gebhart/patrepeval huggingface dataset:
Measurement of the cross section for the production of a W boson in association with b-jets in pp collisions at √s = 7 TeV with the ATLAS detector (2011)

A measurement is presented of the cross section for the production of a W boson with one or two jets, of which at least one must be a b-jet, in pp collisions at s=7TeV. Production via top decay is not included in the signal definition. The measurement is based on 35pb-1 of data collected with the ATLAS detector at the LHC. The W+b-jet cross section is defined for jets reconstructed with the anti-kt clustering algorithm with transverse momentum above 25 GeV and rapidity within ±2.1. The b-jets are identified by reconstructing secondary vertices. The fiducial cross section is measured both for the electron and muon decay channel of the W boson and is found to be 10.2±1.9(stat)±2.6(syst)pb for one lepton flavour. The results are compared with next-to-leading order QCD calculations, which predict a cross section smaller than, though consistent with, the measured value. © 2011 CERN.
Suppression of sucrose synthase affects auxin signaling and leaf morphology in tomato (2017)

Metabolic enzymes have been found to play roles in plant development. Sucrose synthase (SUS) is one of the two enzyme families involved in sucrose cleavage in plants. In tomato, six SUS genes have been found. We generated transgenic tomato plants with RNAi suppression of SlSUS1, SlSUS3 and SlSUS4 genes. Independent transgenic lines with RNAi suppression of more than one SUS gene exhibited morphological effects on their cotyledons and leaf structure, but there were no significant effects on their carbohydrate levels, demonstrating that SUS has a developmental function, in addition to its metabolic function. Shoot apices of the transgenic lines showed elevated expression of JAGGED (JAG) and the auxin transporter PIN1. In a PIN1-GFP fusion reporter/SUS-RNAi hybrid, PIN1-GFP patterns were altered in developing leaves (as compared to control plants), indicating that SlSUS suppression alters auxin signaling. These results suggest possible roles for SUS in the regulation of plant growth and leaf morphology, in association with the auxin-signaling pathway.
A Generalized Maxwell Model for Creep Behavior of Artery Opening Angle (2008)

An artery ring springs open into a sector after a radial cut. The opening angle characterizes the residual strain in the unloaded state, which is fundamental in understanding stress and strain in the vessel wall. A recent study revealed that the opening angle decreases with time if the artery is cut from the loaded state, while it increases if the cut is made from the no-load state due to viscoelasticity. In both cases, the opening angle approaches the same value in 3 h. This implies that the characteristic relaxation time is about 10,000 s. Here, the creep function of a generalized Maxwell model (a spring in series with six Voigt bodies) is used to predict the temporal change of opening angle in multiple time scales. It is demonstrated that the theoretical model captures the salient features of the experimental results. The proposed creep function may be extended to study the viscoelastic response of blood vessels under various loading conditions.
MC2: Multiple Clients on a Multilevel Cache (2008)

In today's networked storage environment, it is common to have a hierarchy of caches where the lower levels of the hierarchy are accessed by multiple clients. This sharing can have both positive or negative effects. While data fetched by one client can be used by another client without incurring additional delays, clients competing for cache buffers can evict each other's blocks and interfere with exclusive caching schemes. Our algorithm, MC <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , combines local, per client management with a global, system-wide, scheme, to emphasize the positive effects of sharing and reduce the negative ones. The local scheme uses readily available information about the client's future access profile to save the most valuable blocks, and to choose the best replacement policy for them. The global scheme uses the same information to divide the shared cache space between clients, and to manage this space. Exclusive caching is maintained for non-shared data and is disabled when sharing is identified. Our simulation results show that the combined algorithm significantly reduces the overall I/O response times of the system.
Fast and Robust UAV to UAV Detection and Tracking From Video (2021)

Unmanned Aerial Vehicle (UAV) technology is being increasingly used in a wide variety of applications ranging from remote sensing, to delivery and security. As the number of UAVs increases, there is a growing need for UAV to UAV detection and tracking systems for both collision avoidance and coordination. Among possible solutions, autonomous “see-and-avoid” systems based on low-cost high-resolution video cameras offer important advantages in terms of light weight and low power consumption. However, in order to be effective, camera based “see-and-avoid” systems require sensitive, robust, and computationally efficient algorithms for autonomous detection and tracking of UAVs from a moving camera. In this article, we propose a general architecture for a highly accurate and computationally efficient UAV to UAV detection and tracking (U2U-D&T) algorithm from a camera mounted on a moving UAV platform. The system is based on a computationally efficient pipeline consisting of a moving target detector, followed by a target tracker. The algorithm is validated using video data collected from multiple fixed-wing UAVs that is manually ground-truthed and is publicly available. Results indicate that the proposed algorithm can be implemented on commodity hardware and robustly achieves highly accurate detection and tracking of even distant and faint UAVs. Open source code for the U2U-D&T algorithm is available at: <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><uri>https://github.com/jingliinpurdue/Fast-and-Robust-UAV-to-UAV-Detection-and-Tracking.git</uri>.</i>
Towards Improving the Testability of Cloud Application Services (2012)

In cloud computing, applications are hosted, deployed, and delivered as services over the Internet. New cloud application services can be developed by tailoring existing ones, while hiding the complexity of the underlying implementation. Cloud applications may be able to adapt to changes in their environment, which should be secure and reliable. The infrastructure on which cloud applications are built is characterized by power, storage, and virtualization. But how does all of this affect the ability to adequately test cloud applications? This chapter investigates the testability of cloud application services. It focuses on the specific problem of reduced controllability and observability of software services hosted in the cloud, and proposes a novel solution referred to as Test Support as-a-Service (TSaaS). A prototype of TSaaS is also presented, and is used to discuss the feasibility, challenges, and benefits of the approach.
Delay-Bandwidth-Aware Metric Abstraction Schemes for OIF E-NNI Multidomain Traffic Engineering (2010)

Multidomain traffic engineering (TE) has the potential not only of guaranteeing the quality of service (QoS) to connections spanning multiple domains but also of effectively utilizing intradomain resources. The hierarchical Optical Internetworking Forum (OIF) External Network-to-Network Interface (E-NNI) control plane platform has emerged as a promising candidate aiming at guaranteeing multidomain QoS provisioning. Recent efforts have been made to extend OIF E-NNI in the multicarrier scenario. However, open issues such as confidentiality, the choice of TE metric, the routing controller (RC) architecture, the path computation method, and the abstraction schemes responsible for selecting the appropriate value of the TE metric to be announced have not been addressed yet. In this study, what we believe to be a novel RC architecture integrating the path computation element (PCE) is proposed to enable the efficient provisioning of end-to-end QoS-guaranteed services. The key role of the TE metric is analyzed and discussed, together with different TE metric abstraction schemes. The end-to-end delay is here considered as the most suitable candidate and a novel family of such schemes, named delay-bandwidth aware (DBA), are proposed and evaluated by means of simulations. Results show the ability of such schemes to globally preserve control plane stability and network resource utilization while advertising a high service level.
Development of high frequency band over 6 GHz for 5G mobile communication systems (2015)

Currently, the next generation (5G) mobile communication system has been actively investigated all over the world, in order to satisfy the future expected requirements, such as super high bit rate. Here, one of the approaches is to utilize the high-SHF (above 6 GHz) and EHF (mainly 30 – 60 GHz) bands. These bands are very attractive because wider frequency bandwidth is relatively easily obtained. Here, in order to determine the carrier frequency bands for 5G, frequency dependency of path loss and channel properties need to be understood. In this paper, we introduce our concept for 5G mobile communication networks, and then show the frequency dependency of propagation loss based on the measurement in urban microcellular environment. In addition, the investigation results of frequency dependency of shadowing effect of human body and scattering effect on rough surface are also shown.
Resistance-Associated Mutations and Polymorphisms among Integrase Inhibitor-Naïve HIV-1 Patients in Kuwait (2017)

Our results highlight the importance of monitoring the emergence of INSTI-RAMS before and after the initiation of INSTI-based therapy.
Interleukin 1 release by human monocytes treated with liposome-encapsulated lipopolysaccharide. (1987)

Liposome therapy offers a unique method of delivering antifungals, antiprotozoans, and macrophage-activating factors directly to reticuloendothelial cells. Although liposomes are entering clinical trials, their effect on Il 1 synthesis and release has yet to be determined. The beneficial, as well as possible pathological, effects of liposome therapy may be due to IL 1 released by reticuloendothelial cells. This study examined the effects of multilamellar phospholipid vesicles on the synthesis and release of IL 1 from human peripheral blood monocytes. Liposomes consisting of phosphatidylcholine and phosphatidylserine in molar ratio of 7:3 did not stimulate IL 1 release, and did not diminish the level of IL 1 release when monocytes were subsequently stimulated with LPS or Staphylococcus aureus. Surprisingly, LPS encapsulated in liposomes failed to stimulate IL 1 release from monocytes. This defect was limited to the release of IL 1, because monocytes stimulated with liposomes containing LPS had control levels of intracellular (cytosolic) and membrane IL 1. By contrast, LPS associated with lyophilized liposomes induced the secretion of IL 1 and behaved similarly to free LPS. These findings indicate that LPS activation of monocytes may involve not only the synthesis of IL 1 but activation of the secretory mechanism for IL 1, and that these two events could be independent, that the density of LPS molecules at the surface of the liposome may influence the degree of monocyte activation as measured by intracellular IL 1 synthesis, membrane accumulation, and secretion into the medium, and that intracellular lipids may not interfere with the secretory mechanism, because liposomes made with phospholipids differing in acyl chain length or the headgroup behaved identically.
IL-13 Controls IL-33 Activity through Modulation of ST2 (2021)

IL-33 is a multifunctional cytokine that mediates local inflammation upon tissue damage. IL-33 is known to act on multiple cell types including group 2 innate lymphoid cells (ILC2s), Th2 cells, and mast cells to drive production of Th2 cytokines including IL-5 and IL-13. IL-33 signaling activity through transmembrane ST2L can be inhibited by soluble ST2 (sST2), which acts as a decoy receptor. Previous findings suggested that modulation of IL-13 levels in mice lacking decoy IL-13Rα2, or mice lacking IL-13, impacted responsiveness to IL-33. In this study, we used <i>Il13</i> <sup>-/-</sup> mice to investigate whether IL-13 regulates IL-33 activity by modulating the transmembrane and soluble forms of ST2. In <i>Il13</i> <sup>-/-</sup> mice, the effects of IL-33 administration were exacerbated relative to wild type (WT). <i>Il13</i> <sup>-/-</sup> mice administered IL-33 i.p. had heightened splenomegaly, more immune cells in the peritoneum including an expanded ST2L<sup>+</sup> ILC2 population, increased eosinophilia in the spleen and peritoneum, and reduced sST2 in the circulation and peritoneum. In the spleen, lung, and liver of mice given IL-33, gene expression of both isoforms of ST2 was increased in <i>Il13</i> <sup>-/-</sup> mice relative to WT. We confirmed fibroblasts to be an IL-13-responsive cell type that can regulate IL-33 activity through production of sST2. This study elucidates the important regulatory activity that IL-13 exerts on IL-33 through induction of IL-33 decoy receptor sST2 and through modulation of ST2L<sup>+</sup> ILC2s.
Secure Signatures and Chosen Ciphertext Security in a Quantum Computing World (2013)

We initiate the study of quantum-secure digital signatures and quantum chosen ciphertext security. In the case of signatures, we enhance the standard chosen message query model by allowing the adversary to issue quantum chosen message queries: given a superposition of messages, the adversary receives a superposition of signatures on those messages. Similarly, for encryption, we allow the adversary to issue quantum chosen ciphertext queries: given a superposition of ciphertexts, the adversary receives a superposition of their decryptions. These adversaries model a natural ubiquitous quantum computing environment where end-users sign messages and decrypt ciphertexts on a personal quantum computer. We construct classical systems that remain secure when exposed to such quantum queries. For signatures, we construct two compilers that convert classically secure signatures into signatures secure in the quantum setting and apply these compilers to existing post-quantum signatures. We also show that standard constructions such as Lamport one-time signatures and Merkle signatures remain secure under quantum chosen message attacks, thus giving signatures whose quantum security is based on generic assumptions. For encryption, we define security under quantum chosen ciphertext attacks and present both public-key and symmetric-key constructions.
Carbohydrate mimetics as potential antiinfective treatments for Staphylococcus aureus (2008)

Antibiotic resistant strains of Staphylococcus aureus are an important cause of nosocomial infections. These strains are currently causing community‐acquired infections, resulting in an increased need for alternative therapies. S. aureus capsules appear to act as important virulence determinants, as bacteria with type 5 and 8 capsules cause 75–90% of nosocomial infections and anti‐capsular antibodies decrease mortality in infected mice. Our research involves construction of analogs of the aminosugars found in S. aureus capsules that we are testing for their ability to prevent capsule synthesis. To measure capsule production, bacteria were incubated with MV‐II‐065 or MV‐II‐063 (both n‐glucosyl 1,2,3‐triazoles with different functional groups), formalinized, trypsinized, and the bacteria used as an antigen in an ELISA. The presence of capsular carbohydrate was determined by incubation with anti‐capsular monoclonal antibodies, followed by a secondary incubation with peroxidase‐conjugate anti‐mouse Ig and a colorimetric substrate. Incubation type 5 S. Aureus with MV‐II‐065 decreased antibody binding, but the compound had no effect on Type 8 capsule synthesis. Studies with MV‐II‐063 (shown below) have indicated inhibition of capsule synthesis in Type 8 bacteria, while type 5 capsule synthesis remains to be tested. In addition to their possible therapeutic potential, the differential effects of these two compounds may be used to investigate the synthetic pathways for these capsules. Support: NIH R15 2003‐2006, YSU PACER.
TH‐C‐BRB‐05: Monte Carlo Simulations for Quality Assurance of Varian TrueBeam 6MV FFF RapidArc SBRT Treatments (2012)

Purpose: To establish feasibility of performing quality assurance for Flattening Filter Free (FFF) RapidArc stereotactic body radiotherapy treatments (SBRT) on a TrueBeam LINAC using Monte Carlo simulations. Methods: Phase‐space files for TrueBeam FFF photon beams were made available by Varian in IAEA‐compliant format. Monte Carlo simulations were performed using BEAMnrc and DOSXYZnrc to validate the 6MV FFF phase space files for use in this study. The phase space data provided by Varian is in cylindrical geometry and required conversion into a format that was compatible with BEAMnrc prior to use. To establish validity of the phase space data, dose calculations in a water phantom for fields ranging from 3×3 cm̂2 to 40 × 40 cm̂2 were performed using DOSXYZnrc. Percent depth doses (PDDs), transverse profiles and output factors were calculated and compared with measurements. Monte Carlo simulations of 6MV FFF SBRT RapidArc plans were performed using a 2mm̂3 voxel size and compared with both ion chamber measurement and Eclipse Treatment Planning System (TPS) dose calculations. 3D gamma analysis (3%,3mm) comparing Monte Carlo and TPS results was performed. Results: Monte Carlo simulations and measured values agreed within 1% and 1.5% for PDDs and profiles respectively for all fields. The agreement between measured and calculated output factors was within 1 % including for highly asymmetric fields. These results indicate that the 6MV FFF phase space data is sufficiently accurate for use in quality assurance in radiation therapy. For the 6 MV FFF RapidArc plans the agreement between MC and both measured and TPS dose calculations was within 2%. Over 95% of the points passed the 3D Gamma test Conclusions: We have demonstrated the feasibility of performing patient specific quality assurance for 6 MV FFF SBRT RapidArc treatments using Monte Carlo simulations for a TrueBeam linac. This project is funded by Varian Medical Systems
Supplementary Figure from Raptinal Induces Gasdermin E–Dependent Pyroptosis in Naïve and Therapy-Resistant Melanoma (2023)

Supplementary Figure from Raptinal Induces Gasdermin E–Dependent Pyroptosis in Naïve and Therapy-Resistant Melanoma
Sensing with Optimal Matrices (2012)

We consider the problem of designing optimal $M \times N$ ($M \leq N$) sensing matrices which minimize the maximum condition number of all the submatrices of $K$ columns. Such matrices minimize the worst-case estimation errors when only $K$ sensors out of $N$ sensors are available for sensing at a given time. For M=2 and matrices with unit-normed columns, this problem is equivalent to the problem of maximizing the minimum singular value among all the submatrices of $K$ columns. For M=2, we are able to give a closed form formula for the condition number of the submatrices. When M=2 and K=3, for an arbitrary $N\geq3$, we derive the optimal matrices which minimize the maximum condition number of all the submatrices of $K$ columns. Surprisingly, a uniformly distributed design is often \emph{not} the optimal design minimizing the maximum condition number.
Non-Native Peptides Capable of Pan-Activating the agr Quorum Sensing System across Multiple Specificity Groups of Staphylococcus epidermidis (2021)

<i>Staphylococcus epidermidis</i> is a leading cause of hospital-acquired infections. Traditional antibiotics have significantly reduced efficacy against this pathogen due to its ability to form biofilms on abiotic surfaces and drug resistance. The accessory gene regulator (<i>agr</i>) quorum sensing system is directly involved in <i>S. epidermidis</i> pathogenesis. Activation of <i>agr</i> is achieved via binding of the autoinducing peptide (AIP) signal to the extracellular sensor domain of its cognate receptor, AgrC. Divergent evolution has given rise to four <i>agr</i> specificity groups in <i>S. epidermidis</i> defined by the unique AIP sequence used by each group (AIPs-I-IV) with observed cross-group activities. As <i>agr</i> agonism has been shown to reduce biofilm growth in <i>S. epidermidis</i>, the development of pan-group activators of the <i>agr</i> system is of interest as a potential antivirulence strategy. To date, no synthetic compounds have been identified that are capable of appreciably activating the <i>agr</i> system of more than one specificity group of <i>S. epidermidis</i> or, to our knowledge, of any of the other Staphylococci. Here, we report the characterization of the structure-activity relationships for <i>agr</i> agonism by <i>S. epidermidis</i> AIP-II and AIP-III and the application of these new SAR data and those previously reported for AIP-I for the design and synthesis of the first multigroup <i>agr</i> agonists. These non-native peptides were capable of inducing the expression of critical biofilm dispersal agents (i.e., phenol-soluble modulins) in cell culture and represent new tools to study the role of quorum sensing in <i>S. epidermidis</i> infections.
Experimental and theoretical STM imaging of xylene isomers on Pd(111) (2002)

We have performed a theoretical and experimental study of the three isomers of xylene, ${\mathrm{C}}_{6}{\mathrm{H}}_{4}{(\mathrm{C}\mathrm{H}}_{3}{)}_{2},$ adsorbed on Pd(111). Using scanning tunneling microscopy (STM), we imaged the characteristic surface structures and investigated the molecular ordering for meta-, para-, and ortho-xylene adsorbed on Pd(111). We used extended H\"uckel theory to predict the characteristic features of individual xylene molecules and to perform binding energy calculations for the preferred molecular orientations. STM observations of the surface features showed good agreement with the predictions, and the binding energy preferences correlated well with experiment.
More with less (2015)

Mobile crowdsourcing is a powerful tool for collecting data of various types. The primary bottleneck in such systems is the high burden placed on the user who must manually collect sensor data or respond in-situ to simple queries (e.g., experience sampling studies). In this work, we present Compressive CrowdSensing (CCS) -- a framework that enables compressive sensing techniques to be applied to mobile crowdsourcing scenarios. CCS enables each user to provide significantly reduced amounts of manually collected data, while still maintaining acceptable levels of overall accuracy for the target crowd-based system. Naïve applications of compressive sensing do not work well for common types of crowdsourcing data (e.g., user survey responses) because the necessary correlations that are exploited by a sparsifying base are hidden and non-trivial to identify. CCS comprises a series of novel techniques that enable such challenges to be overcome. We evaluate CCS with four representative large-scale datasets and find that it is able to outperform standard uses of compressive sensing, as well as conventional approaches to lowering the quantity of user data needed by crowd systems.
Targeted Learning for Causality and Statistical Analysis in Medical Research (2012)

The authors present the use of targeted learning methods for medical research, prepared as a chapter for the upcoming book "Statistics: Discovering Your Future Power." The targeted learning framework involves the explicit specification of the data, model, and parameter. The estimators are double robust and efficient, and can incorporate machine learning procedures such as the super learner.