gebhart/patrepeval huggingface dataset:
Controlling the bunch of filaments formed by high-power femtosecond laser pulse in air (2005)

We have shown that control of stochastic multiple filamentation may be performed with either large - scale spatial modifications of the beam, such as squeezing the whole beam, or relatively small-scale periodic light field perturbations introduced into the transverse beam distribution. We have found that the average conversion efficiency to the supercontinuum grows according to the similar law in both small beam and large beam cases, starting from the point of the parent filament formation. Stability of the supercontinuum signal grows essentially with decreasing initial beam size. Periodic intensity and phase perturbations are used to control stochastic filamentation arising in atmospheric turbulence. Regular phase fluctuations are introduced into the beam in the form of a lens array. With decreasing array period the spatial arrangement is attained earlier in the propagation distance. In addition, the amplitude of multiple filaments has smaller fluctuations relatively to the propagation in the regular medium. In the case of periodic intensity perturbations, control of stochastic filaments is more pronounced as compared with the phase perturbations of the same period. However, introduction of amplitude perturbations leads to the energy loss from the initial pulse.
Multitask Machine Learning of Collective Variables for Enhanced Sampling of Rare Events (2022)

Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to learn collective variables with a multitask neural network, where a common upstream part reduces the high dimensionality of atomic configurations to a low dimensional latent space and separate downstream parts map the latent space to predictions of basin class labels and potential energies. The resulting latent space is shown to be an effective low-dimensional representation, capturing the reaction progress and guiding effective umbrella sampling to obtain accurate free energy landscapes. This approach is successfully applied to model systems including a 5D Müller Brown model, a 5D three-well model, the alanine dipeptide in vacuum, and an Au(110) surface reconstruction unit reaction. It enables automated dimensionality reduction for energy controlled reactions in complex systems, offers a unified and data-efficient framework that can be trained with limited data, and outperforms single-task learning approaches, including autoencoders.
The dnaKJ operon of Agrobacterium tumefaciens: transcriptional analysis and evidence for a new heat shock promoter (1995)

The dnaKJ operon of Agrobacterium tumefaciens was cloned and sequenced and was found to be highly homologous to previously analyzed dnaKJ operons. Transcription of this operon in A. tumefaciens was stimulated by heat shock as well as by exposure to ethanol and hydrogen peroxide. There were two transcripts representing the dnaKJ operon: one containing the dnaK and dnaJ genes and the second containing only the dnaK gene. Primer extension analysis indicated that transcription started from the same site in heat-shocked cells and in untreated cells. The upstream regulatory region of the dnaKJ operon of A. tumefaciens does not contain the highly conserved inverted repeat sequence previously found in the groESL operon of this bacterium, as well as in many other groE and dnaK operons. Sequence analysis of the promoter region of several groESL and dnaK operons from alpha-purple proteobacteria indicates the existence of a putative promoter sequence different from the known consensus promoter sequences recognized by the Escherichia coli vegetative or heat shock sigma factor. This promoter may constitute the heat shock promoter of these alpha-purple proteobacteria.
Efficient Access to Azaindoles and Indoles (2006)

[Structure: see text] An expedient, catalytic method for the synthesis of diverse azaindoles and indoles, starting from readily available and inexpensive starting materials, is described. Conditions were developed for effective reductive alkylation of electron-deficient o-chloroarylamines, substrates previously viewed as poor partners in this reaction. The derived N-alkylated o-chloroarylamines were elaborated to N-alkylazaindoles and N-alkylindoles via a novel one-pot process comprising copper-free Sonogashira alkynylation and a base-mediated indolization reaction.
Abstract B144: NVP-BEZ235, a dual inhibitor of PI3K and mTOR, induces MAPK phosphorylation in HER2-positive cells (2009)

Abstract The PI3K pathway is highly deregulated in human cancer with the most common alterations being amplification of the receptor tyrosine kinases (RTKs) EGFR and HER2 and mutations in PI3K itself or inactivation of the tumor suppressor PTEN. Thus, the rationale exists to develop therapeutic agents targeting the PI3K/AKT pathway. Several small molecule inhibitors targeting PI3K, AKT and mTOR are now in clinical trials. However, these novel compounds may interfere with regulatory feedback loops. One such example involves the activation of AKT following rapamycin analogues treatment, such as everolimus, an allosteric mTOR inhibitor. Blocking mTOR signaling also alters the regulation of other signaling pathways, like the MAPK cascade. The aim of this study was to investigate the mechanism/s by which inhibition of the PI3K pathway leads to activation of MAPK kinase signaling in breast cancer cell lines and its relevance in tumor treatment. We have observed an increased MAPK phosphorylation in HER2 positive BT474, SKBR-3, MDA-361 and MCF-7HER2 cells when treated with NVP-BEZ235, a dual inhibitor of both mTOR and p110, the catalytic component of PI3K. The increase of P-MAPK was observed by western blot and correlated with hyperphosphorylation of several RTKs. PD325901, a MEK1/2 inhibitor, or lapatinib, a HER1/2 tyrosine kinase inhibitor, reverted the NVP-BEZ235-induced MAPK phosphorylation. On the other hand, NVP-AEW541, an IGFR-1 tyrosine kinase inhibitor, did not prevent NVP-BEZ235-dependent HER2 phosphorylation and downstream MAPK activation. Activation of MAPK upon administration of NVP-BEZ235 was also observed in vivo. We are currently investigating the possible involvement of known regulatory feedback loops as well as the individual RTK contribution. Activation of parallel pathways in a condition of PI3K inhibition may reduce potential benefits of these anti-cancer treatments. For this reason, we propose the combination of an anti-HER2 therapy together with PI3K inhibitors for the treatment of HER2 positive tumors. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B144.
Heterozygous mutation of cysteine528 in XPO1 is sufficient for resistance to selective inhibitors of nuclear export (2016)

Exportin-1 (CRM1/XPO1) is a crucial nuclear export protein that transports a wide variety of proteins from the nucleus to the cytoplasm. These cargo proteins include tumor suppressors and growth-regulatory factors and as such XPO1 is considered a potential anti-cancer target. From this perspective, inhibition of the XPO1-mediated nuclear export by selective inhibitor of nuclear export (SINE) compounds has shown broad-spectrum anti-cancer activity. Furthermore, the clinical candidate SINE, selinexor, is currently in multiple phase I/II/IIb trials for treatment of cancer. Resistance against selinexor has not yet been observed in the clinic, but in vitro selection of resistance did not reveal any mutations in the target protein, XPO1. However, introduction of a homozygous mutation at the drug's target site, the cysteine 528 residue inside the XPO1 cargo-binding pocket, by genetic engineering, confers resistance to selinexor. Here we investigated whether this resistance to selinexor is recessive or dominant. For this purpose we have engineered multiple leukemia cell lines containing heterozygous or homozygous C528S substitutions using CRISPR/Cas9-mediated genome editing. Our findings show that heterozygous mutation confers similar resistance against selinexor as homozygous substitution, demonstrating that SINE resistance can be obtained by a single and dominant mutation of the cysteine528 residue in XPO1.
The Effects of Wedged Footwear on Lower Limb Frontal Plane Biomechanics During Running (2012)

KAAIs are reduced with laterally wedged footwear because of lateral shifts in the center of pressure beneath the foot, which then increases ankle inversion moments and decreases peak knee abduction moments. Laterally wedged footwear may therefore offer greater relief to runners with PFPS than medially wedged footwear by reducing KAAIs.
Isolation of a cDNA Clone Coding for the γ-Subunit of Mouse Nerve Growth Factor Using a High-Stringency Selection Procedure (1984)

A new approach was taken to isolate a full-length cDNA encoding the gamma-subunit of nerve growth factor (NGF). An oligonucleotide probe was used first to identify kallikrein-related sequences in a cDNA library derived from male mouse submaxillary gland mRNA. Of 10,000 clones, 860 were identified as being kallikrein-related; these were analyzed further by hybridization to synthetic oligonucleotides using a procedure which eliminates the effects of base composition and thus allows distinction between partial and perfect sequence complementarity. Nine clones hybridized with a gamma-subunit-specific probe at high stringency, and the nucleotide sequence of the longest cDNA insert was determined. Regions of homology and variability within the kallikrein gene family are maintained in this protein and probably reflect the similar functions and different substrates for this family of proteins.
Origin, Current Status, and Future Perspectives of Chemical Cytometry (2010)

This chapter contains sections titled: The Cell and Cytometry Flow and Image Cytometry Chemical Cytometry Chemical Cytometry of DNA and mRNA Metabolic Cytometry Future Perspectives on Instrumentation for Chemical Cytometry Acknowledgments References
Actuation response of polyacrylate dielectric elastomers (2001)

Polyacrylate dielectric elastomers have yielded extremely large strain and elastic energy density suggesting that they are useful for many actuator applications. A thorough understanding of the physics underlying the mechanism of the observed response to an electric field can help develop improved actuators. The response is believed to be due to Maxwell stress, a second order dependence of the stress upon applied electric field. Based on this supposition, an equation relating the applied voltage to the measured force from an actuator was derived. Experimental data fit with the expected behavior, though there are discrepancies. Further analysis suggests that these arise mostly from imperfect manufacture of the actuators, though there is a small contribution from an explicitly electrostrictive behavior of the acrylic adhesive. Measurements of the dielectric constant of stretched polymer reveal that the dielectric constant drops, when the polymer is strained, indicating the existence of a small electrostrictive effect. Finally, measurements of the electric breakdown field were made. These also show a dependence upon the strain. In the unstrained state the breakdown field is 20 MV/m, which grows to 218MV/m at 500% x 500% strain. This large increase could prove to be of importance in actuator design.
Discriminative Machine Translation Using Global Lexical Selection (2009)

Statistical phrase-based machine translation models crucially rely on word alignments. The search for word-alignments assumes a model of word locality between source and target languages that is violated in starkly different word-order languages such as English-Hindi. In this article, we present models that decouple the steps of lexical selection and lexical reordering with the aim of minimizing the role of word-alignment in machine translation. Indian languages are morphologically rich and have relatively free-word order where the grammatical role of content words is largely determined by their case markers and not just by their positions in the sentence. Hence, lexical selection plays a far greater role than lexical reordering. For lexical selection, we investigate models that take the entire source sentence into account and evaluate their performance for English-Hindi translation in a tourism domain.
SUBTOTAL/PARTIAL GLAND PROSTATE CRYOABLATION: RESULTS OF 341 PATIENTS FROM MULTIPLE CENTERS TRACKED WITH THE COLD REGISTRY (2008)

You have accessJournal of Urology1 Apr 2008SUBTOTAL/PARTIAL GLAND PROSTATE CRYOABLATION: RESULTS OF 341 PATIENTS FROM MULTIPLE CENTERS TRACKED WITH THE COLD REGISTRY David Ellis, J Stephen Jones, Louis L Pisters, Aaron E Katz, Stephen Scionti, Franco Lugnani, David M Jackson, and Martin Dineen David EllisDavid Ellis , J Stephen JonesJ Stephen Jones , Louis L PistersLouis L Pisters , Aaron E KatzAaron E Katz , Stephen SciontiStephen Scionti , Franco LugnaniFranco Lugnani , David M JacksonDavid M Jackson , and Martin DineenMartin Dineen View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)61162-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "SUBTOTAL/PARTIAL GLAND PROSTATE CRYOABLATION: RESULTS OF 341 PATIENTS FROM MULTIPLE CENTERS TRACKED WITH THE COLD REGISTRY." The Journal of Urology, 179(4S), p. 397 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 397 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information David Ellis More articles by this author J Stephen Jones More articles by this author Louis L Pisters More articles by this author Aaron E Katz More articles by this author Stephen Scionti More articles by this author Franco Lugnani More articles by this author David M Jackson More articles by this author Martin Dineen More articles by this author Expand All Advertisement PDF downloadLoading ...
Alga-Produced Malaria Transmission-Blocking Vaccine Candidate Pfs25 Formulated with a Human Use-Compatible Potent Adjuvant Induces High-Affinity Antibodies That Block Plasmodium falciparum Infection of Mosquitoes (2015)

A vaccine to prevent the transmission of malaria parasites from infected humans to mosquitoes is an important component for the elimination of malaria in the 21st century, yet it remains neglected as a priority of malaria vaccine development. The lead candidate for Plasmodium falciparum transmission-blocking vaccine development, Pfs25, is a sexual stage surface protein that has been produced for vaccine testing in a variety of heterologous expression systems. Any realistic malaria vaccine will need to optimize proper folding balanced against cost of production, yield, and potentially reactogenic contaminants. Here Chlamydomonas reinhardtii microalga-produced recombinant Pfs25 protein was formulated with four different human-compatible adjuvants (alum, Toll-like receptor 4 [TLR-4] agonist glucopyranosal lipid A [GLA] plus alum, squalene-oil-in-water emulsion, and GLA plus squalene-oil-in-water emulsion) and compared for their ability to induce malaria transmission-blocking antibodies. Alga-produced recombinant Pfs25 plus GLA plus squalene-oil-in-water adjuvant induced the highest titer and avidity in IgG antibodies, measured using alga-produced recombinant Pfs25 as the enzyme-linked immunosorbent assay (ELISA) antigen. These antibodies specifically reacted with the surface of P. falciparum macrogametes and zygotes and effectively prevented parasites from developing within the mosquito vector in standard membrane feeding assays. Alga-produced Pfs25 in combination with a human-compatible adjuvant composed of a TLR-4 agonist in a squalene-oil-in-water emulsion is an attractive new vaccine candidate that merits head-to-head comparison with other modalities of vaccine production and administration.
Detection of pneumococci in the upper respiratory tract: comparison of media and culture techniques (1982)

A survey for carriers of Streptococcus pneumoniae among 573 children was undertaken. Throat and nasopharyngeal cultures from 303 children disclosed pneumococci in 89 (29.4%) nasopharyngeal swabs but in only 8 (2.6%) throat specimens. Carriers of pneumococci were detected with frequencies of 84.4 and 79.9% on aerobically incubated 5% horse blood agar with a 5-micrograms optochin disk and on 5% horse blood agar with 5 mg of gentamicin per liter, respectively. Anaerobically incubated 5% horse blood agar yield pneumococci from 78.2% of 179 carriers. We consider the examination of nasopharyngeal secretions for optochin-susceptible alpha-hemolytic bacteria to be the most sensitive and convenient means for detecting carriers of pneumococci.
Increasing awareness and improving the care of urinary incontinence: highlights from the world health organization 2nd international consultation on incontinence july 1-4, 2001, paris, france. (2003)

In July of 2001, some of the world’s leading urologists and urogynecologists gathered in Paris for the Second International Consultation on Incontinence. The World Health Organization (WHO) organized this meeting. In the summer of 1998, the group first met in Monaco to increase awareness and improve the care of urinary incontinence worldwide.1 At that meeting, committees were formed to assess relevant information on various aspects of urinary incontinence, including epidemiology and voiding dysfunction in the elderly, and to develop guidelines based on these assessments. Also, the first consultation pledged to define strategies in both education and research.2 The principal task of the second consultation was to build on the work of the first consultation and further develop management plans for incontinence. What follows is a discussion of some of the outstanding presentations highlighted at the WHO meeting.
Fractional deviations in precursor stoichiometry dictate the properties, performance and stability of perovskite photovoltaic devices (2018)

The last five years have witnessed remarkable progress in the field of lead halide perovskite materials and devices. Examining the existing body of literature reveals staggering inconsistencies in the reported results among different research groups with a particularly wide spread in the photovoltaic performance and stability of devices. In this work we demonstrate that fractional, quite possibly unintentional, deviations in the precursor solution stoichiometry can cause significant changes in the properties of the perovskite layer as well as in the performance and stability of perovskite photovoltaic devices. We show that while the absorbance and morphology of the layers remain largely unaffected, the surface composition and energetics, crystallinity, emission efficiency, energetic disorder and storage stability are all very sensitive to the precise stoichiometry of the precursor solution. Our results elucidate the origin of the irreproducibility and inconsistencies of reported results among different groups as well as the wide spread in device performance even within individual studies. Finally, we propose a simple experimental method to identify the exact stoichiometry of the perovskite layer that researchers can employ to confirm their experiments are performed consistently without unintentional variations in precursor stoichiometry.
Characterization ofRhizobium tropiciClAT899 Nodulation Factors: The Role ofnodHandnodPQGenes in Their Sulfation (1996)

We have purified and characterized the nodulation factors produced by Rhizobium tropici CIAT899. This strain produces a large variety of nodulation factors, these being a mixture of sulfated or nonsulfated penta- or tetra-chito-oligosaccharides to which any of six different fatty acyl moieties may be attached to nitrogen of the nonreducing terminal residue. In this mixture we have also found methylated or nonmethylated lipo-chitin oligosaccharides. Here we describe a novel lipo-chitin-oligosaccharide consisting of a linear backbone of 4 N-acetylglucosamine residues and one mannose that is the reducing-terminal residue and bearing a C18:1 fatty acyl moiety on the nonreducing terminal residue. In addition, we have identified, cloned, and sequenced R. tropici nodH and nodPQ genes, generated mutations in the nodH and nodQ genes, and tested the mutant strains for nodulation in Phaseolus and Leucaena plants. Our results indicate that the sulfate group present in wild-type Nod factors plays a major role in nodulation of Leucaena plants by strain CIAT899 of R. tropici.
In-situ RBS for oxygen ion implantation systems (2002)

In-situ measurement of backscattered oxygen ions has been studied with the goal of providing real-time in-situ diagnostics of contamination levels during ion implantation. Heavy metal contamination caused by ion beam sputtering of beam defining apertures and beam line construction components is a significant concern for producing high quality SIMOX wafers. If present during implantation, these contaminants will concentrate near the implanted surface with decreasing concentrations down to the end-of-range of the implanted ions, Ultimately, these heavy metals will diffuse to the SOI interfaces and possibly degrade device performance. A 5 mm diameter (2 to 200 /spl mu/A) 65 KeV beam of oxygen ions, used to probe various elemental target materials, produced distinctive edges in the backscattered ion energy spectrum that was measured using an electrostatic analyzer and channeltron detector. Additional samples with thin metal films deposited on silicon substrates were measured showing excellent agreement between theoretical and measured spectra for both thickness and concentration. In this paper we present a description of the experimental apparatus along with the data and analysis. We also discuss the future implementation plans for an in-situ monitor for use in SIMOX implantation.
Quantum computing with antiferromagnetic spin clusters (2003)

We show that a wide range of spin clusters with antiferromagnetic intracluster exchange interaction allows one to define a qubit. For these spin cluster qubits, initialization, quantum gate operation, and readout are possible using the same techniques as for single spins. Quantum gate operation for the spin cluster qubit does not require control over the intracluster exchange interaction. Electric and magnetic fields necessary to effect quantum gates need only be controlled on the length scale of the spin cluster rather than the scale for a single spin. Here, we calculate the energy gap separating the logical qubit states from the next excited state and the matrix elements which determine quantum gate operation times. We discuss spin cluster qubits formed by one- and two-dimensional arrays of $s=1/2$ spins as well as clusters formed by spins $s&gt;1/2.$ We illustrate the advantages of spin cluster qubits for various suggested implementations of spin qubits and analyze the scaling of decoherence time with spin cluster size.
El picasso del nuevo milenio (1998)

Malaga entrara en el ano 2000 con un nuevo museo dedicado a Pablo Picasso. La donacion del legado de Christine Picasso, nuera del pintor, ha sido clave para la inauguracion de esta pinacoteca.
Parameterization for Remeshing Over Dynamically Changing Domains. (2006)

We present a method for incrementally maintaining a global, bijective mapping between an arbitrary triangular input mesh and a dynamically changing domain mesh by use of a meta-mesh. The domain mesh is derived from the input mesh through an arbitrary sequence of local mesh connectivity operations. The mapping can be maintained independent of the choice of metrics for driving the simplification process to derive the domain mesh. In addition, due to the dynamic nature of the mapping, user post-processing can be applied to adjust the final domains.