gebhart/patrepeval huggingface dataset:
Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microarrays Using Pro-Q− Diamond Dye Technology (2005)

The human genome is estimated to contain 30,000 to 75,000 genes, but as a result of alternative mRNA splicing and protein posttranslational modifications, the human proteome may contain a million or more proteins. Of the potential posttranslational modifications, phosphorylation by protein kinases is of increasing importance and interest because of its involvement in many essential cellular processes such as metabolism, transcription, cell-cycle regulation, and apoptosis, as well as intercellular communication. The malfunction of these and other kinase-regulated processes is often manifested in clinical disease states.
Rapid morphologic changes to microglial cells and upregulation of mixed microglial activation state markers induced by P2X7 receptor stimulation and increased intraocular pressure (2021)

P2X7 receptor stimulation induced rapid morphological activation of microglial cells, including process retraction and cell body enlargement, and upregulation of markers linked to both M1- and M2-type activation. Parallel responses accompanied IOP elevation, suggesting ATP release and P2X7 receptor stimulation influence the early microglial response to increased pressure.
Crystalloid versus cold blood cardioplegia in patients operated on for myocardial revascularisation. (1996)

Due to their position deep in the pelvis, the classical surgical treatment of iliac artery aneurysm leads to a high morbidity and mortality rate. The transfemoral percutaneous repair of these aneurysms is now possible thanks to a new device the endoprosystem I from "Mintech". We began in 1994 a study including radiological, cardiac and vascular centers all of them skilled in endovascular procedures. 27 patients entered the study: 1 patient died, 2 attempt failed and 2 presented leakage: the immediate failure rate was then 18.5%. For the late result (min 6, Max 19, mean 12 months) we had 1 thrombosis treated by surgery, 1 restenosis treated by PTA. We did not see any polyester dilatation or reactivation of aneurysm at the scan control at one year. We conclude that the percutaneous treatment of iliac aneurysm is possible and safe but we need long term result to validate the method.
Spiral phyllotaxis: The natural way to construct a 3D radial trajectory in MRI (2011)

While radial 3D acquisition has been discussed in cardiac MRI for its excellent results with radial undersampling, the self-navigating properties of the trajectory need yet to be exploited. Hence, the radial trajectory has to be interleaved such that the first readout of every interleave starts at the top of the sphere, which represents the shell covering all readouts. If this is done sub-optimally, the image quality might be degraded by eddy current effects, and advanced density compensation is needed. In this work, an innovative 3D radial trajectory based on a natural spiral phyllotaxis pattern is introduced, which features optimized interleaving properties: (1) overall uniform readout distribution is preserved, which facilitates simple density compensation, and (2) if the number of interleaves is a Fibonacci number, the interleaves self-arrange such that eddy current effects are significantly reduced. These features were theoretically assessed in comparison with two variants of an interleaved Archimedean spiral pattern. Furthermore, the novel pattern was compared with one of the Archimedean spiral patterns, with identical density compensation, in phantom experiments. Navigator-gated whole-heart coronary imaging was performed in six healthy volunteers. High reduction of eddy current artifacts and overall improvement in image quality were achieved with the novel trajectory.
The Laptop Orchestra as Classroom (2008)

March 01 2008 The Laptop Orchestra as Classroom Ge Wang, Ge Wang *Department of Computer Science, Princeton University, Princeton, New Jersey 08544 USA gewang@cs.princeton.edu, prc@cs.princeton.edu Search for other works by this author on: This Site Google Scholar Dan Trueman, Dan Trueman †Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Search for other works by this author on: This Site Google Scholar Scott Smallwood, Scott Smallwood †Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Search for other works by this author on: This Site Google Scholar Perry R. Cook Perry R. Cook *Department of Computer Science, Princeton University, Princeton, New Jersey 08544 USA gewang@cs.princeton.edu, prc@cs.princeton.edu†Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Search for other works by this author on: This Site Google Scholar Author and Article Information Ge Wang *Department of Computer Science, Princeton University, Princeton, New Jersey 08544 USA gewang@cs.princeton.edu, prc@cs.princeton.edu Dan Trueman †Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Scott Smallwood †Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Perry R. Cook *Department of Computer Science, Princeton University, Princeton, New Jersey 08544 USA gewang@cs.princeton.edu, prc@cs.princeton.edu†Princeton University, Department of Music, Woolworth Center, Princeton, New Jersey 08544 USA dan@music.princeton.edu, skot@music.princeton.edu Online ISSN: 1531-5169 Print ISSN: 0148-9267 © 2008 Massachusetts Institute of Technology2008 Computer Music Journal (2008) 32 (1): 26–37. https://doi.org/10.1162/comj.2008.32.1.26 Connected Content A correction has been published: Erratum: The Laptop Orchestra as Classroom Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn Email Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Ge Wang, Dan Trueman, Scott Smallwood, Perry R. Cook; The Laptop Orchestra as Classroom. Computer Music Journal 2008; 32 (1): 26–37. doi: https://doi.org/10.1162/comj.2008.32.1.26 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsComputer Music Journal Search Advanced Search This content is only available as a PDF. © 2008 Massachusetts Institute of Technology2008 Article PDF first page preview Close Modal You do not currently have access to this content.
A compact UWB CPW-fed antenna with inverted L-shaped slot for WLAN band notched characteristics (2017)

The purpose of this draft is to introduce a compact CPW-fed antenna with WLAN band notched characteristics. For band notched characteristics, an inverted L-shaped structure is used on the surface of radiator. The proposed design has overall size of 25 × 25 × 1.6 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and covers the entire UWB spectrum from 3.02 GHz to 11.34 GHz except the notch band from 4.9 GHz to 6.2 GHz. High concentration of surface current is shown on the inner side of antenna surface and inverted L-shaped stub, when the design is simulated at 5.5 GHz to show the band notch affect. The simulated results in terms of return loss, surface current distribution and VSWR exhibit good antenna performance over the complete spectrum. The validity of the proposed design is also shown by comparing the simulated results with the measured results.
System Spectral Efficiency Analysis of a 2-Link Ad Hoc Network (2007)

This paper analyzes the system spectral efficiency of a 2-link ad hoc network. The analysis shows that there are exactly three operating points that maximize system capacity: either both links transmit with maximum power simultaneously; or one single link transmits with maximum power while the other is silent. The impact of the scheduling policy on the system spectral efficiency is also studied: simultaneous transmission or sequential access where the two links share the medium by dedicated time/frequency slots without causing interference. An exhaustive numerical search over a wide range of pathloss parameters shows that sequential transmission is superior to simultaneous transmission in about two third of the cases. Even when simultaneous transmission outperforms sequential transmission, the gains are typically not substantial. Furthermore, we show that in case of simultaneous transmission power control causes only marginal degradation in terms of system spectral efficiency, while transmitting with maximum power pays off for sequential transmission. This highlights the importance of the joint optimization of power and rate adaptation together with scheduling for power constraint ad hoc networks.
Scalable image reconstruction in optical tomography using deep priors (2021)

Two features desired in 3D optical tomographic image reconstruction algorithm are the ability to reduce imaging artifacts and to do fast processing of large data volumes. Traditional iterative algorithms are impractical in this context due to their heavy computational and memory requirements. We propose and experimentally validate a novel scalable iterative mini-batch algorithm (SIMBA) for fast and high-quality optical tomographic imaging. SIMBA enables high-quality imaging by combining two complementary information sources: the physics of the imaging system characterized by its forward model and the imaging prior characterized by a denoising deep neural net. SIMBA easily scales to very large 3D tomographic datasets by processing only a small subset of measurements at each iteration. We validate SIMBA on intensity diffraction tomography (IDT). Our results show that SIMBA can significantly reduce the computational burden of 3D image formation without sacrificing the imaging quality.
Creating the Mood (2015)

Mood affects the decisions we make and our attitudes toward work and the people with whom we work. The availability of peripheral and focal information also affects the quality and speed of decision-making processes. We are exploring ways to use ambient lighting, music, and images over the course of group meetings in order to understand how these ambient elements affect the quality of meetings, people's attitudes, and the decisions made.
Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations (2017)

Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
Coincident-frequency entanglement via extended phase matching (2005)

We demonstrate a source of entangled photon pairs with identical frequency spectra. An Hong-Ou-Mandel interferometric measurement of this source shows a high visibility of 85% under pulsed pumping and without any spectral filtering.
Mechanism for Specificity by HMG-1 in Enhanceosome Assembly (2000)

Assembly of enhanceosomes requires architectural proteins to facilitate the DNA conformational changes accompanying cooperative binding of activators to a regulatory sequence. The architectural protein HMG-1 has been proposed to bind DNA in a sequence-independent manner, yet, paradoxically, it facilitates specific DNA binding reactions in vitro. To investigate the mechanism of specificity we explored the effect of HMG-1 on binding of the Epstein-Barr virus activator ZEBRA to a natural responsive promoter in vitro. DNase I footprinting, mutagenesis, and electrophoretic mobility shift assay reveal that HMG-1 binds cooperatively with ZEBRA to a specific DNA sequence between two adjacent ZEBRA recognition sites. This binding requires a strict alignment between two adjacent ZEBRA sites and both HMG boxes of HMG-1. Our study provides the first demonstration of sequence-dependent binding by a nonspecific HMG-box protein. We hypothesize how a ubiquitous, nonspecific architectural protein can function in a specific context through the use of rudimentary sequence recognition coupled with cooperativity. The observation that an abundant architectural protein can bind DNA cooperatively and specifically has implications towards understanding HMG-1's role in mediating DNA transactions in a variety of enzymological systems.
A Chemical Strategy toward Novel Brain-Penetrant EZH2 Inhibitors (2022)

Aberrant gene-silencing through dysregulation of polycomb protein activity has emerged as an important oncogenic mechanism in cancer, implicating polycomb proteins as important therapeutic targets. Recently, an inhibitor targeting EZH2, the methyltransferase component of PRC2, received U.S. Food and Drug Administration approval following promising clinical responses in cancer patients. However, the current array of EZH2 inhibitors have poor brain penetrance, limiting their use in patients with central nervous system malignancies, a number of which have been shown to be sensitive to EZH2 inhibition. To address this need, we have identified a chemical strategy, based on computational modeling of pyridone-containing EZH2 inhibitor scaffolds, to minimize P-glycoprotein activity, and here we report the first brain-penetrant EZH2 inhibitor, TDI-6118 (compound <b>5</b>). Additionally, in the course of our attempts to optimize this compound, we discovered TDI-11904 (compound <b>21</b>), a novel, highly potent, and peripherally active EZH2 inhibitor based on a 7 member ring structure.
Validation and Characterization of Five Distinct Novel Inhibitors of Human Cytomegalovirus (2020)

The critical consequences of human cytomegalovirus (HCMV) infection in the transplant population and in congenitally infected infants, the limited treatment options for HCMV, and the rise of resistant mutants toward existing therapies has fueled the search for new anti-HCMV agents. A pp28-luciferase recombinant HCMV was used as a reporter system for high-throughput screening of HCMV inhibitors. Approximately 400 000 compounds from existing libraries were screened. Subsequent validation assays using resynthesized compounds, several virus strains, and detailed virology assays resulted in the identification of five structurally unique and selective HCMV inhibitors, active at sub to low micromolar concentrations. Further characterization revealed that each compound inhibited a specific stage of HCMV replication. One compound was also active against herpes simplex virus (HSV1 and HSV2), and another compound was active against Epstein-Barr virus (EBV). Drug combination studies revealed that all five compounds were additive with ganciclovir or letermovir. Future studies will focus on optimization of these new anti-HCMV compounds along with mechanistic studies.
Steel beam behaviour in standard and natural fires : Comparison of FE modelling and hand calculation procedures (2014)

Steel beam behaviour in standard and natural fires : Comparison of FE modelling and hand calculation procedures
Covalently attached liquids as protective coatings (2020)

Abstract Covalently attached liquids provide a liquid–liquid surface interaction for contacting contaminants, typically achieved through use of a polydimethylsiloxane linear polymer bound to the surface at one end. The attached dimethylsiloxane polymer chain retains liquid‐like mobility through bending and rotational motions, distinguishing the coatings from those formed by crosslinked polydimethylsiloxane or branched polymer chains. Here, covalently attached liquids are reviewed and their potential for application as topcoat treatments is discussed. This review focuses on a new use scenario: prevention of chemical contamination. When allowed to age in place, chemical contaminants tend to penetrate into painted surfaces. Standard decontamination processes can fail to remove the chemicals within the paint layer, resulting in secondary exposure hazards when environmental conditions change. Covalent liquid coatings provide repellency and shedding behaviors. This review highlights the failure of typical wetting evaluations in predicting performance for the new application as well as the potential of the coatings in enhancing chemical resistance for painted surfaces. Potential methods for further improvements are also discussed. Published 2020. This article is a U.S. Government work and is in the public domain in the USA
Effect of either Gamma-Tocotrienol or a Tocotrienol Mixture on the Plasma Lipid Profile in Hamsters (2002)

This study provides further evidence that tocotrienols lower total cholesterol and low density lipoprotein plasma levels in hamsters and that gamma-tocotrienol is a more potent agent than a mixture of tocotrienols.
GMP Manufacturing and IND-Enabling Studies of a Recombinant Hyperimmune Globulin Targeting SARS-CoV-2 (2022)

Conventionally, hyperimmune globulin drugs manufactured from pooled immunoglobulins from vaccinated or convalescent donors have been used in treating infections where no treatment is available. This is especially important where multi-epitope neutralization is required to prevent the development of immune-evading viral mutants that can emerge upon treatment with monoclonal antibodies. Using microfluidics, flow sorting, and a targeted integration cell line, a first-in-class recombinant hyperimmune globulin therapeutic against SARS-CoV-2 (GIGA-2050) was generated. Using processes similar to conventional monoclonal antibody manufacturing, GIGA-2050, comprising 12,500 antibodies, was scaled-up for clinical manufacturing and multiple development/tox lots were assessed for consistency. Antibody sequence diversity, cell growth, productivity, and product quality were assessed across different manufacturing sites and production scales. GIGA-2050 was purified and tested for good laboratory procedures (GLP) toxicology, pharmacokinetics, and in vivo efficacy against natural SARS-CoV-2 infection in mice. The GIGA-2050 master cell bank was highly stable, producing material at consistent yield and product quality up to >70 generations. Good manufacturing practices (GMP) and development batches of GIGA-2050 showed consistent product quality, impurity clearance, potency, and protection in an in vivo efficacy model. Nonhuman primate toxicology and pharmacokinetics studies suggest that GIGA-2050 is safe and has a half-life similar to other recombinant human IgG1 antibodies. These results supported a successful investigational new drug application for GIGA-2050. This study demonstrates that a new class of drugs, recombinant hyperimmune globulins, can be manufactured consistently at the clinical scale and presents a new approach to treating infectious diseases that targets multiple epitopes of a virus.
A Study of the Dispersity of Catalytic Sites in Ethylene/Propylene Copolymerization Through Computer-Assisted13C NMR Analysis (1996)

Abstract A series of ethylene(E)/propylene(P) copolymers covering a large range of compositions is obtained by a new solution copolymerization process. The catalyst system consists of a high-activity, high-regioselectivity and high-stereospecificity Ti complex supported on MgCl2. The cocatalyst is triethylaluminum treated with diphenyldimethoxysilane. The polymers are studied by 13C NMR, and the E- and P-centered triads analyzed via the computer-assisted analytical approach. Through a systematic analysis, one can determine the minimum number of components that are needed to fit the data. Each component would correspond to a family of similar catalytic sites. The reactivity ratios (rE and rP ) of each family of active sites and the component weight factor (related to the catalytic activity) are also determined.
The Frequency and Degree of Cosuppression by Sense Chalcone Synthase Transgenes Are Dependent on Transgene Promoter Strength and Are Reduced by Premature Nonsense Codons in the Transgene Coding Sequence. (1997)

By comparing the effects of strong and weak promoters that drive sense chalcone synthase (Chs) transgenes in large populations of independently transformed plants, we show here that a strong transgene promoter is required for high-frequency cosuppression of Chs genes and for production of the full range of cosuppression phenotypes. In addition, sense Chs transgenes driven by a cauliflower mosaic virus 35S promoter possessing a single copy of the upstream activator region (UAR) were found to produce a significantly lower degree of cosuppression than they did when the transgene promoter possessed two or four copies of the UAR. It has been shown elsewhere that 35S promoter strength increases with increasing UAR copy number. Frameshift mutations producing early nonsense codons in the Chs transgene were found to reduce the frequency and the degree of cosuppression. These results suggest that promoter strength and transcript stability determine the degree of cosuppression, supporting the hypothesis that sense cosuppression is a response to the accumulation of transcripts at high concentrations. This conclusion was shown to apply to single-copy transgenes but not necessarily to inversely repeated transgenes. The results presented here also have significance for efficient engineering of cosuppression phenotypes for use in research and agriculture.
Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects (2014)

The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbor an Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of NatA, the major human NAT involved in the co-translational acetylation of proteins. Structural models and molecular dynamics simulations of the human NatA and its S37P mutant highlight differences in regions involved in catalysis and at the interface between Naa10 and the auxiliary subunit hNaa15. Biochemical data further demonstrate a reduced catalytic capacity and an impaired interaction between hNaa10 S37P and Naa15 as well as Naa50 (NatE), another interactor of the NatA complex. N-Terminal acetylome analyses revealed a decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells, supporting the genetic findings and our hypothesis regarding reduced Nt-acetylation of a subset of NatA/NatE-type substrates as one etiology for Ogden syndrome. Furthermore, Ogden syndrome fibroblasts display abnormal cell migration and proliferation capacity, possibly linked to a perturbed retinoblastoma pathway. N-Terminal acetylation clearly plays a role in Ogden syndrome, thus revealing the in vivo importance of N-terminal acetylation in human physiology and disease.