gebhart/patrepeval huggingface dataset:
Electroacoustic miniaturized DNA-biosensor (2007)

A micrometer-sized electroacoustic DNA-biosensor was developed. The device included a thin semi-crystalline polyethylene terephthalate (PET) dielectric layer with two Ag microband electrodes on one side and a DNA thiol-labeled monolayer adsorbed on a gold surface on the other. A resonance wave was observed at 29 MHz with a network analyzer, upon AC voltage application between the two Ag electrodes, corresponding to electromechanical coupling induced by molecular dipoles of the PET polymer chain in the dielectric layer. It was found that the device size and geometry were well adapted to detect DNA hybridization, by measuring the capacity of the resonance response evolution: hybridization induced polarization of the dielectric material that affected the electromechanical coupling established in the dielectric layer. The 0.2 mm(2) sensor sensitive area allows detection in small volumes and still has higher detection levels for bioanalytical applications, the non-contact configuration adopted avoids electric faradic reactions that may damage biosensor sensitive layers, and finally, PET is a costless raw material, easy to process and well adapted for large scale production. The well-balanced technological and economic advantages of this kind of device make it a good candidate for biochip integration.
Optical near-field and thermal nanolithography using organic dry developing photoresist (2005)

A combination of new organic photoresist films based on naphthoquinone with a conventional AFM using a tapered fibre tip as a near-field source enables the development of 'real time' dry process nano-lithography. The methodology of the adaptation of these films as well as the system configuration for a nano-scale fabrication will be described. Using these materials the exposure can be performed either by the optical near field or nano-thermal effect to achieve positive or negative lithography. Sub-wavelength gratings fabricated using this system with a variable line width down to 45 nm will be demonstrated.
Set of five related photoluminescence defects in silicon formed through nitrogen-carbon interactions (1987)

We study four new defect photoluminescence lines N2 (758.0 meV), N3 (761.5 meV), N4 (767.4 meV), and N5 (772.4 meV) appearing in silicon after nitrogen implantation. The defects are closely related to the N1 (745.6 meV) defect recently associated with single nitrogen and carbon atoms. It is demonstrated here by annealing studies and isotope shifts that the new defects incorporate nitrogen and carbon as well, and that N3, N4, and N5 defects need additional interactions with other impurities (probably oxygen) to form. The optical properties suggest that N1--N5 defects form a set of defects with similar basic N-C configurations.
Data from Genome-Wide Expression Profiling Reveals EBV-Associated Inhibition of MHC Class I Expression in Nasopharyngeal Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;To identify the molecular mechanisms by which EBV-associated epithelial cancers are maintained, we measured the expression of essentially all human genes and all latent EBV genes in a collection of 31 laser-captured, microdissected nasopharyngeal carcinoma (NPC) tissue samples and 10 normal nasopharyngeal tissues. Global gene expression profiles clearly distinguished tumors from normal healthy epithelium. Expression levels of six viral genes (&lt;i&gt;EBNA1, EBNA2, EBNA3A, EBNA3B, LMP1&lt;/i&gt;, and &lt;i&gt;LMP2A&lt;/i&gt;) were correlated among themselves and strongly inversely correlated with the expression of a large subset of host genes. Among the human genes whose inhibition was most strongly correlated with increased EBV gene expression were multiple MHC class I HLA genes involved in regulating immune response via antigen presentation. The association between EBV gene expression and inhibition of MHC class I HLA expression implies that antigen display is either directly inhibited by EBV, facilitating immune evasion by tumor cells, and/or that tumor cells with inhibited presentation are selected for their ability to sustain higher levels of EBV to take maximum advantage of EBV oncogene-mediated tumor-promoting actions. Our data clearly reflect such tumor promotion, showing that deregulation of key proteins involved in apoptosis (BCL2-related protein A1 and Fas apoptotic inhibitory molecule), cell cycle checkpoints (AKIP, SCYL1, and NIN), and metastasis (matrix metalloproteinase 1) is closely correlated with the levels of EBV gene expression in NPC. (Cancer Res 2006; 66(16): 7999-8006)&lt;/p&gt;&lt;/div&gt;
ChemInform Abstract: Three‐Component Synthesis of Cryofluorescent 2,4‐Disubstituted 3H‐1,5‐Benzodiazepines — Conformational Control of Emission Properties. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Draft consensus guidelines for diagnosis and treatment of Shwachman‐Diamond syndrome (2011)

Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by pancreatic exocrine insufficiency and bone marrow failure, often associated with neurodevelopmental and skeletal abnormalities. Mutations in the SBDS gene have been shown to cause SDS. The purpose of this document is to provide draft guidelines for diagnosis, evaluation of organ and system abnormalities, and treatment of hematologic, pancreatic, dietary, dental, skeletal, and neurodevelopmental complications. New recommendations regarding diagnosis and management are presented, reflecting advances in understanding the genetic basis and clinical manifestations of the disease based on the consensus of experienced clinicians from Canada, Europe, and the United States. Whenever possible, evidence-based conclusions are made, but as with other rare diseases, the data on SDS are often anecdotal. The authors welcome comments from readers.
Response to Comment on “Development of a High-Pressure Aerodynamic Lens for Focusing Large Particles (4–10 μm) into the Aerosol Time-of-Flight Mass Spectrometer” (2015)

Copyright 2015 American Association for Aerosol Research
Distance Bounding Protocols on TH-UWB Radios (2010)

Relay attacks pose a real threat to the security of wireless communications. Distance bounding protocols have been designed to thwart these attacks. In this paper, we study the way to adapt distance bounding protocols to time-hopping ultra wide band (TH-UWB) radios. Two protocols are proposed which are based on the milestones of the TH-UWB radio: the time-hopping sequence and the mapping code. The security and the different merits of those protocols are analyzed.
Oscillating endoskeletal antibubbles (2019)

An antibubble is a gas bubble with a liquid droplet inside. Antibubbles have a potential role in ultrasonic imaging, ultrasound-guided drug delivery, and hydrocarbon leakage detection. The liquid core droplets inside antibubbles can be stabilised with a process called Pickering stability. Other systems proposed include spoke crystals to suspend the droplet or endoskeletal structures. In this study, the oscillatory response of microscopic endoskeletal antibubbles to ultrasound has been investigated, primarily to determine whether the presence of an endoskeleton attenuates the oscillation amplitude of the antibubble. Three emulsions containing (anti)bubbles were prepared for evaluation. Each emulsion was pipetted into the observation chamber of a high-speed microscopic observation system. A high-speed camera, operating at 10 million frames per second, was couples to the microscope. During camera recording, the materials were subjected to ultrasound pulses from a laboratory-assembled single-element transducer. The presence of an endoskeleton with droplets hampers the oscillation of antibubbles as compared to identical bubbles without endoskeleton and droplet content.
Rod Sensitivity, Cone Sensitivity, and Photoreceptor Layer Thickness in Retinal Degenerative Diseases (2011)

Both rods and cones can support an intact IS/OS junction and normal photoreceptor thickness measures. The product of ONL and OS thicknesses is proportional to the sensitivity mediated by the less abnormal type of photoreceptor.
Multichannel SQUID magnetometry using double relaxation oscillation SQUID's (1996)

A highly sensitive first-order gradiometer based on double relaxation oscillation SQUID's (DROS's) for multichannel use is presented. The white flux noise level of the bare DROS's is 4.5 /spl mu//spl Phi//sub 0///spl radic/Hz (/spl epsi/=275 h). With wire-wound first-order gradiometers, having a baseline of 40 mm, the white magnetic field noise equals 4 fT//spl radic/Hz. As a result of the high flux-to-voltage transfer of the DROS's of about 1 mV//spl Phi//sub 0/, this low noise level could be obtained with simple room-temperature flux locked loop electronics based on direct voltage readout. The relaxation frequency of the present DROS's is approximately 1 GHz. No degradation of the DROS characteristics caused by interference between relaxation oscillations in two adjacent channels has been observed, although the gradiometers are spaced by less than 1 mm. This shows that DROS's can be used in multichannel SQUID magnetometers.
B<sub>0</sub> shimming of the human heart at 7T (2020)

Challenges in state-of-the-art B<sub>0</sub> shimming of the human heart at 7 T were described. Cardiac phase-specific shimming strategies were found to be superior to vendor-supplied shimming.
Visualization of unstructured text sequences of nursing narratives (2006)

This paper presents a keyword-based information visualization technique for nursing record sequences. Visualizing the trend information rooted in unstructured and fragmented abstract text data is a largely unaddressed problem. In our technique, multiple hierarchical keyword based visualizations are used to explore unstructured text data from nursing records. First, each text data set is broken up into a list of keywords to enable the visualization of keyword occurrences over time and the relative distribution of keywords. A graphical user interface is provided to enable selection and classification of keywords. Users may select one or more data sets to compare, in addition to one or more groups of keywords to add to the visualization. Colors are used to distinguish quickly and easily between groups of keywords present in the visualization. At the second level of hierarchy, keywords for visualization are discovered through a predetermined automatic detection and scoring based mechanism. The aggregate frequency trend of keywords from all data sets is also provided in both hierarchies as a way to visualize overall trends and analyze various events in time.
New EMR approach for a multi domain-multivariable energetic flow (2012)

International audience
Chancen für Hybridkinematiken zwischen Industrieroboter und Werkzeugmaschine (2003)

Kurzfassung Die Absolutgenauigkeit von Industrierobotern ist für bestimmte Aufgaben oft noch unzureichend. Insbesondere bezüglich Offline-Programmierung und Austauschbarkeit können bei hochpräzisen Anwendungen Probleme auftreten, deren Beseitigung oft zeit- und kostenintensiv ist. Durch den Einsatz von Robotern mit Parallelkinematik und fortschrittlicher Kalibriermethoden ist es jedoch möglich, eine Absolutgenauigkeit von 0,1 mm dauerhaft zu gewährleisten, beispielsweise für die hochgenaue Laserbearbeitung.
A Collaborative Visualization Tool to Support Doctors' Shared Decision-Making on Antibiotic Prescription (2017)

The inappropriate prescription of antibiotics may cause severe medical outcomes such as antibiotic resistance. To prevent such situations and facilitate appropriate antibiotic prescribing, we designed and developed an asynchronous collaborative visual analytics tool. It visualizes the antibiotics' coverage spectrum that allows users choose the most appropriate antibiotics. The asynchronous collaboration around visualization mimics the actual collaboration scenarios in clinical settings, and provides supportive information during physician's decision-making process. Our work contributes to the CSCW community by providing a design prototype to support asynchronous collaboration among healthcare professionals, which is crucial but lacks in many of the present clinical decision support systems.
Local adaptation of bone micro-structure and canal network to tendon insertion investigated by image-based micro-FE simulations (2020)

peer reviewed
Measurements of ECH absorption on ATF using a polarization-controlled beam launcher (1989)

Electron cyclotron heating (ECH) is used on the Advanced Toroidal Facility (ATF) experiment at ORNL for plasma formation and heating. A 53.2 GHz gyrotron generates 200 kW cw which is transported to ATF in 6.35 cm evacuated waveguide. Power is launched into ATF using a recently completed polarization controlled beam launcher which can launch a linear polarized beam with a /minus/20 dB diameter of 12 cm at the plasma center. The launcher consists of a Vlasov mode converting antenna, a Teflon-copper laminate polarization rotating grating, and a spherical focusing mirror. The plane of polarization can be remotely adjusted by rotating the grating with a motorized vacuum feedthrough. First pass plasma absorption is monitored in two planes of polarization using a dual-polarized detector looking through a dome shaped scattering cut-off screen. During plasma operation, the detected signals indicate that absorption under ideal conditions is nearly complete. With low density or a shifted resonance zone, absorption is small and there are cases where there is mode coupling to the perpendicular polarization. This is presumably due to shear in the ATF magnetic field. 2 refs., 3 figs.
Fiber composition influence on spontaneous Brillouin scattering properties in double-clad fiber amplifiers (2006)

Brillouin properties of doped fibers are reported for the first time. The characterized fibers present Brillouin frequency shift variation that we attribute to fiber composition. A thermally induced evolution of Brillouin spectrum has been observed.
Enabling compact GTL by 3D-printing of structured catalysts (2020)

This paper uses 3D printing methods to overcome mass and heat transport limitations in small-scale processes for the conversion of syngas to ethanol. Advances in the past two decades in nano-materials technologies had resulted in a new generation of highly active catalysts. These catalysts are formed into porous pellets or monoliths and placed into the reactors which often operate at elevated temperatures and pressures. The key problem with this arrangement is that transport rates are of different orders of magnitudes within the particles which is dominated by (slow) diffusion, and between the particles, which is set by (fast) pressure driven viscous flow. Balancing these timescales requires either (i) making the pellets very small, so that the diffusion path lengths and hence travel times are reduced – but this so severely impacts the pressure drop over the system that it is impractical; or (ii) increasing the residence time in the reactor and/or reducing the reaction rate by limiting the catalyst activity (which is the currently used solution, where typically catalyst carriers dilute the active materials by >90%), but this results in very large reactor sizes. Further, for highly energetic reactions requiring intensive heating or cooling, packed beds and monoliths becomes limited by the poor heat transfer properties of the arrangement. Poor temperature control results in reduced conversion efficiency, and a wider range of products and by-products which in turn require additional downstream separation and purification operations. Here, we discuss 3D printing approach to lay down catalysts into reactor architecture.
Ligament Stability Two to Six Years After Anterior Cruciate Ligament Reconstruction with Autogenous Patellar Tendon Graft and Participation in Accelerated Rehabilitation Program (1995)

We studied patients who participated in our accelerated rehabilitation program after anterior cruciate ligament reconstructive surgery to determine if they showed signs of patellar tendon graft stretching. This program initiated in 1987 emphasizes early full hyperextension, early weightbearing as tolerated, and closed-chain functional activities with rapid return to sports when the patient has attained full range of motion, approximately 65% of strength, and has accomplished the running and agility drills prescribed. A total of 209 patients met the criteria of KT-1000 arthrometer followup at the time full range of motion (5 degrees/0 degrees/135 degrees) was attained and at 2 years or more after surgery. The KT-1000 arthrometer manual maximum difference between the reconstructed and normal knees was used as the indicator of change in the graft length. All patients completed postoperative subjective questionnaires. The mean KT-1000 arthrometer value was 2.06 mm (SD, +/- 2.2) at full range of motion and 2.10 mm (SD, +/- 1.9) at more than 2 years of followup (P = 0.7961). The patients' subjective stability scores averaged 19.6 with 97% reporting no instability episodes. Based on our findings, we conclude that an accelerated rehabilitation program after this type of reconstruction does not affect long-term stability as measured by the KT-1000 arthrometer.
Calculation of turbulence effects in an upward-refracting atmosphere (1990)

The parabolic equation (PE) method is used together with a two-dimensional atmospheric turbulence model to calculate the effect of turbulence on sound propagation. Both a nonrefractive atmosphere and a refractive atmosphere are considered. The nonrefractive calculation serves as a test of the two-dimensional model for turbulence. For a nonrefractive atmosphere, good agreement is obtained with experiment and the theory of Daigle. The calculation with upward refraction is compared to the data of Weiner and Keast who observed that the relative sound-pressure level versus range follows a characteristic ‘‘step’’ function. The calculations, which contain no adjustable parameters, give reasonable agreement with the data. In particular, the shape of the step function is well predicted. In the geometric shadow region, the observed strong dependence on refraction strength and weak dependence on range, height, and frequency are also predicted. It is concluded that, for a receiver deep in a shadow zone and frequencies greater than a few hundred hertz, the measured sound-pressure level is due almost entirely to sound scattered into the shadow zone by atmospheric turbulence. Consequently, for upward refraction and frequencies above a few hundred hertz, turbulence must be included in long-range propagation calculations if one is to obtain useful predictions.
In search of optimal settings for Ho:YAG laser-lithotripsy to maximize the ablation rate, while minimizing the retropulsion (2020)

Although laser lithotripsy is now the preferred treatment option for urolithiasis due to shorter operation time and a better stone-free rate [1], the optimal laser settings for URS (Ureteroscopic lithotripsy) to enable shorter operating times remain unclear. This study aims to identify optimal laser settings for Ho:YAG laser-lithotripsy to maximize the ablation rate while minimizing the retropulsion, as well as to improve the discharge of fragments via the urinary tract. The net result will be an increase in treatment success and patient satisfaction by ameliorating the stone-free rate. In vitro investigations of Ho:YAG laser-induced stone ablation and retropulsion were performed with a bench top model first introduced by Sroka’s group [2]. A commercial Ho:YAG laser system (Lumenis VersaPulse PowerSuite 100W, Lumenis Ltd., Yokneam, Israel) was used as the laser pulse source, with pulse energy from 0.2 J up to 1.5 J and repetition rate from 5 to 40 Hz. A DOE with two replicate points and two lack-of-fit points was performed on artificial BEGO stones of sample size 14 under reproducible experimental conditions (fiber size: 365 &mu;m, S-LLF365 SureFlex Fiber, Boston Scientific Corporation, San Jose, CA, USA). The best fit to the experimental data was analyzed utilizing the design of experiment software, which can produce the numerical formulas for the response surfaces of ablation rate and retropulsion in terms of laser pulse parameters [3]. The coded numerical formulas for the response surfaces of ablation speed and retropulsion velocity are generated. The coded equation is useful for identifying the relative impact of the factors by comparing their coefficients. Upon examination of the laser ablation of stone phantoms (BEGO), the laser pulse energy is 1.4 times the impact of the frequency, and laser pulse peak power’s impact is the same as the frequency; while for retropulsion, the laser pulse energy is 5.8 times as the impact of the frequency, and laser pulse peak power’s impact is 13 times as the frequency; A series of laser settings for relatively efficient laser lithotripsy were identified in terms of laser pulse energy and peak power. The laser pulse energy or peak power in reference to frequency has a higher impact coefficient to stone retropulsion as compared to stone ablation in Ho:YAG laser-lithotripsy. The most effective way to reduce stone retropulsion during laser lithotripsy is to reduce the laser pulse peak power (which has the highest impact coefficient in the coded response equation).
Using Ontologies in a Cognitive-Grounded System: Automatic Action Recognition in Video-Surveillance. (2012)

Abstract—This article presents an integrated cognitive system for automatic video surveillance: in particular, we focus on the task of classifying the actions occurring in a scene. For this purpose, we developed a semantic infrastructure on top of a hybrid computational ontology of actions. The article outlines the core features of this infrastructure, illustrating how the processing mechanisms of the cognitive system benefit from knowledge capabilities in fulfilling the recognition goal. Ultimately, the paper shows that ontologies can enhance a cognitive architecture’s functionalities, allowing for high-level performance in complex task execution. I.
Comparative Transcriptomic Responses to Chronic Cadmium, Fluoranthene, and Atrazine Exposure in Lumbricus rubellus (2008)

Transcriptional responses of a soil-dwelling organism (the earthworm Lumbricus rubellus) to three chemicals, cadmium (Cd), fluoranthene (FA), and atrazine (AZ), were measured following chronic exposure, with the aim of identifying the nature of any shared transcriptional response. Principal component analysis indicated full or partial separation of control and exposed samples for each compound but not for the composite set of all control and exposed samples. Partial least-squares discriminant analysis allowed separation of the control and exposed samples for each chemical and also for the composite data set, suggesting a common transcriptional response to exposure. Genes identified as changing in expression level (by the least stringent test for significance) following exposure to two chemicals indicated a substantial number of common genes (> 127). The three compound overlapping gene set, however, comprised only 25 genes. We suggest that the low commonality in transcriptional response may be linked to the chronic concentrations (approximately 10% EC50) and chronic duration (28 days) used. Annotations of the three compound overlapping gene set indicated that genes from pathways most often associated with responses to environmental stress, such as heat shock, phase I and II metabolism, antioxidant defense, and cation balance, were not represented. The strongest annotation signature was for genes important in mitochondrial function and energy metabolism.