2 h.
Theoretical and experimental studies of a surface acoustic wave flow sensor (2012)

A novel SAW flow sensor is proposed based on pressure measurement. The relationship between the flow rate and the pressure difference along the flow path is evaluated. The results show a linear relationship between the flow rate and pressure difference, which agrees with the past research results. Strain analysis and FEM simulation show that phase delay depends linearly on the flow rate passing the SAW sensor, whereas SAW frequency decreases linearly upon the increase of flow rate. Phase delay experiment results agree with analysis and simulation, and the frequency change falls in a reasonable range around the predicted curve.
Catalytically active lubricants (2023)

Provided herein are lubricant compositions and methods of using the same. These lubricant compositions are useful for providing improved anti-friction and anti-wear properties.
Low Electron Effective Masses and Energy Gap inCdxHg1−xTe (1961)

Received 10 November 1961DOI:https://doi.org/10.1103/PhysRevLett.7.403©1961 American Physical Society
Biphasic Effects of the Natural Estrogen 17β-Estradiol on Hepatic Cholesterol Metabolism in Intact Female Rats (2000)

The protective influence of estrogens in cardiovascular disease is believed to be partly due to beneficial effects on cholesterol metabolism. Much of the experimental data are based on models in which synthetic estrogens have been used in pharmacological doses, and therefore, the physiological role of estrogens in cholesterol metabolism is uncertain. To evaluate this important issue, we performed experiments in intact female rats with use of the natural estrogen 17beta-estradiol (E2) administered either subcutaneously or orally. After physiological doses of E2 (< or =0.04 mg. kg(-1). d(-1)) were administered, plasma levels of high density lipoprotein (HDL) cholesterol and apolipoprotein (apo) A-I were increased. In the liver, 3-hydroxy-3-methylglutaryl coenzyme A reductase and cholesterol 7alpha-hydroxylase activities were increased, as well as cholesterol 7alpha-hydroxylase mRNA levels. These effects were abolished during treatment with higher doses of E2, whereas apo A-I mRNA increased in a dose-dependent way. After treatment with pharmacological doses of E2 (> or =0.2 mg. kg(-1). d(-1)), the number of hepatic low density lipoprotein receptors increased and plasma cholesterol was reduced. These effects were similar after both oral and subcutaneous administration of E2. Our results show that the responses to E2 are biphasic: plasma HDL, apo A-I, and hepatic enzyme activities governing bile acid and cholesterol synthesis increased only at physiological doses of E2. At pharmacological doses of E2, hepatic low density lipoprotein receptors are stimulated and plasma cholesterol is reduced. Therefore, under physiological conditions, E2 exerts its major effects on hepatic cholesterol metabolism through mechanisms other than stimulation of low density lipoprotein receptor expression.
Auralization of Tonal Rotor Noise Components of a Quadcopter Flyover (2015)

The capabilities offered by small unmanned vertical lift aerial vehicles, for example, quadcopters, continue to captivate entrepreneurs across the private, public, and civil sectors. As this industry rapidly expands, the public will be exposed to these devices (and to the noise these devices generate) with increasing frequency and proximity. Accordingly, an assessment of the human response to these machines will be needed shortly by decision makers in many facets of this burgeoning industry, from hardware manufacturers all the way to government regulators. One factor of this response is that of the annoyance to the noise that is generated by these devices. This paper presents work currently being pursued by NASA toward this goal. First, physics-based (CFD) predictions are performed on a single isolated rotor typical of these devices. The result of these predictions are time records of the discrete tonal components of the rotor noise. These time records are calculated for a number of points that appear on a lattice of locations spread over the lower hemisphere of the rotor. The source noise is then generated by interpolating between these time records. The sound from four rotors are combined and simulated-propagation techniques are used to produce complete flyover auralizations.
Metal–Metal Electronic Coupling in syn and anti Stereoisomers of Mixed‐Valent (FeCp)2‐, (RhL2)2‐, and (FeCp)(RhL2)‐as‐Indacenediide Ions (2007)

The extent of metal-metal electronic coupling was quantified for a series of syn and anti stereoisomers of (FeCp)(2)-, (RhL(2))(2)- and (FeCp)(RhL(2))- (L(2)=1,5-cyclooctadiene (cod), L=CO) as-indacenediide mixed-valent ions by spectroelectrochemical and DFT studies. The effect of the syn/anti orientation of the metal units with respect to the planar aromatic ligand indicates that electron transfer occurs through the bridge rather than through space. The nature of the metal was found to be crucial: while homobimetallic diiron species are localised valence-trapped ions (Class II), the dirhodium analogues are almost delocalised mixed-valent ions (borderline and Class III). Finally, despite their redox asymmetry, even in the heterobimetallic iron-rhodium as-indacenediide complexes, strong metal-metal coupling is present. In fact, oxidation of the iron centre is accompanied by electron transfer from rhodium to iron and formation of a reactive 17-electron rhodium site. syn and anti Fe-Rh as-indacenediide complexes are rare examples of heterobimetallic systems which can be classified as borderline Class II/Class III species.
Multiple model moving horizon estimation approach to prognostics in coupled systems (2011)

The key objectives of this paper are to analyze and implement a novel moving horizon model predictive estimation scheme based on constrained nonlinear optimization techniques for inferring the survival functions and residual useful life (RUL) of components in coupled systems. The approach employs a data-driven prognostics framework that combines failure time data, static and dynamic (time-series) parametric data, and the Multiple Model Moving Horizon Estimation (MM-MHE) algorithm for predicting the survival functions of components based on their usage profiles. Validation of the approach has been provided based on data from an electronic throttle control (ETC) system. The proposed prognostic approach is modular and has the potential to be applicable to a wide variety of systems, ranging from automobiles to aerospace.
Optical parametric oscillators for medical applications (1996)

In recent years optical parametric oscillators (OPOs) have undergone a renaissance largely due to the discovery of new nonlinear materials capable of wide continuous tuning ranges spanning from the UV to the near-infrared spectral regions. To date, however, OPOs have not been exploited in the medical field despite their advantages over the dye laser in terms of tuning range and solid state structure. We consider the development of an OPO based on barium borate (BBO) which can be tailored to suit applications in medicine. Converting the maximum number of pump photons to tunable signal and idler photons is of great importance to secure high-fluence radiation necessary for many treatments. With this in mind, we report on an all- solid-state system using BBO which has been optimized by computer modeling with the potential of delivering amplification factors of typically up to 20 over a continuous tuning range of 700 nm to 1000 nm. As an example of its biomedical application, we describe the selective excitation of biomolecules and chromophores for cell destruction using malachite green isothiocyanate labelled bacteria. The potential for development is reviewed towards other medical applications such as diagnostic sensing and phototherapy.
Distinct Neural Circuits for the Formation and Retrieval of Episodic Memories (2017)

The formation and retrieval of a memory is thought to be accomplished by activation and reactivation, respectively, of the memory-holding cells (engram cells) by a common set of neural circuits, but this hypothesis has not been established. The medial temporal-lobe system is essential for the formation and retrieval of episodic memory for which individual hippocampal subfields and entorhinal cortex layers contribute by carrying out specific functions. One subfield whose function is poorly known is the subiculum. Here, we show that dorsal subiculum and the circuit, CA1 to dorsal subiculum to medial entorhinal cortex layer 5, play a crucial role selectively in the retrieval of episodic memories. Conversely, the direct CA1 to medial entorhinal cortex layer 5 circuit is essential specifically for memory formation. Our data suggest that the subiculum-containing detour loop is dedicated to meet the requirements associated with recall such as rapid memory updating and retrieval-driven instinctive fear responses.
Supports of Extremal Doubly and Triply Stochastic Measures - Master's Project (2007)

c○2007 by Nathan Killoran. Doubly stochastic measures are Borel probability measures on the unit square which push forward via the canonical projections to Lebesgue measure on each axis. The set of doubly stochastic measures is convex, so its extreme points are of particular interest. I review necessary and sufficient conditions for a set to support an extremal doubly stochastic measure, and include a proof that such a set can be decomposed into a countable collection of graphs and antigraphs of functions, called a ‘limb-numbering system. ’ I also investigate how this structure partially generalizes to triply stochastic measures on the unit cube. A doubly stochastic matrix is a real matrix whose entries are positive and whose rows and columns individually sum to one. A classical theorem first due to Birkhoff [1], but also attributed to von Neumann [2], states that the set of doubly stochastic matrices is the convex hull of the set of n × n permutation matrices.
Comparing methods to extract technical content for technological intelligence (2012)

We are developing indicators for the emergence of science and technology (S&T) topics. We are targeting various S&T information resources, including metadata (i.e., bibliographic information) and full text. We explore alternative text analysis approaches - principal components analysis (PCA) and topic modeling - to extract technical topic information. We analyze the topical content to pursue potential applications and innovation pathways. In this presentation we compare alternative ways of consolidating messy sets of key terms [e.g., using Natural Language Processing (NLP) on abstracts and titles, together with various keyword sets]. Our process includes combinations of stopword removal, fuzzy term matching, association rules, and tf-idf weighting. We compare PCA results to topic modeling results. Our key test set consists of 4104 Web of Science records on Dye-Sensitized Solar Cells (DSSCs). Results suggest good potential to enhance our technical intelligence payoffs from database searches on topics of interest.
Automatic Ontology Matching via Upper Ontologies: A Systematic Evaluation (2009)

“Ontology matching” is the process of finding correspondences between entities belonging to different ontologies. This paper describes a set of algorithms that exploit upper ontologies as semantic bridges in the ontology matching process and presents a systematic analysis of the relationships among features of matched ontologies (number of simple and composite concepts, stems, concepts at the top level, common English suffixes and prefixes, and ontology depth), matching algorithms, used upper ontologies, and experiment results. This analysis allowed us to state under which circumstances the exploitation of upper ontologies gives significant advantages with respect to traditional approaches that do no use them. We run experiments with SUMO-OWL (a restricted version of SUMO), OpenCyc, and DOLCE. The experiments demonstrate that when our “structural matching method via upper ontology” uses an upper ontology large enough (OpenCyc, SUMO-OWL), the recall is significantly improved while preserving the precision obtained without upper ontologies. Instead, our “nonstructural matching method” via OpenCyc and SUMO-OWL improves the precision and maintains the recall. The “mixed method” that combines the results of structural alignment without using upper ontologies and structural alignment via upper ontologies improves the recall and maintains the F-measure independently of the used upper ontology.
1946-1996 : Cinquante ans de départementalisation outre-mer (1997)

Ensemble de contributions coordonnées visant à une évaluation systématique du processus de départementalisation outre-mer. Trois angles d'analyse sont privilégiées: les politiques publiques (économie, éducation, action sociale, santé publique, migration), la vie politique (acteurs, enjeux et règles) et les conflits idéologiques et de représentation identitaire (cadres anthropologiques d'expression identitaire, patrimonialisme, concuurences Etat/autorités locales).