gebhart/patrepeval huggingface dataset:
Integrated genomic analyses of de novo pathways underlying atypical meningiomas (2017)

Meningiomas are mostly benign brain tumours, with a potential for becoming atypical or malignant. On the basis of comprehensive genomic, transcriptomic and epigenomic analyses, we compared benign meningiomas to atypical ones. Here, we show that the majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent SMARCB1 mutations. These tumours harbour increased H3K27me3 signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells, thereby phenocopying a more primitive cellular state. Consistent with this observation, atypical meningiomas exhibit upregulation of EZH2, the catalytic subunit of the PRC2 complex, as well as the E2F2 and FOXM1 transcriptional networks. Importantly, these primary atypical meningiomas do not harbour TERT promoter mutations, which have been reported in atypical tumours that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas and potential therapeutic targets.
Formation of Microbubbles for Targeted Ultrasound Contrast Imaging: Practical Translation Considerations (2018)

For preparation of ligand-decorated microbubbles for targeted ultrasound contrast imaging, it is important to maximize the amount of ligand associated with the bubble shell. We describe optimization of the use of a biocompatible cosurfactant in the microbubble formulation media to maximize the incorporation of targeting ligand-lipid conjugate into the microbubble shell, and thus reduce the fraction of ligand not associated with microbubbles, following amalgamation preparation. The influence of the concentration of a helper cosurfactant propylene glycol (PG) on the efficacy of microbubble preparation by amalgamation and on the degree of association of fluorescent PEG-lipid with the microbubble shell was tested. Three sets of targeted bubbles were then prepared: with VCAM-1-targeting peptide VHPKQHRGGSK(FITC)GC-PEG-DSPE, cyclic RGDfK-PEG-DSPE, selective for α<sub>V</sub>β<sub>3</sub>, and control cRADfK-PEG-DSPE, without such affinity. Microbubbles were prepared by 45 s amalgamation, with DSPC and PEG stearate as the main components of the shell, with 15% PG in aqueous saline. In vitro microbubble targeting was assessed with a parallel plate flow chamber with a recombinant receptor coated surface. In vivo targeting was assessed in MC-38 tumor-bearing mice (subcutaneous tumor in hind leg), 10 min after intravenous bolus of microbubble contrast agent (20 million particles per injection). Ultrasound imaging of the tumor and control nontarget muscle tissue in a contralateral leg was performed with a clinical scanner. Amalgamation technique with PG cosurfactant produced microbubbles at concentrations exceeding 2 × 10<sup>9</sup> particles/mL, and ∼50-60% or more of the added fluorescein-PEG-DSPE or VCAM-1-targeted fluorescent peptide was associated with microbubbles, about 2 times higher than that in the absence of PG. After intravenous injection, peptide-targeted bubbles selectively accumulated in the tumor vasculature, with negligible accumulation in nontumor contralateral leg muscle, or with control nontargeted microbubbles (assessed by contrast ultrasound imaging). For comparison, administration of RGD-decorated microbubbles prepared by traditional sonication, and purified from free peptide-PEG-lipid by repeated centrifugation, resulted in the same accumulation pattern as for translatable amalgamated microbubbles. Following amalgamation in the presence of PG, efficient transfer of ligand-PEG-lipid to microbubble shell was achieved and quantified. Purification of microbubbles from free peptide-PEG-lipid was not necessary, as proven by in vitro and in vivo targeting studies, so PG cosurfactant amalgamation technique generated peptide-targeted microbubbles are amenable for bedside preparation and clinical translation. The pathway to clinical translation is simplified by the fact that most of the materials used in this study either are on the United States Food and Drug Administration GRAS list or can be procured as pharmaceutical grade substances.
Transmission Performance Evaluation of 43Gb/s RZ-DPSK Transponder using Electrical Equalizer (2007)

We have experimentally confirmed that 43Gb/s RZ-DPSK transponder using electrical equalizer could provide good transmission performances for various applications. By optimizing the equalizer setting, it suppressed the main degradation factor effect in each system application.
Importance des corps gras dans le domaine des tensioactifs (2006)

This article is willing to show through different industrial examples the role played by the oleochemistry in the development of new surfactants. This field offers indeed a large choice of alkyl chains that can be transformed. Linked to a polar head such as a polyol, a carbohydrate or a protein derivative, these alkyl chains lead to performing bio-surfactants that show interesting toxicological and ecotoxicological profiles. This natural lipophilic source allows thus to adjust some physico-chemical parameters of the surfactant such as its geometry, its hydrophilic lipophilic balance, the type of functional groups linking its hydrophilic part to its lipophilic part, its molecular weight, etc. The emulsifying, foaming, solubilizing, biological properties can be valued in cosmetics (as excipients or actives), in the areas of veterinary additives, of detergents, in the food industry, etc.
Student loneliness through the pandemic: How, why and where? (2022)

Loneliness has emerged as a problem for individuals and society. A group whose loneliness has recently grown in severity and visibility is students in higher education. Complementing media reports and surveys of students' lockdown loneliness, this paper presents qualitative research findings on students loneliness during the COVID-19 pandemic. It explores the how, why and where of student loneliness through research co-produced with undergraduate and postgraduate students. Student-researchers investigated loneliness as a function of relationships and interactions through self-interviews and peer interviews (<i>n </i>= 46) and through objects, chosen by participants to represent their experiences of lockdown. This research led to three conclusions, each with a geographical focus. First, as the spaces in which students live and study were fragmented, interactions and relationships were disrupted. Second, students struggled to put down roots in their places of study. Without a sense of belonging-to the city and institution where they studied, and the neighbourhood and accommodation where they lived-they were more likely to experience loneliness. Third, many students were unable to progress through life transitions associated with late adolescence including leaving home, learning social skills, forming sexual relationships and emerging into adulthood. Those facing bigger changes such as bereavement struggled to process these events and spoke of feeling 'neither here nor there'-in limbo. But students displayed resilience, finding ways to cope with and mitigate their loneliness. Their coping strategies speak to the efforts of policymakers and practitioners-including those in universities, government, health and wellbeing services, and accommodation services-who are seeking ways to tackle students' (and other peoples') loneliness.
Clinically Confirmed Type 2 Diabetes Mellitus and Colorectal Cancer Risk: A Population-Based, Retrospective Cohort Study (2006)

In this population-based, retrospective cohort study, clinically confirmed type 2 DM was associated with increased CRC risk, predominantly among men. Cigarette smoking appeared to positively modify DM-associated CRC risk, which to our knowledge has not been previously reported. These data suggest that further investigation of potential interactions between endogenous and exogenous factors involved in colorectal carcinogenesis may help to clarify the magnitude and extent of CRC risk experienced by persons with type 2 DM.
Channelopathies: Decoding Disease Pathogenesis (2010)

The deconvolution of corrupted biological pathways in disease and the translation of patient-specific molecular mechanisms into tailored management algorithms have begun to extend the reach of individualized medicine from principles to practice. A case in point is the emergent deciphering of the pathobiology underlying life-threatening human diseases caused by dysfunction in adenosine triphosphate (ATP)-sensitive potassium (K(ATP)) channels. In a recent paper in Science, researchers used humanized mouse models to recapitulate a pathogenic K(ATP) channel mutation and pinpoint tissue-restricted lesions that stratify the consequences of genetic variation on disease traits. Advances in the molecular medicine of K(ATP) channelopathies offer new perspectives for personalized diagnosis and therapy.
3D Visual Perception for Self-Driving Cars using a Multi-Camera System:\n Calibration, Mapping, Localization, and Obstacle Detection (2017)

Cameras are a crucial exteroceptive sensor for self-driving cars as they are\nlow-cost and small, provide appearance information about the environment, and\nwork in various weather conditions. They can be used for multiple purposes such\nas visual navigation and obstacle detection. We can use a surround multi-camera\nsystem to cover the full 360-degree field-of-view around the car. In this way,\nwe avoid blind spots which can otherwise lead to accidents. To minimize the\nnumber of cameras needed for surround perception, we utilize fisheye cameras.\nConsequently, standard vision pipelines for 3D mapping, visual localization,\nobstacle detection, etc. need to be adapted to take full advantage of the\navailability of multiple cameras rather than treat each camera individually. In\naddition, processing of fisheye images has to be supported. In this paper, we\ndescribe the camera calibration and subsequent processing pipeline for\nmulti-fisheye-camera systems developed as part of the V-Charge project. This\nproject seeks to enable automated valet parking for self-driving cars. Our\npipeline is able to precisely calibrate multi-camera systems, build sparse 3D\nmaps for visual navigation, visually localize the car with respect to these\nmaps, generate accurate dense maps, as well as detect obstacles based on\nreal-time depth map extraction.\n
Range-Separated Stochastic Resolution of Identity: Formulation and Application to Second Order Green's Function Theory (2020)

We develop a range-separated stochastic resolution of identity approach for the $4$-index electron repulsion integrals, where the larger terms (above a predefined threshold) are treated using a deterministic resolution of identity and the remaining terms are treated using a stochastic resolution of identity. The approach is implemented within a second-order Greens function formalism with an improved $O(N^3)$ scaling with the size of the basis set, $N$. Moreover, the range-separated approach greatly reduces the statistical error compared to the full stochastic version ({\it J. Chem. Phys.} {\bf 151}, 044144 (2019)), resulting in computational speedups of ground and excited state energies of nearly two orders of magnitude, as demonstrated for hydrogen dimer chains.
An ORF323 with homology to crtE, specifying prephytoene pyrophosphate dehydrogenase, is encoded by cyanelle DNA in the eukaryotic alga Cyanophora paradoxa (1991)

Carotenoids are essential constituents of the light-harvesting and light-protective systems of photosynthetic organisms. The biochemistry of carotenoid biosynthesis in eukaryotes is known, whereas evidence for the genes specifying this biosynthetic pathway is scant. We report here the nucleotide sequence and expression of a gene likely encoding crtE (prephytoene pyrophosphate dehydrogenase). The reaction product of this enzyme is phytoene, a C40 carotenoid precursor common to all organisms. The gene is found in the cyanelle (plastid) DNA of an eukaryotic alga, Cyanophora paradoxa. The expression into protein of cyanelle crtE has been demonstrated in vitro. The identity and similarity scores of CrtE from cyanelles with the corresponding protein from the photosynthetic bacterium Rhodobacter capsulatus are 28.6 and 68.5%, respectively.
Novel one-step syntheses of cryptands and bis(aza-12-crown-4 ethers) (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel one-step syntheses of cryptands and bis(aza-12-crown-4 ethers)Krzysztof E. Krakowiak and Jerald S. BradshawCite this: J. Org. Chem. 1991, 56, 11, 3723–3725Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/jo00011a054https://doi.org/10.1021/jo00011a054research-articleACS PublicationsRequest reuse permissionsArticle Views220Altmetric-Citations18LEARN 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-Alertsclose Get e-Alerts
Chemical imaging of single 4,7,12,15-tetrakis[2.2]paracyclophane by spatially resolved vibrational spectroscopy (2007)

Single 4,7,12,15-tetrakis[2.2]paracyclophane were deposited on NiAl(110) surface at 11 K. Two adsorbed species with large and small conductivities were detected by the scanning tunneling microscope (STM). Their vibrational properties were investigated by inelastic electron tunneling spectroscopy (IETS) with the STM. Five vibrational modes were observed for the species with the larger conductivity. The spatially resolved vibrational images for the modes show striking differences, depending on the coupling of the vibrations localized on different functional groups within the molecule to the electronic states of the molecule. The vibrational modes are assigned on the basis of ab initio calculations. No IETS signal is resolved from the species with the small conductivity.
Thermal power plane enabling dual-side electrical interconnects for high-performance chip stacks: Implementation (2014)

We report on the design, implementation and performance of a laminate named Thermal Power Plane and solder joints that enable dual-side electrical interconnects (EIC) to a chip stack. This novel packaging topology with a laminate on both sides of the chip stack doubles the number of EIC thus supporting increased communication bandwidth and power density. In addition, in a two-die stack, all power TSVs can be eliminated with the advantage of gained silicon active area. The use of two laminates also enables individual test & burn-in of the dies before stack formation. The TPP needs to provide efficient heat removal and current feed in the out-of-plane and in-plane direction, respectively. An 8+1 coreless build-up laminate with aligned and stacked thermal laminate vias (TLVs) was designed and implemented. Bar-, chevron- and mesh-like copper planes with varying TLV densities were characterized. The mesh design resulted in minimal warpage and voltage drop. The bar and chevron designs result in the lowest thermal resistance. In combination with rail-shaped solder interconnects interfacing between TPP and top chip, the overall thermal resistance of the junction to cold plate of the dual-side EIC approach can outperform that of the standard single-side EIC package. The electrical DC characteristics of the TPP was also evaluated experimentally. The sheet resistance of 0.21 MΩ allows the supply of the required currents within the voltage uniformity requirements. In general, the experimental evaluation supports the feasibility of the proposed dual-side EIC concept supporting further performance and efficiency scaling of highperformance chip stacks.
The Secure Communication Interoperability Protocol (SCIP) over an HF Radio Channel (2006)

The secure communication interoperability protocol (SCIP) is a newly emerging application layer interoperability standard that is being developed for secure voice and voice band data communication between international coalition partners. It was designed to operate independently of the characteristics of underlying media layers. This paper will present the results of the first phase of an investigation into the performance of SCIP over a high frequency radio link. A simulation using the Watterson model for HF propagation was created and is described. Voice quality performance data was gathered over a range of radio configurations and channel conditions. Performance data is presented along with discussion and recommendations on future work
Supplementary Figures 1-5 from ABCG2/BCRP Expression Modulates d-Luciferin–Based Bioluminescence Imaging (2023)

Supplementary Figures 1-5 from ABCG2/BCRP Expression Modulates d-Luciferin–Based Bioluminescence Imaging
60GHz highly reliable power amplifier with 13dBm P<sub>sat</sub> 15% peak PAE in 65nm CMOS technology (2015)

A 60 GHz highly reliable single-ended two-stage Power Amplifier (PA) is fabricated for the Wireless Personal Area Network (WPAN) applications. The PA consists of a cascode power stage to reduce voltage drop and improving long-term reliability, and a common source driver stage. Output, inter-stage and input impedance matching networks are implemented with distributed elements (microstrip and slow-wave transmission lines). The PA achieves a saturated output power (Psat) of 13dBm and a maximum Power Added Efficiency (PAEmax) of 15% with 13dB gain. It consumes only 84mW and occupies 0.4mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of die area.
Biological applications of microscopic magnetic resonance imaging (1993)

The ability of MRI to provide three dimensional images of thick opaque samples in a noninvasive manner has made it an extremely important clinical tool. In addition, the large number of types of contrast mechanisms in a MR experiment offer the clinician and research scientist the possibility of adapting the image contrast to fit the problem of interest. While typical resolutions employed clinically are on the order of a millimeter, the notion of using MRI at microscopic resolutions arose early in the development of this technique. Spatial information is encoded in both the frequency and phase of the nuclear magnetic resonance signal by selective application of magnetic field gradients. Spatial resolution in biological samples is typically limited by a number of physical effects as well as signal-to-noise ratio (S/N) considerations. Estimate of the theoretical limits of resolution in the MR image arising from these phenomena range from 2 to 0.5μm. The practical spatial resolution is currently determined by the S/N which is often limited by the amount of time available to actually acquire the image (i.e. the temporal resolution). For example, a reasonable S/N clinical MR image can be obtained in about 5 minutes with a voxel (volume element) size of (1mm). We are interested in voxels down to ∼1μm on a side. Because most of the proton MR signal arises from water in biological samples and water concentration is roughly constant, the S/N change in the image will be proportional to the volume change: a factor of 10 −9 . Of course, this is true only if all experimental parameters are the same.
Catalytic potential and disturbance rejection of glycolytic kinases in the human red blood cell (2017)

Abstract The allosteric regulation of metabolic enzymes plays a key role in controlling the flux through metabolic pathways. The activity of such enzymes is traditionally described by allosteric rate laws in complex kinetic models of metabolic network function. As an alternative, we describe the fraction of the regulated enzyme that is in an active form by developing a detailed reaction network of all known ligand binding events to the enzyme. This fraction is the fundamental result of metabolic regulation as it represents the “tug of war” among the various regulators and substrates that determine the utilization of the enzyme. The active fraction corresponds to the utilization of the catalytic potential of the enzyme. Using well developed kinetic models of human red blood cell (RBC) glycolysis, we characterize the catalytic potential of its three key kinases: hexokinase (HEX), phosphofructokinase (PFK), and pyruvate kinase (PYK). We then compute their time-dependent interacting catalytic potentials. We show how detailed kinetic models of the management of the catalytic potential of the three kinases elucidates disturbance rejection capabilities of glycolysis. Further, we examine the sensitivity of the catalytic potential through an examination of existing personalized RBC models, providing a physiologically-meaningful sampling of the feasible parameter space. The graphical representation of the dynamic interactions of the individual kinase catalytic potential adjustment provides an easy way to understand how a robust homeostatic state is maintained through interacting allosteric regulatory mechanisms.
Solution Biasing for Optimized Cloud Workload Placement (2016)

We consider the cloud workload placement problem, which is a mapping of logical to physical entities, that satisfies some constraints and optimizes an objective function. We describe an efficient solution technique that is based on random search methods and uses biased statistical sampling methods. In particular, the proposed technique utilizes (1) importance sampling as a mechanism for characterizing the optimal solution through marginal distributions, (2) independent sampling via a modified Gibbs sampler with intra-sample dependency, and (3) a jumping distribution that uses conditionals derived from the relationship constraints given in the user request and cloud system topology, and the importance sampling marginal distributions as posterior distributions. We demonstrate the feasibility of our methodology using several large-size simulation experiments. In a case where an optimal solution may be obtained, we show that our method is within 20% of optimality. Since the magnitude of biasing impacts the quality of placement, we investigate the tradeoff between biasing and optimality of placement solutions.
Developing Oncology Drugs Using Virtual Patients of Vascular Tumor Diseases (2011)

This chapter contains sections titled: Introduction Modeling Angiogenesis Use of Rigorous Mathematical Analysis to Gain Insight into Drug Development Use of Angiogenesis Models in Theranostics Use of Angiogenesis Models in Drug Salvage Summary and Conclusions References