gebhart/patrepeval huggingface dataset:
Plasmonic toroidal excitation with engineering metamaterials (2017)

Natural toroidal molecules, such as biomolecules and proteins, possess toroidal dipole moments that are hard to be detected, which leads to extensive studies of artificial toroidal materials. Recently, toroidal metamaterials have been widely investigated to enhance toroidal dipole moments while the other multipoles are eliminated due to the spacial symmetry. In this talk, we will show several cases on the plasmonic toroidal excitation by engineering the near-field coupling between metamaterials, including their promising applications. In addition, a novel design for a toroidal metamaterial with engineering anapole mode will also be discussed.
Nonlinear exceptional-point lasing with ab-initio Maxwell-Bloch theory (2022)

We present a general analysis for finding and characterizing nonlinear exceptional point (EP) lasers above threshold, using steady-state ab-initio Maxwell-Bloch equations. For a system of coupled slabs, we show that a nonlinear EP is obtained for a given ratio between the external pumps in each resonator, and that it is associated with a kink in the output power and lasing frequency, confirming coupled-mode theory predictions. Through numerical linear stability analysis, we confirm that the EP laser can be stable for a large enough inversion relaxation rate. We further show that the EP laser can be characterized by scattering a weak signal off the lasing cavity, so that the scattering frequency spectrum exhibits a quartic divergence. Our approach can be applied to arbitrary scatterers with multi-level gain media.
From Research to Proof-of-Concept: Analysis of a Deployment of FPGAs on a Commercial Search Engine. (2021)

FPGAs are quickly becoming available in the cloud as a one more heterogeneous processing element complementing CPUs and GPUs. There are many reports in the literature showing the potential for FPGAs to accelerate a wide variety of algorithms, which combined with their growing availability, would seem to also indicate a widespread use in many applications. Unfortunately, there is not much published research exploring what it takes to integrate an FPGA into an existing application in a cost-effective way and keeping the algorithmic performance advantages. Building on recent results exploring how to employ FPGAs to improve the search engines used in the travel industry, this paper analyses the end-to-end performance of the search engine when using FPGAs, as well as the necessary changes to the software and the cost of such deployments. The results provide important insights on current FPGA deployments and what needs to be done to make FPGAs more widely used. For instance, the large potential performance gains provided by an FPGA are greatly diminished in practice if the application cannot submit request in the most optimal way, something that is not always possible and might require significant changes to the application. Similarly, some existing cloud deployments turn out to use a very imbalanced architecture: a powerful FPGA connected to a not so powerful CPU. The result is that the CPU cannot generate enough load for the FPGA, which potentially eliminates all performance gains and might even result in a more expensive system. In this paper, we report on an extensive study and development effort to incorporate FPGAs into a search engine and analyse the issues encountered and their practical impact. We expect that these results will inform the development and deployment of FPGAs in the future by providing important insights on the end-to-end integration of FPGAs within existing systems.
X-ray diffraction analysis of the inactivation of chymotrypsin by 3-benzyl-6-chloro-2-pyrone (1986)

The inactivation of chymotrypsin by 3-benzyl-6-chloro-2-pyrone has been studied. A covalent adduct is formed that deacylates slowly with a half-life of 23 h. X-ray diffraction analysis at 1.9-A resolution of the inactivator-enzyme complex shows that the gamma-oxygen of the active-site serine (serine-195) is covalently attached to C-1 of (Z)-2-benzylpentenedioic acid, the benzyl group of the inactivator is held in the hydrophobic specificity pocket of the enzyme, and the free carboxylate forms a salt bridge with the active-site histidine (histidine-57). The conformational changes that occur in the protein as a result of complexation are described. It is proposed that formation of the salt bridge prevents access of water and, therefore, hydrolysis of the acyl-enzyme.
Effects of Visual Display on Joint Excursions Used to Play Virtual Dodgeball (2016)

Differences in visual display type and participant perspective influence how participants perform in Virtual Dodgeball. Because VR use within rehabilitation settings is often designed to help restore movement following orthopedic or neurologic injury, these findings provide an important caveat regarding the need to consider the potential influence of presentation format and perspective on motor behavior.
Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma (2017)

To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4-NUT in NMC patient cells but not detectable in 293T cells. EP300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic chromatin complex in BRD4-NUT patient cells. Adding key functional significance to our biochemical findings, we independently discovered a <i>ZNF532-NUT</i> translocation fusion in a newly diagnosed NMC patient. ChIP sequencing of the major players NUT, ZNF532, BRD4, EP300, and H3K27ac revealed the formation of ZNF532-NUT-associated hyperacetylated megadomains, distinctly localized but otherwise analogous to those found in BRD4-NUT patient cells. Our results support a model in which NMC is dependent on ectopic NUT-mediated interactions between EP300 and components of BRD4 regulatory complexes, leading to a cascade of misregulation.
Preparation of Soy Protein Hydrolysates through alcalase treatment using Response Surface Methodology with Alzheimer's β‐amyloid (Aβ 1–42) Peptide Aggregation inhibition property (2013)

Soy protein isolate (SPI), has the highest protein content and wide range of health benefits. Soy peptides have been studied for their various beneficial effects including anti‐cancer, anti‐hypertensive, anti‐diabetic etc properties. However there is no literature regarding their anti‐Alzheimer's disease properties. Alzheimer's disease is the most common form of dementia and is the seventh leading cause of death in the United States and expected to become the sixth leading cause of death by 2013. In this study we aim to evaluate the anti‐aggregative property of alcalase hydrolysates of SPI. Since the anti‐aggregative properties against Alzheimer's β‐amyloid peptide (Aβ 1–42) depends on the peptide composition of the hydrolysates and the enzyme used, the effect of process conditions on SPI hydrolyzed with alcalase was investigated systematically using response surface methodology. Hydrolysis conditions for optimal β‐amyloid aggregation inhibition were defined using the response surface model of central composite design (CCD). The optimum conditions obtained by the model for hydrolysate (with maximum anti‐beta amyloid aggregation activity) preparation was found to be pH=8, Time=1 hr, E/S=0.5%, Temperature= 50 C which was in perfect correlation with the experimental model. This is by far one of the first studies to show that soy protein hydrolysates possess bio‐activity against beta amyloid peptide found in patients with Alzheimer's disease. Grant Funding Source : ABI
[Magnetic resonance tomography imaging of the inner ear of patients with sensorineural hearing loss or vertigo]. (2001)

The introduced TSE sequence can be used to delineate the anatomy of the inner ear as well as pathological changes. The technique appears to be useful for preoperative planning.
A General Model for Estimating the Laminated Steel Losses Under PWM Voltage Supply (2010)

The new model is based on a modified Steinmetz equation and employs a hysteresis-loss multiplicative coefficient and a combined coefficient for eddy-current and excess losses, both coefficients being variable with induction and frequency. The material model coefficients are first identified through multifrequency tests with sine-wave excitation. The iron-loss increase due to pulsewidth-modulation supply is estimated using global waveform parameters of the nonsinusoidal voltage. The study includes three different grades of non-grain-oriented electric steel. The data cover a wide range of fundamental frequency from 10 to 600 Hz and induction from 0.05 to 2 T. The errors of the computational model are small at relatively low fundamental frequency and increase thereafter. The main advantages of the model are its simplicity of use and minimal data requirements.
Injectable Biodegradable Hydrogels from Vitamin D-Functionalized Polycarbonates for the Delivery of Avastin with Enhanced Therapeutic Efficiency against Metastatic Colorectal Cancer (2014)

Humanized vascular endothelial growth factor (VEGF) antibody (bevacizumab; Avastin) is a highly effective monoclonal antibody against metastatic colorectal cancer and several other advanced late stage cancers. However, limited aqueous solubility and short circulation half-life of the antibody result in long infusion time (30-90 min) and frequent injections. Such direful medical procedures often cause considerable patient inconvenience and prolonged pharmacy preparation. Subcutaneous delivery of Avastin using injectable hydrogels can continuously provide Avastin to treat the malignancy and mitigate antibody degradation. In this study, ABA triblock copolymers of vitamin D-functionalized polycarbonate and poly(ethylene glycol), that is, VDm-PEG-VDm were synthesized and employed to form physically cross-linked injectable hydrogels for encapsulation and subcutaneous delivery of Avastin in a sustained fashion. Antitumor studies were performed using two different HCT116 xenograft mouse models: a subcutaneous and an intraperitoneal metastatic tumor models. The therapeutic efficacy of Avastin-loaded hydrogel injected subcutaneously (s.c.) was compared to an Avastin solution injected via either intravenous (i.v.) or intraperitoneal (i.p.) route. In the subcutaneous tumor model, the Avastin-loaded hydrogel resulted in greater tumor suppression as compared to i.v. and i.p. administration of Avastin solution. The biodistribution pattern of the hydrogel delivery system was also different from the other formulations as there was significantly higher accumulation in the tumor tissue and lesser accumulation within the liver and kidneys as compared to Avastin delivered through i.v. and i.p. administration. Furthermore, in vivo studies carried out on mice with peritoneal metastasis demonstrated that Avastin-loaded hydrogel and weekly administration of Avastin solution resulted in higher survival (87 and 77% over 62 days, respectively) when compared to the control, blank hydrogel and bolus Avastin solution (i.v.; 50-60%). The antimetastatic activity of Avastin delivered using a one-time injection of the hydrogel was as effective as that of 4× weekly injections (i.v.) of Avastin. The reduced injection frequency provided by the subcutaneous formulation may enhance patient convenience and compliance for metastatic cancer therapy.
Correlation between nec1 Gene Copy Number Detected in Soils by Quantitative Competitive Quenching Probe PCR and Incidence of Potato Common Scab Disease (2006)

We surveyed the soils from 54 potato fields in Nagasaki during the 2003 and 2004 spring croppings, and examined the relationship between the detectable copy number of the nec1 gene at harvest and the incidence of scab disease in each field. The nec1 gene in soil samples was quantified by a quantitative competitive quenching probe PCR (QCQP-PCR) method, using primers specific to the nec1 gene and fluorescence quenching-based probes. A significant positive correlation (r2=0.8195) was observed between the detectable copy number of the nec1 gene and the incidence of disease in tubers from 21 fields in 2003. In 23 of 25 fields where the incidence of disease was >10%, more than 103 copies of nec1 per g-soil were detected. Of the nine fields where the incidence of disease was <10%, eight had fewer than 103 gene copies. The nec1 gene was not detected in 20 fields where no disease was found. These results suggest that scab disease occurs more frequently in fields where more than 103 copies of nec1 per g-dry soil are detected.
A Review on the Formulation and Analysis of Anti-Diabetic Agent: Gliclazide (2013)

Gliclazide is a second generation sulfonylurea, which is used as antidiabetics drug. It is orally administrated and used for the treatment of non-insulin-dependent diabetes mellitus (NIDDM) and has duration of action of 12 h or more. Beside its hypoglycaemic effects, gliclazide was reported to have many other important effects, such as: suppression of platelet functions, antithrombotic actions, decreased the production of tumour necrosis factor (TNF) α by endothelial cells and other effects. The unique activities of gliclazide has open a new avenue for the drug development research. This work is aimed to provide comprehensive information about gliclazide and its current research activities.
Synthesis and Study of Zirconium Viologen Phosphonate Thin Films Containing Colloidal Platinum (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Study of Zirconium Viologen Phosphonate Thin Films Containing Colloidal PlatinumJonathan L. Snover and Mark E. ThompsonCite this: J. Am. Chem. Soc. 1994, 116, 2, 765–766Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/ja00081a046https://doi.org/10.1021/ja00081a046research-articleACS PublicationsRequest reuse permissionsArticle Views176Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Rice RS2‐9, which is bound by transcription factor OSH1, blocks enhancer–promoter interactions in plants (2021)

Insulators characterized in Drosophila and mammals have been shown to play a key role in the restriction of promiscuous enhancer-promoter interactions, as well as reshaping the topological landscape of chromosomes. Yet the role of insulators in plants remains poorly understood, in large part because of a lack of well-characterized insulators and binding factor(s). In this study, we isolated a 1.2-kb RS2-9 insulator from the Oryza sativa (rice) genome that can, when interposed between an enhancer and promoter, efficiently block the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and Nicotiana tabacum (tobacco). In the rice genome, the genes flanking RS2-9 exhibit an absence of mutual transcriptional interactions, as well as a lack of histone modification spread. We further determined that O. sativa Homeobox 1 (OSH1) bound two regions of RS2-9, as well as over 50 000 additional sites in the rice genome, the majority of which resided in intergenic regions. Mutation of one of the two OSH1-binding sites in RS2-9 impaired insulation activity by up to 60%, whereas the mutation of both binding sites virtually abolished insulator function. We also demonstrated that OSH1 binding sites were associated with 72% of the boundaries of topologically associated domains (TADs) identified in the rice genome, which is comparable to the 77% of TAD boundaries bound by the insulator CCCTC-binding factor (CTCF) in mammals. Taken together, our findings indicate that OSH1-RS2-9 acts as a true insulator in plants, and highlight a potential role for OSH1 in gene insulation and topological organization in plant genomes.
Latest high performance X-ray tubes for medical imaging (2014)

Why still vacuum technology to generate Bremsstrahlung, nearly 120 years after Conrad Roentgen's discovery? How do X-ray source and detection contribute to modern medical imaging? How do latest medical X-ray tubes work and look like? What's next? Will we see replacements of bremsstrahlung from practical sources for medical imaging in the clinical environment? After touching historic achievements to demonstrate the high level which the technology has today, we will shortly dive into physics of X-ray generation, study key characteristics, material boundary conditions, manufacturing technology. A particular focus area will be the generation of free electrons under the adverse conditions inside an X-ray tube, grid switching and focusing of the beam. The high level of residual gas as well as ion and discharge processes severely limit the range of suitable technologies. Other topics will be overall design concepts of glass and metal frame, single ended and dual polar tubes with reflection targets. We will touch the principle of rotating anode tubes, their bearings, anode discs, motors, cooling, heat balance, electron emitters and beam focusing, focal spot characteristics, off-focal radiation, and discuss the improvements of image quality by focal spot deflection.
Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies (2014)

Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, cofactor and RNA polymerase occupancy, as well as the distribution of histone marks. Consortia such as the ENCyclopedia Of DNA Elements (ENCODE) have produced large datasets using manual protocols. However, future measurements of hundreds of additional factors in many cell types and physiological states call for higher throughput and consistency afforded by automation. Such automation advances, when provided by multiuser facilities, could also improve the quality and efficiency of individual small-scale projects. The immunoprecipitation process has become rate-limiting, and is a source of substantial variability when performed manually. Here we report a fully automated robotic ChIP (R-ChIP) pipeline that allows up to 96 reactions. A second bottleneck is the dearth of renewable ChIP-validated immune reagents, which do not yet exist for most mammalian transcription factors. We used R-ChIP to screen new mouse monoclonal antibodies raised against p300, a histone acetylase, well-known as a marker of active enhancers, for which ChIP-competent monoclonal reagents have been lacking. We identified, validated for ChIP-seq, and made publicly available a monoclonal reagent called ENCITp300-1.
Protein Technologies: Proteome Analysis by Capillary Electrophoresis (2002)

This chapter contains sections titled: Introduction Capillary Electrophoresis Capillary Electrophoresis for Protein-nalysis Single-Cell Analysis Two-Dimensional Separations Conclusions References
Heat Transfer Mechanisms In Relation ToLaser Surface Melting Of Nitrided Steel (1970)

Surface laser upgrading techniques involving laser melting is becoming increasingly significant in industry. Such process generally aims at improving the surface properties, especially by enhancing the hardness of the surface layer, its resistance to wear and corrosion and/or its property gradients. Temperature rise inside the material and surface cooling rate are two important factors which affect the surface properties significantly. Consequently, investigation into heat transfer mechanism during laser melting process becomes necessary for surface upgrading. In the present study, heat transfer model, including conduction, melting and evaporation, based on electron kinetic theory is introduced for pulsed laser heating process. In the analysis, thermal properties are modified to include the nitrided compounds in the surface zone. Heat transfer medium is selected as plasma nitrided tool steel. A numerical method is employed to compute the temperature rise inside the material.
CD16 and NKG2D co-clustering facilitates quality of primary NK cell responses (2022)

Abstract Cooperation between CD16 and NKG2D receptors has been demonstrated both in animal and NK cell line models leading to an enhanced cytotoxicity and tumor elimination. However, the mechanisms of the receptor cooperation are not known, and whether the receptors form co-clusters has not been determined either. We exposed human primary polyclonal NK cells with CD16 158V/V-genotype to planar lipid bilayers (PLB) presenting Herceptin and anti-NKG2D Ab in the presence of ICAM-1. NK cells interacting with Herceptin-containing PLBs + ICAM-1 formed mostly unstable synapse, i.e., kinapses, while stimulation with anti-NKG2D alone or Herceptin+anti-NKG2D bilayers + ICAM-1 led to formation of mature synapses showing complete segregation of the receptors from ICAM-1, increased synapse stability, and efficient NK cell cytotoxicity. The cells exposed to PLBs with both anti-NKG2D and Herceptin ligands were mostly confined within the initial contact area while the cells responding to Herceptin alone were significantly more motile. Regardless of stimulatory ligands displayed on PLB, the frequency of adhered cells was very similar, but the degranulation was observed within 40% of kinapses and 80% of mature synapses, suggesting that degranulation efficiency is linked to synapse stability. Importantly, more efficient degranulation was associated with rapid and sustained Ca2+ signaling as opposed to oscillating Ca2+ signaling observed for NK cells showing less efficient degranulation. Our data demonstrated that Herceptin alone functions as a weak agonist, while co-activation of CD16 and NKG2D results in rapid and sustained Ca2+ signaling that mediates stable synaptic interface and efficient cytolytic activity by human NK cells. Supported by Grant from NIH U01AI148117
Ventricular septal defect. A review of current thoughts. (1968)

Ventricular septal defect, alone or in combination with other cardiac malformations, is the commonest form of congenital heart disease in man. Morphogenically, the ventricular septum is composed of three parts: (a) the conal septum, (b) the septum of the endocardial cushions, and (c) the muscular septum proper. Consequently, most cono-truncal abnormalities (transposition of the great arteries, tetralogy of Fallot, common truncus arteriosus) include a defect of the ventricular septum and, similarly, most endocardial cushion defects (and all complete AV canals) have a ventricular compo- nent. Isolated ventricular septal defects may occur in any of the three parts. The majority of the complex intracardiac malformations are associated with a ventricular septal defect.