gebhart/patrepeval huggingface dataset:
PriMO-5G: making firefighting smarter with immersive videos through 5G (2019)

In this paper, we introduce PriMO-5G which is an EU-Korea collaboration project studying the use of 5G technologies and unmanned aerial vehicles (UAVs) or drones to enhance the safety and efficiency of firefighting operations. We start by describing envisaged use cases of smart firefighting focusing on how the 5G communications with drones can help the firefighting. Inspired by the use cases, we identify several research challenges that call for new solutions in 5G radios and cores for mission-critical services. Then, a discussion of a new framework for defining key performance indicators (KPIs) follows. Finally, we introduce our effort and future plans for the demonstration of the technologies that the PriMO-5G develops.
Scalable dynamical systems for multi-agent steering and simulation (2002)

We present a methodology for agent modeling that is scalable and efficient. It is based on the integration of nonlinear dynamical systems and kinetic data structures. The method consists of three-layers that model steering, flocking, and crowding agent behaviors among moving and static obstacles in 2 and 3D. The first layer, the local layer is based on the the use of nonlinear dynamical systems theory and models low level behaviors, it is fast and efficient, and does not depend on the total number of agents in the environment. The use of dynamical systems allows the use of continuous numerical parameters with which we can modify the interaction of each agent with the environment. This creates controllable distinctive behaviors. The second layer, a global environment layer consists of a specifically designed kinetic data structure to track efficiently the immediate environment of each agent and know which obstacles/agents are near or visible to the given agent. This layer reduces the complexity in the local layer. In the third layer, a global planning layer, the problem of target tracking is generalized in a way that allows navigation in maze-like terrains, avoidance of local minima and cooperation between agents. We implement this layer based on two approaches that are suitable for different applications. One is to track the closest single moving or static target. The second is to use a pre-specified vector field. This vector can be generated automatically (with harmonic functions, for example) or based on user input to achieve the desired output. We demonstrate the power of the approach through a series of experiments simulating single/multiple agents and crowds moving towards moving/static targets in complex environments.
A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase (2011)

The His274→Tyr (H274Y) oseltamivir (Tamiflu) resistance mutation causes a substantial decrease in the total levels of surface-expressed neuraminidase protein and activity in early isolates of human seasonal H1N1 influenza, and in the swine-origin pandemic H1N1. In seasonal H1N1, H274Y only became widespread after the occurrence of secondary mutations that counteracted this decrease. H274Y is currently rare in pandemic H1N1, and it remains unclear whether secondary mutations exist that might similarly counteract the decreased neuraminidase surface expression associated with this resistance mutation in pandemic H1N1. Here we investigate the possibility of predicting such secondary mutations. We first test the ability of several computational approaches to retrospectively identify the secondary mutations that enhanced levels of surface-expressed neuraminidase protein and activity in seasonal H1N1 shortly before the emergence of oseltamivir resistance. We then use the most successful computational approach to predict a set of candidate secondary mutations to the pandemic H1N1 neuraminidase. We experimentally screen these mutations, and find that several of them do indeed partially counteract the decrease in neuraminidase surface expression caused by H274Y. Two of the secondary mutations together restore surface-expressed neuraminidase activity to wildtype levels, and also eliminate the very slight decrease in viral growth in tissue-culture caused by H274Y. Our work therefore demonstrates a combined computational-experimental approach for identifying mutations that enhance neuraminidase surface expression, and describes several specific mutations with the potential to be of relevance to the spread of oseltamivir resistance in pandemic H1N1.
GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction (2023)

High-throughput DNA and RNA sequencing are revolutionizing precision oncology, enabling personalized therapies such as cancer vaccines designed to target tumor-specific neoepitopes generated by somatic mutations expressed in cancer cells. Identification of these neoepitopes from next-generation sequencing data of clinical samples remains challenging and requires the use of complex bioinformatics pipelines. In this paper, we present GeNeo, a bioinformatics toolbox for genomics-guided neoepitope prediction. GeNeo includes a comprehensive set of tools for somatic variant calling and filtering, variant validation, and neoepitope prediction and filtering. For ease of use, GeNeo tools can be accessed via web-based interfaces deployed on a Galaxy portal publicly accessible at https://neo.engr.uconn.edu/. A virtual machine image for running GeNeo locally is also available to academic users upon request.
Corrections to “High-Throughput Random Access Using Successive Interference Cancellation in a Tree Algorithm” (2022)

In the above article, the authors propose <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$d$ </tex-math></inline-formula> -ary SICTA and derive the expected conditional length of the collision resolution interval, optimal splitting probability and the maximum stable throughput (MST) for <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$d \geq 2$ </tex-math></inline-formula> under stationary ergodic packet arrivals. In this correction, we show that the premise of the analysis for <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$d &gt; 2$ </tex-math></inline-formula> and consequentially the results presented for <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$d &gt; 2$ </tex-math></inline-formula> do not hold.
Stevenson’s Rule (2016)

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Judder-Induced Edge Flicker at Zero Spatial Contrast (2004)

Judder is a motion artifact that degrades the quality of video imagery. Smooth motion appears jerky and can appear to flicker along the leading and trailing edge of the moving object. In a previous paper, we demonstrated that the strength of the edge flicker signal depended upon the brightness of the scene and the contrast of the moving object relative to the background. Reducing the contrast between foreground and background reduced the flicker signal. In this report, we show that the contrast signal required for judder-induced edge flicker is due to temporal contrast and not simply to spatial contrast. Bars made of random dots of the same dot density as the background exhibit edge flicker when moved at sufficient rate.
ChemInform Abstract: CHEMICALLY SIGNIFICANT INTERACTIONS BETWEEN RUTHENIUM IONS IN OXO‐BRIDGED COMPLEXES OF RUTHENIUM(III) (1975)

Abstract Die u‐oxoverbrückten Ru(III)‐Komplexe (II), (III) und (IV) werden dargestellt und durch Elementaranalyse, Leitfähigkeitsmessungen, magnetische und elektronenspektroskopische Daten charakterisiert.
grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses (2011)

The shape of a plant is largely determined by regulation of lateral branching. Branching architecture can vary widely in response to both genotype and environment, suggesting regulation by a complex interaction of autonomous genetic factors and external signals. Tillers, branches initiated at the base of grass plants, are suppressed in response to shade conditions. This suppression of tiller and lateral branch growth is an important trait selected by early agriculturalists during maize domestication and crop improvement. To understand how plants integrate external environmental cues with endogenous signals to control their architecture, we have begun a functional characterization of the maize mutant grassy tillers1 (gt1). We isolated the gt1 gene using positional cloning and found that it encodes a class I homeodomain leucine zipper gene that promotes lateral bud dormancy and suppresses elongation of lateral ear branches. The gt1 expression is induced by shading and is dependent on the activity of teosinte branched1 (tb1), a major domestication locus controlling tillering and lateral branching. Interestingly, like tb1, gt1 maps to a quantitative trait locus that regulates tillering and lateral branching in maize and shows evidence of selection during maize domestication. Branching and shade avoidance are both of critical agronomic importance, but little is known about how these processes are integrated. Our results indicate that gt1 mediates the reduced branching associated with the shade avoidance response in the grasses. Furthermore, selection at the gt1 locus suggests that it was involved in improving plant architecture during the domestication of maize.
Detection of low titre TBII in patients with Graves’ disease using recombinant human TSH receptor (2002)

Low TBII titres can now be followed more accurately during the course of treatment, which will also allow better longitudinal studies on the importance of TBII for the diagnosis as well as the prognosis of GD with respect to remission or relapse.
Unraveling the Effect of Conformational and Electronic Disorder in the Charge Transport Processes of Semiconducting Polymers (2018)

Abstract Charge transport in semiconducting polymers is inextricably linked to their microstructure, making the characterization of polymer morphology at all length‐scales essential for understanding the factors that limit mobility in these materials. Indeed, charge transport depends both on the ability of polarons to delocalize at the approximately nanometer length‐scale and navigate a complex energetic and morphological mesoscale landscape. While characterization of the mesoscale morphology of polymers is well‐established, studies of the local chain packing and nanoscale disorder, which affect delocalization, can be significantly more difficult to carry out. Through infrared charge modulation spectroscopy and theoretical modeling, the effect of the local chain environment on polaron delocalization is directly measured and quantified. Using a series of polymers based on the model system, poly(3‐hexylthiophene), the link between disorder and polaron localization is systematically explored. Polaron delocalization is correlated with known trends in mobility, revealing that while charge delocalization is always beneficial, the formation of tie‐chains is necessary to reach the highest mobilities in semicrystalline polymers. The results provide direct evidence for the importance of both nanoscale (charge carrier delocalization) and mesoscale (tie‐chains) orders, demonstrating the need to distinguish the key length‐scale limiting charge transport in the design of new, high mobility polymers.
High spatial density few-mode multi-core fiber with low differential mode delay characteristics (2016)

Inter-core crosstalk suppressed 4-LP mode 12-core fiber with the highest relative core multiplicity factor is realized using a feasible cladding diameter. We obtain low differential mode delay characteristics by optimizing the trench-assisted graded-index core profile.
The Role of Gas Diffusion Layer in Cationic Contamination and Mitigation in Polymer Electrolyte Fuel Cells (2014)

To understand the role of the gas diffusion layer (GDL) in cation contamination, three methods were used to soak the PEFC MEA with a cationic solution, with the major difference being whether the CCM was completely/partially exposed to the cationic solution or separated by the GDL and gasket. Significant performance drop was observed with the CCMs which were in direct/partially contact with the Ca 2+ solution, and no significant change in performance occurred where the CCM was separated by the GDL and gasket. It seems that the GDL acts as a barrier to the transport of Ca +2 into the CCM, possibly due to very highly hydrophobic nature of the GDL. When a surfactant was added to the cationic solution to increase the wettability of the GDL, a drop in the performance was observed which verified that the hydrophobic GDL hindered the transport of Ca 2+ into the CCM. When the CCM was reprotonated, the performance was almost fully recovered.
Limits to surface-enhanced Raman scattering near arbitrary-shape scatterers: erratum (2020)

In this erratum, we correct two minor algebraic errors from our previous published manuscript [ Opt. Express 27 , 35189 ( 2019 ) 10.1364/OE.27.035189 ], which do not affect the main results or conclusions, and make a corresponding small change to one figure.
A formal ontology for re-use of software architecture documents (2003)

Software architecture has been established as a viable level of representation for reuse in practical software engineering efforts. The main reason for this is that an architectural view of software is sufficiently abstract to have many instantiations. Even with technologies such as CORBA and JavaBeans, which emphasize reuse of components, the realization of widespread reuse has been severely limited. While architectural reuse has been successful, it has thus far suffered from an ad-hoc semantics, and even savvy architecture practitioners are unsure precisely what is being reused. We have been engaged in research into reuse of software documents, such as design documents, statements of work, contracts, etc., that capture and reuse architectural level knowledge of software solutions. We have found that, given a sufficiently robust knowledge based tool for maintaining documents, a formal ontology or meta-model for software architectures is required to achieve reuse of these architecture-level documents. We present such an ontology.
Multilevel screen design using direct binary search (2002)

Screening is an efficient halftoning algorithm that is easy to implement. With multilevel devices, there is a potential to improve the overall image quality by using multilevel screening, which allows us to choose among multiple native tones at each addressable pixel. We propose a methodology for multilevel screen design using direct binary search (DBS). We refer to one period of the screen as a multitone cell. We define a multitone schedule, which for each absorptance level specifies the fraction of each native tone used in the multitone cell. Traditional multitoning uses only one native tone in smooth areas corresponding to absorptance values near the native tones, an approach that introduces contouring artifacts. To reduce contouring, we employ schedules that use more than one native tone at each absorptance level. On the basis of the multitone schedule, multitone patterns are designed level by level by adding native tones under the stacking constraint. At each level the spatial arrangement of the native tones is determined by a modified DBS search. We explore several different multitone schedules that illustrate the image-quality trade-offs in multitone screen design.
Size-Dependent Self-Assembly of Anisotropic Silica-Coated Hybrid Nanoparticles (2015)

The self-organization of colloids into defined structures offers the possibility to develop novel materials with exciting properties. However, this requires the understanding and application of the forces governing interparticle association. A novel approach for a size-dependent anisotropic assembly between nanoparticles is achieved. Janus-like iron oxide/polystyrene hybrid nanocolloids are prepared by heterophase polymerization and selectively coated with silica on the iron oxide face to gradually form a cavity. Hence, a shallow surface around the hydrophobic polymer face is created, enabling smaller particles of the same nature to be locked by shape complementarity and colloidal steric stabilization. Further coating with silica fixes these assemblies and allows quantitative analysis of the interaction on a nanoscale.
Sites and Mechanisms of Action of Diuretics in the Kidney (1981)

Utilization of classical clearance methodology for the determination of diuretic mechanism and site of action is based on four kinds of observations: (1) the effects of diuretic agents on the concentrating and diluting mechanism; (2) an analysis of the pattern of anionic excretion produced by the drug; (3) determination of the action of the agent on acid excretion and on acid-base status; (4) an evaluation of the effects of the diuretic on potassium excretion. Agents (such as acetazolamide) that act in the proximal convoluted tubule cause an enhancement of solute-free water generation (CH2O), induce a phosphaturia and an increase in bicarbonate excretion, alkalinize the urine, and cause a kaliuresis. Those agents which inhibit sodium chloride transport in the loop of Henle (for example, furosemide and ethacrynic acid) reduce both CH2O and the abstraction of tubular water from the collecting duct (TCH2O). They are the most potent natriuretic agents currently available, causing increments in the excretion of sodium in the urine of 15 to 25 per cent of filtered load. Those drugs which act in the early portion of the distal convolution (the thiazides, metolazone) reduce CH2O modestly or not at all and have no effect on TCH2O. They are capable of increasing urinary sodium by 5 to 8 per cent of the filtered load. The special-purpose agents such as triamterene and spironolactone are only mildly effective as natriuretic agents. While they augment fractional sodium excretion by only 2 to 3 per cent, they are useful because of their capacity to reduce urinary potassium excretion, either by a direct renal tubular effect (triamterene) or by competitive inhibition of aldosterone (spironolactone).
Myoarchitectonic Approach for Lumbar Spine : Effect of Preservation of Supra-and Interspinous Ligament vs. Multifidus Attachment (2011)

Objective : Concerns for instability following decompression for lumbar stenosis have led to development of procedures with minimal destruction of the elements of the spine and muscles. Fenestration, consisting of partial laminotomy and medial facetectomy, achieved lower incidence of postoperative instability compared to laminectomy. We had performed fenestration for patients with neurogenic claudication until 2005 when we developed a new procedure, myoarchitectonic spinolaminoplasty (MSLP), to preserve all musculoskeletal interactions including that of multifidus. In this study, clinical and radiological outcome of patients who underwent fenestration or MSLP were retrospectively compared.
Fabrication of mid-infrared frequency-selective surfaces by soft lithography (2001)

We describe the fabrication of large areas (4 cm(2)) of metallic structures or aperture elements that have ~100-350-nm linewidths and act as frequency-selective surfaces. These structures are fabricated with a type of soft lithography-near-field contact-mode photolithography-that uses a thin elastomeric mask having topography on its surface and is in conformal contact with a layer of photoresist. The mask acts as an optical element to create minima in the intensity of light delivered to the photoresist. Depending on the type of photoresist used, lines of, or trenches in, photoresist are formed on the substrate by exposure, development, and lift-off. These surfaces act as bandpass or bandgap filters in the infrared.
Chimeric camel/human heavy-chain antibodies protect against MERS-CoV infection (2018)

Middle East respiratory syndrome coronavirus (MERS-CoV) continues to cause outbreaks in humans as a result of spillover events from dromedaries. In contrast to humans, MERS-CoV-exposed dromedaries develop only very mild infections and exceptionally potent virus-neutralizing antibody responses. These strong antibody responses may be caused by affinity maturation as a result of repeated exposure to the virus or by the fact that dromedaries-apart from conventional antibodies-have relatively unique, heavy chain-only antibodies (HCAbs). These HCAbs are devoid of light chains and have long complementarity-determining regions with unique epitope binding properties, allowing them to recognize and bind with high affinity to epitopes not recognized by conventional antibodies. Through direct cloning and expression of the variable heavy chains (VHHs) of HCAbs from the bone marrow of MERS-CoV-infected dromedaries, we identified several MERS-CoV-specific VHHs or nanobodies. In vitro, these VHHs efficiently blocked virus entry at picomolar concentrations. The selected VHHs bind with exceptionally high affinity to the receptor binding domain of the viral spike protein. Furthermore, camel/human chimeric HCAbs-composed of the camel VHH linked to a human Fc domain lacking the CH1 exon-had an extended half-life in the serum and protected mice against a lethal MERS-CoV challenge. HCAbs represent a promising alternative strategy to develop novel interventions not only for MERS-CoV but also for other emerging pathogens.
A lightweight incremental analysis and profiling framework for embedded devices (2014)

Embedded systems such as mobile devices are currently ubiquitous. The performance potential of these devices is rapidly improving by incorporating multi-core and GPU technologies, and is rapidly catching up with the workstation platforms. Nevertheless, the heterogeneity of the underlying hardware as well as the low-power constraints severely limit performance portability. In this paper we consider the case of leveraging JIT compilers to provide portable parallelization while hiding the corresponding expensive runtime analysis. We propose a novel lightweight JIT framework that exploits the device idle time and the large storage space generally available on these devices. The framework performs 'incremental' analysis while the processor is idle (such as during charging time), and exploits the storage space to cache intermediate analysis results. Such approach requires reengineering existing complex optimization analysis methods. For this paper, we focus on the traditional loop parallelization analysis, and implement a working prototype into the LLVM framework, integrating a lightweight dynamic profiling method to identify hotspots. Initial results demonstrate the low overhead of our method for parallelizing simple loops on an embedded GPU.