gebhart/patrepeval huggingface dataset:
Designing affordances for the navigation of detail-on-demand hypervideo (2004)

We introduced detail-on-demand video as a simple type of hypervideo that allows users to watch short video segments and to follow hyperlinks to see additional detail. Such video lets users quickly access desired information without having to view the entire contents linearly. A challenge for presenting this type of video is to provide users with the appropriate affordances to understand the hypervideo structure and to navigate it effectively. Another challenge is to give authors tools that allow them to create good detail-on-demand video. Guided by user feedback, we iterated designs for a detail-on-demand video player. We also conducted two user studies to gain insight into people's understanding of hypervideo and to improve the user interface. We found that the interface design was tightly coupled to understanding hypervideo structure and that different designs greatly affected what parts of the video people accessed. The studies also suggested new guidelines for hypervideo authoring.
Development and validation of an immuno-PET tracer for patient stratification and therapy monitoring of antibody-drug conjugate therapy. (2013)

11006 Background: SAR566658 is an antibody-drug immunoconjugate consisting of a humanized monoclonal antibody (huDS6) against the tumor-associated MUC1-sialoglycotope, CA6, conjugated to a cytotoxic maytansinoid (DM4). SAR566658 is currently undergoing phase I clinical trials in patients with CA6-positive solid tumors. A companion diagnostic based on huDS6 may facilitate patient stratification and early evaluation of therapeutic efficacy. The present study describes the development and preclinical evaluation of three novel Copper-64 (t ½ = 12.7h) labeled antibody fragments (two Fabs and a diabody) derived from the huDS6 antibody. One fragment was chosen based on imaging figures of merit for further specificity evaluations. Methods: The affinity of all fragments and their DOTA conjugates to CA6 was validated using flow cytometry. The DOTA conjugates were labeled with Copper-64 and evaluated in human serum stability studies, in vivo small animal PET imaging and 24-hour biodistribution studies in nude mice bearing either CA6 positive (WISH) or CA6 negative (A2780) subcutaneous tumors. The specificity of the lead tracer was evaluated in vivo via blocking studies and isotype controls. Results: All fragments and their DOTA conjugates had high affinity (K d = 4-20 nM) for WISH cells. 64 Cu-DOTA-B-Fab gave superior results in radio-synthesis (RCY - 60%, SA - 55 GBq/µmole, >99% purity), serum stability (94±5%, n=3) and biodistribution profile. Its two isotype controls gave statistically significant (P<0.05) uptake values in WISH but not A2780 tumors (see table). Blocking with B-Fab or huDS6 prior to tracer administration afforded a 23% (p<0.05, n=8) and 26% (p<0.05, n=7) decrease in WISH tumor uptake, respectively. Conclusions: These preclinical studies suggest that 64 Cu-DOTA-B-Fab may be a suitable companion diagnostic for SAR566658 in cancer patients and requires further investigation.[Table: see text]
Mode-based multi-hypothesis head tracking using parametric contours (2003)

The paper describes a probabilistic mode-based multi-hypothesis tracking (MHT) algorithm. The modes are the local maximums refined from initial samples in a parametric state space. Because the modes are highly representative, this technique allows us to use a small number of hypotheses to effectively model nonlinear probabilistic distributions. To ensure real-time tracking performance, we propose a novel parametric causal contour model and an efficient dynamic programming scheme to refine the initial contours to nearby modes. Furthermore, to overcome the common drawback of conventional MHT techniques, i.e., producing only the maximum likelihood estimates instead of the desired posterior, we introduce the highly effective importance sampling framework into MHT, and develop a novel procedure to estimate the posterior from the importance function. Experiments on a challenging real-world video sequence demonstrate that the proposed tracking technique is both robust in complex environment (e.g., clutter background and partial occlusion) and efficient in computation.
MicroRNA‐124a is a key regulator of proliferation and monocyte chemoattractant protein 1 secretion in fibroblast‐like synoviocytes from patients with rheumatoid arthritis (2009)

The results of this study suggest that miR-124a is a key miRNA in the posttranscriptional regulatory mechanisms of RA synoviocytes.
Polymer Additive Assisted Fabrication of Compact and Ultra-Smooth Perovskite Thin Films with Fast Lamp Annealing (2021)

Perovskite solar cells (PVSC) have drawn increasing attention due to their high photovoltaic performance and low-cost fabrication with solution processability. A variety of methods have been developed to make uniform and dense perovskite thin films, which play a critical role on device performance. Herein, we demonstrate a polymer additive assisted approach with Polyamidoamine (PAMAM) dendrimers to facilitate the growth of uniform, dense, and ultra-smooth perovskite thin films. Furthermore, a lamp annealing approach has been developed to rapidly anneal perovskite films using an incandescent lamp, resulting in comparable or even better device performance compared to the control hotplate annealing. The facile polymer additive assisted method and the rapid lamp annealing technique offer a clue for the large-scale fabrication of efficient PVSCs.
Development of conductive adhesive materials for via fill applications (2002)

As mobile computing and telecommunication electronics are spreading fast, a demand for microelectronics packaging schemes for high density, fine pitch, high performance and low cost becomes even more severe. Specifically, the conventional printed circuit board (PCB) with plated-through-hole (PTH) vias is difficult to justify its manufacturing cost as well as the packaging density requirement. To meet this challenge, several new manufacturing schemes of high density and high performance PCB have been recently introduced such as surface laminar circuit (SLC), array layer inner via hole (ALIVH) and others. This new PCB fabrication process is categorized as sequential build-up (SBU) or build-up multilayer (BUM) using laminate-based substrates, where via holes are filled with a conductive paste material to make reliable vertical or Z-interconnects. In this paper, a new electrically conducting paste material to be used for via filling is introduced. The new conducting material consists of a conducting filler powder coated with a low melting point metal or alloy, a mixture of several thermoset resins, and other minor organic additives. By varying the filler content and resin chemistry, several formulations have been produced to fill via holes with a high aspect ratio. Via fill experiments have been performed to demonstrate void-free microstructure with good electrical continuity. Various bulk properties such as thermal, electrical and mechanical have also been characterized to understand the material behavior during via filling as well as the field service.
Efficacy of Killed Virus Vaccine, Live Attenuated Chimeric Virus Vaccine, and Passive Immunization for Prevention of<i>West Nile virus</i>Encephalitis in Hamster Model (2002)

Results of experiments evaluating the efficacy of three immunization strategies for the prevention of West Nile virus (WNV) encephalitis are reported. Immunization strategies evaluated included a killed virus veterinary vaccine, a live attenuated chimeric virus vaccine candidate, and passive immunization with WNV-immune serum; all were tested by using a hamster model of the disease. Each product protected the animals from clinical illness and death when challenged with a hamster-virulent éwild-type WNV strain 1 month after initial immunization. The live attenuated chimeric virus vaccine candidate induced the highest humoral antibody responses, as measured by hemagglutination inhibition, complement fixation, and plaque reduction neutralization tests. Although the duration of protective immunity was not determined in this study, our preliminary results and the cumulative experience of other virus vaccines suggest that the live attenuated chimeric virus provides the longest lasting immunity.
A pneumococcal surface protein (PspB) that exhibits the same protease sensitivity as streptococcal R antigen (1988)

A monoclonal antibody against Streptococcus pneumoniae, designated T4A49, detected a 64,000-molecular-weight protein that was immunologically unrelated to the previously described surface protein PspA. This new protein, designated PspB, was pepsin sensitive and trypsin resistant, as is the R antigen of type 28 group A streptococci.
The addressing characteristics of an alternating current plasma display panel adopting a ramping reset pulse (2001)

The characteristics of the address discharge of an alternating current plasma display panel (ac PDP) adopting a ramping reset pulse were studied using two-dimensional (2-D) numerical simulation. We investigated the principal parameters of the reset pulse for a successful address discharge. In this paper, we suggest a new parameter, the terminal voltage of the ramping reset pulse, and its effects on the minimum address voltage and current flow characteristics during the address discharge. The minimum addressing voltage decreased with increase in the ramping-down time and with increase in the terminal voltage of the ramping reset pulse, which were explained with the wall charge characteristics obtained by a 2-D simulation and confirmed through an ac PDP experiment.
Activity analysis based on low sample rate smart meters (2011)

Activity analysis disaggregates utility consumption from smart meters into specific usage that associates with human activities. It can not only help residents better manage their consumption for sustainable lifestyle, but also allow utility managers to devise conservation programs. Existing research efforts on disaggregating consumption focus on analyzing consumption features with high sample rates (mainly between 1 Hz ~ 1MHz). However, many smart meter deployments support sample rates at most 1/900 Hz, which challenges activity analysis with occurrences of parallel activities, difficulty of aligning events, and lack of consumption features. We propose a novel statistical framework for disaggregation on coarse granular smart meter readings by modeling fixture characteristics, household behavior, and activity correlations. This framework has been implemented into two approaches for different application scenarios, and has been deployed to serve over 300 pilot households in Dubuque, IA. Interesting activity-level consumption patterns have been identified, and the evaluation on both real and synthetic datasets has shown high accuracy on discovering washer and shower.
Fast ordering of large categorical datasets for better visualization (2001)

An important issue in visualizing categorical data is how to order categorical values. The focus of this paper is on constructing such orderings efficiently without compromising their visual quality.
Diagnosis of Zika Virus Infection by Peptide Array and Enzyme-Linked Immunosorbent Assay (2018)

Zika virus (ZIKV) is implicated in fetal stillbirth, microcephaly, intracranial calcifications, and ocular anomalies following vertical transmission from infected mothers. In adults, infection may trigger autoimmune inflammatory polyneuropathy. Transmission most commonly follows the bite of infected <i>Aedes</i> mosquitoes but may also occur through sexual intercourse or receipt of blood products. Definitive diagnosis through detection of viral RNA is possible in serum or plasma within 10 days of disease onset, in whole blood within 3 weeks of onset, and in semen for up to 3 months. Serological diagnosis is nonetheless critical because few patients have access to molecular diagnostics during the acute phase of infection and infection may be associated with only mild or inapparent disease that does not prompt molecular testing. Serological diagnosis is confounded by cross-reactivity of immune sera with other flaviviruses endemic in the areas where ZIKV has recently emerged. Accordingly, we built a high-density microarray comprising nonredundant 12-mer peptides that tile, with one-residue overlap, the proteomes of Zika, dengue, yellow fever, West Nile, Ilheus, Oropouche, and chikungunya viruses. Serological analysis enabled discovery of a ZIKV NS2B 20-residue peptide that had high sensitivity (96.0%) and specificity (95.9%) versus natural infection with or vaccination against dengue, chikungunya, yellow fever, West Nile, tick-borne encephalitis, or Japanese encephalitis virus in a microarray assay and an enzyme-linked immunosorbent assay (ELISA) of early-convalescent-phase sera (2 to 3 weeks after onset of symptomatic infection).<b>IMPORTANCE</b> The emergence of Zika virus (ZIKV) as a teratogen is a profound challenge to global public health. Molecular diagnosis of infection is straightforward during the 3-week period when patients are viremic. However, serological diagnosis thereafter of historical exposure has been confounded by cross-reactivity. Using high-density peptide arrays that tile the proteomes of a selection of flaviviruses to identify a ZIKV-specific peptide, we established two assays that enable sensitive and specific diagnosis of exposure to ZIKV. These assays may be useful in guiding clinical management of mothers at risk for potential exposure to ZIKV and enable insights into the epidemiology of ZIKV infections.
Compressed Sensing Based Joint-Compensation of Power Amplifier's Distortions in OFDMA Cognitive Radio Systems (2013)

Linearization of user equipment power amplifiers driven by orthogonal frequency division multiplexing signals is addressed in this paper. Particular attention is paid to the power efficient operation of an orthogonal frequency division multiple access cognitive radio system and realization of such a system using compressed sensing. Specifically, precompensated overdriven amplifiers are employed at the mobile terminal. Over-driven amplifiers result in in-band distortions and out of band interference. Out of band interference mostly occupies the spectrum of inactive users, whereas the in-band distortions are mitigated using compressed sensing at the receiver. It is also shown that the performance of the proposed scheme can be further enhanced using multiple measurements of the distortion signal in single-input multi-output systems. Numerical results verify the ability of the proposed setup to improve error vector magnitude, bit error rate, outage capacity and mean squared error.
Abstract 4626: Optimal Dose of Adv-hHCN4 Creates Stable and Long-lasting Biopacing Activity in Cultured Ventricular Cardiomyocytes (2008)

Purpose: Hyperpolarization-activated cyclic nucleotide-gated (HCN) genes have been successfully used as a strategy for recreating cardiac biological pacemakers in animal models. However, optimal dose of HCN and toxicity from HCN overexpression have not been investigated. Therefore, we assessed the effects of various titers of adenoviral human HCN4-GFP vector (Adv-hHCN4) on cardiomyocytes. Methods: Neonatal rat ventricular myocytes (NRVMs) were isolated, selected and cultured on microelectrode arrays to assess their automaticities. Morphology and apoptosis with and without HCN or Ca 2+ channel inhibitor were also assessed. Results: Beating rates significantly increased in NRVMs after hHCN4 infection (Fig. 1 ). For example, the rates were gradually increased to 235±11 beat/min on day 7 after hHCN4 infection with 1×10 5 PFU/array. In contrast, control cells showed low rates. NRVMs with ≥10 6 PFU/array Adv-hHCN4 reached faster rates early and subsequently stopped beating (Fig. 1 ). In addition, myocytes with ≥10 6 PFU/array Adv-hHCN4 underwent significant apoptosis (>50%) which potentially resulted from hHCN4 overexpression and was blocked by the HCN channel blocker Cs + (1 mM), but not by the Ca 2+ channel inhibitor nifedipine. In addition, myocytes infected with ≥10 6 PFU/array Adv-GFP maintained normal morphology and rate. Our data demonstrate that hHCN4 transfer significantly and dose-dependently increased beating rates of NRVMs. However, overexpression of HCN could cause apoptosis. Therefore, an optimal dose of HCN gene is important for reducing toxicity and creating stable and long-lasting biopacing activity in cardiomyocytes in vitro, and probably also in vivo. Figure 1. Effects of hHCN4 infection on automaticities of neonatal rat ventricular myocytes. Each data point represents an averaged beating rate (mean ± SE) from 8 to 10 arrays. Various titers (1×10 5 to 1×10 7 PFU/500,000 cells per array) of Adv-Hhcn4 (expect control) were added to the arrays after measurements on day 0 (see the arrow)
Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy (2018)

Although a number of advances have been made in RNA sequencing and structural characterization, the lack of a method for directly determining the sequence and structure of single RNA molecules has limited our ability to probe heterogeneity in gene expression at the level of single cells. Here we present a method for direct nucleotide identification and structural label mapping of single RNA molecules <i>via</i> Quantum Molecular Sequencing (QMSeq). The method combines non-perturbative quantum tunneling spectroscopy to probe the molecular orbitals of ribonucleotides, new experimental biophysical parameters that fingerprint these molecular orbitals, and a machine learning classification algorithm to distinguish between the ribonucleotides. The algorithm uses tunneling spectroscopy measurements on an unknown ribonucleotide to determine its chemical identity and the presence of local chemical modifications. Combining this with structure-dependent chemical labeling presents the possibility of mapping both the sequence and local structure of individual RNA molecules. By optimizing the base-calling algorithm, we show a high accuracy for both ribonucleotide discrimination (>99.8%) and chemical label identification (>98%) with a relatively modest molecular coverage (35 repeat measurements). This lays the groundwork for simultaneous sequencing and structural mapping of single unknown RNA molecules, and paves the way for probing the sequence-structure-function relationship within the transcriptome at an unprecedented level of detail.
Spare Capacity Allocation in Two-Layer Networks (2007)

In this paper we consider the problem of provisioning spare capacity in two-layer backbone networks using shared backup path protection. First, two spare capacity allocation (SCA) optimization problems are formulated as integer linear programming (ILP) models for the cases of protection at the top layer against failures at the bottom layer. The first model captures failure propagation using overlay information between two layers for backup paths to meet diversity requirements. The second model improves bandwidth efficiency by moving spare capacity sharing from the top layer to the bottom layer. This exposes a tradeoff between bandwidth efficiency and extra cross-layer operation. Next, the SCA model for common pool protection is developed to allow spare capacity sharing between two layers. Our previous SCA heuristic technique, successive survivable routing (SSR) is extended for these optimization problems. Numerical results for a variety of networks indicate that the common pool protection is attractive to enhance bandwidth efficiency without loss of survivability and that the SSR heuristic quickly results in near optimal solutions
Quantitative Inference in a Mechanical Design “Compiler” (1989)

Abstract This paper introduces the theory underlying a computer program that takes as input a schematic of a mechanical or hydraulic power transmission system, plus specifications and a utility function, and returns catalog numbers from predefined catalogs for the optimal selection of components implementing the design. Unlike programs for designing single components or systems, this program provides the designer with a high level “language“ in which to compose new designs. It then performs much of the detailed design process. The process of “compilation”, or transformation from a high to a low level description, is based on a formalization of quantitative inferences about hierarchically organized sets of artifacts and operating conditions. This allows design compilation without the exhaustive enumeration of alternatives. The paper introduces the formalism, illustrating its use with examples. It then outlines some differences from previous work, and summarizes early tests and conclusions.
Structure-activity analysis of synthetic autoinducing thiolactone peptides from <i>Staphylococcus aureus</i> responsible for virulence (1999)

The synthesis of virulence factors and other extracellular proteins responsible for pathogenicity in Staphylococcus aureus is under the control of the agr locus. A secreted agr-encoded peptide, AgrD, processed from the AgrD gene product, is known to be an effector of self-strain activation and cross-strain inhibition of the agr response. Biochemical analysis of AgrD peptides isolated from culture supernatants has suggested that they contain an unusual thiol ester-linked cyclic structure. In the present work, chemical synthesis is used to confirm that the mature AgrD peptides contain a thiolactone structure and that this feature is absolutely necessary for full biological activity. The AgrD synthetic thiolactone peptides exhibited biological activity in vivo in a mouse protection test. Structure-activity studies have allowed key aspects of the peptide structure involved in the differential activation and inhibition functions to be identified. Accordingly, we propose a model for activation and inhibition of the agr response in which the former, but not the latter, involves specific acylation of the agr transmembrane receptor, AgrC.
A method to achieve spatial linearity and uniform resolution at the edges of monolithic scintillation crystal detectors (2014)

We have performed Monte Carlo simulations of the scintillation light transport between adjacent monolithic LYSO crystals that are optically coupled together using coupling media of varying refractive index. The scintillation light from the crystals was read out by SiPM arrays from the large crystal face. Scintillation event positioning results show that this optical coupling technique preserves the shape of the light spread function near and across the interface between the two crystals in order to substantially reduce the edge-artifacts observed in monolithic scintillation crystals, while not degrading the timing performance.
[Bmim]Br Accelerated One-Pot Three-Component Cascade Protocol for the Construction of Spirooxindole–Pyrrolidine Heterocyclic Hybrids (2020)

Our synthetic approach for the assembly of structurally complex spirooxindole heterocyclic hybrids was based on an ionic liquid, [bmim]Br mediated one-pot three-component cascade reaction strategy involving 1,3-dipolar cycloaddition reaction of <i>N</i>-1-(2-pyridinylmethyl)-3,5-bis[(<i>E</i>)-arylmethylidene]tetrahydro-4(1<i>H</i>)-pyridinones and azomethine ylide generated in situ from isatin and L-phenyl alanine, affording a series of spirooxindole-pyrrolidine heterocyclic hybrids in good-to-excellent yields. In addition to serving as the reaction medium, [bmim]Br also functioned as a catalyst in this cycloaddition reaction and hence accelerated the reaction rate affording the cycloadducts in short reaction time.