gebhart/patrepeval huggingface dataset:
Evaluation of gene mutations beyond KRAS as predictive biomarkers of response to panitumumab in a randomized, phase III monotherapy study of metastatic colorectal cancer (mCRC). (2011)

3530 Background: KRAS mutation is an established biomarker for lack of response to antiepidermal growth factor receptor (EGFR) antibodies in mCRC. We used next generation sequencing to investigate whether mutation of other genes known to be altered in CRC predict response to panitumumab. Methods: Banked formalin fixed paraffin embedded patient tumor samples from a randomized, phase III monotherapy clinical trial that compared panitumumab + best supportive care (BSC) with BSC alone (the 408 study) were sequenced. After disease progression, patients randomized to the BSC alone arm could enroll in an optional panitumumab extension study (the 194 study). Tumor samples previously analyzed for KRAS codon 12 and 13 mutations were sequenced for mutations in 9 genes: AKT1, BRAF, CTNNB1, EGFR, KRAS (codon 61), NRAS, PIK3CA, PTEN, and TP53. This analysis presents pooled efficacy data from the 408 and 194 studies by genotype. Results: In the 408 study (multimarker data presented at AACR 2010), 463 patients were randomized to panitumumab + BSC (n = 231) or BSC alone (n = 232); 176 of these BSC alone patients enrolled in the 194 study. In total, 288 patients had multimarker data available; 257 of these were treated with panitumumab monotherapy on either study (147 from study 408 and 110 from study 194). In this treated population, 22/138 (15.9%) patients with wild type (WT) KRAS tumors compared with 0/103 (0%) with mutant (MT) KRAS (codons 12, 13) tumors had an objective response (OR). OR rates (ORR) for other single genotypes within the KRAS WT subset are shown (Table). Conclusions: Implications of tumor genotype at the 9 loci for clinical outcomes (ORR and progression free survival) with panitumumab and detailed results from the aggregate analysis of the 408 and 194 studies will be presented. Genotype N ORR (%) WT KRAS (codons 12, 13) WT KRAS (codon 61) 138 15.9 MT KRAS (codon 61) 6 16.7 WT KRAS (codons 12, 13, 61) WT AKT1 121 16.5 MT AKT1 1 0 WT BRAF 107 16.8 MT BRAF 13 0 WT CTNNB1 118 15.3 MT CTNNB1 2 50.0 WT EGFR 134 16.4 MT EGFR 0 Not applicable WT NRAS 126 17.5 MT NRAS 9 0 WT PIK3CA 117 14.5 MT PIK3CA 10 20.0 WT PTEN 122 16.4 MT PTEN 9 11.1 WT TP53 50 14.0 MT TP53 84 16.7
An electrochemical approach to graphene oxide coated sulfur for long cycle life (2015)

Owing to the possibilities of achieving high theoretical energy density and gravimetric capacity, sulfur has been considered as a promising cathode material for rechargeable lithium batteries. However, sulfur shows rapid capacity fading due to the irreversible loss of soluble polysulfides and the decrease in active sites needed for conducting agents. Furthermore, the low electrical conductivity of sulfur hampers the full utilization of active materials. Here we report that graphene oxide coated sulfur composites (GO-S/CB) exhibit improved electrochemical stability as well as enhanced rate performance, evidenced by various electrochemical analyses. The cyclic voltammetry and the galvanostatic cycling analysis revealed that the GO plays key roles in homogenizing the nanocomposite structures of the electrodes, in improving the electrochemical contact, and in minimizing the loss of soluble polysulfide intermediates. An electrochemical impedance spectroscopy analysis also confirms the enhanced structural stability of the GO-S/CB composites after battery operation. As a result, the GO-S/CB exhibited excellent cycle stability and specific capacity as high as ∼723.7 mA h g(-1) even after 100 cycles at 0.5 C.
Identification of Natural Compounds with Anti-Hepatitis B Virus Activity from <i>Rheum palmatum</i> L. Ethanol Extract (2007)

The results suggested that RPE could effectively inhibit HBV. The combined anthraquinone chrysophanol 8-O-beta-D-glucoside is the major active compound in RPE and could be a promising candidate for the development of new anti-HBV drugs in the treatment of HBV infection.
Novel Prosthesis Using Silk Fibroin for Small Caliber Vascular (2005)

A novel prosthesis using silk fibroin with blending heparin and sulfonated silk fibroin was studied. Anticoagulation activities of heparin/silk fibroin and sulfonated silk fibroin/silk fibroin vascular and mechanical property results showed that heparin/silk fibroin and sulfonated silk fibroin/silk fibroin vascular could meet the requirement of small caliber grafts. This study indicated that silk fibroin could be used for developing tissue engineering biological vascular grafts that could use for human coronary or low extremity artery bypasses.
2D-to-3D Projection for Monocular and Multi-View 3D Object Detection in Outdoor Scenes (2021)

In this article, we introduce the task of multi-view RGB-based 3D object detection as an end-to-end optimization problem. In a multi-view formulation of the 3D object detection problem, several images of a static scene are used to detect objects in the scene. To address the 3D object detection problem in a multi-view formulation, we propose a novel 3D object detection method named ImVoxelNet. ImVoxelNet is based on a fully convolutional neural network. Unlike existing 3D object detection methods, ImVoxelNet works directly with 3D representations and does not mediate 3D object detection through 2D object detection. The proposed method accepts multi-view inputs. The number of monocular images in each multi-view input can vary during training and inference; actually, this number might be unique for each multi-view input. Moreover, we propose to treat a single RGB image as a special case of a multi-view input. Accordingly, the proposed method can also accept monocular inputs with no modifications. Through extensive evaluation, we demonstrate that the proposed method successfully handles a variety of outdoor scenes. Specifically, it achieves state-of-the-art results in car detection on KITTI (monocular) and nuScenes (multi-view) benchmarks among all methods that accept RGB images. The proposed method operates in real-time, which makes it possible to integrate it into the navigation systems of autonomous devices. The results of this study can be used to address tasks of navigation, path planning, and semantic scene mapping.
Selective Hydrogenation of Amides to Amines and Alcohols Catalyzed by Improved Iron Pincer Complexes (2016)

A comparative study on the synthesis, stability, and catalytic activity of various iron pincer complexes with the general formula [(R-PNHP)Fe(H) (CO) (BH4)] is reported, where R denotes the substituent of the terminal PR2-groups (R = tBu, Cy, iPr, Ph, Et). By the example of the synthesized precatalysts, it is shown that the nature of the ligands has a surprising influence on the catalytic properties of the complexes. Bulky ligands and less electron donating ligands affect the stability of the complexes, which preferably react under the loss of CO or H2 to deactivated products. In return, the reduced steric demand and the strong σ-donating properties of the Et-substituted precatalyst (2a) lead to an improved activity in the hydrogenation of esters to alcohols, compared to that of the previously reported iPr-substituted complexes. The improved activity of complex 2a is clearly demonstrated in the direct hydrogenation of amides to alcohols and amines under mild conditions.
Epidemiology and Evolution of Beta-Lactamases (2014)

Genes participating in the synthesis and metabolism of the cell wall might have a common ancestor with well-disseminated beta-lactamase genes (bla genes) in pathogenic bacteria. Moreover, some of the most successful beta-lactamases have evolved by mobilization from chromosomal bla genes in environmental bacteria, and their evolution in pathogenic bacteria has been accelerated by the extensive use of beta-lactams in the clinical field over the past 70 years. The most widespread plasmid-mediated beta-lactamases are also represented in some of these subgroups such as penicillinase from Staphylococcus aureus (group 2a) or TEM-1 and SHV-1 enzymes (group 2b) and those that have suffered important evolutionary processes in the past years such as extended spectrum beta-lactamases (ESBLs) (group 2be). The ancient evolution of beta-lactamases can now be hypothesized with the aid of structural phylogenetic analysis. The majority of bla genes encoding B1 and B2 beta-lactamases are located on the chromosome but have been recently mobilized at least twice to plasmids, once for the VIM-group and once for the IMP group. The number of studies of phylogenetic groups in Klebsiella pneumoniae isolates is scarce and has mainly focused on their relationship with chromosomal beta-lactamases. The production of virulence markers has been associated with specific clones. This is the case of extraintestinal pathogenic CTX-M-producing Escherichia coli isolates that were compared in a recent study with non-ESBL producers.
Eudragit RL and RS Pseudolatices: Properties and Performance in Pharmaceutical Coating as a Controlled Release Membrane for Theophylline Pellets (1989)

Theophylline Active pellets were coated with Eudragit RL and RS pseudolatices in a fluidized bed. The effects of polymer ratio, additional oven drying, addition of dispersed solids, and addition of water miscible organic solvents on sustained drug release through the lates film were determined by using a modified U.S.P. Paddle dissolution method.The release rate of theophylline can be varied by changing the polymer ratio. permeability to the drug increases with an increase in the content of Eudragit RL. Additional oven drying at 60°C for 10 hours caused no significant change in the dissolution profiles. The addition of dispersed solids such as talcum and silica resulted in an increase in drug release rate. There is no significant change in dissolution profiles when 50% methanol or acetone was added to the Eudragit RS pseudolatex.
Solar thermophotovoltaics: reshaping the solar spectrum (2018)

Recently, there has been increasing interest in utilizing solar thermophotovoltaics (STPV) to convert sunlight into electricity, given their potential to exceed the Shockley-Queisser limit. Encouragingly, there have also been several recent demonstrations of improved system-level efficiency as high as 6.2%. In this work, we review prior work in the field, with particular emphasis on the role of several key principles in their experimental operation, performance, and reliability. In particular, for the problem of designing selective solar absorbers, we consider the trade-off between solar absorption and thermal losses, particularly radiative and convective mechanisms. For the selective thermal emitters, we consider the tradeoff between emission at critical wavelengths and parasitic losses. Then for the thermophotovoltaic (TPV) diodes, we consider the trade-off between increasing the potential short-circuit current, and maintaining a reasonable opencircuit voltage. This treatment parallels the historic development of the field, but also connects early insights with recent developments in adjacent fields.With these various components connecting in multiple ways, a system-level end-to-end modeling approach is necessary for a comprehensive understanding and appropriate improvement of STPV systems. This approach will ultimately allow researchers to design STPV systems capable of exceeding recently demonstrated efficiency values.
Electromagnetic micromirror array with single-crystal silicon mirror plate and aluminum spring (2003)

We have designed and fabricated an addressable 4 × 4 array of micromirrors capable of providing up to 90° of angular deflection. Each micromirror comprises a single-crystalline silicon mirror plate supported by aluminum springs, which provides an extremely flat reflective surface and a compliant spring material that enables the integration of the device into a limited area without mitigating its performance (i.e., total angular deflection). The device is fabricated using a combination of surface and bulk micromachining processes, such as electroplating, bulk wet etching and XeF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> etch processes. Selective actuation is accomplished by the use of an electrostatic clamping force on each mirror plate. A mirror rotation angle of more than 80° can be obtained by applying an external magnetic field, and this angle can be further increased by the use of an electrostatic force. The designed structure can be used in microphotonic applications.
Abstract 5774: Effect of extrinsic and intrinsic solid stress on tumor spheroid growth (2017)

Abstract Growth-induced intrinsic solid stress and adaptive response to extrinsic mechanical cues have been recognized as major hurdles to overcome in cancer treatment and any approach that could significantly modulate these parameters would have an impact in improving therapies. An attracting in vitro model to explore this issue is the Multicellular Tumor Spheroid, a 3D culture model reproducing the non-vascularized microtumor environment, proliferation gradient and cellular interactions. To explore and assess spheroid growth-induced solid stress, we couple biological approach to the application of mechanics and modeling. We adapted a method, which consist in partial sectioning of the microtumor and measuring tissue relaxation parameters. Using this strategy, we showed that cell proliferation induced the accumulation of intrinsic mechanical constraint. To investigate the consequence of the accumulation of solid stress at the cell scale, we analyzed 3D cellular organization within spheroids. Using 3D light sheet microscopy (LSM) visualization on optically cleared spheroids combined with 3D reconstruction and automatic algorithms, we were able to determine cell density, nuclear orientation and nuclear shape in whole 3D spheroids. We found that stress accumulation is associated with an increase in cell density and a regionalization of nuclei organization. We also explored the impact of extrinsic stress in 3D culture condition under constraint. We found that mechanical constraint and cytoskeleton control nuclei orientation and using live 3D LSM microscopy we show that mechanical constraint induces an actin cytoskeleton-dependent prometaphase delay. We anticipate that this work will provide key information and parameters to improve our knowledge of the crosstalk between mechanical parameters and tumor growth. Citation Format: Ludivine Guillaume, Annaick Desmaison, Bernard Ducommun, Valérie Lobjois. Effect of extrinsic and intrinsic solid stress on tumor spheroid growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5774. doi:10.1158/1538-7445.AM2017-5774
Dynamics and control of the zero inertia powertrain (2001)

Due to rotating inertias within the engine and transmission, the response of a vehicle during large engine speed transients may appear reluctant or even counteracting.\nReminiscent of comparable behaviour in aircraft jet-propulsion, this phenomenon is also referred to as jet-start.\nTo overcome this behaviour, a CVT powertrain is augmented with a plenetary gear set and a compact steel flywheel.\nThe new transmission seamlessly combines two contradictory features: the driveability in terms of the pedal-to-wheel response is greatly improved and a large leap towards optimal fuel economy can be made.\nThis is achieved by cruising the vehicle at extremely low engine speeds, using the large ratiocoverage of the CVT.\nThe flywheel acts as a "peak shaver" during speed shifts: it delivers power during engine acceleration and absorbs kinetic energy during engine decelerations. In this paper, system dynamics and control aspects of the new powertrain are discussed.
Supplying volunteer consultancy expertise to developing countries (2004)

Not all volunteer engineering services are provided purely for community-related projects. Developing economies also need a flourishing private sector, yet many of their businesses lack the skills to overcome technical and managerial challenges and are unable to buy in the necessary advice. This paper describes the wide-ranging volunteer consultancy services provided by British Executive Services Overseas to organisations in both the public and private sectors worldwide. The assignments also provide a valuable opportunity for volunteers and their sponsors to get involved at the earliest stages of major development projects.
Branchio‐oto‐renal syndrome associated mutations in Eyes Absent 1 result in loss of phosphatase activity (2006)

The Eyes Absent (Eya) proteins are tyrosine phosphatases and transcriptional activators involved in cell-fate determination and organ development. Mutations in the gene encoding Eya homologue 1 have been implicated in the multi-organ developmental disorder branchio-oto-renal syndrome (BOR) and in ocular defects. Here we report that BOR-associated mutations lead to a loss of phosphatase activity in Eya1 proteins, while mutations associated with ocular defects yield Eya1 proteins with near normal levels of phosphatase activity. Furthermore we demonstrate that the N-terminal domain attenuates the catalytic activity of Eya suggesting a mechanism of regulation.
Infrared generation by filamentation in air of a spectrally shaped laser beam (2011)

We demonstrated the generation of infrared radiation by filamentation of a spectrally shaped femtosecond laser beam. The spectrum is divided in two distinctive parts using an acousto-optic programmable dispersive filter (AOPDF) as a pulse shaper, resulting in two pulses of different colors. One pulse is frequency doubled and the beams are then focused to produce an optical filament. Efficient infrared generation occurred in the filament zone through the four-wave mixing interaction. This in-line setup allowed perfect spatial overlap of the pulses, fine control of the relative delay and the remote control of the infrared spectral distribution through spectral shaping of the initial femtosecond laser beam via the AOPDF.
Echocardiographic predictors of nonrheumatic atrial fibrillation. The Framingham Heart Study. (1994)

In this elderly, population-based sample, left atrial enlargement, increased left ventricular wall thickness, and reduced left ventricular fractional shortening were predictive of risk for nonrheumatic atrial fibrillation. These echocardiographic precursors offer prognostic information beyond that provided by traditional clinical atrial fibrillation risk factors.
Decrease in Membrane Phospholipid Unsaturation Induces Unfolded Protein Response (2010)

Various kinds of fatty acids are distributed in membrane phospholipids in mammalian cells and tissues. The degree of fatty acid unsaturation in membrane phospholipids affects many membrane-associated functions and can be influenced by diet and by altered activities of lipid-metabolizing enzymes such as fatty acid desaturases. However, little is known about how mammalian cells respond to changes in phospholipid fatty acid composition. In this study we showed that stearoyl-CoA desaturase 1 (SCD1) knockdown increased the amount of saturated fatty acids and decreased that of monounsaturated fatty acids in phospholipids without affecting the amount or the composition of free fatty acid and induced unfolded protein response (UPR), evidenced by increased expression of C/EBP homologous protein (CHOP) and glucose-regulated protein 78 (GRP78) mRNAs and splicing of Xbox-binding protein 1 (XBP1) mRNA. SCD1 knockdown-induced UPR was rescued by various unsaturated fatty acids and was enhanced by saturated fatty acid. Lysophosphatidylcholine acyltransferase 3 (LPCAT3), which incorporates preferentially polyunsaturated fatty acids into phosphatidylcholine, was up-regulated in SCD1 knockdown cells. Knockdown of LPCAT3 synergistically enhanced UPR with SCD1 knockdown. Finally we showed that palmitic acid-induced UPR was significantly enhanced by LPCAT3 knockdown as well as SCD1 knockdown. These results suggest that a decrease in membrane phospholipid unsaturation induces UPR.
Visualizing and Understanding Neural Models in NLP (2015)

While neural networks have been successfully applied to many NLP tasks the resulting vector-based models are very difficult to interpret. For example it's not clear how they achieve {\em compositionality}, building sentence meaning from the meanings of words and phrases. In this paper we describe four strategies for visualizing compositionality in neural models for NLP, inspired by similar work in computer vision. We first plot unit values to visualize compositionality of negation, intensification, and concessive clauses, allow us to see well-known markedness asymmetries in negation. We then introduce three simple and straightforward methods for visualizing a unit's {\em salience}, the amount it contributes to the final composed meaning: (1) gradient back-propagation, (2) the variance of a token from the average word node, (3) LSTM-style gates that measure information flow. We test our methods on sentiment using simple recurrent nets and LSTMs. Our general-purpose methods may have wide applications for understanding compositionality and other semantic properties of deep networks , and also shed light on why LSTMs outperform simple recurrent nets,
A Method for Making Inorganic and Hybrid (Organic/Inorganic) Fibers and Vesicles with Diameters in the Submicrometer and Micrometer Range via Sol−Gel Chemistry and Electrically Forced Liquid Jets (2003)

Electrically driven liquid jets are combined with sol-gel methods to design vesicles and fibers made from inorganic oxides and hybrid materials with diameters in the micrometer and submicrometer range. The proposed materials synthesis method benefits greatly from the maturity of sol-gel chemistry and the generalities of a structure-directing phenomenon that is physical in nature.
Verisig: verifying safety properties of hybrid systems with neural network controllers (2018)

This paper presents Verisig, a hybrid system approach to verifying safety properties of closed-loop systems using neural networks as controllers. Although techniques exist for verifying input/output properties of the neural network itself, these methods cannot be used to verify properties of the closed-loop system (since they work with piecewise-linear constraints that do not capture non-linear plant dynamics). To overcome this challenge, we focus on sigmoid-based networks and exploit the fact that the sigmoid is the solution to a quadratic differential equation, which allows us to transform the neural network into an equivalent hybrid system. By composing the network's hybrid system with the plant's, we transform the problem into a hybrid system verification problem which can be solved using state-of-the-art reachability tools. We show that reachability is decidable for networks with one hidden layer and decidable for general networks if Schanuel's conjecture is true. We evaluate the applicability and scalability of Verisig in two case studies, one from reinforcement learning and one in which the neural network is used to approximate a model predictive controller.
Phase Transitions in Multiferroic BiFeO3 Crystals, Thin‐Layers, and Ceramics. Enduring Potential for a Single Phase, Room‐Temperature Magnetoelectric ′Holy Grail′ (2007)

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