gebhart/patrepeval huggingface dataset:
Voxel-based statistical analysis and quantification of amyloid PET in the Japanese Alzheimer’s disease neuroimaging initiative (J-ADNI) multi-center study (2019)

Abstract Background Amyloid PET plays a vital role in detecting the accumulation of in vivo amyloid-β (Aβ). The quantification of Aβ accumulation has been widely performed using the region of interest (ROI)-based mean cortical standardized uptake value ratio (mcSUVR). However, voxel-based statistical analysis has not been well studied. The purpose of this study was to examine the feasibility of analyzing amyloid PET scans by voxel-based statistical analysis. The results were then compared to those with the ROI-based mcSUVR. In total, 166 subjects who underwent 11 C-PiB PET in the J-ADNI multi-center study were analyzed. Additionally, 18 Aβ-negative images were collected from other studies to form a normal database. The PET images were spatially normalized to the standard space using an adaptive template method without MRI. The mcSUVR was measured using a pre-defined ROI. Voxel-wise Z -scores within the ROI were calculated using the normal database, after which Z -score maps were generated. A receiver operating characteristic (ROC) analysis was performed to evaluate whether Z -sum (sum of the Z -score) and mcSUVR could be used to classify the scans into positive and negative using the central visual read as the reference standard. PET scans that were equivocal were regarded as positive. Results Sensitivity and specificity were respectively 90.8% and 100% by Z -sum and 91.8% and 98.5% by mcSUVR. Most of the equivocal scans were subsequently classified by both Z -sum and mcSUVR as false negatives. Z -score maps correctly delineated abnormal Aβ accumulation over the same regions as the visual read. Conclusions We examined the usefulness of voxel-based statistical analysis for amyloid PET. This method provides objective Z -score maps and Z -sum values, which were observed to be helpful as an adjunct to visual interpretation especially for cases with mild or limited Aβ accumulation. This approach could improve the Aβ detection sensitivity, reduce inter-reader variability, and allow for detailed monitoring of Aβ deposition. Trial registration The number of the J-ADNI study is UMIN000001374
Gamma gene promoter and enhancer structure in Seattle variant of hereditary persistence of fetal hemoglobin (1988)

A variant of hereditary persistence of fetal hemoglobin (HPFH), first described in a patient from Seattle, was studied by structural analysis of the gamma-globin genes. A family study suggested that the determinant for this form of HPFH, in which the HbF contains both G gamma- and A gamma-globin chains, segregated with the beta S gene. No deletions or other abnormalities were detected in the fetal to adult globin gene region by genomic mapping studies. All four gamma-globin genes were isolated from a cosmid library, and allelic pairs of gamma-globin genes were distinguished by linkage to either the beta S- or beta A-globin gene. Nucleotide sequence analysis of the four gamma-globin gene promoters revealed a total of three discrepancies compared with a reference sequence, but these were judged unlikely to be the underlying determinants. Sequence analysis of the enhancer region located 3' to the A gamma-globin gene from the putative HPFH chromosome revealed three base substitutions, whereas this region was normal in the A gamma-globin gene linked to the beta A gene. These data raise the possibility that an alteration of enhancer function rather than promoter function could be the basis for this condition.
Metrics and Methods for Evaluation of Over-The-Air Performance of MIMO User Equipment (2012)

Commercial User Equipment (UE) testing and certification has become more complex for state-of-the-art mobile communication standards such as 3rd Generation Partnership Project (3GPP) Long-Term Evolution (LTE) due to the extensive use of Multiple Input-Multiple Output (MIMO) transmission techniques. The variety of different MIMO operating modes and the almost unlimited choice of possible multipath channel conditions under which UE performance may be evaluated are not accounted for by established Single Input-Single Output (SISO) Over-The-Air (OTA) performance metrics like Total Isotropic Sensitivity (TIS) and Total Radiated Power (TRP). As pointed out in this contribution, meaningful metrics and cost-effective, low-complexity measurement methods can, nevertheless, be derived by focusing on characterization of the physical attributes of UE and by adopting statistical metrics. Starting from a brief review of the most important MIMO operating modes in the 3GPP LTE standard, the relation between UE properties and UE performance, which is observed in these operating modes, is discussed. Two complementary metrics and corresponding measurement procedures for evaluation of MIMO OTA performance are presented in order to address the diversity of possible propagation scenarios. Measurement results from preliminary implementations of the two proposed measurement procedures, including comparison between different LTE devices, are presented.
Train Positioning Using Video Odometry (2014)

Reliable Data Systems have developed a video-based odometry system that enables trains to measure velocities and distances travelled without the need for trackside infrastructure. The Study Group was asked to investigate ways of improving the accuracy of such a system, and to suggest any improvements that might be made. The work performed in the week followed along these strands: (a). Elimination of errors in video odometery induced by pitch and height; (b) Robust calculation of (i) the train velocity and (ii) the track curvature; (c). Accurate determination of the position of a train on a track by assimilating Curvature information; (d). Determining where on UK’s railway map a train journey takes place, based purely on video odometry and (e). Drawing a track map.
FLT4 Receptor Tyrosine Kinase Gene Mapping to Chromosome Band 5q35 in Relation to the t(2;5), t(5;6), and t(3;5) Translocations (1993)

FLT4 is a recently cloned receptor tyrosine kinase cDNA, which is characterized by seven immunoglobulin-like loops in its extracellular domain. We have previously mapped the FLT4 gene to chromosome segment 5q33-qter using somatic cell hybrids. Here we have refined the localization to band 5q35 by fluorescence in situ hybridization and show that the gene is translocated to chromosomes 2 and 6 in the t(2;5)(p23;q35) and t(5;6)(q35;p21) translocations, respectively, of Ki-I-positive lymphomas, as well as to chromosome 3 in the t(3;5)(q25.1;q34) translocation, which is occasionally found in myelodysplastic syndromes and acute myeloid leukemia. No evidence was obtained for a rearrangement or deregulation of the translocated FLT4 gene. We further show that abundant FLT4 mRNA expression occurs only in erythroid and megakaryoblastoid cell lines among nine leukemia cell lines studied.
Blink (2011)

Reducing the energy footprint of data centers continues to receive significant attention due to both its financial and environmental impact. There are numerous methods that limit the impact of both factors, such as expanding the use of renewable energy or participating in automated demand-response programs. To take advantage of these methods, servers and applications must gracefully handle intermittent constraints in their power supply. In this paper, we propose blinking---metered transitions between a high-power active state and a low-power inactive state---as the primary abstraction for conforming to intermittent power constraints. We design Blink, an application-independent hardware-software platform for developing and evaluating blinking applications, and define multiple types of blinking policies. We then use Blink to design BlinkCache, a blinking version of memcached, to demonstrate the effect of blinking on an example application. Our results show that a load-proportional blinking policy combines the advantages of both activation and synchronous blinking for realistic Zipf-like popularity distributions and wind/solar power signals by achieving near optimal hit rates (within 15% of an activation policy), while also providing fairer access to the cache (within 2% of a syn- chronous policy) for equally popular objects.
Development of the Barrel Type Bellows. (2000)

This paper presents the development of the bending bellows named “barrel type bellows” for the multi-functional vacuum tube. Conventional bellows with a bending axis outside of the bellows is imposed the complex motions of bending and sliding, and the stress concentrates on the pleat near the end portions. Based on the numerical analysis, it is found that the concentrated stress is reduced by making the outer diameter increase continuously from the both ends toward the center. As a result, the offset width of the bellows decreases and the vacuum tube becomes small. The endurance test shows that the operating cycles are over 30, 000, which roughly corresponds to that predicted from the calculated stress and the fatigue data of the thin stainless sheet in Refs. 2) and 4).
Thermal conductivity and compressive strain of foam neoprene insulation under hydrostatic pressure (2005)

The purpose of this study was to show that the thermal properties of foam neoprene under hydrostatic pressure cannot be predicted by theoretical means, and that uni-axial pressure cannot simulate hydrostatic compression. The thermal conductivity and compressive strain of foam neoprene were measured under hydrostatic pressure. In parallel, uni-axial compressive strain data were collected. The experimental set-up and data were put into perspective with past published studies. It was shown that uni-axial compression yielded strains 20–25% greater than did hydrostatic compression. This suggests the need for direct hydrostatic pressure measurement. For comparison to hydrostatic experimental data, a series of thermal conductivity theories of two phase composites based on particulate phase geometry were utilized. Due to their dependence on the porosity and constituent thermal conductivities, a model to predict porosity under hydrostatic pressure was used and an empirical correlation was derived to calculate the thermal conductivity of pure neoprene rubber from experimental data. It was shown that, although some agreement between experimental data and thermal conductivity theories was present, no particular theory can be used because they all fail to model the complex structure of the pores. It was therefore concluded that an experimental programme, such as reported here, is necessary for direct measurement.
Ab initiopseudopotential solid-state calculations of highly electronegative first-row elements (1989)

Density-functional pseudopotential total-energy calculations have been a powerful tool in studies of the electronic and structural properties of semiconductors and simple metals. The inclusion of highly electronegative first-row elements such as oxygen and fluorine has not, in general, been tractable. In this paper we address the inherent difficulties and demonstrate that they can be overcome. Focusing on oxygen-silicon systems the precision of our method is demonstrated particularly through the study of angular stability of Si-O-Si bridge bonds in silica. The results predict bending to an equilibrium angle of 140\ifmmode^\circ\else\textdegree\fi{}\ifmmode\pm\else\textpm\fi{}5\ifmmode^\circ\else\textdegree\fi{}, as observed, with an energy gain of only \ensuremath{\sim}0.15 eV.
Cartilaginous spheroid-assembly design considerations for endochondral ossification: towards robotic-driven biomanufacturing (2021)

Spheroids have become essential building blocks for biofabrication of functional tissues. Spheroid formats allow high cell-densities to be efficiently engineered into tissue structures closely resembling the native tissues. In this work, we explore the assembly capacity of cartilaginous spheroids (<i>d</i>∼ 150<i>µ</i>m) in the context of endochondral bone formation. The fusion capacity of spheroids at various degrees of differentiation was investigated and showed decreased kinetics as well as remodeling capacity with increased spheroid maturity. Subsequently, design considerations regarding the dimensions of engineered spheroid-based cartilaginous mesotissues were explored for the corresponding time points, defining critical dimensions for these type of tissues as they progressively mature. Next, mesotissue assemblies were implanted subcutaneously in order to investigate the influence of spheroid fusion parameters on endochondral ossification. Moreover, as a step towards industrialization, we demonstrated a novel automated image-guided robotics process, based on targeting and registering single-spheroids, covering the range of spheroid and mesotissue dimensions investigated in this work. This work highlights a robust and automated high-precision biomanufacturing roadmap for producing spheroid-based implants for bone regeneration.
Introduction to the JEEG – NSG Geotechnical Assessment and Geo-environmental Engineering Geophysics Special Issue (2013)

Experts say that the near-surface geophysics community will witness a rapid growth over the next decade. The recent surge in the development of new technologies and analysis tools lends weight to that theory, and today we have numerous means to solve many of the complex engineering problems associated with the natural and built environments. Assessing the stability and integrity of structures such as buildings, bridges, dams, roads, water ways, foundations, underground excavations, mines, landfills, and sinkholes often requires a multi-disciplinary approach and collaboration between experts in geophysics, hydrology, geotechnical and environmental engineering, and geology. A trend to objectify the information about the condition of a structure is beginning to emerge: the development of tools to appraise and integrate data from sources of similar and dissimilar nature.

This Special Joint-Issue of the Journal of Environmental and Engineering Geophysics and Near Surface Geophysics entitled “Geotechnical Assessment and Geo-environmental Engineering” is a selection of original contributions organized under two themes. Near Surface Geophysics presents eight articles on the application of the electrical resistivity techniques to determine the geotechnical properties of the ground, and the integration of geophysical and geotechnical data. The Journal of Environmental and Engineering Geophysics contains seven papers that investigate the stability of structures using seismic techniques.

The articles presented in this special joint-issue were selected from a pool of over forty manuscript submissions never published before. The papers are peer-reviewed by a panel of experts from around the world and are at the forefront of the current state-of-knowledge. We hope that both researchers and professionals responsible for site and geomaterials characterization will find the information contained in this collection of practical use.

In the paper “ Seismic surface-wave prospecting methods for sinkhole hazard assessment along the Dead Sea shoreline ”, Ezersky et al. present the results of a surface-wave investigation …
Background Reduction in STED-FCS Using a Bivortex Phase Mask (2020)

Fluorescence correlation spectroscopy (FCS) is a valuable tool to study the molecular dynamics in living cells. When used together with a super-resolution stimulated emission depletion (STED) microscope, STED-FCS can measure diffusion processes on the nanoscale in living cells. In two-dimensional (2D) systems like the cellular plasma membrane, a ring-shaped depletion focus is most commonly used to increase the lateral resolution, leading to more than 25-fold decrease in the observation volume, reaching the relevant scale of supramolecular arrangements. However, STED-FCS faces severe limitations when measuring diffusion in three dimensions (3D), largely due to the spurious background contributions from undepleted areas of the excitation focus that reduce the signal quality and ultimately limit the resolution. In this paper, we investigate how different STED confinement modes can mitigate this issue. By simulations as well as experiments with fluorescent probes in solution and in cells, we demonstrate that the coherent-hybrid (CH) depletion pattern created by a bivortex phase mask reduces background most efficiently and thus provides superior signal quality under comparable reduction of the observation volume. Featuring also the highest robustness to common optical aberrations, CH-STED can be considered the method of choice for reliable STED-FCS-based investigations of 3D diffusion on the subdiffraction scale.
Highly Regioselective Indoline Synthesis under Nickel/Photoredox Dual Catalysis (2015)

Nickel/photoredox catalysis is used to synthesize indolines in one step from iodoacetanilides and alkenes. Very high regioselectivity for 3-substituted indoline products is obtained for both aliphatic and styrenyl olefins. Mechanistic investigations indicate that oxidation to Ni(III) is necessary to perform the difficult C-N bond-forming reductive elimination, producing a Ni(I) complex, which in turn is reduced to Ni(0). This process serves to further demonstrate the utility of photoredox catalysts as controlled single electron transfer agents in multioxidation state nickel catalysis.
Nitride VECSELs as Light Sources for Biomedical Applications (2013)

In-well-pumped blue InGaN/GaN vertical-external-cavity surface-emitting lasers are demonstrated. The laser structures were grown on bulk GaN substrates by using metal-organic vapor phase epitaxy near atmospheric pressure. The active zone consisted of up to 20 InGaN quantum wells distributed in a resonant periodic gain configuration. High-reflectivity dielectric distributed Bragg-reflectors were used as mirrors. Laser emission with a single longitudinal mode at 440 nm was achieved by exclusively pumping the quantum wells with the 384 nm emission line of a dye-/N2-laser.
Soft Electron Beam Lithography (Soft-eBL) Patterning of 0- and 1-D Nanostructures of Magnetic and Ferroelectric Oxides (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
Using a biologically annotated library to analyze the anticancer mechanism of serine palmitoyl transferase (SPT) inhibitors (2017)

Mechanistic understanding is crucial to anticancer drug discovery. Here, we reveal that inhibition of serine palmitoyl transferase (SPT), the rate-limiting enzyme in sphingolipid synthesis, induced death in a lung cancer cell line via a necrosis-dependent pathway. To elucidate the mechanism of cell death induced by SPT inhibition, a biologically annotated library of diverse compounds was screened with an SPT inhibitor. This analysis identified suppressors of SPT inhibitor-mediated cell death. Further analysis using hit compounds from this screening revealed that SPT inhibitors induce COX-2 expression, leading to necrosis-dependent cell death. SPT inhibitors might therefore represent novel candidates for cancer therapy via necrosis pathway regulation. Our data illustrate that compound combination screening of biologically annotated libraries could be used for mechanistic elucidation.
Voltage-controlled IPMC actuators for accommodating intra-ocular lens systems (2017)

An ion polymer–metal composite (IPMC) actuator has unique performance characteristics that were applied in this study for use within the eye. Cataracts are a common eye disease causing clouding of the lens. To treat cataracts, surgeons replace clouded lenses with intraocular lenses (IOLs). However, patients who receive this treatment must still wear reading glasses for tasks requiring close-up vision. We suggest a new voltage-controlled accommodating IOL consisting of an IPMC actuator to change the lens' focus. We examined the relationship between the displacement performance of an IPMC actuator and the accommodating range of the IOL using in vitro experiments. We show that this system has an accommodating range of approximately 1.15 D under an applied voltage of ±1.2 V. By Lagrange interpolation, we estimate that with an IPMC actuator displacement of 0.14 mm, we can achieve a refractive power of 4 D, which is equivalent to the accommodating range of a 40 year old person.
Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach (2011)

Neuropilin-1 (NRP-1) is a receptor that plays an essential role in angiogenesis, vascular permeability, and nervous system development. Previous studies have shown that peptides with an N-terminal Arg, especially peptides with the four-residue consensus sequence R/K/XXR/K, bind to NRP-1 cell surfaces. Peptides containing such consensus sequences promote binding and internalization into cells, while blocking the C-terminal Arg (or Lys) prevents the internalization. In this study, we use molecular dynamics simulations to model the structural properties of the NRP-1 complex with a prototypic CendR peptide, RPAR. Our simulations show that RPAR binds NRP-1 through specific interactions of the RPAR C-terminus: three hydrogen bonds and a salt bridge anchor the ligand in the receptor pocket. The modeling results were used as the starting point for a systematic computational study of new RPAR analogues based on chemical modifications of their natural amino acids. Comparison of the structural properties of the new peptide-receptor complexes with the original organization suggests that some of the analogues can increase the binding affinity while reducing the natural sensitivity of RXXR to endogenous proteases.
Comparaison du couple massique de diverses architectures de machines synchrones à aimants (2005)

National audience
A comparative study of inhibition of acetylcholinesterase, trypsin, neuropathy target esterase, and spleen cell activation by structurally related organophosphorus compounds (1994)

Organophosphorus (OP) compounds can bind to and inactivate several target molecules other than acetylcholinesterase (AChE). In the present study, five sets of structurally related organophosphorus compounds were used to evaluate the relationships between organophosphorus binding sites of AChE, neuropathy target esterase (NTE), trypsin, and the target molecule(s) involved in inhibition of splenocyte activation by OP compounds. The concentration of each OP compound required to inhibit enzyme activity or splenocyte activation by concanavalin A by 50% was determined. The pattern of IC50 values indicated that AChE, trypsin, NTE, and the molecule(s) involved in inhibition of splenocyte activation are distinct with regard to patterns of inhibition by OP compounds. However, there was a striking similarity in the patterns of inhibition for trypsin and NTE with substantial differences for only 2 of 20 compounds. This pattern suggests similarity in the active sites of these molecules. There were also similarities in the IC50 patterns for lymphocyte activation and trypsin or NTE activity. However, the correlation was not as strong as between NTE and trypsin, and the data suggested the possibility of multiple target molecules for inhibition of splenocyte activation by OP compounds. More importantly, there was essentially no correlation between the pattern of IC50 values for AChE and splenocyte activation. This strongly suggests that acetylcholine and AChE of the type found in the brain are not important in the regulation of splenocyte activation by concanavalin A.