gebhart/patrepeval huggingface dataset:
EFFICIENT SALIENCY DETECTION USING REGIONAL COLOR AND SPATIAL INFORMATION (2013)

In this paper, we propose an efficient saliency model using regional color and spatial information. The original image is first segmented into a set of regions using a superpixel segmentation algorithm. For each region, its color saliency is evaluated based on the color similarity measures with other regions, and its spatial saliency is evaluated based on its color distribution and spatial position. The final saliency map is generated by combining color saliency measures and spatial saliency measures of regions. Experimental results on a public dataset containing 1000 images demonstrate that our computationally efficient saliency model outperforms the other six state-of-the-art models on saliency detection performance. Index Terms—Saliency detection, saliency model, color saliency, spatial saliency. 1.
Label-Free LC–MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis (2015)

Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control (HC), and other neurological disease (OND) subjects using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1712 CSF proteins were detected and relatively quantified by spectral counting. Levels of several proteins with diverse biological functions were significantly altered in sALS samples. Enrichment analysis was used to link these alterations to biological pathways, which were predominantly related to inflammation, neuronal activity, and extracellular matrix regulation. We then used our CSF proteomic profiles to create a support vector machines classifier capable of discriminating training set ALS from non-ALS (HC and OND) samples. Four classifier proteins, WD repeat-containing protein 63, amyloid-like protein 1, SPARC-like protein 1, and cell adhesion molecule 3, were identified by feature selection and externally validated. The resultant classifier distinguished ALS from non-ALS samples with 83% sensitivity and 100% specificity in an independent test set. Collectively, our results illustrate the utility of CSF proteomic profiling for identifying ALS protein/pathway alterations and candidate disease biomarkers.
Drugs Targeting the A3 Adenosine Receptor: Human Clinical Study Data (2022)

The A3 adenosine receptor (A3AR) is overexpressed in pathological human cells. Piclidenoson and namodenoson are A3AR agonists with high affinity and selectivity to A3AR. Both induce apoptosis of cancer and inflammatory cells via a molecular mechanism entailing deregulation of the Wnt and the NF-κB signaling pathways. Our company conducted phase I studies showing the safety of these 2 molecules. In the phase II studies in psoriasis patients, piclidenoson was safe and demonstrated efficacy manifested in significant improvements in skin lesions. Namodenoson is currently being developed to treat liver cancer, where prolonged overall survival was observed in patients with advanced liver disease and a Child-Pugh B score of 7. A pivotal phase III study in this patient population has been approved by the FDA and the EMA and is currently underway. Namodenoson is also being developed to treat non-alcoholic steatohepatitis (NASH). A Phase IIa study has been successfully concluded and showed that namodenoson has anti-inflammatory, anti-fibrosis, and anti-steatosis effects. A phase IIb study in NASH is currently enrolling patients. In conclusion, A3AR agonists are promising drug candidates in advanced stages of clinical development and demonstrate safety and efficacy in their targeted indications.
Ultra-High-Image-Density, Large-Size Organic Light-Emitting Device Panels Based on Highly Reliable Gate Driver Circuits Integrated by Using InGaZnO Thin-Film Transistors (2019)

Large-size, organic light-emitting device (OLED) panels based on highly reliable gate driver circuits integrated using InGaZnO thin-film transistors (TFTs) were fabricated to achieve ultra-high image density (UHD). These large-size OLED panels were driven by using a novel gate driver circuit not only for displaying images but also for sensing TFT characteristics for external compensation. Regardless of the negative threshold voltage of the TFTs, the proposed gate driver circuit in OLED panels functioned precisely, resulting from a decrease in the leakage current. The falling time of the circuit is approximately 1.6 μs, which is fast enough to drive UHD OLED displays at 120 Hz. 120 Hz is most commonly used as the operating voltage because images consisting of 12 frames per second can be quickly shown on the display panel without any image sticking. The reliability tests showed that the lifetime of the proposed integrated gate driver is at least 1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> h.
Large-scale synthesis of single-walled carbon nanohorns by submerged arc (2004)

We report on the synthesis of single-walled carbon nanohorns (SWNHs) by arc discharge between two graphite electrodes submerged in liquid nitrogen. The product in its powder form was found to consist of spherical aggregates with sizes in the range of 50–100 nm. The nanohorns are characterized by transmission electron microscopy (TEM), Raman and electron energy loss spectroscopies and surface area measurements. TEM observations revealed that the internal structure of the aggregates could be described as a mixture of 'dahlia-like' and 'bud-like'. A structural transition above 300 °C was inferred from the Raman data. Here we show that a simple technique that does not require relatively expensive laser and vacuum equipment provides an economical alternative for the synthesis of SWNHs.
Nonparametric Radio Maps Reconstruction Via Elastic Net Regularization with Multi-Kernels (2018)

Radio maps can provide insightful information about the wireless environment to improve flexibility and intelligence of wireless networks. Channel gain cartography aims at reconstructing the path loss of any two points in space given a finite number of measurements. In this paper, a linear tomographic projection method is used to model the shadowing attenuation between any two points in a map. More specifically, the shadowing attenuation is considered to be the weighted integral of an underlying spatial loss field (SLF). The learning process is nonparametric in the sense that no model for the associated weights function of the SLF is assumed. The problem is posed as a regression problem with elastic nets regularization, i.e., a linear combination of ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> and ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> regularization terms. Further, the multi-kernel framework is used as a nonlinear approach and an algorithm that addresses a non-convex problem by iterating between two convex ones is proposed. The algorithm relies on the alternating direction method of multipliers (ADMM) to iteratively find a solution. Numerical evaluation with synthetic data shows great potential and outperforms state of the art approaches.
Novel Serotonin-3 Receptor Antagonists (1991)

A structurally novel series of serotonin-3 (5-HT3) receptor antagonists is described. A computer pharmacophore model for ligands binding to this receptor has been developed and utilized to explain observed structure-activity relationships as well as demonstrated predictive utility. A novel azabicyclic 5-HT3 receptor ligand prototype [2-(4-amino-5-chloro-2-methoxybenzamidomethyl)-1-azabicyclo[2.2.2]oct-2-ene] has also been discovered, and its selective synthesis, which proceeds through a thermodynamically disfavored allylic azide, is described. 1. Introduction 2. Biological Assays - Definitions 3. Discovery of the Lead Structure 7 (3-[2-(Guanidinomethyl)-1,3-thiazol-4-yl]indole) and Approach to Its Modification 4. Definition and Application of an Initial Computer Pharmacophore Model for Selective 5-HT3 Receptor Ligands 5. Structure - Activity Relationship (SAR) Studies 6. Synthesis of a Novel Azabicyclic Prototype 7. Summary
Presence of carcinoma in situ (CIS) in bladder cancer biopsies and its relationship to pathologic complete response (pCR) rates to neoadjuvant chemotherapy (neo-CTx). (2013)

286 Background: Despite an improved overall survival with neo-CTx for muscle-invasive urothelial carcinoma (miUC) patients (pts) prior to cystectomy, the adoption of neo-CTx in suitable pts has been suboptimal. While associated with a more aggressive phenotype in early stage UC, the prognostic role of CIS in miUC is less clear. In particular, the effect of concurrent CIS in pts undergoing neo-CTx prior to cystectomy is unknown. Methods: A retrospective review of the Indiana University Simon Cancer Center urology and medical oncology clinical databases was performed spanning the years 1991 – 2012. Subjects with miUC, pathology reports available for both transurethral resection of bladder tumor (TURBT) and cystectomy procedures, and confirmed receipt of neo-CTx were included in this analysis. Pts with clinically positive lymph nodes (LN+) were included provided they underwent cystectomy with curative intent. Associations between pCR and pt baseline age, gender, race, clinical stage (T2N0 vs. T3/T4/N+), chemotherapy regimen received (cisplatin combination therapy (CisCTx) vs. non-cisplatin based), and presence of CIS on TURBT sample were tested by multinomial logistic regression analysis with statistical significance set at p&lt;0.05. Results: 72 miUC pts satisfying the inclusion criteria were identified. Cohort demographics included: median age – 59 yrs, 76% male, 93% Caucasian, 63% T2N0, 32% LN+, 81% CisCTx neo-CTx regimen, 32% CIS on TURBT, pCR for entire cohort 18%. The presence of CIS on TURBT was significantly associated with decreased rates of pCR (1/23 vs. 12/49) p=0.002. TURBT CIS was not associated with decreased rates of less than pT2N0 (12/23 vs. 18/49) p=0.562. Seven pts (30%) with CIS on TURBT sample achieved pTisN0 at cystectomy. Conclusions: The presence of CIS in TURBT specimens is associated with decreased rates of pCR at cystectomy in miUC pts treated with neo-CTx. The finding of pTisN0 at cystectomy is common after neo-CTx in pts with CIS in preop TURBT specimens. Validation of the prognostic significance of TURBT CIS on pCR rates and characterization of pTisN0 clinical course in TURBT CIS pts after neo-CTx is warranted.
SmartSynth (2013)

This paper presents SmartSynth, a novel end-to-end programming system for synthesizing smartphone automation scripts from natural language descriptions. Our approach is unique in two key aspects. First, it involves a carefully designed domain-specific language that incorporates standard constructs from smartphone programming platforms to balance its expressivity and the ability to synthesize scripts from natural language. Second, our synthesis algorithm integrates techniques from two research areas: (1) It infers the set of components and their partial dataflow relations from the natural language description using techniques from the Natural Language Processing community; and (2) It uses techniques from the Program Synthesis community to infer missing dataflow relations via type-based synthesis and constructs scripts in a process akin to reverse parsing. SmartSynth also performs conversational interactions with the user when multiple top-ranked scripts exist or it cannot map part of the description to any component. Evaluated on 50 tasks collected from smartphone help forums, our system produces the intended scripts in real time for over 90% of the 640 natural language descriptions obtained from a user study for those tasks. SmartSynth has also been adapted to TouchDevelop, an end user-targeted programming environment on mobile platforms, with very promising results (see http://www.cs.ucdavis.edu/~su/smartsynth.mp4 for a video demo). We believe that SmartSynth is a step toward fully personalized use of smartphones' increasingly rich functionalities.
Adsorption Behavior of Arsenate at Transition Metal Cations Captured by Amino-Functionalized Mesoporous Silicas (2003)

We show that Fe3+, Co2+, Ni2+, and Cu2+ fixed by diamino-functionalized MCM-41 and MCM-48 work as adsorption centers for arsenate ions. The stoichiometry of the N/metal cation was determined as well as the As/metal cation for the adsorption of arsenate. The effectiveness of the removal of arsenate from a dilute solution is ordered according to Fe3+ > H+ ∼ Co2+ > Ni2+ ∼ Cu2+, which is slightly different from the adsorption capacity: Fe3+ > Co2+ ∼ H+ > Ni2+ > Cu2+. The distribution coefficients, Kd, exceed 200 000 at [arsenate] < 100 ppm in Fe/NN-MCM-41. The Fe center binds nearly three arsenate ions, which allows the adsorption capacity of Fe/NN-MCM-48 to be one of the largest at 2.5 mmol (g of adsorbent)-1 among the adsorbents of arsenate. The difference between the meso-framework structures appears in their adsorption capacity; cation/NN-MCM-48 adsorbs a larger amount of arsenate than cation/NN-MCM-41. This is mainly caused by the difference of cation content in these functionalized mesoporous silicas. A sudden decrease in Kd for Fe/NN-MCM-41 at a coverage around θ = 0.3 suggests a difference in the stabilization constant between the first and the second arsenates while Kd(θ) in Ni and Cu/NN-MCM-41 decreased gradually. The equilibrium constants, b (=ka/kd), were plotted against the coverage (Langmuir plots), where Fe3+ showed a minimum at θ = 0.65 while b in the Ni2+ and Cu2+ sites was almost constant. The inhibition by coexisting anions such as SO42- and Cl- was evaluated by the suppression of the adsorption capacity. Differences between the suppression among the cations were found. We analyzed the local structure of the adsorption centers in Fe and Co captured in NN-MCM-41 by EXAFS spectroscopy.
AFS Roots: The Father of All the Fishes (2020)

FisheriesVolume 45, Issue 2 p. 90-100 AFS 150th Anniversary Celebration AFS Roots: The Father of All the Fishes Brian R. Murphy, Brian R. Murphy AFS President Elect murphybr@vt.edu Virginia Polytechnic Institute and State University, 310 West Campus Drive, Blacksburg, VA, 24061Search for more papers by this author Brian R. Murphy, Brian R. Murphy AFS President Elect murphybr@vt.edu Virginia Polytechnic Institute and State University, 310 West Campus Drive, Blacksburg, VA, 24061Search for more papers by this author First published: 27 February 2020 https://doi.org/10.1002/fsh.10413Citations: 3Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Citing Literature Volume45, Issue2February 2020Pages 90-100 RelatedInformation
Using Ga-Based Intelligent Control Means to Enhance Human-Machine Interfaces (2005)

Abstract A GA (genetic algorithm) search procedure was employed to explore a best set of sensory feedback parameters in designing ahuman-machine interface for improved performance. The optimization concerned two objective functions of interest, which incorporated tradeoffs between speed and accuracy in tracking. APareto-optimal front was calculated involving the two cost functions selected. This approach differs from the traditional minimum of anon-convex cost function (scalaz) describing the desired closed loop performance. Also, this methodology used a parsimonious experimental design method. By making a few runs with a limited number of subjects, a response model was first developed. This model was then simulated and a complex vector response surface was generated by the performance variables of interest. The GA seazch procedure was then used to locate the minimum of this response surface. Finally, in a post hoc experimental study to confirm that the selected design parameters were the best from the cl...
Boron Nitride Nanotubes (1995)

The successful synthesis of pure boron nitride (BN) nanotubes is reported here. Multi-walled tubes with inner diameters on the order of 1 to 3 nanometers and with lengths up to 200 nanometers were produced in a carbon-free plasma discharge between a BN-packed tungsten rod and a cooled copper electrode. Electron energy-loss spectroscopy on individual tubes yielded B:N ratios of approximately 1, which is consistent with theoretical predictions of stable BN tube structures.
Indoor Localization and Mapping: Towards Tracking Resilience Through a Multi-SLAM Approach (2020)

International audience
Classical approximation schemes for the ground-state energy of quantum and classical Ising spin Hamiltonians on planar graphs (2007)

We describe an efficient approximation algorithm for evaluating the ground-state energy of the classical Ising Hamiltonian with linear terms on an arbitrary planar graph. The running time of the algorithm grows linearly with the number of spins and exponentially with 1/epsilon, where epsilon is the worst-case relative error. This result contrasts the well known fact that exact computation of the ground-state energy for the two-dimensional Ising spin glass model is NP-hard. We also present a classical approximation algorithm for the Local Hamiltonian Problem or Quantum Ising Spin Glass problem on a planar graph with bounded degree which is known to be a QMA-complete problem. Using a different technique we find a classical approximation algorithm for the quantum Ising spin glass problem on the simplest planar graph with unbounded degree, the star graph.
Maskless lithography: a low-energy electron-beam direct writing system with a common CP aperture and the recent progress (2003)

In order to realize SoC (System on a Chip) fabrication at low cost with quick-TAT (Turn-Around-Time) we have proposed a maskless lithography (ML2) strategy, a low-energy electron-beam direct writing (LEEBDW) system with a common character projection (CP) aperture. This paper presents a status report on our proof-of-concept (POC) system. We have developed a compact EB column consisting small electrostatic lenses and deflectors. The experimental results for our POC system indicated that the patterns corresponding to 50nm-node logic devices can be obtained with CP exposure at the incident energy of 5 keV. The technique to reduce the raw process time using a SEM function of LEEBDW system is also reported.
A Direct Brain-Machine Interface for 2D Cursor Control Using a Kalman Filter (2004)

A Kalman filter was exploited to model the probabilistic relationship between neural firing in motor cortex and hand kinematics in a Macaque monkey. In previous off-line experiments this Bayesian decoding method was used to estimate 2D hand kinematics from the firing rates of a population of cells in the arm area of primary motor cortex. Here we extended this work to the case of on-line, closed-loop, neural control of cursor motion. In this task a single monkey moved a cursor on a computer monitor using either a manipulandum or its neural activity recorded with a chronically implanted micro-electrode array. The monkey was presented with a target in a random location on a monitor and then moved a feedback cursor to the location of the target at which point the target disappeared and then reappeared in a new location. During neural control the decoding algorithm was switched between the Kalman filter and a commonly used linear regression method. With the linear regresssion method, the monkey was able to acquire 22.8 targets per minute while with the Kalman filter decoder the monkey was able to 33.5 targets/min. While the Kalman filter decoder provided better on-line task performance, we observed the decoded cursor position was nosier under brain control as compared with manual control using the manipulandum. To smooth the cursor motion without decreasing accuracy we developed a method that exploited smoothed neural firing rates. This smoothing method and its validity were quantitatively evaluated with recorded data.
Low-loss, wide and low-ripple passband arrayed-waveguide grating with tandem MZI-synchronized configuration (2009)

A novel AWG with a wide passband is proposed. The measured insertion loss and 0.5-dB bandwidth are 2.8 dB and 59 GHz. Thanks to the low amplitude and phase ripples, this AWG can be used in a 40G ROADM.
Selective Topography Directed Cell Adhesion on Spider Silk Surfaces (2022)

Abstract For tissue engineering applications, guided cell interaction with a biomaterial surface is one essential feature since, in natural tissue, cells constantly interact with their extracellular matrix, which provides different topographical, mechanical and biochemical stimuli. Therefore, the introduction of topographical surface features is one promising approach to direct material‐cell interactions. In this study, maskless lithography and soft lithographic methods are used to produce recombinant spider silk films with size gradient patterns, including grooves, circles, squares, triangles, and stars, to enhance specific cell attachment. The influence of surface features on cell behavior is analyzed using eight different cell lines. It can be shown that surface indentations provide cellular attachment sites and guiding structures for restructuring, aligning, and adopting cell morphology, with a relation of cell to feature size for some of the cell lines investigated. Therefore, specific topographical surface modifications can be used to guide selective cell adhesion, allowing the generation of tissue‐specifically modified implant surfaces in the future.
A study of the macro and micro immunoglobulins to Brucella abortus and their transfer from cow to calf via the colostrum. (1978)

Samples of adult bovine serum, colostrum, the serum of unsuckled and suckled calves were subjected to gel filtration through Sephadex G 200. All samples (except those of unsuckled calves) contained antibodies to Brucella abortus. Four phases were recorded in normal adult serum corresponding to IgM, IgG, Albumin and a fourth phase of smaller nitrogen-containing molecules. In colostrum phase 2 was relatively large and phase 3 was absent indicating absence of albumin. In the serum of the unsuckled calves phase 2 was absent, indicating a virtual absence of IgG. Agglutinins and Complement fixing antibodies were found in the fractions of both phase 1 and phase 2. Incomplete antibodies occurred only in phase 2, which suggested that they occurred only as 7S molecules. By immunising pregnant heifers shortly before calving with formalin Killed Strain 19 vaccine, it was found that serum IgM may be secreted in colostrum and in this manner transferred to the calf on suckling. It is considered that the immunoglobulins of importance in protecting the young calf from Br. abortus, and also in neutralising Strain 19 vaccination, are of the IgG incomplete (7S) class. These antibodies appear to be less heat-labile than 7S agglutinins.
32-channel reconfigurable optical add/drop multiplexer on a chip (2005)

We report on a single-chip 32-channel reconfigurable optical add/drop multiplexer (ROADM) based on a polymer planar lightwave circuit platform. This subsystem on a chip consists of 32x8 switches and arrays of 32 add/drop switches, variable optical attenuators (VOA's), power taps, and photodiodes. The architecture, design and optical performance are presented.