gebhart/patrepeval huggingface dataset:
Characterizing human retinotopic mapping with conformal geometry: a preliminary study (2014)

Functional magnetic resonance imaging (fMRI) has been widely used to measure the retinotopic organization of early visual cortex in the human brain. Previous studies have identified multiple visual field maps (VFMs) based on statistical analysis of fMRI signals, but the resulting geometry has not been fully characterized with mathematical models. Here we test whether VFMs V1 and V2 obey the least restrictive of all geometric mappings; that is, whether they are anglepreserving and therefore maintain conformal mapping. We measured retinotopic organization in individual subjects using standard traveling-wave fMRI methods. Visual stimuli consisted of black and white, drifting checkerboards comprising rotating wedges and expanding rings to measure the cortical representations of polar angle and eccentricity, respectively. These representations were then projected onto a 3D cortical mesh of each hemisphere. By generating a mapped unit disk that is conformal of the VFMs using spherical stereographic projection and computing the parameterized coordinates of the eccentricity and polar angle gradients, we computed Beltrami coefficients to check whether the mapping from the visual field to the V1 and V2 cortical representations is conformal. We find that V1 and V2 exhibit local conformality. Our analysis of the Beltrami coefficient shows that selected regions of V1 and V2 that contain reasonably smooth eccentricity and polar angle gradients do show significant local conformality, warranting further investigation of this approach for analysis of early and higher visual cortex. These results suggest that such a mathematical model can be used to characterize the early VFMs in human visual cortex.
A Selective ATP-Binding Cassette Subfamily G Member 2 Efflux Inhibitor Revealed via High-Throughput Flow Cytometry (2012)

Chemotherapeutics tumor resistance is a principal reason for treatment failure, and clinical and experimental data indicate that multidrug transporters such as ATP-binding cassette (ABC) B1 and ABCG2 play a leading role by preventing cytotoxic intracellular drug concentrations. Functional efflux inhibition of existing chemotherapeutics by these pumps continues to present a promising approach for treatment. A contributing factor to the failure of existing inhibitors in clinical applications is limited understanding of specific substrate/inhibitor/pump interactions. We have identified selective efflux inhibitors by profiling multiple ABC transporters against a library of small molecules to find molecular probes to further explore such interactions. In our primary screening protocol using JC-1 as a dual-pump fluorescent reporter substrate, we identified a piperazine-substituted pyrazolo[1,5-a]pyrimidine substructure with promise for selective efflux inhibition. As a result of a focused structure-activity relationship (SAR)-driven chemistry effort, we describe compound 1 (CID44640177), an efflux inhibitor with selectivity toward ABCG2 over ABCB1. Compound 1 is also shown to potentiate the activity of mitoxantrone in vitro as well as preliminarily in vivo in an ABCG2-overexpressing tumor model. At least two analogues significantly reduce tumor size in combination with the chemotherapeutic topotecan. To our knowledge, low nanomolar chemoreversal activity coupled with direct evidence of efflux inhibition for ABCG2 is unprecedented.
Pulsed, Inductively Generated, Streaming Plasma Ion Source for Heavy Ion Fusion Linacs (2006)

This report describes a compact, high current density, pulsed ion source, based on electrodeless, inductively driven gas breakdown, developed to meet the requirements on normalized emittance, current density, uniformity and pulse duration for an ion injector in a heavy-ion fusion driver. The plasma source produces >10 μs pulse of Argon plasma with ion current densities >100 mA/cm2 at 30 cm from the source and with strongly axially directed ion energy of about 80 eV, and sub-eV transverse temperature. The source has good reproducibility and spatial uniformity. Control of the current density during the pulse has been demonstrated with a novel modulator coil method which allows attenuation of the ion current density without significantly affecting the beam quality. This project was carried out in two phases. Phase 1 used source configurations adapted from light ion sources to demonstrate the feasibility of the concept. In Phase 2 the performance of the source was enhanced and quantified in greater detail, a modulator for controlling the pulse shape was developed, and experiments were conducted with the ions accelerated to >40 kV.
Transformation of Saccharomyces cerevisiae with linear DNA killer plasmids from Kluyveromyces lactis (1982)

Protoplasts of Saccharomyces cerevisiae were mixed with linear DNA plasmids, pGKl1 and pGKl2, isolated from a Kluyveromyces lactis killer strain and treated with polyethylene glycol. Out of 2,000 colonies regenerated on a nonselective medium, two killer transformants were obtained. The pGKl plasmids and the killer character were stably maintained in one (Pdh-1) of them. Another transformant, Pdl-1, was a weak killer, and the subclones consisted of a mixture of weak and nonkiller cells. The weak killers were characterized by the presence of pGKl1 in a decreased amount, and nonkillers were characterized by the absence of pGKl1. The occurrence of two new plasmids which migrated faster than pGKl1 in an agarose gel was observed in Pdl-1 and its subclones, whether weak or nonkillers. Staining with 4',6-diamidino-2-phenylindole revealed that the pGKl plasmids exist in the cytosol of transformant cells with numerous copy numbers.
Diffusion‐based MR methods for bone structure and evolution (2007)

A new approach to MR trabecular bone characterization is presented. This method probes the diffusion of spins through internal magnetic field gradients due to the susceptibility contrast between the bone and water (or marrow) phases. The resulting spin magnetization decay encodes properties of the underlying structure. This method, termed decay due to diffusion in the internal field (DDIF), is well established as a probe of pore size and structure. In the present work its application is shown for in vitro experiments on excised bovine tibiae samples. A comparison with pulsed field gradient (PFG) measurement of restricted diffusion shows a strong correlation of DDIF with the surface-to-volume ratio (SVR) of bones. Calculation of the internal magnetic field within the bone structure also supports this interpretation. These NMR measurements compare well with the image analysis from microscopic computed tomography (muCT). The SVR is not accessible in the clinically standard densitometry measurements, and provides vital information on bone strength and therefore on its fracture risk. The DDIF and PFG methods derive this information from a straightforward pulse sequence that does not employ either high applied field gradients or microimaging, and thus may have clinical potential.
XTC MRI: Sensitivity improvement through parameter optimization (2007)

Xenon polarization Transfer Contrast (XTC) MRI pulse sequences permit the gas exchange of hyperpolarized xenon-129 in the lung to be measured quantitatively. However, the pulse sequence parameter values employed in previously published work were determined empirically without considering the now-known gas exchange rates and the underlying lung physiology. By using a theoretical model for the consumption of magnetization during data acquisition, the noise intensity in the computed gas-phase depolarization maps was minimized as a function of the gas-phase depolarization rate. With such optimization the theoretical model predicted an up to threefold improvement in precision. Experiments in rabbits demonstrated that for typical imaging parameter values the optimized XTC pulse sequence yielded a median noise intensity of only about 3% in the depolarization maps. Consequently, the reliable detection of variations in the average alveolar wall thickness of as little as 300 nm can be expected. This improvement in the precision of the XTC MRI technique should lead to a substantial increase in its sensitivity for detecting pathological changes in lung function.
Full-fidelity flexible object-oriented XML access (2009)

Developers need to programmatically access persistent XML data. Object-oriented access is often the preferred method. Translating XML data into objects or vice-versa is a hard problem due to the data model mismatch and the difficulty of query translation. We propose a framework that addresses this problem by transforming object-based queries and updates into queries and updates on XML using flexible, declarative mappings between classes and XML schema types. The same mappings are used to shred XML fragments from query results into client-side objects. Information in the XML store that is not mapped using the mapping language, such as comments and processing instructions, are also made available in the object representation.
High silica dispersive optical fiber and its application as an in-line short pass fiber filter (2003)

Summary form only given. In this study, a dispersive fiber based on a high silica glass host is fabricated for the first time. The dispersive characteristics of the index difference was achieved using the index variation of SiO/sub 2/-B/sub 2/O/sub 3/ and SiO/sub 2/-F glass. To make a short-pass filter, the core and cladding compositions were chosen as SiO/sub 2/-B/sub 2/O/sub 3/ and SiO/sub 2/-F respectively.
Challenges in the Analysis of Surface-Borehole EM Measurements. Reviewing the Field Distortion due to Metallic Casing (2019)

Summary In this paper a discussion is presented of the main aspects describing the challenges expected and encountered in recording and analyzing STB/BTS data in the presence of the steel casing. To this end, numerical simulations of the casing effect are analysed in relation to the many unknown of the system, i.e. casing, overburden and reservoir properties. The discussion highlights the evident need to either remove the distorting component of the field due to the current flow in the casing, or to directly model the response of the entire system, i.e. including the localized highly conductive anomaly of the metallic casing. In the former case, an estimate of the casing effect could be obtained from the recorded data, but the accuracy may not be enough to remove the casing response while keeping a x100 weaker response of the reservoir. In the later case, aside from the numerical burden of the modelling exercise, the properties of the casing may not be known accurately enough to discriminate the subsurface response from the total field dominated by the casing effect.
Quality of eyeglass prescriptions from a low-cost wavefront autorefractor evaluated in rural India: results of a 708-participant field study (2019)

Average VAs from autorefractor-prescribed eyeglasses were one letter worse than those from subjective refraction. More than half of all participants either had no preference or preferred eyeglasses prescribed by the autorefractor. This marginal difference in quality may warrant autorefractor-based prescriptions, given the portable form factor, short measurement time, low cost and minimal training required to use the autorefractor evaluated here.
Completeness in SMT-based BMC for software programs (2008)

Bounded Model Checking (BMC) is incomplete without a completeness threshold (CT) bound. Previous methods, using recurrence diameter for obtaining CT, check for existence of a longest loop-free path at every depth k. For terminating software programs, we propose an efficient method for obtaining CT that requires solving a formula of size O(k) at some depths only, as compared to previous methods that require solving a formula of O(k2) (or O(klogk)) size at every depth. We augment previous methods for BMC simplifications using model transformation and control flow information, with context-sensitive analysis. This results in more BMC simplifications and further reduction in the number of CT checks. We have implemented our techniques in a Satisfiability Modulo Theory (SMT)-based BMC framework. Our controlled experiments on real-world software programs show that our proposed formulation provides significant improvements over previous approaches.
African Swine Fever Virus Georgia Isolate Harboring Deletions of MGF360 and MGF505 Genes Is Attenuated in Swine and Confers Protection against Challenge with Virulent Parental Virus (2015)

The main problem for controlling ASF is the lack of vaccines. Studies focusing on understanding ASFV virulence led to the production of genetically modified recombinant viruses that, while attenuated, are able to confer protection in pigs challenged with homologous viruses. Here we have produced an attenuated recombinant ASFV derived from highly virulent ASFV strain Georgia (ASFV-G) lacking only six of the multigene family 360 (MGF360) and MGF505 genes (ASFV-G-ΔMGF). It is demonstrated, by first time, that deleting specific MGF genes alone can completely attenuate a highly virulent field ASFV isolate. Recombinant virus ASFV-G-ΔMGF effectively confers protection in pigs against challenge with ASFV-G when delivered once via the intramuscular (i.m.) route. The protection against ASFV-G is highly effective by 28 days postvaccination. This is the first report of an experimental vaccine that induces solid protection against virulent ASFV-G.
The VIA vibrating beam accelerometer: a new quartz micromachined sensor (2003)

ONERA, the French National Establishment for Aerospace Research, under the financial support of the DGA (The French MoD Procurement Agency), has been developing a micro-machined quartz vibrating beam accelerometer called VIA (Vibrating Inertial Accelerometer). This sensor exploits the frequency change of a quartz resonator when submitted to an acceleration. The main targeted applications are the guidance and the attitude control of tactical missiles, as well as the inertial navigation of aircraft, helicopters and ground vehicles (coupled with radio-electric positioning systems such as the GPS receiver). The VIA concept has been selected to meet these objectives. First, the monolithic configuration of the transducers is well suited to chemical etching process and miniaturization. Secondly, the choice of vibrating beams as sensitive elements, combined with excellent quartz mechanical properties, gives a very good stability of the scale factor. Third, the performed optimisation of the transducer leads to a very good insulation of the active part with respect to the mounting areas of the transducer, suitable to bias stability. In order to reduce the thermal sensitivity, the accelerometer is composed of two transducers operating in differential mode.
A transformation vector for the production of marker‐free transgenic plants containing a single copy transgene at high frequency (2000)

We represent here the GST-MAT vector system. The R recombinase gene of the site-specific recombination system R/RS from Zygosaccharomyces rouxii was fused to the chemical inducible promoter of the glutathione-S-transferase (GST-II-27) gene from Zea mays. Upon excision, the isopentenyltransferase (ipt) gene that is used as a selectable marker gene is removed. When the cauliflower mosaic virus 35S promoter (CaMV 35S) was used to express R recombinase, 67% of the marker-free transgenic plants had more than three transgene copies. Because the CaMV 35S promoter transiently and efficiently excised the ipt gene before callus and adventitious bud formation, the frequency of emergence of the ipt-shooty explants with a single T-DNA copy might be reduced. In this study we show that the GST-MAT vector efficiently produced transgenic ipt-shooty explants from 37 (88%) out of 42 differentiated adventitious buds and marker-free transgenic plants containing the GUS gene from five (14%) out of 37 ipt-shooty lines. Furthermore, the GST-MAT vector also induced two marker-free transgenic plants without the production of ipt-shooty intermediates. Southern blot analysis showed that six (86%) out of seven marker-free transgenic plants had a single GUS gene. This result suggests that the GST-MAT vector is useful to generate high frequency, marker-free transgenic plants containing a single transgene.
Film-Cooling Effectiveness on Squealer Rim Walls and Squealer Cavity Floor of a Gas Turbine Blade Tip Using Pressure Sensitive Paint (2005)

Effects of shaped holes on the tip pressure side, coolant jet impingement on the pressure side squealer rim from tip holes and varying blowing ratios for a squealer blade tip were examined on film-cooling effectiveness. The film-cooling effectiveness distributions were measured on the blade tip, near tip pressure side and the inner pressure side rim wall using Pressure Sensitive Paint technique. Air and nitrogen gas were used as the film cooling gases and the oxygen concentration distribution for each case was measured. The film cooling effectiveness information was obtained from the difference of the oxygen concentration between air and nitrogen gas cases by applying the mass transfer analogy. The internal coolant-supply passages of the squealer tipped blade were modeled similar to those in the GE-E3 rotor blade with two separate serpentine loops supplying coolant to the film cooling holes. A row of compound angled cylindrical film cooling holes was arranged along the camber line on the tip and another row of compound angled shaped film cooling holes was arranged along the span of the pressure side just below the tip. The average blowing ratio of the cooling gas was controlled to be 0.5, 1.0 and 2.0. Tests were conducted in a five-bladed linear cascade in a blow down facility with a tip gap clearance of 1.5%. The free stream Reynolds number, based on the axial chord length and the exit velocity, was 1,138,000 and the inlet and the exit Mach number were 0.25 and 0.6, respectively. Turbulence intensity level at the cascade inlet was 9.7%. Numerical predictions were also performed using Fluent to simulate the experiment at the same inlet flow conditions. Predictions for film cooling are presented. Results show a good correlation between experimental and predicted data. The shape and location of the film cooling holes along with varying blowing ratios can have significant effects on film-cooling performance.
A Multi-Step Predictive Model to Estimate Li-Ion State of Charge for Higher C-Rates (2019)

Energy Storage or battery management systems for Li-ion batteries require accurate prediction of state of charge (SOC). Existing methods predict SOC for a given charging/discharging rate (C-rate) using experimentally obtained values of cell current and voltage. However, in scenarios where there is a lack of such historical data, these methods perform poorly because of inadequate training data. This paper proposes a combinatorial model involving autoregressive integrated moving average (ARIMA) and a nonlinear autoregressive network with exogenous inputs (NARX-net). ARIMA is used to first predict cell current and cell voltage for the desired higher C-rate (C/10) only using the voltage and current from historical, lower C-rates (C/2 to C/8) of an actual 3.7V, 3.5Ah Li-ion battery. The NARX-net is used to predict SOC using the voltage and current values predicted by ARIMA. To train NARX-net, four algorithms are used, and their performance is evaluated by comparing the predicted SOC values with those obtained experimentally for C/10. Results show that the proposed data-driven model is effective at predicting SOC for Li-ion batteries given some preliminary historical data on current and voltage of previous, lower C-rates.
Targeted Profiling of RNA Translation (2018)

This unit describes a reverse transcription-quantitative PCR (RT-qPCR)-based method for gene-targeted measurement of RNA translation levels. The method includes washing and lysing cells with a buffer containing cycloheximide to enrich ribosomal accumulation at translation initiation sites (TIS), followed by enzymatic treatment to generate ribosomal footprints, reverse transcription targeted towards TIS of specific transcripts of interest to generate complementary DNA (cDNA), and qPCR to measure the abundance of these footprints. This method enables time- and cost-effective assessment of changes in translation levels across focused panels of genes and across numerous samples. © 2018 by John Wiley & Sons, Inc.
Power Allocation for Underlay Device-to-Device Communication Over Multiple Channels (2017)

In underlay device-to-device (D2D) communication, a D2D pair reuses the cellular spectrum, causing interference to existing cellular users. The achieved D2D rate and the added interference to cellular users need to be jointly considered for optimal resource and power allocations. Unlike most existing work which only consider the simplified scenario of assigning each D2D pair a single channel or resource block (RB), we consider multiple RBs from different cellular users can be assigned to each D2D pair. We formulate the problem of optimal power allocation over multiple RBs at the D2D transmitter to maximize the sum-rate of D2D and cellular users, under the D2D transmitter power constraint and minimum signal-to-noise-and-interference ratio (SINR) requirement at each reused RB for all affected cellular users in all cells. To further lower the required overhead in a practical setting, we consider a second optimization problem for power allocation solution to maximize the D2D rate under the same constraints as the sum-rate maximization problem. We obtain the asymptotic power solution for the sum-rate maximization and the semiclosed-form optimal power solution for the D2D rate maximization. Our proposed optimization solutions are applicable to both uplink and downlink cellular spectrum sharing as well as to mutlicell with multiple D2D pairs scenarios. Our simulation studies demonstrates the effectiveness of the two proposed methods for both uplink and downlink resource sharing, and further shed light into how the maximum rate is impacted by the system parameters such as available D2D transmit power, number of D2D pairs, minimum SINR requirements, and the cell size.
ADAM 12 may be used to reduce the false positive rate of first trimester combined screening for Down syndrome (2009)

ADAM12 is a moderately effective DS marker. It is not a cost-effective addition to CUB screening, but may be used to reduce the FPR in selected high-risk cases.
Bayesian Estimation Based Parameter Estimation for Composite Load (2019)

Accurate identification of parameters of load models is essential in power system computations, including simulation, prediction, and stability and reliability analysis. Conventional point estimation based composite load modeling approaches suffer from disturbances and noises and provide limited information of the system dynamics. In this work, a statistic (Bayesian Estimation) based distribution estimation approach is proposed for both static (ZIP) and dynamic (Induction Motor) load modeling. When dealing with multiple parameters, Gibbs sampling method is employed. In each iteration, the proposal samples each parameter while keeps others fixed. The proposed method provides a distribution estimation of load models coefficients and is robust to measurement errors.