gebhart/patrepeval huggingface dataset:
Stop testing for autoantibodies to the VGKC-complex: only request LGI1 and CASPR2 (2020)

Autoantibodies to leucine-rich glioma-inactivated 1 (LGI1) and contactin-associated protein like-2 (CASPR2) are associated with clinically distinctive syndromes that are highly immunotherapy responsive, such as limbic encephalitis, faciobrachial dystonic seizures, Morvan's syndrome and neuromyotonia. These autoantibodies target surface-exposed domains of LGI1 or CASPR2, and appear to be directly pathogenic. In contrast, voltage-gated potassium channel (VGKC) antibodies that lack LGI1 or CASPR2 reactivities ('double-negative') are common in healthy controls and have no consistent associations with distinct syndromes. These antibodies target intracellular epitopes and lack pathogenic potential. Moreover, the clinically important LGI1 and CASPR2 antibodies comprise only ~15% of VGKC-positive results, meaning that most VGKC-antibody positive results mislead rather than help. Further, initial VGKC testing misses some cases that have LGI1 and CASPR2 antibodies. These collective observations confirm that laboratories should stop testing for VGKC antibodies and instead, test only for LGI1 and CASPR2 antibodies. This change in practice will lead to significant patient benefit.
Modeling the Maximum Lateral Extent of Encroachment and Probability of Passenger-Vehicle Rollover on Slopes (2019)

The 1967 “Yellow Book” points out that “[f]or adequate safety it is desirable to provide an unencumbered recovery area up to 30 feet from the edge of the traveled way.” The 1974 Yellow Book points out that a 30-ft recovery area is not a one-size-fits-all guideline. This paper examines the probability of an errant vehicle trajectory extending laterally to a location of interest (e.g., across the median, to the barrier, to a fixed object, etc.) and the likelihood the vehicle will rollover prior to reaching that point as a function of the foreslope. The influence of encroachment speed and angle, vehicle type, and slope on the probable lateral extent was examined using survival analysis of simulated vehicle trajectories. Field collected data were used to scale the simulated data to better represent field collected encroachment speeds and angles. The work presented in this paper represents a significant enrichment to the understanding of the lateral extent of errant vehicle trajectories during an encroachment and the probability of rollover by slope and distance traveled on the slope. These models can be used for guideline development and extended in the future to include ditches and other complex terrain features. The two figures presented in this paper which represent the conclusions of this research are a significant step toward reducing the computational burden of analyzing roadside safety alternatives thereby significantly reducing the reliance on computer programs such as Roadside Analysis Program.
Investigation of Variable Mach Number Wind Tunnel with Symmetric Sliding Block Nozzles (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-0716.vid The Continuously Varying Mach Number Tunnel (CVMT) was commissioned at National Centre for Combustion Research and Development (NCCRD), Indian Institute of Technology Madras. The CVMT is capable of generating variable Mach number flow continuously. This ground test facility is of intermittent, blow-down, enclosed free-jet type. The nozzle profile was designed using the Method of Characteristics (MOC) simulations. The nozzle blocks are translated towards and away from each other symmetrically. The continuous movement of nozzle blocks results in the varying Mach number. The CVMT is characterized using two methods. In the first method, the flow is calibrated using a Pitot rake. In this case, the CVMT is calibrated for different Mach numbers without dynamic movement of the nozzle. In the second method, the CVMT is calibrated with a simple wedge for different Mach numbers with dynamic movement of the nozzle. The resulting Mach numbers with both the methods agree well with each other. In this paper, the design method, nozzle translation mechanism and characterization of the Variable Mach number tunnel with symmetric sliding block nozzle are presented.
A preliminary approach in the prediction of orthodontic bone remodeling by coupling experiments, theory and numerical models (2019)

International audience
Tanzania HIV Investment Case (IC) 2.0: Using modeling to explore optimization under severe resource constraints (2022)

Background After years of increased human immunodeficiency virus (HIV) investments in Tanzania, the United States Presidents Emergency Program for the AIDS Response (PEPFAR) and the Global Fund to Fight AIDS, Tuberculosis, and Malaria (GFATM) have signaled that their financing will plateau or decline in the coming years, despite remaining challenges to reaching the Fast-Track 95-95-95 goals. To plan for these challenges, the Tanzania Ministry of Health and local partners requested an update to the country’s HIV investment case, recognizing that domestic financing will also be severely constrained over the coming decade. Methods Using the Goals model, five program scenarios (2019-30) were modeled and their health impacts and costs compared. Two scenarios were coverage-driven, Constant Coverage (CC) and the National Strategy (NS) while the three remaining scenarios explored how limited resources could be optimized through prioritization of prevention interventions, raising efficiency of treatment, and expanding cost-effective testing modalities. The resource envelopes used for resource-constrained scenarios were: same funding as the CC scenario, declining donor funds, and declining donor funds offset by domestic resource mobilization. Results Implementing the NS is estimated to cost US$8.1 billion over 2019-30, a 40% increase over the CC scenario. If the same funds needed to maintain CC were optimized, the NS goals could be achieved for US$2.5 billion less. If donor funds decline and domestic funding is not mobilized, even with optimization new HIV infections would increase by 7% and acquired immunodeficiency syndrome (AIDS)-related deaths by 24%. However, if the government can mobilize an average year on year increase of US$10.8 million, optimization would allow the country to achieve its ambitious Fast-Track goals. Conclusions If donor funds for HIV decline as announced, the Government needs to proactively optimize the response and invest more domestic resources to compensate, in order to achieve HIV epidemic control. Otherwise, national goals could be compromised. Other high burden countries can consider a similar investment case approach in the current era of fiscal constraints, which have been further exacerbated by COVID-19.
Real-time Visualization of Wave Propagation. (2006)

In this work we present a method to visualize the wave propagation mechanisms of wireless networks at interactive rates. The user can move around transmitting nodes and immediately sees the resulting field strength for the complete scenario. This can be used for rapid optimization of antenna placement, or for visualizing the coverage of mobile stations, as they move through a simulation. In a preprocessing step we compute the wave propagation for a distinct set of transmitter positions. Whereas in the visualization phase we use these precomputed maps to do a fast interpolation using a current graphics card.
Pharmacologic inhibition of LAT1 predominantly suppresses transport of large neutral amino acids and downregulates global translation in cancer cells (2022)

L-type amino acid transporter 1 (LAT1; SLC7A5), which preferentially transports large neutral amino acids, is highly upregulated in various cancers. LAT1 supplies cancer cells with amino acids as substrates for enhanced biosynthetic and bioenergetic reactions and stimulates signalling networks involved in the regulation of survival, growth and proliferation. LAT1 inhibitors show anti-cancer effects and a representative compound, JPH203, is under clinical evaluation. However, pharmacological impacts of LAT1 inhibition on the cellular amino acid transport and the translational activity in cancer cells that are conceptually pivotal for its anti-proliferative effect have not been elucidated yet. Here, we demonstrated that JPH203 drastically inhibits the transport of all the large neutral amino acids in pancreatic ductal adenocarcinoma cells. The inhibitory effects of JPH203 were observed even in competition with high concentrations of amino acids in a cell culture medium. The analyses of the nutrient-sensing mTORC1 and GAAC pathways and the protein synthesis activity revealed that JPH203 downregulates the global translation. This study demonstrates a predominant contribution of LAT1 to the transport of large neutral amino acids in cancer cells and the suppression of protein synthesis by JPH203 supposed to underly its broad anti-proliferative effects across various types of cancer cells.
Discrimination of clinically significant calcium salts using MARS spectral CT (2017)

Calcium compounds within tissues are usually a sign of pathology, and calcium crystal type is often a pointer to the diagnosis. There are clinical advantages in being able to determine the quantity and type of calcifications non-invasively in cardiovascular, genitourinary and musculoskeletal disorders, and treatment differs depending on the crystal type and quantity. The problem arises when trying to distinguish between different calcium compounds within the same image due to their similar attenuation properties. There are spectroscopic differences between calcium salts at very low energies. As calcium oxalate and calcium hydroxyapatite can co-exist in breast and musculoskeletal pathologies of the breast, we wished to determine whether Spectral CT could distinguish between them in the same image at clinical X-ray energy ranges. Energy thresholds of 15, 22, 29 and 36keV and tube voltages of 50, 80 and 110kVp were chosen, and images were analysed to determine the percentage difference in the attenuation coefficients of calcium hydroxyapatite samples at concentrations of 54.3, 211.7, 808.5 and 1169.3mg/ml, and calcium oxalate at a concentration of 2000 mg/ml. The two lower concentrations of calcium hydroxyapatite were distinguishable from calcium oxalate at all energies and all tube voltages, whereas the ability to discriminate oxalate from hydroxyapatite at higher concentrations was dependent on the threshold energy but only mildly dependent on the tube voltage used. Spectral CT shows promise for distinguishing clinically important calcium salts.
Framework for Quantification of the Dynamics of Root Colonization by Pseudomonas fluorescens Isolate SBW25 (2020)

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap. A model system was developed to acquire quantitative data on the colonization process of lettuce (<i>Lactuca sativa</i> L. cultivar. All Year Round) roots by <i>Pseudomonas fluorescens</i> isolate SBW25. A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization. This allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally. All techniques proposed are generic and similar analyses could be applied to study various combinations of plants and bacteria, or to assess competition between species. In the future this could allow for selection of microbial traits that improve early colonization and maintenance of targeted isolates in cropping systems, with potential applications for the development of biological fertilizers.
Sphere Lower Bound for Rotated Lattice Constellations in Fading Channels (2007)

We study the error probability performance of rotated lattice constellations in frequency-flat Nakagami-$m$ block-fading channels. In particular, we use the sphere lower bound on the underlying infinite lattice as a performance benchmark. We show that the sphere lower bound has full diversity. We observe that optimally rotated lattices with largest known minimum product distance perform very close to the lower bound, while the ensemble of random rotations is shown to lack diversity and perform far from it.
A Fixed-Threshold Approach to Generate High-Resolution Vegetation Maps for IKONOS Imagery (2008)

Vegetation distribution maps from remote sensors play an important role in urban planning, environmental protecting and related policy making. The normalized difference vegetation index (NDVI) is the most popular approach to generate vegetation maps for remote sensing imagery. However, NDVI is usually used to generate lower resolution vegetation maps, and particularly the threshold needs to be chosen manually for extracting required vegetation information. To tackle this threshold selection problem for IKONOS imagery, a fixed-threshold approach is developed in this work, which integrates with an extended Tasseled Cap transformation and a designed image fusion method to generate high-resolution (1-meter) vegetation maps. Our experimental results are promising and show it can generate more accurate and useful vegetation maps for IKONOS imagery.
SHG microscopic observation of Pb(Zn1/3Nb2/3)O3–9%PbTiO3single crystal (2011)

Abstract Non-destructive and contactless observations of the domain structures in a single crystal of solid solution Pb(Zn1/3Nb2/3)O3–9%PbTiO3 (PZN–9PT) was performed using the scanning second-harmonic generation (SHG) microscopy with the spatial resolution of optical wavelength scale. A novel method of the 2D mapping of SHG polarization dependence (Pol-D) is proposed. The result indicates that the Pol-Ds correspond well to the observed SHG images of domain structures. The directions of ferroelectric spontaneous polarizations are quantitatively analysed by comparing SHG images and the Pol-Ds. It is confirmed that PZN-9PT has the monoclinic symmetry at room temperature. Keywords: ferroelectricsrelaxormorphotropic phase boundaryPZN-PTSHG microscope Acknowledgements This research is partly supported by the “Academic Frontier” Project of the Ministry of Education, Culture, Sports, Science and Technology. J. Kaneshiro is grateful for the support of Grants-in-Aid for Research Fellow of the Japan Society for the Promotion of Science. The authors thank Dr Y. Yamashita for providing the PZN-9PT single crystal.
Resolving the Incomplete Charging Behavior of Redox-Mediated Li-O2 Batteries via Sustainable Protection of Li Metal Anode (2022)

Lithium-oxygen batteries (LOBs) have attracted worldwide attention due to their high specific energy. However, the poor rechargeability and cycling stability of LOBs hinders their practical use in applications. Here, we explore the incomplete charging behavior of redox-mediated LOBs operated at a feasible capacity for a practical level (3.25 mAh cm<sup>-2</sup>) and resolve it using a sustainable lithium protection strategy. The incomplete charging behavior, promoted by self-discharge of redox mediators (RMs), hampers the reversible cycling of LOBs, which was investigated through multiangle <i>in situ</i> and <i>ex situ</i> analyses. Meanwhile, the proposed lithium protection strategy, introducing an inorganic/organic hybrid artificial composite layer with a preformed stable interface between the lithium metal and the composite layer, enhances the stability of the lithium metal anode during the prolonged cycling by preventing the chemical/electrochemical interactions of RMs on the lithium metal surface, thus improving the overall rechargeability of LOBs. This work provides guidelines for the effective use of RMs with an adequate lithium protection strategy to achieve sustainable cycling of LOBs, creating a feasible approach for the practical use of LOBs with high areal capacity.
Epilogue (2009)

Although I do not think that every aspect of James's practical faith is equally plausible or compelling, much less that every aspect of his religious and moral views can or should be affirmed, I confess my admiration for the sheer originality and scope of his philosophical vision. James was among the first philosophers of religion to approach the subject from an empirical and humanistic point of view, though, as we have seen time and again, he resisted any tendency toward scientific positivism or toward what Paul Ricoeur famously called “the hermeneutics of suspicion.” James was also among the first philosophers to develop an anti- evidentialist and anti-foundationalist religious epistemology, rejecting not only the presupposition that religious belief cannot be warranted if it does not rest upon sufficient evidence, but also the presupposition that having religious knowledge requires having infallible and incorrigible religious beliefs. This stance is basic to both his will to believe doctrine and his pragmatic account of religion, and I am inclined to think that James was right (or at any rate reasonable) in holding such a view. But in my view the most innovative aspect of James's philosophy of religion is its attempt to reconcile a commitment to religious realism with what we might call a commitment to religious humanism – that is, to combine a realistic view of the objects of religious belief with the view that human interests and purposes ineluctably shape our conceptions of and manner of relating to those objects. In short, religion is about an unseen order on James's view, but it is also about us and our values.
Analysis of least-time and minimum-hop routing for clustered temporal networks (2002)

Networks of low-altitude multiple satellites (LAMS) have been envisioned to provide such diverse tasks as global positioning, paging, weather tracking, surveillance, and environmental observation and disaster assessment. One theoretical model for such dynamically reconfiguring networks, allowing the investigation of packet routing, is the clustered temporal network (CTN). The store-and-forward routing in such a network requires a quite different algorithmic approach to that of static networks which have been studied extensively. While solutions for optimal paths can be found only by NP complexity algorithms, a polynomial algorithm using spanning graphs in conjunction with the CTN model, and yielding very good, but not necessarily optimal, solutions have been previously found. The time-complexities of the algorithm using a full spanning graph, which yields optimal solutions relative to the CTN model, and a reduced spanning graph that yields good but sub-optimal solutions are investigated empirically. The algorithm using the reduced spanning graph is shown, through stochastic simulation and descriptive statistics, to be significantly faster than the algorithm using the full spanning graph. It is also shown that the space-complexity of the reduced spanning graph data structure is significantly less than the corresponding full spanning graph. Finally, the average path latencies and hop counts of the generated paths are compared for the full and reduced spanning graphs, and show very little difference. The studies are performed for networks of 5-80 nodes (satellites).
Autonomous Vehicle and Real Time Road Lanes Detection and Tracking (2015)

Advanced Driving Assistant Systems, intelligent and autonomous vehicles are promising solutions to enhance road safety, traffic issues and passengers' comfort. Such applications require advanced computer vision algorithms that demand powerful computers with high-speed processing capabilities. Keeping intelligent vehicles on the road until its destination, in some cases, remains a great challenge, particularly when driving at high speeds. The first principle task is robust navigation, which is often based on system vision to acquire RGB images of the road for more advanced processing. The second task is the vehicle's dynamic controller according to its position, speed and direction. This paper presents an accurate and efficient road boundaries and painted lines' detection algorithm for intelligent and autonomous vehicle. It combines Hough Transform to initialize the algorithm at each time needed, and Canny edges' detector, least-square method and Kalman filter to minimize the adaptive region of interest, predict the future road boundaries' location and lines parameters. The scenarios are simulated on the Pro-SiVIC simulator provided by Civitec, which is a realistic simulator of vehicles' dynamics, road infrastructures, and sensors behaviors, and OPAL-RT product dedicated for real time processing and parallel computing.
High Aspect Ratio GaN Fin Microstructures with Nonpolar Sidewalls by Continuous Mode Metalorganic Vapor Phase Epitaxy (2016)

Three-dimensional GaN micro- and nanorods with a high aspect ratio have recently gained substantial interest in light-emitting diode research, due to their reduced defect density, their nonpolar sidewalls, and their increased active area. Here, we present an alternative geometry for high aspect ratio three-dimensional nanostructures: vertically standing GaN “walls”, so-called GaN fins. With high aspect ratios, these GaN fins exhibit the same interesting characteristics as their rod counterparts mentioned above. Beyond that, because of their geometry, the respective material analysis and device processing can be expected to be less complex. We are able to demonstrate the highly reproducible selective area growth of these fins by continuous mode metalorganic vapor phase epitaxy. Fin heights of more than 50 μm (aspect ratios of nearly 14) could be achieved, and growth rates are as high as 22.8 μm/h in the beginning of the growth. The sidewalls are smooth nonpolar <112̅0> a-planes, suitable for optoelectronic devices due to the missing quantum-confined Stark effect and less edge effects compared to rods. We investigate the influence of pattern orientation and geometry on the fin morphology. Moreover, the influence of silane flow, which is known to enhance the vertical growth rate, and other growth parameters are systematically explored.
NIW: A Net2Plan-Based Library for NFV over IP over WDM Networks (2019)

Software-Defined Networking (SDN) and Network Function Virtualization (NFV) technologies enable a major technological breakthrough for telecom operators' networks. In this paper, we present the NFV over IP over WDM (NIW) library, an open-source framework for SDN/NFV metropolitan networks, created in the context of the Metro-Haul project. NIW is a library added to the Net2Plan open-source network planning software, specifically to model, provision, design and evaluate SDN/NFV networks. We introduce the major components and functionalities of NIW in a tutorial manner, including an Excel file loader meant to ease data loading for its manipulation through NIW data structure and its available methods. Finally, an illustrative example shows the basic library usage taking into account NFV over IP over WDM network resources in a reference topology.