gebhart/patrepeval huggingface dataset:
Template-Based Monocular 3D Shape Recovery Using Laplacian Meshes (2015)

We show that by extending the Laplacian formalism, which was first introduced in the Graphics community to regularize 3D meshes, we can turn the monocular 3D shape reconstruction of a deformable surface given correspondences with a reference image into a much better-posed problem. This allows us to quickly and reliably eliminate outliers by simply solving a linear least squares problem. This yields an initial 3D shape estimate, which is not necessarily accurate, but whose 2D projections are. The initial shape is then refined by a constrained optimization problem to output the final surface reconstruction. Our approach allows us to reduce the dimensionality of the surface reconstruction problem without sacrificing accuracy, thus allowing for real-time implementations.
Homolytic Pathways Drive Peroxynitrite-Dependent Trolox C Oxidation (2004)

Peroxynitrite is a powerful oxidant implicated as a mediator in nitric oxide ((*)NO)- and superoxide (O(2)(*)(-))-dependent toxicity. Peroxynitrite homolyzes after (i) protonation, yielding hydroxyl ((*)OH) and nitrogen dioxide ((*)NO(2)) free radicals, and (ii) reaction with carbon dioxide (CO(2)), yielding carbonate radical anion (CO(3)(*)(-)) and (*)NO(2). Additionally, peroxynitrite reacts directly with several biomolecules. It is currently accepted that alpha-tocopherol is one important antioxidant in lipid compartments and its reactions with peroxynitrite or peroxynitrite-derived radicals may be relevant in vivo. Previous reports on the peroxynitrite reaction with Trolox C (TxOH)--an alpha-tocopherol water soluble analogue--suggested a direct and fast reaction. This was unexpected to us as judged from the known reactivities of peroxynitrite with other phenolic compounds; thus, we thoroughly investigated the kinetics and mechanism of the reaction of peroxynitrite with TxOH and its modulation by CO(2). Direct electron paramagnetic resonance studies revealed that Trolox C phenoxyl radical (TxO(*)) was the only paramagnetic species detected either in the absence or in the presence of CO(2). Stopped-flow spectrophotometry experiments revealed a sequential reaction mechanism, with the intermediacy of TxO(*) and the production of Trolox C quinone (TxQ). Reactions were zero-order with respect to TxOH and first-order in peroxynitrite and CO(2), demonstrating that the reaction of peroxynitrite with TxOH is indirect. In agreement, TxOH was unable to inhibit the direct peroxynitrite-mediated oxidation of methionine to methionine sulfoxide. TxOH oxidation yields to TxO(*) and TxQ with respect to peroxynitrite were approximately 60 and approximately 31%, respectively, and increased to approximately 73 and approximately 40%, respectively, in the presence of CO(2). At peroxynitrite excess over TxOH, the kinetics and mechanism of oxidation are more complex and involve the reactions of CO(3)(*)(-) with TxO(*) and the possible intermediacy of unstable NO(2)-TxOH adducts. Taken together, our results strongly support that H(+)- or CO(2)-catalyzed homolysis of peroxynitrite is required to cause TxOH, and hence, alpha-tocopherol oxidation.
Outside Back Cover: Multipronged functional proteomics approaches for global identification of altered cell signalling pathways in B‐cell chronic lymphocytic leukaemia (2016)

DOI: 10.1002/pmic.201500372 The characterization of Chronic Lymphocytic Leukaemia (CLL) at genomic level has been performed throughout the last decades providing a broad knowledge of the disease. Nevertheless, studies concerning proteins have been limited in this cancer. Thus, the use of affinity (antibody microarrays) and MS/MS proteomic strategies has allowed the establishment of preliminary proteomic profiles of different CLL stages increasing the knowledge about the disease. For more details, see the article by Paula Díez et al. on page 1193.
Photonic Nanostructures and Devices Based on Photonic Crystals (2005)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. Noda, "Photonic Nanostructures and Devices Based on Photonic Crystals," in Integrated Photonics Research and Applications/Nanophotonics for Information Systems, Technical Digest (Optica Publishing Group, 2005), paper NThB1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Myocardial Akt Activation and Gender (2001)

Cardiovascular disease risk is higher in men than women, but the basis for this discrepancy remains controversial. Estrogenic stimulation of the myocardium or isolated cardiomyocytes has been purported to exert multiple beneficial effects associated with inhibition of maladaptive responses to pathogenic insults. This report describes a significant difference between the sexes in myocardial activation of Akt, a protein kinase that regulates a broad range of physiological responses including metabolism, gene transcription, and cell survival. We find that young women possess higher levels of nuclear-localized phospho-Akt(473) relative to comparably aged men or postmenopausal women. Both localization of phospho-Akt(473) in myocardial nuclei of sexually mature female mice versus males and Akt kinase activity in nuclear extracts of hearts from female mice versus males are elevated. Cytosolic localization of phospho-forkhead, a downstream nuclear target of Akt, is also increased in female relative to male mice, suggesting a potential mechanism for cardioprotective nuclear signaling resulting from Akt activation. Phospho-Akt(473) levels and localization at cardiac nuclei are similarly increased in transgenic mice with myocardium-specific expression of insulin-like growth factor I, a proven stimulus for Akt activation. Phospho-Akt(473) is also localized to the nucleus of cultured cardiomyocytes after exposure to 17beta-estradiol or genistein (a phytoestrogen in soy protein-based diets), and neonatal exposure of litters to genistein elevated nuclear phospho-Akt(473) localization. The activation of Akt in a gender-dependent manner may help explain differences observed in cardiovascular disease risk between the sexes and supports the potential beneficial effects of estrogenic stimulation.
Phase Screen Effects in Enhanced Backscattering (1996)

The enhanced backscattering (EBS) phenomenon is investigated in the complex case of structures modeled as ensembles of random phase screens, lenses, and volume-scattering media. Effects on the peak shape and magnitude are discussed and possible solutions to problems encountered in using EBS to characterize random media are suggested.
Inverse designed plasmonic metasurface with parts per billion optical hydrogen detection (2022)

Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical hydrogen sensors, in which hydrogen is absorbed inside optically-lossy Pd nanostructures and for which state-of-the-art detection limits are only at the low parts-per-million (ppm) range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive optical (gas) detection.
ChemInform Abstract: Bis(tris(m‐(sodium sulfonato)phenyl)phosphine) Hexacarbonyl Dicobalt, Co2(CO)6(P(m‐C6H4SO3Na)3)2, in a Supported Aqueous Phase for the Hydroformylation of 1‐Hexene. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Epitope mapping of envelope glycoprotein E1 of hog cholera virus strain Brescia (1993)

Four antigenic domains (A, B, C and D) on envelope glycoprotein E1 (gp51-54) of hog cholera virus strain Brescia have been specified by using 13 monoclonal antibodies (MAbs) that recognize non-conserved and conserved epitopes. It was shown that the non-conserved epitopes map to the N-terminal half of E1 by analysis of chimeric E1 proteins of strains Brescia and C. Conserved epitopes, however, could not be mapped using this approach. Here we describe mapping of both conserved and non-conserved epitopes on E1 by the use of an extensive set of single and double deletion mutants of E1 of strain Brescia. Deletion mutants were transiently expressed in COS1 cells and analysed by immunostaining with the 13 MAbs directed against strain Brescia and four MAbs directed against strain C. All MAbs bound to the N-terminal half of E1, i.e. amino acids 690 to 866 encoded by the sequence of strain Brescia. Domain B and one epitope in domain C are located between residues 690 and 773. Other epitopes in domain C are located on an extended region, i.e. between residues 690 and 800. Conserved epitopes of domain A are mapped between residues 766 and 866, whereas the only non-conserved epitope in this domain is located between residues 766 and 813. Domain D, represented by one MAb, is located in the same region as this non-conserved epitope of domain A, i.e. between residues 766 and 800. The results suggest the presence of two distinct antigenic units on E1, one consisting of domains B and C and the other consisting of domain A.
Isolation between three antennas at 700 MHz: for handheld terminals (2014)

To address the antenna design challenges posed by many frequency bands, introduced with long‐term evolution deployment, this study proposes the use of separate transmit (Tx) and receive (Rx) narrow‐band antennas. In addition, a diversity Rx (Dx) antenna is needed for multiple‐input multiple‐output performance. Although the isolation between two antennas at low frequencies (700 MHz) is crucial for the successful implementation of 4G in handheld terminals, it becomes more challenging when considering isolation among three antennas (one Tx and two Rx antennas) at low frequencies. Hence, a method that improves the isolation between the ports of one Tx and two Rx antennas is presented here.
Ever Wondered What Playing Video Games Does to Your Brain? (2013)

Children today interact with media an average of 7 hours a day, every day including weekends. That is more than the weekly time adults spend at work. What is the impact of so much media consumption? Research in this field is still in its infancy, but an emerging field on video game and the brain suggests that we are in for some surprises.
Quantification of live cell membrane compartmentalization with high-speed single lipid tracking through interferometric Scattering Microscopy (2021)

Abstract The specific details of the lateral diffusion dynamics in cellular plasma membrane are an open topic in modern biophysics. Many studies have documented several different behaviours, including free (Brownian) motion, confined diffusion, transiently confined (hop) diffusion, anomalous diffusion, and combinations thereof. Here we have employed Interferometric Scattering Microscopy (ISCAT) to explore the lateral diffusion dynamics in the plasma membrane of living cells of a biotinylated lipid analogue that had been labelled with streptavidin-coated gold nanoparticles (20 and 40nm in diameter) at a sampling rate of 2kHz. The data was analysed with an unbiased statistics-driven mean squared displacement analysis pipeline that was designed to identify both the most likely diffusion mode for a specific data set, and the best fit parameters of the most likely model. We found that the prevalent diffusion mode of the tracked lipids, independent of the particle size, is compartmentalized diffusion, although the use of the larger tags resulted in tighter confinement and reduced diffusion rates. Through our analysis and comparison with simulated data, we quantify significant physical parameters, such as average compartment size, dynamic localization uncertainty, and the diffusion rates. We hereby further demonstrate the use of a confinement strength metric that makes it possible to compare diffusivity measurements across techniques and experimental conditions. Statement of Significance This work offers new details on the data analysis of lipid diffusion on cellular membranes in vitro, through Interferometric Scattering microscopy. With this technique, we performed single particle tracking (SPT) experiments at 2kHz sampling rate. We analyzed the data through an unbiased statistics-driven protocol. The data shows that the diffusion motion of the tracked lipids follows mainly the “hopping” diffusion behaviour, whereby transient confinement zones hinder the particle dynamics. Matching the experimental data with diffusion simulations, we have been able to verify the physical parameters inferred by the experimental data analysis. Finally, we showcase a framework to compare SPT data with other techniques, to offer a complete overview of plasma membrane dynamics.
Rydberg excitation assisted light shift blockade in Rb atoms for realizing a collective state quantum bit and quantum memory (2014)

Previously, we had proposed the technique of light shift imbalance induced blockade which leads to a condition where a collection of non-interacting atoms under laser excitation remains combined to a superposition of the ground and the fist excited states, thus realizing a collective state quantum bit which in turn can be used to realize a quantum computer. In this paper, we show first that the light shift imbalance by itself is actually not enough to produce such a blockade, and explain the reason by the limitation of our previous analysis had reached this constraint. We then show that by introducing Rydberg interaction, it is possible to achieve such a blockade for a wide range of parameters. Analytic arguments used to establish these results are confirmed by numerical simulations. The fidelity of coupled quantum gates based on such collective state qubits is highly insensitive to the exact number of atoms in the ensemble. As such, this approach may prove be viable for scalable quantum computing based on neutral atoms.
A Meaningful Indoor Path-Loss Formula (2013)

A simple indoor path-loss formula is proposed that is both simple and physically sound, as it accounts for major propagation processes taking place in indoor environment: namely wave-divergence and obstruction. The formula is shown to well reproduce the path-loss versus distance trend in different indoor environments. Moreover, its parameters are closely related to major environment characteristics, and therefore the formula can be parameterized in simple cases even without resorting to measurement-based tuning.
Acquisitive modals (2009)

The paper explores the fact that ‘get’ etymons may acquire modal meanings. It tries to fit this fact into the modal map proposal of van der Auwera & Plungian (1998) and concludes that the map has to be revised, in part because the lexical input, the predicates meaning ‘get/acquire’ allow more than one reading, an agentive and a receptive one. The paper focuses on the two areas in which so-called ‘acquisitiv modality’ is very prominent, viz. Northern Europe and South(east) Asia.
Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs (2012)

In this paper we present a new approach for tightening upper bounds on the partition function. Our upper bounds are based on fractional covering bounds on the entropy function, and result in a concave program to compute these bounds and a convex program to tighten them. To solve these programs effectively for general region graphs we utilize the entropy barrier method, thus decomposing the original programs by their dual programs and solve them with dual block optimization scheme. The entropy barrier method provides an elegant framework to generalize the message-passing scheme to high-order region graph, as well as to solve the block dual steps in closed-form. This is a key for computational relevancy for large problems with thousands of regions.
Effects of Threading Dislocation Density on the Gate Leakage of AlGaN/GaN Heterostructures for High Electron Mobility Transistors (2011)

AlGaN/GaN heterostructures were regrown on three semi-insulating GaN templates with threading dislocation densities of ∼2 × 10 10, ∼5 × 108,and ∼5 × 107 cm-2. Regrowths were carried out under Ga-rich conditions by plasma-assisted molecular beam epitaxy to determine the effects of threading dislocation density on leakage through Schottky contacts on the AlGaN/GaN heterostructures. A similar AlGaN/GaN heterostructure was directly grown on 4H-SiC under Ga-rich conditions for comparison with the regrown heterostructures. High electron mobility transistors were fabricated. Decreasing the threading dislocation density from ∼2 × 1010 to ∼5 × 107 cm-2 yielded up to a 45-fold decrease in the average reverse Schottky diode current at -10 V bias. © 2011 The Japan Society of Applied Physics.
High-throughput antibody screening from complex matrices using intact protein electrospray mass spectrometry (2020)

Toward the goal of increasing the throughput of high-resolution mass characterization of intact antibodies, we developed a RapidFire-mass spectrometry (MS) assay using electrospray ionization. We achieved unprecedented screening throughput as fast as 15 s/sample, which is an order of magnitude improvement over conventional liquid chromatography (LC)-MS approaches. The screening enabled intact mass determination as accurate as 7 ppm with baseline resolution at the glycoform level for intact antibodies. We utilized this assay to characterize and perform relative quantitation of antibody species from 248 samples of 62 different cell line clones at four time points in 2 h using RapidFire-time-of-flight MS screening. The screening enabled selection of clones with the highest purity of bispecific antibody production and the results significantly correlated with conventional LC-MS results. In addition, analyzing antibodies from a complex plasma sample using affinity-RapidFire-MS was also demonstrated and qualified. In summary, the platform affords high-throughput analyses of antibodies, including bispecific antibodies and potential mispaired side products, in cell culture media, or other complex matrices.
ChemInform Abstract: Diastereoselective Photocyclization to Dihydroindolinols. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Abstract 4482: Discovery of an irreversible PI3Kα-specific Inhibitor (2011)

Abstract The PI3K pathway, which regulates cell growth, proliferation and survival, is activated in many types of human tumors by mutational activation of PI3Kα, PTEN inactivation, or activation of upstream receptor tyrosine kinases. Several PI3K inhibitors are currently in clinical development, but most are pan-PI3K inhibitors. Tumor biology data suggests that targeting PI3Kα specifically should be efficacious, and there may be advantages to not disrupting other members of the complex PI3K signaling cascade. Using structure-based drug design (SBDD), we have discovered a series of small molecules that selectively inhibit PI3Kα via the formation of an irreversible covalent bond. In addition to the enhanced pharmacodynamics achieved through permanent silencing of targets, covalent inhibitors also exhibit key advantages in terms of isoform selectivity and translational biomarker opportunities. SBDD was used to design small molecules which bond to an amino acid present uniquely in the α-isoform of PI3K. Mass spectrometry verified covalent bond formation to PI3Kα but not to the other isoforms. PI3K enzyme activity was measured using an HTRF assay. PI3Kα inhibition was evaluated in SKOV-3 cells by measuring P-AktSer473 levels. Washout experiments were performed to assess prolonged duration of action in cells. Effects on cell proliferation were assessed in cell lines bearing different mutations, such as SKOV-3 (PIK3CA H1047R), PC3 (PTEN-null) and others. SKOV-3 xenograft studies were performed in mice to measure P-AktSer473 inhibition and tumor growth inhibition in vivo. A biotinylated covalent probe molecule specific for PI3Kα was used to verify and quantitate target occupancy by the covalent inhibitor, both in vitro and ex vivo. Using trypsin digestion and MS-MS analysis, we confirmed that the designed inhibitors covalently bonded to the protein at the desired amino acid that is unique to PI3Kα. The covalent bonding resulted in potent inhibition of the PI3Kα enzyme activity and inhibition of P-AktSer473 in cells (EC50 &amp;lt; 100nM). Moreover, the inhibition of PI3Kα activity continued after compound removal, confirming prolonged duration of activity. Only cell lines driven by PI3Kα were potently inhibited by PI3Kα-selective inhibitors. A lead compound also demonstrated in vivo inhibition of PI3Kα and tumor growth inhibition in an SKOV-3 xenograft model, and a biotinylated covalent probe molecule verified that PI3Kα was covalently inhibited by the compound in vivo. Selective irreversible inhibitors of PI3Kα demonstrate prolonged duration of action and activity in vivo. This targeted approach should yield a first-in-class selective covalent PI3Kα inhibitor with clinical advantages. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4482. doi:10.1158/1538-7445.AM2011-4482
Thermal cyclic etching of silicon nitride using formation and desorption of ammonium fluorosilicate (2016)

Abstract Novel selective cyclic etching of SiN over SiO 2 via the formation and desorption of ammonium fluorosilicate was developed. The formation of ammonium fluorosilicate was observed using X-ray photoelectron spectroscopy after hydrofluorocarbon-based radical exposure. Etching of SiN was observed after ammonium fluorosilicate was removed by thermal annealing. Cyclic etching tests were carried out by repeated radical exposure and thermal annealing. The etching depth increased on increasing the number of cycles. It was found that the cyclic etching is self-limiting because the etching depth does not depend on the radical exposure time but on the number of cycles.
Association of Retinal Nerve Fiber Layer Thinning With Current and Future Cognitive Decline (2018)

A thinner RNFL is associated with worse cognitive function in individuals without a neurodegenerative disease as well as greater likelihood of future cognitive decline. This preclinical observation has implications for future research, prevention, and treatment of dementia.
A Simple Load-Balancing Scheme with High Scaling Efficiency (2019)

This chapter describes an image partitioning scheme that can be used to distribute the work of computing pixel values across multiple processing units. The resulting workload distribution scheme is simple to implement, yet effective.