gebhart/patrepeval huggingface dataset:
Toward More General Embeddings for Protein Design: Harnessing Joint Representations of Sequence and Structure (2021)

A bstract Protein embeddings learned from aligned sequences have been leveraged in a wide array of tasks in protein understanding and engineering. The sequence embeddings are generated through semi-supervised training on millions of sequences with deep neural models defined with hundreds of millions of parameters, and they continue to increase in performance on target tasks with increasing complexity. We report a more data-efficient approach to encode protein information through joint training on protein sequence and structure in a semi-supervised manner. We show that the method is able to encode both types of information to form a rich embedding space which can be used for downstream prediction tasks. We show that the incorporation of rich structural information into the context under consideration boosts the performance of the model by predicting the effects of single-mutations. We attribute increases in accuracy to the value of leveraging proximity within the enriched representation to identify sequentially and spatially close residues that would be affected by the mutation, using experimentally validated or predicted structures.
Pulmonary Vein Isolation Guided by Real‐Time Three‐Dimensional Transesophageal Echocardiography (2011)

The present case illustrates pulmonary vein isolation guided by real-time three-dimensional transesophageal echocardiography. This imaging modality allowed to navigate in a point-by-point fashion around pulmonary veins to assess both catheter location in relation to pulmonary vein ostia and stability of catheter tip. Also, it offered high-resolution visualization of a thickened, prominent tissue that surrounded the left upper pulmonary vein (the ligament of Marshall). The ability to visualize this anatomical structure along with intracardiac recording of electrical signals allowed to safely modulate in loco radiofrequency energy delivery, thus achieving electrical isolation of the pulmonary vein.
Understanding Semantics in Feature Selection for Fault Diagnosis in Network Telemetry Data (2023)

Expert systems for fault diagnosis are computationally expensive to build and maintain, and lack scalability and inherent adaptability to unknown events or modifications in the topology of the monitored system. While data-driven feature selection mechanisms can facilitate diagnosis without the hardship of developing and maintaining expert systems, purely data-driven mechanisms lack understanding of semantic importance within a feature set, and would benefit from additional domain knowledge. Part of this additional knowledge can be extracted from metadata. The proposed approach combines data-driven metrics and semantic information contained in the feature names to produce selections of features which best represent an underlying event. This study extends a cross entropy based optimization method to join semantic importance with data behavior. A benchmarking architecture is introduced to evaluate the benefits of semantic analysis, and demonstrate the performance and robustness of semantic feature selection on different types of faults in network telemetry datasets, modeled with the YANG data modeling language. The results illustrate the interest of such a complementary meta-data analysis for data-driven fault diagnosis, and highlight the robustness of the studied approach against variations in the input feature set.
Asymptotic Optimality of Likelihood-Based Cross-Validation (2004)

Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d. observations from the true density among a collection of candidate density estimators. General examples are the selection of a model indexing a maximum likelihood estimator, and the selection of a bandwidth indexing a nonparametric (e.g. kernel) density estimator. In this article, we establish a finite sample result for a general class of likelihood-based cross-validation procedures (as indexed by the type of sample splitting used, e.g. V-fold cross-validation). This result implies that the cross-validation selector performs asymptotically as well (w.r.t. to the Kullback-Leibler distance to the true density) as a benchmark model selector which is optimal for each given dataset and depends on the true density. Crucial conditions of our theorem are that the size of the validation sample converges to infinity, which excludes leave-one-out cross-validation, and that the candidate density estimates are bounded away from zero and infinity. We illustrate these asymptotic results and the practical performance of likelihood-based cross-validation for the purpose of bandwidth selection with a simulation study. Moreover, we use likelihood-based cross-validation in the context of regulatory motif detection in DNA sequences.
Postsynthetic Modification: A Versatile Approach Toward Multifunctional Metal-Organic Frameworks (2009)

An isoreticular metal-organic framework (IRMOF-3) containing 2-amino-1,4-benzenedicarboxylic acid (NH(2)-BDC) as a building block is shown to undergo chemical modification with a diverse series of anhydrides and isocyanates. The modification of IRMOF-3 by these reagents has been evidenced by using a variety of methods, including NMR and electrospray ionization mass spectrometry, and the structural integrity of the modified MOFs has been confirmed by thermogravimetric analysis, powder X-ray diffraction, and gas sorption analysis. The results show that a variety of functional groups can be introduced onto the MOF including amines, carboxylic acids, and chiral groups. Furthermore, it is shown that tert-butyl-based asymmetric anhydrides can be used to selectively deliver chemical payloads to the IRMOF. Finally, the results demonstrate that at least four different chemical modifications can be performed on IRMOF-3 and that the reaction conditions can be modulated to control the relative abundance of each group. The findings presented here demonstrate several important features of postsynthetic modification on IRMOF-3, including (1) facile introduction of a wide range of functional groups using simple reagents (e.g., anhydrides and isocyanates), (2) the introduction of multiple (as many as four different) substituents into the MOF lattice, and (3) control over reaction conditions to preserve the crystallinity and microporosity of the resultant MOFs. The findings clearly illustrate that postsynthetic modification represents a powerful means to access new MOF compounds with unprecedented chemical complexity, which may serve as the basis of multifunctional materials.
Polymerizability, copolymerizability, and properties of cyanoacrylate‐telechelic polyisobutylenes I: three‐arm star cyanoacrylate‐telechelic polyisobutylene (2007)

Abstract This series of papers concern new materials for possible biological applications created by combining the chemistry of highly reactive cyanoacrylates (CAs) with polyisobutylene (PIB) rubbers. First, a new strategy for the synthesis of CA–telechelic PIBs is described. Subsequently, the strategy is employed for the synthesis of low viscosity (syringible) CA–telechelic three‐arm star PIB [Ø(PIB–CA) 3 ]. The intermediates of the synthesis route are characterized by 1 H NMR spectroscopy. Injecting liquid Ø(PIB–CA) 3 into living tissue (fresh chicken egg) produces a bolus of crosslinked PIB rubber. The spectacular oxidative resistance of this rubber is documented by its resistance to concentrated HNO 3 . A structural model of the crosslinked rubber obtained upon contacting Ø(PIB–CA) 3 with proteinaceous tissue is proposed. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Developing Actively Targeted Nanoparticles to Fight Cancer: Focus on Italian Research (2021)

Active targeting is a valuable and promising approach with which to enhance the therapeutic efficacy of nanodelivery systems, and the development of tumor-targeted nanoparticles has therefore attracted much research attention. In this field, the research carried out in Italian Pharmaceutical Technology academic groups has been focused on the development of actively targeted nanosystems using a multidisciplinary approach. To highlight these efforts, this review reports a thorough description of the last 10 years of Italian research results on the development of actively targeted nanoparticles to direct drugs towards different receptors that are overexpressed on cancer cells or in the tumor microenvironment. In particular, the review discusses polymeric nanocarriers, liposomes, lipoplexes, niosomes, solid lipid nanoparticles, squalene nanoassemblies and nanobubbles. For each nanocarrier, the main ligands, conjugation strategies and target receptors are described. The literature indicates that polymeric nanoparticles and liposomes stand out as key tools for improving specific drug delivery to the site of action. In addition, solid lipid nanoparticles, squalene nanoparticles and nanobubbles have also been successfully proposed. Taken together, these strategies all offer many platforms for the design of nanocarriers that are suitable for future clinical translation.
The effect of moderate‐dose corticosteroids in preventing severe flares in patients with serologically active, but clinically stable, systemic lupus erythematosus: Findings of a prospective, randomized, double‐blind, placebo‐controlled trial (2006)

These preliminary data support our hypothesis that in a subset of clinically stable SLE patients with a combination of elevated C3a and anti-dsDNA levels, short-term corticosteroid therapy may avert a severe flare.
Abstract P32 (2014)

AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK
Formulation with CpG Oligodeoxynucleotides Prevents Induction of Pulmonary Immunopathology following Priming with Formalin-Inactivated or Commercial Killed Bovine Respiratory Syncytial Virus Vaccine (2005)

Commercial killed bovine respiratory syncytial virus (K-BRSV) and formalin-inactivated BRSV (FI-BRSV) tend to induce Th2-type immune responses, which may not be protective and may even be detrimental during subsequent exposure to the virus. In this study we assessed the ability of CpG oligodeoxynucleotides (ODNs) to aid in the generation of effective and protective BRSV-specific immune responses. Mice were immunized subcutaneously with FI-BRSV formulated with CpG ODN, Emulsigen (Em), CpG ODN and Em, or non-CpG ODN and Em. Two additional groups were immunized with K-BRSV or K-BRSV and CpG ODN. After two vaccinations, the mice were challenged with BRSV. FI-BRSV induced Th2-biased immune responses characterized by production of serum immunoglobulin G1 (IgG1) and IgE, as well as interleukin-4 (IL-4), by in vitro-restimulated splenocytes. Formulation of FI-BRSV with CpG ODN, but not with non-CpG ODN, enhanced serum IgG2a and IFN-gamma production by splenocytes, whereas serum IgE was reduced. Although the immune response induced by K-BRSV was not as strongly Th2 biased, the addition of CpG ODN to this commercial vaccine also resulted in a more Th1-type response. Furthermore, the addition of CpG ODN to the BRSV vaccine formulations resulted in enhanced neutralizing antibody responses. Significant production of IL-5, eotaxin, and eosinophilia was observed in the lungs of FI-BRSV- and K-BRSV-immunized mice. However, IL-5 and eotaxin levels, as well as the number of eosinophils, were decreased in the mice vaccinated with the CpG ODN-formulated vaccines. Finally, when formulated with CpG ODN, both FI-BRSV and K-BRSV significantly reduced virus production after challenge with BRSV.
Urethral mobilization and advancement for midshaft to distal hypospadias. (2002)

The hypospadias technique described, which uses wide urethral and glanular mobilization and advancement, can be useful for repair of midshaft to distal hypospadias with or without chordee with minimal complications and excellent cosmetic results.
Effect of Increased Weight Reduction on Shrinkage of Injection-Molded Parts Using Microcellular Foaming Process (2008)

Shrinkage is a common problem in injection-molded parts. This study finds a way to reduce the linear and volumetric shrinkage by using microcellular foaming process. Experiments were conducted by using unfilled and filled (25% short glass fiber reinforced) acetal copolymer samples to demonstrate the effect. The overall improvement in shrinkage was observed therefore the result of increasing weight reduction in the samples. Therefore weight reduction can be utilized to achieve higher-dimensional tolerances of polymer parts and filled polymer can be used if greater mechanical properties are also a matter of concern.
[New semi-automatic ROI setting system for brain PET images based on elastic model]. (1994)

We have developed a semi-automatic ROI setting system for brain PET images. It is based on the elastic network model that fits the standard ROI atlas into individual brain image. The standard ROI atlas is a set of segments that represent each anatomical region. For transformation, the operator needs to set only three kinds of district anatomical features: manually determined midsagittal line, brain contour line determined with SNAKES algorithm semi-automatically, a few manually determined specific ROIs to be used for exact transformation. Improvement of the operation time and the inter-operator variance were demonstrated in the experiment by comparing with the conventional manual ROI setting. The operation time was reduced to 50% in almost all cases. And the inter-operator variance was reduced to one seventh in the maximum case.
[FIP1L1::PDGFRA-positive chronic eosinophilic leukemia presenting with multiple ulcers of oral cavity and gastrointestinal tract]. (2022)

A 66-year-old man developed multiple erosions and pain in the lips and mouth, fever, and black stools. There was persistent bleeding from the lip erosions. When he was admitted to our hospital, his white blood cell count increased to 53,420/µl with 3% eosinophils, and hemoglobin decreased to 3.1 g/dl. Bone marrow biopsy revealed an elevated eosinophil level (24.0%) with markedly toxic granules. Gastrointestinal endoscopy revealed multiple ulcers and erosions in the pharynx, esophagus, stomach, and colon. Histopathological diagnosis indicated nonspecific inflammation with poor infiltration of eosinophils. Bone marrow FISH test was positive for 4q12 deletion (FIP1L1::PDGFRA), leading to the diagnosis of FIP1L1::PDGFRA-positive chronic eosinophilic leukemia. Following initiation of oral administration of imatinib 100 mg/day, the number of eosinophils decreased rapidly, and normalized 2 days after the start of imatinib. The mucosal lesions showed significant improvement and were diagnosed as leukemia-associated lesions. Based on the clinical course of our patient, multiple oral cavity and gastrointestinal ulcers could be the initial presentation in this leukemia.
Simultaneous Parameter Mapping, Modality Synthesis, and Anatomical Labeling of the Brain with MR Fingerprinting (2016)

Magnetic resonance fingerprinting (MRF) quantifies various properties simultaneously by matching measurements to a dictionary of precomputed signals. We propose to extend the MRF framework by using a database to introduce additional parameters and spatial characteristics to the dictionary. We show that, with an adequate matching technique which includes an update of selected fingerprints in parameter space, it is possible to reconstruct parametric maps, synthesize modalities, and label tissue types at the same time directly from an MRF acquisition. We compare (1) relaxation maps from a spatiotemporal dictionary against a temporal MRF dictionary, (2) synthetic diffusion metrics versus those obtained with a standard diffusion acquisition, and (3) anatomical labels generated from MRF signals to an established segmentation method, demonstrating the potential of using MRF for multiparametric brain mapping.
1,24(S)-dihydroxyvitamin D2, an endogenous vitamin D2 metabolite, inhibits growth of breast cancer cells and tumors. (2005)

1,24(OH)2D2 inhibits growth of breast cancer cells via VDR-dependent mechanisms; its complete lack of toxicity and significant antitumor activity supports further development for chemotherapeutic applications.
Photosensing Properties of Pentacene OFETs Based on a Novel PMMA Copolymer Gate Dielectric (2014)

In the present work, bottom-gate top-contact organic field effect transistors (OFETs) were fabricated by evaporating a pentacene semiconductor film on top of a new insulating poly(methyl methacrylate) (PMMA) copolymer containing methacrylate units. The PMMA copolymer was synthesized in order to combine the well-known insulating properties of PMMA with the possibility to be efficiently photocured enabling photopatterning-based organic circuitry integration processes. The properties of the pentacene layer deposited on ITO/PMMA copolymer stack were studied through morphological and structural analyses. Device photoresponses and photoexcitated transients were investigated and compared to reference devices based on standard PMMA gate dielectric.
Elevation of extracellular magnesium rapidly raises intracellular free nbsp Mg sup 2 sup nbsp in human aortic endothelial cells is extracellular Mg sup 2 sup a regulatory cation (1997)

Extracellular magnesium ions [Mg2+]o are known to regulate functions of endothelial cells, but whether [Mg2+]o can alter intracellular free ionized magnesium [Mg2+]i in these cells remains unknown. The present studies, using digital imaging microscopy and the Mg2+ fluorescent probe, mag-fura-2, determined effects of elevation of [Mg2+]o on [Mg2+]i in cultured human aortic endothelial cells. With normal Mg2+(1.2 mM)-containing incubation media, [Mg2+]i was 0.51+/-0.04 mM with a heterogeneous distribution. The ratio of [Mg2+]i/[Mg2+]o was 0.52+/-0.07. Elevation of [Mg2+]o up to 4.8 mM increased [Mg2+]i to 0.80+/-0.07 mM in 2-10 min and lowered the ratio of [Mg2+]i/[Mg2+]o to 0.16+/-0.02. Irrespective of the observed increments of [Mg2+]i, a subcellular heterogeneous distribution of [Mg2+]i was always evident in all cells tested. Our results suggest that [Mg2+]o can regulate [Mg2+]i more rapidly than heretofore believed, supporting the hypothesis that extracellular Mg2+ can exert regulatory effects on endothelial cell functions and probably act as extracellular regulatory cations
Competitive and cost effective high-k based 28nm CMOS technology for low power applications (2009)

In this paper, we present a cost-effective 28 nm CMOS technology for low power (LP) applications based on a high-k, single-metal-gate-first architecture. We report raw gate densities up to 4200 kGate/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and, using the ARM Cortex-R4F as a reference, we report achievement of an overall 2.4x area reduction in 28 nm from 45 nm technology. Our high-density SRAM bit-cell (area= 0.120mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) has a demonstrated Static Noise Margin (SNM) of 213 mV at 1 V. Fully compatible with power/leakage management techniques intensively used in low power designs, the transistor drive currents are increased +35% & +10%, for nFET and pFET respectively, with respect to a 28 nm LP poly/SiON reference. Compatible with LP system-on-chip requirements, ultra low-cost, high performance analog devices are reported which leverage a dramatic improvement in matching factor (AVT~2mV.um) versus our previously-reported result. An optimized interconnection scheme based on Extreme Low k (ELK) dielectric (k~2.4) and advanced metallization allows high density wiring with competitive R-C versus our previous technology.
Experimental Liquid Densities of n-Pentane, n-Octane, and n-Nonane and Their Binary Mixtures from (273.15 to 363.15) K at 0.1 MPa (2011)

This paper presents experimental liquid densities for n-pentane, n-octane, and n-nonane and their binary mixtures from (273.15 to 363.15) K over the entire composition range (for the mixtures) at atmospheric pressure. The experimental apparatus is a vibrating-tube densimeter. It is possible to compare the results to a generalized correlation for liquid densities of n-alkanes and to molecular dynamics simulations. The average absolute percentage deviation is (0.06 and 0.8) % using the equation and the simulation results.
Duplicate transcription factors GT1 and VRS1 regulate branching and fertile flower number in maize and Brachypodium distachyon (2023)

Abstract Crop engineering and de novo domestication using genome editing are new frontiers in agriculture. However, outside of well-studied crops and model systems, prioritizing engineering targets remains challenging. Evolution can serve as our guide, revealing high-priority genes with deeply conserved roles. Indeed, GRASSY TILLERS1 ( GT1 ), SIX-ROWED SPIKE1 ( VRS1 ), and their homologs have repeatedly been targets of selection in domestication and evolution. This repeated selection may be because these genes have an ancient, conserved role in regulating growth repression. To test this, we determined the roles of GT1 and VRS1 homologs in maize ( Zea mays ) and the distantly related grass brachypodium ( Brachypodium distachyon ) using CRISPR-Cas9 gene editing and mutant analysis. GT1 and VRS1 have roles in floral development in maize and barley, respectively. Grass flowers are borne in branching structures called spikelets. In maize spikelets, carpels are suppressed in half of all initiated ear flowers. These spikelets can only produce single grains. We show that gt1; vrs1-like1 ( vrl1 ) mutants have derepressed carpels in ear flowers. Importantly, these plants can produce two grains per spikelet. In brachypodium, bdgt1; bdvrl1 mutants have more branches, spikelets, and flowers than wildtype plants, indicating conserved roles for GT1 and VRS1 homologs in growth suppression. Indeed, maize GT1 can suppress growth in Arabidopsis thaliana , separated from the grasses by ca . 160 million years of evolution. Thus, GT1 and VRS1 maintain their potency as growth regulators across vast timescales and in distinct developmental contexts. Modulating the activity of these and other conserved genes may be critical in crop engineering.
Efficiency Improvement of a Dual-input LLC Converter for PV Applications using Burst-mode Control Strategy (2019)

Although LLC resonant converter is well-known for its high efficiency, its light load efficiency still cannot meet the ever-growing market requirements. This paper applies a burstmode (pulse-skipping) control strategy to improve the light load efficiency of a dual-input LLC resonant converter which interfaces with two PV panels. This topology is a dual half-bridge LLC circuit with four active switches. A phase-shift pulse width modulation (PWM) control is employed to implement independent maximum power point tracking (MPPT) for each PV panel and suitable burst-on time for each load condition is selected to maximize the efficiency of burst-mode operation. The switching frequency and phase shift are varied to control the converter voltage gain. Zero-voltage-switching (ZVS) is realized in all switches over the entire range of source voltage and load conditions. A 200-W prototype was setup to verify the proposed control strategy. The input voltage range was selected to be 25 V to 45 V with an output voltage regulated at 200 V DC. Experimental results show that the proposed burst-mode control strategy can significantly improve the converter light load efficiency by around 6% maximum and waveforms match the simulation results fairly well.
Chromatic Aberration Correction by Combination Concave Lens (2010)

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.