gebhart/patrepeval huggingface dataset:
Summarization and Classification of CNN.com Articles using the TF*IDF Family of Metrics (2016)

TF*IDF (term frequency times inverse document frequency) is a common metric used to automatically discover keywords in documents for use in classification and other text processing applications. We are interested in determining whether these measures can help in determining the most relevant sentences for summarization and classification purposes. However, there are many ways to define TF*IDF, and to date no attempt to relatively&#x2014;and systematically&#x2014;gauge the value of these different forms has been performed. We investigate a comprehensive family of 112 TF*IDF measures (corresponding to an a priori estimate of 20 degrees of freedom among these measures) applied to 3000 CNN articles belonging in 12 classes such as Business, Sport, and World. The assumption is that at least some sets of these measures must be effective for document summarization and classification. The goal is to identify the summaries provided by TF*IDF measures that best match human generated summaries as well as find effective TF*IDF definitions for classification purposes.
Google's Cloud Vision API Is Not Robust To Noise (2017)

Google has recently introduced the Cloud Vision API for image analysis. According to the demonstration website, the API "quickly classifies images into thousands of categories, detects individual objects and faces within images, and finds and reads printed words contained within images." It can be also used to "detect different types of inappropriate content from adult to violent content." In this paper, we evaluate the robustness of Google Cloud Vision API to input perturbation. In particular, we show that by adding sufficient noise to the image, the API generates completely different outputs for the noisy image, while a human observer would perceive its original content. We show that the attack is consistently successful, by performing extensive experiments on different image types, including natural images, images containing faces and images with texts. For instance, using images from ImageNet dataset, we found that adding an average of 14.25% impulse noise is enough to deceive the API. Our findings indicate the vulnerability of the API in adversarial environments. For example, an adversary can bypass an image filtering system by adding noise to inappropriate images. We then show that when a noise filter is applied on input images, the API generates mostly the same outputs for restored images as for original images. This observation suggests that cloud vision API can readily benefit from noise filtering, without the need for updating image analysis algorithms.
Discovery of 4,4-Disubstituted Quinazolin-2-ones as T-Type Calcium Channel Antagonists (2010)

A novel series of quinazolinone T-type calcium channel antagonists have been prepared and evaluated using in vitro and in vivo assays. Optimization of the screening hit 3 by modifications of the 3- and 4-positions of the quinazolinone ring afforded potent and selective antagonists that displayed in vivo central nervous system efficacy in epilepsy and tremor models, as well as significant effects on rat active wake as measured by electrocorticogram.
ChemInform Abstract: Photochemical Reactions of Triarylmethyl Peroxides. Part 2. α‐ and β‐Naphthyldiphenylmethyl Peroxide. (1988)

Abstract Photolysis of bis(triarylmethyl) peroxide (I) gives the phenols (II) and (III), the ketones (IV) and (V), and the olefin (VI), together with some other by‐products.
Iridium(I) Pyridyl Azolate Complexes with Saturated Red Metal‐to‐Ligand Charge Transfer Phosphorescence; Fundamental and Potential Applications in Organic Light‐Emitting Diodes (2006)

Preparation of a new series of neutral metal complexes [(cod)Ir(fppz)] (1), [(cod)Ir(bppz)] (2), [(cod)Ir(fptz)] (3) and [(cod)Ir(bptz)] (4), bearing one cod ligand and a pyridyl azolate chelate are reported. A single-crystal X-ray diffraction study of 3 reveals the expected distorted square-planar geometry. The lowest absorption band consists of IrI atom increased triplet dpi-->pi* transitions (3MLCT), the assignment of which is firmly supported by the theoretical approaches. Complexes 1-4 exhibit weak phosphorescence in degassed solution at room temperature, whereas much more intense, solid-state phosphorescence appears in the range 622-649 nm. The pure MLCT emission was used as a prototypical model to address its remarkable spectral differences from the IrIII isoquinoline pyrrolide complex (5), which has mainly 3pipi phosphorescence. Complex 3 was used as a dopant to fabricate red-emitting phosphorescent organic light-emitting diodes (OLEDs). For the 7 % doped device, a maximum brightness of 3010 cd m-2 was achieved at an applied voltage of 15 V and with CIE coordinates of (0.56, 0.33), demonstrating for the first time the potential of neutral IrI complexes in OLED applications.
Silica-Supported Nitrogen-Enriched Porous Benzimidazole-Linked and Triazine-Based Polymers for the Adsorption of CO2 (2020)

Two crystalline and five amorphous benzimidazole polymers (BINP) were synthesized and conjugated to porous silica via amine and aldehyde-based materials by a simple reflux procedure. The resulting polymers were subject to thermal analysis for monitoring and quantification of the adsorption and desorption of CO<sub>2</sub>. All the polymers were capable of adsorbing CO<sub>2</sub> from a flowing stream of only 80 mL/min at 25 °C. The adsorbed CO<sub>2</sub> onto the polymers were effectively desorbed at room temperature, illustrating the potential application of such polymers for repeated adsorption/desorption of CO<sub>2</sub>. The CO<sub>2</sub> adsorption capacities of these polymers were dependent upon their nitrogen content, specific surface area, and pore size. The available nitrogen atoms for binding to the carbon of CO<sub>2</sub> via tetrel bonds also plays an important role in the capture of this gas. Minimal and much lower CO<sub>2</sub> adsorption was also noted with two crystalline polymers, compared to the five amorphous counterparts. Intermolecular hydrogen bonding and π-π interaction effectively prevented the polymer N sites of the crystalline polymers from interacting with polarized CO<sub>2</sub> molecules.
Eastern Chimpanzees, but Not Bonobos, Represent a Simian Immunodeficiency Virus Reservoir (2012)

Chimpanzees in west central Africa (Pan troglodytes troglodytes) are endemically infected with simian immunodeficiency viruses (SIVcpzPtt) that have crossed the species barrier to humans and gorillas on at least five occasions, generating pandemic and nonpandemic forms of human immunodeficiency virus type 1 (HIV-1) as well as gorilla SIV (SIVgor). Chimpanzees in east Africa (Pan troglodytes schweinfurthii) are also infected with SIVcpz; however, their viruses (SIVcpzPts) have never been found in humans. To examine whether this is due to a paucity of natural infections, we used noninvasive methods to screen wild-living eastern chimpanzees in the Democratic Republic of the Congo (DRC), Uganda, and Rwanda. We also screened bonobos (Pan paniscus) in the DRC, a species not previously tested for SIV in the wild. Fecal samples (n = 3,108) were collected at 50 field sites, tested for species and subspecies origin, and screened for SIVcpz antibodies and nucleic acids. Of 2,565 samples from eastern chimpanzees, 323 were antibody positive and 92 contained viral RNA. The antibody-positive samples represented 76 individuals from 19 field sites, all sampled north of the Congo River in an area spanning 250,000 km(2). In this region, SIVcpzPts was common and widespread, with seven field sites exhibiting infection rates of 30% or greater. The overall prevalence of SIVcpzPts infection was 13.4% (95% confidence interval, 10.7% to 16.5%). In contrast, none of the 543 bonobo samples from six sites was antibody positive. All newly identified SIVcpzPts strains clustered in strict accordance to their subspecies origin; however, they exhibited considerable genetic diversity, especially in protein domains known to be under strong host selection pressure. Thus, the absence of SIVcpzPts zoonoses cannot be explained by an insufficient primate reservoir. Instead, greater adaptive hurdles may have prevented the successful colonization of humans by P. t. schweinfurthii viruses.
Heterologous Expression of Pseudomonas putida Methyl-Accepting Chemotaxis Proteins Yields Escherichia coli Cells Chemotactic to Aromatic Compounds (2018)

<i>Escherichia coli</i>, commonly used in chemotaxis studies, is attracted mostly by amino acids, sugars, and peptides. We envisioned modifying the chemotaxis specificity of <i>E. coli</i> by expressing heterologous chemoreceptors from <i>Pseudomonas putida</i> enabling attraction either to toluene or benzoate. The <i>mcpT</i> gene encoding the type 40-helical bundle (40H) methyl-accepting chemoreceptor for toluene from <i>Pseudomonas putida</i> MT53 and the <i>pcaY</i> gene for the type 40H receptor for benzoate and related molecules from <i>P. putida</i> F1 were expressed from the <i>trg</i> promoter on a plasmid in motile wild-type <i>E. coli</i> MG1655. <i>E. coli</i> cells expressing McpT accumulated in chemoattraction assays to sources with 60 to 200 μM toluene, although less strongly than the response to 100 μM serine, but statistically significantly stronger than that to sources without any added attractant. An McpT-mCherry fusion protein was detectably expressed in <i>E. coli</i> and yielded weak but distinguishable membranes and polar foci in 1% of cells. <i>E. coli</i> cells expressing PcaY showed weak attraction to 0.1 to 1 mM benzoate, but 50 to 70% of cells localized the PcaY-mCherry fusion to their membrane. We conclude that implementing heterologous receptors in the <i>E. coli</i> chemotaxis network is possible and, upon improvement of the compatibility of the type 40H chemoreceptors, may bear interest for biosensing.<b>IMPORTANCE</b> Bacterial chemotaxis might be harnessed for the development of rapid biosensors, in which chemical availability is deduced from cell accumulation to chemoattractants over time. Chemotaxis of <i>Escherichia coli</i> has been well studied, but the bacterium is not attracted to chemicals of environmental concern, such as aromatic solvents. We show here that heterologous chemoreceptors for aromatic compounds from <i>Pseudomonas putida</i> at least partly functionally complement the <i>E. coli</i> chemotaxis network, yielding cells attracted to toluene or benzoate. Complementation was still inferior to native chemoattractants, like serine, but our study demonstrates the potential for obtaining selective sensing for aromatic compounds in <i>E. coli</i>.
ChemInform Abstract: Stereocontrol in Horner‐Wadsworth‐Emmons Condensations of a gem‐Dimethylcyclopropyl Aldehyde with α‐Substituted Phosphono Acetates. (1990)

Abstract The cyclopropanecarbaldehyde (II), obtained by ozonolysis of (+)‐2‐carene, is sensitive towards oxygen and bases.
Intermediate- and high-affinity interleukin-2 receptors expressed in an IL-4-dependent T-cell line induce different signals. (1993)

In order to understand the respective roles of IL-2R alpha and IL-2R beta subunits in transmission of the interleukin-2 (IL-2)-mediated growth signals, we have established two IL-4-dependent murine T-cell clones stably expressing the human IL-2R beta chain and three clones stably expressing the human IL-2R alpha chain. Whereas parental LD8 cells (which express only the murine IL-2R beta chain) do not proliferate in response to IL-2, cell lines stably expressing human IL-2R beta or the chimeric IL-2R alpha beta complex proliferate in response to IL-2. Stably transfected cells expressing the chimeric high-affinity receptor (human IL-2R alpha and murine IL-2R beta) expressed de novo endogenous murine IL-2R alpha when cultured in the presence of IL-2 but not IL-4. Both chimeric and endogenous receptors are functional in response to IL-2, since only addition of both anti-human and anti-murine IL-2R alpha monoclonal antibodies (mAb) inhibited IL-2-induced proliferation. Taken together, our results strongly suggest that human and murine IL-2R beta molecules are different since interaction of IL-2 with human p70 IL-2R is sufficient for transduction of proliferative signals in the absence of p55 IL-2R or, alternatively, that over-expression of the IL-2R beta chain renders cells responsive to IL-2. In addition, IL-2 stimulation of T cells through different forms of IL-2R results in the induction of distinct cellular responses.
Development of a Tool for Component Positioning in THA Surgeries (2013)

Improper component positioning during total hip arthroplasties is the most common surgical error that takes place during the procedure. Though developments in the individual components have taken place, the positioning of these components during the surgery continues to be a challenge for surgeons, resulting in dislocations with a frequency between 1-10 % [1,2,3]. A practical and elegant solution in the form of a guidance tool was developed to be used by surgeons during placement of the acetabular cup component. The tool accounts for differing patient anatomy and patient position.
(INVITED) On the evolution of nanoparticles in nanoparticle-doped optical fibers (2022)

The doping of dielectric nanoparticles (NPs) into the cores of silica fibers doped with a rare earth (RE) has proven to be an effective approach for controlling the spectroscopic performance of the rare earth. However, little is understood about the chemical and structural evolution of the NPs during fiber preform fabrication, or how any process-induced changes in the NPs affect the optical properties of the resultant fiber. In this work, rare-earth-doped alkaline-earth (AE) fluoride [RE:(AE)F2, RE = Yb, Eu; AE = Ca, Sr, Ba] nanoparticles were synthesized, suspension-doped in a silica preform fabricated using modified chemical vapor deposition (MCVD), and their evolution from as-synthesized to processed into a final preform were thoroughly studied. A thermal profile of the preform during fabrication was developed based on optical-pyrometer temperature measurements and used for time/temperature/structural correlations. A series of characterization methods, including x-ray diffraction, electron microscopy, optical spectroscopy, and thermochemical analyses were employed to study the NP phase and structure evolution. The fluoride NPs are shown to react with the core-glass soot, eventually oxidizing and amorphizing under the thermal treatment associated with the preform fabrication. This work sets the foundation for understanding the composition and structure of RE:(AE)F2 NPs in silica optical fiber cores, and aids in the understanding and tailoring of the optical properties of the resultant fiber.
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution (2021)

The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to preorganize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies to predict and design conformational and binding properties of macrocycles as functional scaffolds for peptidomimetics. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly preorganized all-<i>trans</i> amide conformation, whose formation is likely limited by the slow rate of <i>cis</i>/<i>trans</i> isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na<sup>+</sup> has a higher affinity to the macrocycle than K<sup>+</sup>, with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.
Data traffic based route selection for real-time data delivery in wireless sensor networks (2010)

Surveillance and reconnaissance applications such as military in wireless sensor networks require timely transfer of important data (i.e., the detection of enemy troops and vehicles) to a remote base station or sink node. Unfortunately, picking up the reliable routing path to deliver the data in realtime is difficult because of various interferences, often environmental changes, and so on. Thus, routing protocols based on the link quality to select the routing path are affected by those kinds of factors. In this paper, we propose a reliable routing mechanism that provides real-time transfer of the important data. In other words, we provide the weighted link quality metric that reflect the TX/RX traffic flow to select the reliable route over the routing path. Moreover, we also provide a cross-layer routing protocol design in order to reduce the data queue processing time and to send out the priority data at both network and MAC layer.
Novel Extracellular x-Prolyl Dipeptidyl-Peptidase (DPP) from Streptococcus gordonii FSS2: an Emerging Subfamily of Viridans Streptococcal x-Prolyl DPPs (2001)

ABSTRACT Streptococcus gordonii is generally considered a benign inhabitant of the oral microflora, and yet it is a primary etiological agent in the development of subacute bacterial endocarditis (SBE), an inflammatory state that propagates thrombus formation and tissue damage on the surface of heart valves. Strain FSS2 produced several extracellular aminopeptidase and fibrinogen-degrading activities during growth in culture. In this report we describe the purification, characterization, and cloning of a serine class dipeptidyl-aminopeptidase, an x-prolyl dipeptidyl-peptidase (Sg-xPDPP, for S. gordonii x-prolyl dipeptidyl-peptidase), produced in a pH-controlled batch culture. Purification of this enzyme by anion exchange, gel filtration, and hydrophobic interaction chromatography yielded a protein monomer of approximately 85 kDa, as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (PAGE) under denaturing conditions. However, under native conditions, the protein appeared to be a homodimer on the basis of gel filtration and PAGE. Kinetic studies indicated that purified enzyme had a unique and stringent x-prolyl specificity that is comparable to both the dipeptidyl-peptidase IV/CD26 and lactococcal x-prolyl dipeptidyl-peptidase families. Nested PCR cloning from an S. gordonii library enabled the isolation and sequence analysis of the full-length gene. A 759-amino-acid polypeptide with a theoretical molecular mass of 87,115 Da and a calculated pI of 5.6 was encoded by this open reading frame. Significant homology was found with the PepX gene family from Lactobacillus and Lactococcus spp. and putative x-prolyl dipeptidyl-peptidases from other streptococcal species. Sg-xPDPP may serve as a critical factor for the sustained bacterial growth in vivo and furthermore may aid in the proteolysis of host tissue that is commonly observed during SBE pathology.
Phytoplankton Hotspot Prediction With an Unsupervised Spatial Community\n Model (2017)

Many interesting natural phenomena are sparsely distributed and discrete.\nLocating the hotspots of such sparsely distributed phenomena is often difficult\nbecause their density gradient is likely to be very noisy. We present a novel\napproach to this search problem, where we model the co-occurrence relations\nbetween a robot's observations with a Bayesian nonparametric topic model. This\napproach makes it possible to produce a robust estimate of the spatial\ndistribution of the target, even in the absence of direct target observations.\nWe apply the proposed approach to the problem of finding the spatial locations\nof the hotspots of a specific phytoplankton taxon in the ocean. We use\nclassified image data from Imaging FlowCytobot (IFCB), which automatically\nmeasures individual microscopic cells and colonies of cells. Given these\nindividual taxon-specific observations, we learn a phytoplankton community\nmodel that characterizes the co-occurrence relations between taxa. We present\nexperiments with simulated robot missions drawn from real observation data\ncollected during a research cruise traversing the US Atlantic coast. Our\nresults show that the proposed approach outperforms nearest neighbor and\nk-means based methods for predicting the spatial distribution of hotspots from\nin-situ observations.\n
Evaluating feasibility of functional near-infrared spectroscopy in dolphins (2023)

Brain measurements in juvenile or subadult dolphins, or smaller dolphin species, may be possible using specialized fNIRS devices that support optode separations of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>></mml:mo><mml:mn>100</mml:mn><mml:mtext> </mml:mtext><mml:mi>mm</mml:mi></mml:mrow></mml:math>. We speculate that many measurement repetitions will be required to overcome hemodynamic signals originating predominantly from the muscle layer above the skull. NIRS measurements of muscle tissue are feasible today with source-detector separations of 50 mm, or even less.
Chapter 2. NDI as a DNA Intercalator (2017)

Naphthalene diimide (NDI) has been widely studied as a DNA threading intercalator. While an intercalator binds DNA by insertion in between base pairs, a threading intercalator also binds with substituents residing simultaneously in the DNA major and minor grooves. The ease with which NDI can be modified through its two imide functionalities has allowed it to be used as a scaffold for threading polyintercalation, where multiple NDI intercalators are connected through linkers that are designed to alternate binding between the major and minor grooves, analogous to the way a snake might climb a ladder. The Iverson lab in particular has been exploring NDI threading polyintercalation based on tethering NDI units in a head-to-tail manner with peptide linkers. Peptide linkers derived from library screens have led to threading NDI polyintercalators that display exquisite sequence specificity. Further, the modular nature of the threading polyintercalator design enables binding to relatively long DNA sequences. Recognition of a 22 base-pair sequence and a dissociation half-life of around 60 days have been achieved with different threading NDI polyintercalators, representing the longest recognition sequence and slowest dissociation rate yet reported for synthetic, non-nucleic acid-based molecules.
Magnetically levitated slice motors - an overview (2009)

This publication gives a comprehensive overview over different concepts of magnetically levitated motors with slice-shaped rotors that differ in their construction and the way the bearing and drive forces are created. After a description of the technical principle of the topologies the motor concepts are then compared by different criteria such as the acceleration behavior, the compactness and the complexity of the control. The qualitative comparison is supported by performance measurements on the laboratory prototypes.
Scaling theory for double-gate SOI MOSFET's (1993)

A scaling theory for double-gate SOI MOSFETs, which gives guidance for device design (silicon thickness t/sub si/; gate oxide thickness t/sub ox/) that maintains a subthreshold factor for a given gate length is discussed. According to the theory, a device can be designed with a gate length of less than 0.1 mu m while maintaining the ideal subthreshold factor. This is verified numerically with a two-dimensional device simulator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>