gebhart/patrepeval huggingface dataset:
Evaluation of Components of Gingival Crevicular Fluid as Diagnostic Tests (1997)

Gingival crevicular fluid (GCF) is an inflammatory exudate that can be collected at the gingival margin or within the gingival crevice. The biochemical analysis of the fluid offers a noninvasive means of assessing the host response in periodontal disease. In recent years, the relationship of measures of the inflammatory response in GCF to risk for development of active periodontal disease (defined as clinical attachment loss or radiographic bone loss) has been studied in longitudinal trials. The greatest interest has focused on prostaglandin E2, an arachidonic acid metabolite; beta-glucuronidase and neutrophil elastase, markers of lysosomal enzyme release from neutrophils; and aspartate aminotransferase, a cytoplasmic enzyme indicative of cellular necrosis. Analysis of the data allows a number of conclusions to be drawn concerning the potential diagnostic significance of GCF: 1) an exuberant host inflammatory response is associated with progressive disease in patients with periodontitis; 2) collection of GCF using small precut strips is a reproducible and reliable collection technique; 3) the total amount of the mediator and not concentration of the mediator in the GCF sample can be reported when timed samples are collected; and 4) technology exists for GCF-based diagnostic tests to be performed in the dental office. Nevertheless, many questions remain. Still to be determined are: 1) the relationship of test results to the development of periodontitis in patients with gingivitis; 2) the level of test accuracy needed to justify use of these tests; 3) the unit of observation (patient, site) that is being evaluated by the test; and 4) the need for such tests as perceived by clinicians. While these questions are formidable, introduction of GCF-based diagnostic tests will provide clinicians with an improved, quantitative means of evaluating patients and offer specific criteria to assess the effectiveness of treatment.
3D generic object categorization, localization and pose estimation (2007)

We propose a novel and robust model to represent and learn generic 3D object categories. We aim to solve the problem of true 3D object categorization for handling arbitrary rotations and scale changes. Our approach is to capture a compact model of an object category by linking together diagnostic parts of the objects from different viewing points. We emphasize on the fact that our "parts" are large and discriminative regions of the objects that are composed of many local invariant features. Instead of recovering a full 3D geometry, we connect these parts through their mutual homographic transformation. The resulting model is a compact summarization of both the appearance and geometry information of the object class. We propose a framework in which learning is done via minimal supervision compared to previous works. Our results on categorization show superior performances to state-of-the-art algorithms such as [23]. Furthermore, we have compiled a new 3D object dataset that consists of 10 different object categories. We have tested our algorithm on this dataset and have obtained highly promising results.
CD3 bispecific antibody–induced cytokine release is dispensable for cytotoxic T cell activity (2019)

T cell-retargeting therapies have transformed the therapeutic landscape of oncology. Regardless of the modality, T cell activating therapies are commonly accompanied by systemic cytokine release, which can progress to deadly cytokine release syndrome (CRS). Because of incomplete mechanistic understanding of the relationship between T cell activation and systemic cytokine release, optimal toxicity management that retains full therapeutic potential remains unclear. Here, we report the cell type-specific cellular mechanisms that link CD3 bispecific antibody-mediated killing to toxic cytokine release. The immunologic cascade is initiated by T cell triggering, whereas monocytes and macrophages are the primary source of systemic toxic cytokine release. We demonstrate that T cell-generated tumor necrosis factor-α (TNF-α) is the primary mechanism mediating monocyte activation and systemic cytokine release after CD3 bispecific treatment. Prevention of TNF-α release is sufficient to impair systemic release of monocyte cytokines without affecting antitumor efficacy. Systemic cytokine release is only observed upon initial exposure to CD3 bispecific antibody not subsequent doses, indicating a biological distinction between doses. Despite impaired cytokine release after second exposure, T cell cytotoxicity remained unaffected, demonstrating that cytolytic activity of T cells can be achieved in the absence of cytokine release. The mechanistic uncoupling of toxic cytokines and T cell cytolytic activity in the context of CD3 bispecifics provides a biological rationale to clinically explore preventative treatment approaches to mitigate toxicity.
Peptide Bond Isosteres:  Ester or (<i>E</i>)-Alkene in the Backbone of the Collagen Triple Helix (2005)

[structure: see text] Collagen is the most abundant protein in animals. Interstrand N-H...O=C hydrogen bonds between backbone amide groups form a ladder in the middle of the collagen triple helix. Isosteric replacement of the hydrogen-bond-donating amide with an ester or (E)-alkene markedly decreases the conformational stability of the triple helix. Thus, this recurring hydrogen bond is critical to the structural integrity of collagen. In this context, an ester isostere confers more stability than does an (E)-alkene.
Mechanism of Insect Resistance to the Microbial Insecticide <i>Bacillus thuringiensis</i> (1990)

Receptor binding studies show that resistance of a laboratory-selected Plodia interpunctella strain to a Bacillus thuringiensis insecticidal crystal protein (ICP) is correlated with a 50-fold reduction in affinity of the membrane receptor for this protein. The strain is sensitive to a second type of ICP that apparently recognizes a different receptor. Understanding the mechanism of resistance will provide strategies to prevent or delay resistance and hence prolong the usefulness of B. thuringiensis ICPs as environmentally safe insecticides.
Hey, You, Get Off of My Market: Detecting Malicious Apps in Official and Alternative Android Markets (2012)

In this paper, we present a systematic study for the detection of malicious applications (or apps) on popular Android Markets. To this end, we first propose a permissionbased behavioral footprinting scheme to detect new samples of known Android malware families. Then we apply a heuristics-based filtering scheme to identify certain inherent behaviors of unknown malicious families. We implemented both schemes in a system called DroidRanger. The experiments with 204, 040 apps collected from five different Android Markets in May-June 2011 reveal 211 malicious ones: 32 from the official Android Market (0.02% infection rate) and 179 from alternative marketplaces (infection rates ranging from 0.20% to 0.47%). Among those malicious apps, our system also uncovered two zero-day malware (in 40 apps): one from the official Android Market and the other from alternative marketplaces. The results show that current marketplaces are functional and relatively healthy. However, there is also a clear need for a rigorous policing process, especially for non-regulated alternative marketplaces.
Superoxide Dismutases: Role in Redox Signaling, Vascular Function, and Diseases (2011)

Excessive reactive oxygen species Revised abstract, especially superoxide anion (O₂•-), play important roles in the pathogenesis of many cardiovascular diseases, including hypertension and atherosclerosis. Superoxide dismutases (SODs) are the major antioxidant defense systems against (O₂•-), which consist of three isoforms of SOD in mammals: the cytoplasmic Cu/ZnSOD (SOD1), the mitochondrial MnSOD (SOD2), and the extracellular Cu/ZnSOD (SOD3), all of which require catalytic metal (Cu or Mn) for their activation. Recent evidence suggests that in each subcellular location, SODs catalyze the conversion of (O₂•-), H2O2, which may participate in cell signaling. In addition, SODs play a critical role in inhibiting oxidative inactivation of nitric oxide, thereby preventing peroxynitrite formation and endothelial and mitochondrial dysfunction. The importance of each SOD isoform is further illustrated by studies from the use of genetically altered mice and viral-mediated gene transfer. Given the essential role of SODs in cardiovascular disease, the concept of antioxidant therapies, that is, reinforcement of endogenous antioxidant defenses to more effectively protect against oxidative stress, is of substantial interest. However, the clinical evidence remains controversial. In this review, we will update the role of each SOD in vascular biologies, physiologies, and pathophysiologies such as atherosclerosis, hypertension, and angiogenesis. Because of the importance of metal cofactors in the activity of SODs, we will also discuss how each SOD obtains catalytic metal in the active sites. Finally, we will discuss the development of future SOD-dependent therapeutic strategies.
Electrospray-printed nanostructured graphene oxide gas sensors (2015)

We report low-cost conductometric gas sensors that use an ultrathin film made of graphene oxide (GO) nanoflakes as transducing element. The devices were fabricated by lift-off metallization and near-room temperature, atmospheric pressure electrospray printing using a shadow mask. The sensors are sensitive to reactive gases at room temperature without requiring any post heat treatment, harsh chemical reduction, or doping with metal nanoparticles. The sensors' response to humidity at atmospheric pressure tracks that of a commercial sensor, and is linear with changes in humidity in the 10%-60% relative humidity range while consuming <6 μW. Devices with GO layers printed by different deposition recipes yielded nearly identical response characteristics, suggesting that intrinsic properties of the film control the sensing mechanism. The gas sensors successfully detected ammonia at concentrations down to 500 ppm (absolute partial pressure of ∼5 × 10(-4) T) at ∼1 T pressure, room temperature conditions. The sensor technology can be used in a great variety of applications including air conditioning and sensing of reactive gas species in vacuum lines and abatement systems.
情感的力量——评艾丽丝·默多克《钟》 (2011)

像伟大的现实主义者托尔斯泰、艾略特、詹姆斯一样,艾丽丝·默多克关注的是如何在一个不断加速变化,并且道德信仰不断缺失的世界里道德地生活。她写小说并研究哲学,而她的小说揭露的多为思想面临生活所迫而导致的命运的改变。默多克的才能就是把社会讽刺和她性格中富有
Viral polypeptides detected by a complement-dependent neutralizing murine monoclonal antibody to human cytomegalovirus (1985)

Murine monoclonal antibodies were produced which coimmunoprecipitated, under reducing conditions, 130,000- and 55,000-dalton (Da) polypeptides from cells infected with human cytomegalovirus (CMV) strain AD169. A 92,000-Da species, possibly a biosynthetic intermediate, was also detectable. One of the monoclonal antibodies, 15D8, neutralized CMV AD169 only in the presence of guinea pig complement. A second monoclonal antibody, 14E10, coimmunoprecipitated the 130,000- and 55,000-Da polypeptides but did not neutralize viral infectivity. By sequential immunoprecipitation, both monoclonal antibodies have been shown to recognize the same polypeptides. Monoclonal antibody 15D8 detected the 130,000- and 55,000-Da polypeptides in five of six clinical strains and three laboratory strains tested. The 14E10 monoclonal antibody detected the 130,000-Da protein in four of six CMV clinical isolates and in strain AD169 but did not immunoprecipitate any polypeptides from extracts of cells infected with either Towne or Davis laboratory strains. In kinetic studies, the synthesis of the 130,000-Da polypeptide preceded the appearance of the 55,000-Da polypeptide. In infected cells radiolabeled with a pulse of L-[35S]methionine, the isotope was initially detected in the 130,000-Da polypeptide but could be chased into the 55,000-Da polypeptide. These polypeptides exist in the intracellular and extracellular virus as disulfide-linked multimers. Extracellular virus contained a high-molecular-weight (greater than 200,000 Da) multimer composed entirely of 55,000-Da polypeptides. In extracts from infected cells an additional high-molecular-weight multimer was detected consisting of disulfide-linked 130,000-Da polypeptides.
Comparison of DNA Sequencing and a Line Probe Assay for Detection of Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Patients Failing Highly Active Antiretroviral Therapy (2001)

The resistance of human immunodeficiency virus type 1 (HIV-1) to drugs is a major cause of antiretroviral treatment failure. We have compared direct sequencing to a line probe assay (LiPA) for the detection of drug resistance-related mutations in 197 clinical samples, and we have investigated the sequential appearance of mutations under drug pressure. For 26 patients with virological failure despite the use of two nucleoside analogues and one protease inhibitor (indinavir [n = 6], ritonavir [n = 10], and saquinavir [n = 10]), genotypic resistance assays were carried out retrospectively every 3 months for up to 2 years by using direct sequencing (TruGene; Visible Genetics) and a LiPA for detection of mutations in the reverse transcriptase (INNO-LiPA HIV-1 RT; Innogenetics) and the protease (INNO-LiPA HIV Protease, prototype version; Innogenetics) genes. Comparison of the results from both assays found rare major discrepancies (<1% of codons analyzed). INNO-LiPA detected more wild-type-mutant mixtures than sequencing but suffered from a high rate of codon hybridization failures for the reverse transcriptase. LiPA detected earlier and more frequently than sequencing the transient mixed virus population that contained I84V, which appears before V82A in the protease sequence. Mutations M461, G48V, and L90M were often transient and drug pressure related. In conclusion, direct sequencing and LiPAs give concordant results for most clinical isolates. LiPAs are more sensitive for the detection of mixed virus populations. Mutation I84V appears in minor populations in the early steps of the pathways of resistance to indinavir and ritonavir. The fact that some mutations can be found only transiently and in minor virus populations highlights the importance of a low detection limit for resistance assays.
Hybrid segmentation and exploration of the human lungs (2004)

Segmentation of the tracheo-bronchial tree of the lungs is notoriously difficult. This is due to the fact that the small size of some of the anatomical structures is subject to partial volume effects. Furthermore, the limited intensity contrast between the participating materials (air, blood, and tissue) increases the segmentation of difficulties. In this paper, we propose a hybrid segmentation method which is based on a pipeline of three segmentation stages to extract the lower airways down to the seventh generation of the bronchi. User interaction is limited to the specification of a seed point inside the easily detectable trachea at the upper end of the lower airways. Similarly, the complementary vascular tree of the lungs can be segmented. Furthermore, we modified our virtual endoscopy system to visualize the vascular and airway system of the lungs along with other features, such as lung tumors.
Another jigsaw piece towards solving the iron metabolism puzzle:the cloning of the iron exporter,<i>ferroportin1</i> (2000)

Over the last 4 years, a flurry of genetic studies have brought about revolutions in our understanding of the molecular processes involved in iron (Fe) metabolism. In 1996, Feder and colleagues discovered that the gene HFE is mutated in the Fe-overload disease hemochromatosis.1 During 1997, two groups discovered that a previously cloned gene (Nramp2) encoded an Fe transporter involved in Fe uptake.2–4 This molecule has been called the divalent metal transporter 1 (DMT1), and is involved in the uptake of Fe across the apical enterocyte membrane and also Fe transport across the endosomal membrane after its release from transferrin (Tf).2–4 After a brief hiatus in 1998, another gene, known as hephaestin, was found in 1999 that plays some role in Fe transport in the intestinal enterocyte.5 In the latest discovery, Donovan and colleagues have positionally cloned a gene called ferroportin1 that encodes a membrane-spanning molecule which could be involved in the export of Fe from cells.6 These discoveries have provided the jigsaw pieces of a puzzle that still remains to be completely solved.
Silicon Surface and Interface Issues for Nanoelectronics (2005)

To a large extent, the silicon revolution is based on the wonderful properties of the silicon/silicon dioxide interface. The importance of this structure has been documented and cited in many articles and books on the history of technology.
MPEG2 4:2:2@ML - from concept to an implementation (1996)

There is a growing interest in using MPEG2 in the studio and post production environment. We describe Tektronix' contribution to the standard, starting from the introduction of the concept of 4:2:2 Profile@Main Level, all the way to a hardware realization of 4:2:2 Profile@Main Level. Operating up to 50 Mb/s, MPEG-2 4:2:2 Profile@ML provides higher quality to support multigeneration and digital special effects, in addition to providing higher spatial and chroma resolution.
Labile iron in parenteral iron formulations: a quantitative and comparative study (2004)

Approximately 2-6% of total iron in commonly used IV iron compounds is available for in vitro iron donation to Tf. This fraction may contribute to evidence of bioactive iron in patients after IV iron administration.
Incorporation of an Intramolecular Hydrogen-Bonding Motif in the Side Chain of 4-Aminoquinolines Enhances Activity against Drug-Resistant <i>P. </i><i>f</i><i>alciparum</i> (2006)

Previous data showing that several chloroquine analogues containing an intramolecular hydrogen-bonding motif were potent against multidrug-resistant P. falciparum led to the exploration of the importance of this motif. A series of 116 compounds containing four different alkyl linkers and various aromatic substitutions with hydrogen bond accepting capability was synthesized. The series showed broad potency against the drug-resistant W2 strain of P. falciparum. In particular, a novel series containing variations of the alpha-aminocresol motif gave eight compounds with IC50 values more potent than 5 nM against the W2 strain. Such simple modifications, significantly altering the pKa and sterics of the basic side chain in chloroquine analogues, may prove to be part of a strategy for overcoming the problem of worldwide resistance to affordable antimalarial drugs.
Estimating mean scatterer spacing with the frequency-smoothed spectral autocorrelation function (1995)

The quasiperiodicity of regularly spaced scatterers results in characteristic patterns in the spectra of backscattered ultrasonic signals from which the mean scatterer spacing can be estimated. The mean spacing has been considered for classifying certain biological tissue. This paper addresses the problem of estimating the mean scatterer spacing from backscattered ultrasound signals using the frequency-smoothed spectral autocorrelation (SAC) function. The SAC function exploits characteristic differences between the phase spectrum of the resolvable quasiperiodic scatterers and the unresolvable uniformly distributed (diffuse) scatterers to improve estimator performance over other estimators that operate directly on the magnitude spectrum. Mean scatterer spacing estimates are compared for the frequency-smoothed SAC function and a cepstral technique using an AR model. Simulation results indicate that SAC-based estimates converge more reliably over smaller amounts of data than cepstrum-based estimates. An example of computing an estimate from liver tissue scans is also presented for the SAC function and the AR cepstrum.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers (2006)

Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.
Template Synthesis of Polypyrrole‐Coated Spinel LiMn2 O 4 Nanotubules and Their Properties as Cathode Active Materials for Lithium Batteries (1997)

Tubules of 200 nm outer diameter spinel were prepared by thermal decomposition of an aqueous solution containing lithium nitrate and manganese nitrate at 1:2 molar ratio using a nanoporous alumina membrane as a template. After dissolving the template membrane, the resulting nanotubule array of was coated with polypyrrole to investigate the galvanostatic charge‐discharge characteristics. The polypyrrole‐coated tubule electrodes exhibited higher capacities than the polypyrrole‐coated thin‐film electrode prepared under the same conditions, except for the use of the alumina membrane; it was ca. 2.5 times greater at and became ca. 12 times greater with an increase in current density to . The observed high capacity of the tubule electrode seems to have resulted from two kinds of effects: a decrease in real current density of high specific surface area at the tubule electrode and a decrease in thickness of solid phase for ions to diffuse through during the charging and discharging reactions.
A Near-Field Dual Polarized (TE–TM) Microwave Imaging System (2013)

In this paper, we introduce a novel dual polarized microwave imaging system. The system is comprised of a circular array of multiplexed antennas, distributed evenly around an object-of-interest (OI), along with a novel plurality of probes located at the antennas' apertures. Each probe consists of several p-i-n diodes biased in two different states (open and short). The probes are used to measure field scattered by an OI based on the modulated scatterer technique. Half of the probes are oriented vertically with the second half oriented horizontally. The presence of the two probe-orientations enables the imaging system to collect two orthogonal field polarizations, transverse electric (TE) and transverse magnetic (TM), without the need for mechanical rotation. In order to illuminate the object with all possible polarizations of the electromagnetic field, the transmitting antennas are placed at a slant angle with respect to the longitudinal plane of the imaging chamber. Near-field data are collected using each probe set, then calibrated. We show that the calibrated data for each polarization can be used to reconstruct the dielectric profile of various objects using either two-dimensional TE or TM inversion algorithms.