gebhart/patrepeval huggingface dataset:
Abstract KP02: Functional genomics, cancer biology and targets (2015)

Abstract Recent advances in genomics now make it possible to consider enumerating all of the genetic lesions in specific cancers. These approaches will yield critical information regarding the identification, number, and types of alterations found in human tumors and are increasingly being applied prospectively to patient samples in the clinic. At the same time, complementary approach to decipher the molecular basis of malignant transformation depends upon the application of genome scale tools to annotate the function of genes involved in cancer initiation and progression. Over the past several years, we have developed genome scale loss-of-function libraries and open reading frame expression libraries that permit a systematic evaluation of genes involved in cancer initiation and maintenance. Using these libraries, we have now performed screens in a panel of human ovarian cancer cell lines to systematically identify cancer vulnerabilities. By combining these functional approaches with information derived from mapping the structural abnormalities present in cancer genomes, we have identified several new oncogenes that contribute to cancer development. The ability to systematically manipulate gene expression at genome scale now provides opportunities to investigate the function of genes involved in cancer initiation and maintenance, which will provide a framework for therapeutic strategies. Citation Format: William C. Hahn. Functional genomics, cancer biology and targets [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr KP02.
Logarithmic intensity and speckle-based motion contrast methods for human retinal vasculature visualization using swept source optical coherence tomography (2012)

We formulate a theory to show that the statistics of OCT signal amplitude and intensity are highly dependent on the sample reflectivity strength, motion, and noise power. Our theoretical and experimental results depict the lack of speckle amplitude and intensity contrasts to differentiate regions of motion from static areas. Two logarithmic intensity-based contrasts, logarithmic intensity variance (LOGIV) and differential logarithmic intensity variance (DLOGIV), are proposed for serving as surrogate markers for motion with enhanced sensitivity. Our findings demonstrate a good agreement between the theoretical and experimental results for logarithmic intensity-based contrasts. Logarithmic intensity-based motion and speckle-based contrast methods are validated and compared for in vivo human retinal vasculature visualization using high-speed swept-source optical coherence tomography (SS-OCT) at 1060 nm. The vasculature was identified as regions of motion by creating LOGIV and DLOGIV tomograms: multiple B-scans were collected of individual slices through the retina and the variance of logarithmic intensities and differences of logarithmic intensities were calculated. Both methods captured the small vessels and the meshwork of capillaries associated with the inner retina in en face images over 4 mm(2) in a normal subject.
Study of coupled split-ring resonator arrays for circular polarization selective surface (2015)

Recently, a novel class of circular polarization selective surface (CPSS) has been proposed, composed of two planar metallodielectric arrays of split ring resonators (SRR). The coupling between the two arrays is a key factor that defines the performance of the CPSS. Here we present a study of the coupling between two planar SRR arrays for various geometrical parameters and discuss their impact on CPSS performance.
Performance of Standardized Relative CBV for Quantifying Regional Histologic Tumor Burden in Recurrent High-Grade Glioma: Comparison against Normalized Relative CBV Using Image-Localized Stereotactic Biopsies (2020)

Standardization of relative CBV achieves similar performance compared with normalized relative CBV and offers an important step toward workflow optimization and consensus methodology.
Matching networks for wireless power transfer and related techniques (2023)

In one implementation, an analytical approach to determining an improved and/or optimal design of a matching network in a capacitive or inductive WPT system is provided. In one implementation, for example, a framework is provided to enable stage(s) of the network to simultaneously provide gain and compensation. The multistage matching network efficiency can be improved and/or optimized, such as by using the method of Lagrange multipliers, resulting in the optimum distribution of gain and compensation among the L-section stages.
LLN Minimal Fragment Forwarding - draft-ietf-6lo-minimal-fragment-00 (2018)

International audience
Corrigendum to: Improved upper bounds for the number of points on curves over finite fields (2007)

fin strictement personnelle du copiste est constitutive d'une infraction pnale. Toute copie ou impression de ce fichier doit contenir la prsente mention de copyright.
Short-term monocular deprivation strengthens the patched eye's contribution to binocular combination (2013)

Binocularity is a fundamental property of primate vision. Ocular dominance describes the perceptual weight given to the inputs from the two eyes in their binocular combination. There is a distribution of sensory dominance within the normal binocular population with most subjects having balanced inputs while some are dominated by the left eye and some by the right eye. Using short-term monocular deprivation, the sensory dominance can be modulated as, under these conditions, the patched eye's contribution is strengthened. We address two questions: Is this strengthening a general effect such that it is seen for different types of sensory processing? And is the strengthening specific to pattern deprivation, or does it also occur for light deprivation? Our results show that the strengthening effect is a general finding involving a number of sensory functions, and it occurs as a result of both pattern and light deprivation.
Accuracy of a First-Generation Intravenous Blood Glucose Monitoring System in Subjects with Diabetes Mellitus: A Multicenter Study (2013)

This clinical performance evaluation demonstrates that the IVBG system provides accurate and safe continuous BG measurements in healthy insulin-treated patients with diabetes.
Integrin αVβ3 can substitute for collagen‐binding β1‐integrins in vivo to maintain a homeostatic interstitial fluid pressure (2018)

Accumulated data indicate that cell-mediated contraction of reconstituted collagenous gels in vitro can serve as a model for cell-mediated control of interstitial fluid pressure (P<sub>IF</sub> ) in vivo. A central role for collagen-binding β<sub>1</sub> -integrins in both processes has been established. Furthermore, integrin α<sub>V</sub> β<sub>3</sub> takes over the role of collagen-binding β<sub>1</sub> -integrins in mediating contraction after perturbations of collagen-binding β<sub>1</sub> -integrins in vitro. Integrin α<sub>V</sub> β<sub>3</sub> is also instrumental for normalization of dermal P<sub>IF</sub> that has been lowered due to mast cell degranulation with compound 48/80 (C48/80) in vivo. Here we demonstrate a role of integrin α<sub>V</sub> β<sub>3</sub> in maintaining a long term homeostatic dermal P<sub>IF</sub> in mice lacking the collagen-binding integrin α<sub>11</sub> β<sub>1</sub> (α11<sup>-/-</sup> mice). Measurements of P<sub>IF</sub> were performed after circulatory arrest. Furthermore, cell-mediated integrin α<sub>V</sub> β<sub>3</sub> -directed contraction of collagenous gels in vitro depends on free access to a collagen site known to bind several extracellular matrix (ECM) proteins that form substrates for α<sub>V</sub> β<sub>3</sub> -directed cell attachment, such as fibronectin and fibrin. A streptococcal collagen-binding protein, CNE, specifically binds to and blocks this site on the collagen triple helix. Here we show that whereas CNE perturbed α<sub>V</sub> β<sub>3</sub> -directed and platelet-derived growth factor BB-induced normalization of dermal P<sub>IF</sub> after C48/80, it did not affect α<sub>V</sub> β<sub>3</sub> -dependent maintenance of a homeostatic dermal P<sub>IF</sub> . These data imply that dynamic modification of the ECM structure is needed during acute patho-physiological modulations of P<sub>IF</sub> but not for long-term maintenance of a homeostatic P<sub>IF</sub> . Our data thus show that collagen-binding β<sub>1</sub> -integrins, integrin α<sub>V</sub> β<sub>3</sub> and ECM structure are potential targets for novel therapy aimed at modulating oedema formation and hypovolemic shock during anaphylaxis.
TH-A-141-08: Instrument Design to Measure the Optical Properties of Reflectance and Transmittance (2013)

Purpose: To estimate performance of crystaline scintillator‐based pixelated detectors depending on the optical properties of the crystal surface (cut, etched, polished) and the septum material between each crystal. We propose a new device design to measure the optical reflectance and transmittance properties of candidate crystal‐septum structures. Methods: Using a measurement device including a laser and an arc of photodiode detectors, the reflectance of two sandwich samples that each mimic a pixel was measured: CdWCO4‐glue‐ESR‐glue‐CdWCO4 and CdWO4‐glue‐(Al‐sputtered‐ESR)‐glue‐CdWO4. Reflectance was normalized to that of ESR (a multi‐layer optical film, highly specular reflector). To provide the required range of incident light angles at the interface of interest, a BGO hemisphere with a high index of refraction (n=2.2) was glued (Meltmount, n=1.7) to the top surface of the sandwich. Results: The sandwich structure demonstrated constant reflectivity over all laser angles with reflectances of 95% and 60% for ESR and Al‐sputtered‐ESR sandwiches respectively. This is because the highest incident angle achieved at the crystal‐glue interface was only 25.8 degrees due to the large difference in refractive indices between air (n=1) and CdWO4 (n=2.2), which is below the critical angle for total internal reflection. With the BGO hemisphere added, there are two boundaries where total internal reflection can occur, and three levels of reflectivity were detected with the steps corresponding to the critical angles of 45 degrees and 54 degrees. Normalization is required to remove the influence of the Meltmount and BGO crystal from the measured reflectivities. Conclusion: The optical reflectance due to surface conditions and septum materials can be accurately measured via the addition of a high‐refractive‐index hemisphere to a sandwich structure that has equivalent characteristics to the finished pixel matrix. Reflectance and transmittance are both important to develop an efficient pixelated detector, therefore the instrument has been modified and being assembled to measure them. This work is supported by National Institutes of Health (NIH R01 CA138426) and the Richard M. Lucas Foundation. There is no conflict of interest to disclose.
Robust adaptive beamformer exploiting symmetric structure of array (2008)

A novel robust adaptive beamformer with new constraints on array magnitude response is proposed. The constraints on array magnitude are non-convex. This problem is solved by exploiting the symmetric array structure. With conjugate-symmetric array weight, the constraints on the array magnitude response is derived as linear constraints. The advantage of the proposed method is that arbitrary width of the array robust response region is available. Even the constraints on the conjugate-symmetric structure of array weight consume some degrees of freedom (DOFs), from the numerical results, it is shown that the array still has very high output signal-to-interference-plus-noise ratio (SINR).
Channel predictive proportional fair scheduling (2008)

Recent work on channel modeling and prediction has shown the feasibility of predicting the mobile radio channel, quite accurately, several milliseconds ahead in time for realistic Doppler spreads. Motivated by these results we consider opportunistic scheduling algorithms that exploit both current and future channel estimates. We demonstrate how this extra channel information can be used to improve the scheduling. Simulations show that the proposed algorithm can improve the inherent tradeoff between throughput, fairness and delay. The current approach builds on proportional fair scheduling but can also be generalized to other criteria.
Differential effects of P2‐purinoceptor antagonists on phospholipase C‐ and adenylyl cyclase‐coupled P2Y‐purinoceptors (1994)

1. Stimulation of P2Y-purinoceptors on turkey erythrocytes and many other cell types results in activation of phospholipase C. In contrast, we have observed recently that P2Y-purinoceptors on C6 rat glioma cells are not coupled to phospholipase C, but rather, inhibit adenylyl cyclase. 2. In this study we investigated the pharmacological selectivity of the P2-purinoceptor antagonists, suramin, reactive blue 2, and pyridoxal phosphate 6-azophenyl 2',4'-disulphonic acid (PPADS) for phospholipase C- and adenylyl cyclase-coupled P2Y-purinoceptors. 3. In C6 glioma cells, suramin and reactive blue 2 competitively antagonized the inhibitory effect of 2MeSATP on adenylyl cyclase (pKB = 5.4 +/- 0.2 and 7.6 +/- 0.1, respectively), whereas PPADS at concentrations up to 100 microM had no effect. 4. In contrast, in the turkey erythrocyte preparation, PPADS at concentrations up to 30 microM was a competitive antagonist of P2Y-purinoceptor-stimulated phospholipase C activity (pKB = 5.9 +/- 0.1). Suramin and reactive blue 2 produced both a shift to the right of the concentration-effect of 2MeSATP for the activation of phospholipase C and a significant decrease in the maximal inositol phosphate response. 5. Turkey erythrocytes also express a phospholipase C-coupled beta-adrenoceptor. Concentrations of PPADS that competitively inhibited the P2Y-purinoceptor-mediated response had only minimal effects on the activation of phospholipase C by beta-adrenoceptors. In contrast, suramin and reactive blue 2 produced a non-competitive inhibition, characterized by decreases in the maximal response to isoprenaline with no change in the potency of this beta-adrenoceptor agonist. 6. The differential effect of PPADS on P2Y-purinoceptors of C6 glioma cells and turkey erythrocytes adds further support to the idea that different P2Y-purinoceptor subtypes mediate coupling to adenylylcyclic and phospholipase C.
Fractography of clinical failures of indirect resin composite endocrown and overlay restorations (2021)

Fractography on clinical fractures of resin composites was enlightening. Occlusal surface fatigue degradation from cyclic loading, mode I fracture from applied mastication forces on cuspal planes, and stress concentration within the crown's central groove, indicate limitations of use of these materials for endocrowns in posterior teeth.
Development of an Ultrasonic Phased Array System for Wellbore Integrity Evaluation and Near-Wellbore Fracture Network Mapping of Injection and Production Wells in Geothermal Energy Systems (2016)

This paper documents our progress developing an ultrasound phased array system in combination with a model-based iterative reconstruction (MBIR) algorithm to inspect the health of and characterize the composition of the near-wellbore region for geothermal reservoirs. The main goal for this system is to provide a near-wellbore in-situ characterization capability that will significantly improve wellbore integrity evaluation and near well-bore fracture network mapping. A more detailed image of the fracture network near the wellbore in particular will enable the selection of optimal locations for stimulation along the wellbore, provide critical data that can be used to improve stimulation design, and provide a means for measuring evolution of the fracture network to support long term management of reservoir operations. Development of such a measurement capability supports current hydrothermal operations as well as the successful demonstration of Engineered Geothermal Systems (EGS). The paper will include the design of the phased array system, the performance specifications, and characterization methodology. In addition, we will describe the MBIR forward model derived for the phased array system and the propagation of compressional waves through a pseudo-homogenous medium.
Systematic comparison of family history and polygenic risk across 24 common diseases (2022)

Family history is the standard indirect measure of inherited susceptibility in clinical care, whereas polygenic risk scores (PRSs) have more recently demonstrated potential for more directly capturing genetic risk in many diseases. Few studies have systematically compared how these overlap and complement each other across common diseases. Within FinnGen (N = 306,418), we leverage family relationships, up to 50 years of nationwide registries, and genome-wide genotyping to examine the interplay of family history and genome-wide PRSs. We explore the dynamic for three types of family history across 24 common diseases: first- and second-degree family history and parental causes of death. Covering a large proportion of the burden of non-communicable diseases in adults, we show that family history and PRS are independent and not interchangeable measures, but instead provide complementary information on inherited disease susceptibility. The PRSs explained on average 10% of the effect of first-degree family history, and first-degree family history 3% of PRSs, and PRS effects were independent of both early- and late-onset family history. The PRS stratified the risk similarly in individuals with and without family history. In most diseases, including coronary artery disease, glaucoma, and type 2 diabetes, a positive family history with a high PRS was associated with a considerably elevated risk, whereas a low PRS compensated completely for the risk implied by positive family history. This study provides a catalogue of risk estimates for both family history of disease and PRSs and highlights opportunities for a more comprehensive way of assessing inherited disease risk across common diseases.
A highly distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes (2011)

Cephalopods possess a sophisticated array of mechanisms to achieve camouflage in dynamic underwater environments. While active mechanisms such as chromatophore patterning and body posturing are well known, passive mechanisms such as manipulating light with highly evolved reflectors may also play an important role. To explore the contribution of passive mechanisms to cephalopod camouflage, we investigated the optical and biochemical properties of the silver layer covering the eye of the California fishery squid, Loligo opalescens. We discovered a novel nested-spindle geometry whose correlated structure effectively emulates a randomly distributed Bragg reflector (DBR), with a range of spatial frequencies resulting in broadband visible reflectance, making it a nearly ideal passive camouflage material for the depth at which these animals live. We used the transfer-matrix method of optical modelling to investigate specular reflection from the spindle structures, demonstrating that a DBR with widely distributed thickness variations of high refractive index elements is sufficient to yield broadband reflectance over visible wavelengths, and that unlike DBRs with one or a few spatial frequencies, this broadband reflectance occurs from a wide range of viewing angles. The spindle shape of the cells may facilitate self-assembly of a random DBR to achieve smooth spatial distributions in refractive indices. This design lends itself to technological imitation to achieve a DBR with wide range of smoothly varying layer thicknesses in a facile, inexpensive manner.
212 Manufacturing of Porous Aluminum with Complicated Geometry by Using Die (2010)

Porous aluminum is a multifunctional material with lightweight and high energy absorption properties. In this study, near-net-shape porous aluminum using die was fabricated by friction stir processing (FSP) route precursor method. Rectangular near-net-shape porous aluminum with a porosity of approximately 70%, which was light enough to float on water, was successfully fabricated at a holding temperature of 1003K and at a holding time of 15 min.
Mechanical Properties of Mo&ndash;Nb&ndash;TiC <I>In-situ</I> Composites Synthesized by Hot-Pressing (2000)

Mo-40 mol%TiC and Mo-20 mol%Nb-40 mol%TiC in-situ composites were synthesized by hot-pressing mixed Mo, Nb and TiC powders. Both composites consist of two phases, Mo solid solution (A2) and TiC (B1), after hot-pressing at 2073 K and 70 MPa for 2 h followed by annealing at 2073 K for 24 h. Porosity of hot-pressed compacts decreased by Nb addition to Mo-40 mol%TiC. The composites have different microstructural features. Clusters consisting of fine bcc particles are observed in sizes similar to original Nb powder in Mo-20 mol%Nb-40 mol%TiC, while there are no clusters in Mo-40 mol%TiC. These composites show excellent strength superior to monolithic TiC at high temperatures. The addition of Nb to Mo-40 mol%TiC suppresses effectively intergranular fracture above 1473 K. Furthermore, fracture toughness of these composites is higher than that of monolithic TiC. Fracture toughness of Mo-20 mol%Nb-40 mol%TiC is slightly lower than that of Mo-40 mol%TiC. The obtained results are discussed in relation to microstructural characteristics.
Polystyrene Templated Porous Titania Wells for Quantum Dot Heterojunction Solar Cells (2014)

Polystyrene spheres are used to template TiO2 with a single layer of 300 nm wells which are infilled with PbS quantum dots to form a heterojunction solar cell. The porous well device has an efficiency of 5.7% while the simple planar junction is limited to 3.2%. Using a combination of optical absorption and photocurrent transient decay measurement we determined that the performance enhancement comes from a combination of enhanced optical absorption and increased carrier lifetime.