gebhart/patrepeval huggingface dataset:
Abstract C190: A novel monoclonal antibody for colon cancer therapy. (2013)

Abstract In our recent research activities, we identified 89 novel candidate markers for prevalent cancers by a systematic Tissue microarray analysis (TMA) of a large collection of polyclonal antibodies (approximately 1600) raised against membrane-associated and secreted human proteins currently marginally characterized. Monoclonal antibodies were generated towards 20 distinct antigens that are being characterized and validated for diagnostic and therapeutic applications. Here we describe a monoclonal antibody (mAb) targeting a protein of the protocadherin- family in colo-rectal cancer (CRC). The antibody specifically recognizes its target protein in cancer tissues, with concomitant negligible or marginal reactivity in normal colon. The protein was not previously described as CRC target. IHC data from CRC samples of approximately 200 patients, (collected at the bio-bank of the institute for Pathology of Basel, Switzerland and at the European Institute of Pathology of Milan, Italy) showed that the antibody binds up to 80% CRC cases (stages from 1 to 4) with high or moderate intensity. In most cases, the antibody gives plasma membrane by Immune Histochemistry (IHC). An expanded analysis on approximately 1000 CRC cases is ongoing to assess whether the membranous IHC staining associates with specific clinic-pathological parameters. IHC analysis of 35 normal human tissues revealed that it gives intracellular staining in skeletal muscle, pituitary glands and prostate, whereas it gives background irrelevant staining in the other 32 tissues. The antibody is able to bind the surface of different colon cancer cells in vitro and in vivo. Upon binding it is efficiently internalized by colon cancer cells, suggesting that it can be exploited for the development of Antibody-Drug-Conjugate (ADC). Moreover, it inhibits tumor growth in athymic nude mice bearing HCT15 and HT29 colon cancer xenografts. Overall, data indicate that this monoclonal antibody could be developed for a targeted therapy of colo-rectal cancers, alone or in combinatorial strategies. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C190. Citation Format: Alberto Grandi, Susanna Campagnoli, Matteo Parri, Elisa De Camilli, Ilaria Naldi, Lisa Gherardini, Caterina Cinti, Luigi Terracciano, Boquan Jin, Paolo Sarmientos, Giuseppe Viale, Guido Grandi, Piero Pileri, Renata Maria Grifantini. A novel monoclonal antibody for colon cancer therapy. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C190.
Reports of the Workshops of the 31st AAAI Conference on Artificial Intelligence (2017)

The AAAI‐17 workshop program included 17 workshops covering a wide range of topics in AI. Workshops were held Sunday and Monday, February 4– 5, 2017, at the Hilton San Francisco Union Square in San Francisco, California, USA.
Molecular Genetic Marker‐Based Analysis of the Grass‐Endophyte Symbiosis (2005)

This chapter contains section titled: Development and Characterization of SSR Systems Analysis of Intraspecific Genetic Diversity Phylogenetic Analysis Co-Genotyping Of Grass-Endophyte Symbioses Summary Acknowledgments References
A Neutron Diffraction and Molecular Dynamics Investigation of Acetate-Based Ionic Liquids as Solvents for Glucose (2010)

The liquid state structure of the ionic liquid, 1-ethyl-3-methylimidazolium acetate, and the solute/solvent structure of glucose dissolved in the ionic liquid at a 1:6 molar ratio have been investigated at 323 K by molecular dynamics simulations and neutron diffraction experiments using H/D isotopically substituted materials. Interactions between hydrogen-bond donating cation sites and polar, directional hydrogen-bond accepting acetate anions are examined. Ion-ion radial distribution functions for the neat ionic liquid, calculated from both MD and derived from the empirical potential structure refinement model to the experimental data, show the alternating shell-structure of anions around the cation, as anticipated. Spatial probability distributions reveal the main anion-to-cation features as in-plane interactions of anions with imidazolium ring hydrogens and cation-cation planar stacking. Interestingly, the presence of the polarised hydrogen-bond acceptor anion leads to increased anion-anion tail-tail structuring within each anion shell, indicating the onset of hydrophobic regions within the anion regions of the liquid.
A rich and bountiful harvest: Key discoveries in plant cell biology (2021)

The field of plant cell biology has a rich history of discovery, going back to Robert Hooke's discovery of cells themselves. The development of microscopes and preparation techniques has allowed for the visualization of subcellular structures, and the use of protein biochemistry, genetics, and molecular biology has enabled the identification of proteins and mechanisms that regulate key cellular processes. In this review, seven senior plant cell biologists reflect on the development of this research field in the past decades, including the foundational contributions that their teams have made to our rich, current insights into cell biology. Topics covered include signaling and cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology. In addition, these scientists illustrate the pathways to discovery in this exciting research field.
Use of Genetic Tags to Evaluate Stocking Success for Reservoir Walleyes (1983)

Abstract In recent years, recruitment of walleyes Stizostedion vitreum vitreum in Claytor Lake, Virginia, has resulted from both natural reproduction and periodic stockings of age-0 fish from the midwestern United States. Malate dehydrogenase (MDH) allele frequencies of six walleye cohorts were assessed by starch gel electrophoresis. Augmented cohorts were found to possess MDH allele frequencies significantly different from unstocked cohorts, and both augmented and unstocked cohorts differed in allele frequencies from the juvenile fish that had been stocked during that period. Success of supplemental stocking was evaluated by quantifying shifts in cohort allele frequencies due to the stocking of juvenile fish with allele frequencies different from resident fish. Supplemental stocking of juvenile walleyes contributed an average 67% of year-class strength to augmented cohorts in Claytor Lake during 1976–1979. This investigation demonstrates the utility of genetic tags for evaluating stocking efficiency, eve...
Feature-based and channel-based analyses of intrinsic variability in speaker verification (2009)

We explore how intrinsic variations (those associated with the speaker rather than the recording environment) affect textindependent speaker verification performance. In a previous paper we introduced the SRI-FRTIV corpus and provided speaker verification results using a Gaussian mixture model (GMM) system on telephone-channel speech. In this paper we explore the use of other speaker verification systems on the telephone channel data and compare against the GMM baseline. We found the GMM system to be one of the more robust across all conditions. Systems relying on recognition hypotheses had a significant degradation in low vocal effort conditions. We also explore the use of the GMM system on several other channels. We found improved performance on table-top microphones compared to the telephone channel in furtive conditions and gradual degradations as a function of the distance from the microphone to the speaker. Therefore distant microphones further degrade the speaker verification performance due to intrinsic variability. Index Terms: speaker recognition, vocal effort, speaking style, intrinsic variation, furtive speech, interview speech, read speech, oration
Cell-Autonomous Regulation of Neutrophil Migration by the D6 Chemokine Decoy Receptor (2013)

Chemokines, acting on their cognate receptors on infiltrating leukocytes, drive the inflammatory response. We have been interested in determining roles and potential mechanisms for the atypical chemokine-scavenging receptor D6 in the regulation of inflammation. In this study, we show that a psoriasis-like pathology that arises in inflamed skins of D6-deficient mice is characterized by a massive and aberrant localization of neutrophils to the dermal/epidermal junction, which is associated with development of the pathology. Such misplacement of neutrophils is also seen with D6-deficient mice in other inflammatory models, suggesting a role for D6 in the spatial positioning of neutrophils within inflamed sites. We further show that D6 functions cell autonomously in this context and that D6, expressed by neutrophils, limits their migrational responses to CCR1 ligands such as CCL3. Our data therefore indicate that D6 is able to play a cell-autonomous role as a migratory rheostat restricting migration of D6-expressing cells such as neutrophils toward ligands for coexpressed inflammatory chemokine receptors. These data have important implications for our understanding of the roles for D6 in regulating inflammation and for our understanding of the control of spatial positioning of leukocytes at inflamed sites.
Aliovalent Doping of CeO2 Improves the Stability of Atomically Dispersed Pt (2021)

Atomically dispersed supported catalysts hold considerable promise as catalytic materials. The ability to employ and stabilize them against aggregation in complex process environments remains a key challenge to the elusive goal of 100% atom utilization in catalysis. Herein, using a Gd-doped ceria support for atomically dispersed surface Pt atoms, we establish how the combined effects of aliovalent doping and oxygen vacancy generation provide dynamic mechanisms that serve to enhance the stability of supported single-atom configurations. Using correlated, in situ X-ray absorption, photoelectron, and vibrational spectroscopy methods for the analysis of samples on the two types of support (with and without Gd doping), we establish that the Pt atoms are located proximal to Gd dopants, forming a speciation that serves to enhance the thermal stability of Pt atoms against aggregation.
Nano-taper mode-size converter (2003)

We demonstrate a nano-taper coupler for compact mode-size conversion between fiber and submicron waveguide. The micron-long silicon-on-insulator based nano-taper coupler enhances the coupling efficiency by one order of magnitude compared to that of the waveguide.
Nanofabrication and Characterization for Applications in Biochemistry and Molecular Electronics (1997)

As man-made structures are made increasingly smaller it becomes possible to conduct measurements on single cells, molecules and eventually atoms. In this thesis prerequisites for making this possible are discussed. The underlying thought is that the structures should be used in biological and organic based applications. The discussion is kept in three domains: fabrication, characterization and applications. Fabrication of small structures is mainly accomplished using standard techniques from the semiconductor industry such as UV-lithography or electron beam lithography. For biological and sensor applications the size is important, not the level of complexity. Therefore, a wider range of fabrication methods is available than for manufacturing integrated circuits. Chemical treatment of surfaces, alternative material systems and small scale metallic etching is presented here. The discussion on characterization is focused on scanning probe microscopy and in particular on scanning force microscopy (SFM). SFM allows atomic or nearly atomic resolution on non-conducting samples. In addition it gives a material dependent contrast. This has had a large impact in the bioscience field. The resulting images are deceptively convincing and show in great detail the sample surface as well as mappings of specific force interactions. On the other hand the critical evaluation of images has not had as large a development as the acquiring of images themselves. Artifacts arise due to the finite size of the tip and the rotation of the tip during acquisition. In the thesis examples of artifacts are presented and the effects of the tip and the cantilever on the geometry will be discussed. It is found that for patches which present higher friction, the twisting of the cantilever will contribute to a larger apparent width in the image. By miniaturizing electrode structures, quantitative improvements on sensor structures is the result as well as qualitatively new phenomena. Many of the effects relevant to sensor technology is discussed in the thesis. The standard techniques from the semiconductor industry cannot be directly transferred to biochemical applications or molecular electronics. The material selection is very important. Here some examples of the use of silicon electrodes as well as nanostructured surfaces will be presented.
Preliminary Study of Proton Radiography Imaging Qualities Using GEANT4 Monte Carlo Simulations (2011)

Proton radiography imaging qualities have been studied using Monte Carlo simulations. A specific phantom, made of different common tissues, was implemented for simulations using the Massachusetts General Hospital treatment proton beam, pure 230- and 490-MeV proton beams, and a pure 100-keV X-ray beam. Along with spatial resolution, the signal-to-noise ratio and the contrast-to-noise ratio were specified and compared for each tissue type and geometry, using filtered radiographs taking into account only primary proton interactions, both primary and secondary proton interactions, and both contributions while performing angular and energetic cuts. This work particularly highlights the faculty for proton radiography to image both low- and high-density tissues. This could play an important role in diagnosing specific tumor types, such as lung cancer, for which conventional radiography operates poorly.
High-Mileage Light-Duty Fleet Vehicle Emissions: Their Potentially Overlooked Importance (2016)

State and local agencies in the United States use activity-based computer models to estimate mobile source emissions for inventories. These models generally assume that vehicle activity levels are uniform across all of the vehicle emission level classifications using the same age-adjusted travel fractions. Recent fuel-specific emission measurements from the SeaTac Airport, Los Angeles, and multi-year measurements in the Chicago area suggest that some high-mileage fleets are responsible for a disproportionate share of the fleet's emissions. Hybrid taxis at the airport show large increases in carbon monoxide, hydrocarbon, and oxide of nitrogen emissions in their fourth year when compared to similar vehicles from the general population. Ammonia emissions from the airport shuttle vans indicate that catalyst reduction capability begins to wane after 5-6 years, 3 times faster than is observed in the general population, indicating accelerated aging. In Chicago, the observed, on-road taxi fleet also had significantly higher emissions and an emissions share that was more than double their fleet representation. When compounded by their expected higher than average mileage accumulation, we estimate that these small fleets (<1% of total) may be overlooked as a significant emission source (>2-5% of fleet emissions).
A Two-Layer Gene Circuit for Decoupling Cell Growth from Metabolite Production (2016)

We present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable.
Histologic and Immunopathologic Findings in Sympathetic Ophthalmia (1985)

<h3>To the Editor.</h3> —I read with great interest the article by Müller-Hermelink et al<sup>1</sup>in the SeptemberArchives. According to the authors, they are describing the apparent "early" histologic and immunopathologic events in sympathetic ophthalmia. From the reported clinical ocular findings in their patient, it is very difficult to unequivocally argue for or against the diagnosis of sympathetic ophthalmia. However, I would like to emphasize that the classification of the reported pathologic findings in the enucleated eye as "early events" are unfounded. If our surmise concerning the role of the immune system in the pathology of sympathetic ophthalmia is correct, once a clinical diagnosis of uveal involvement in the sympathizing (noninjured) eye is made, the events that take place in the inciting (injured) eye must have reached the "mature" stage of expression. Therefore, "early" events of clinical symptoms of sympathetic phenomena in the sympathizing eye are a sound possibility.
Crystalline Actin Tubes. V. The Effect of Th4+ on Actin and the Role of Ionic Charge in Tube Formation1 (1982)

NMR and UV spectroscopy reveal that the tetravalent thorium ion interacts with actin in an identical fashion to the trivalent lanthanide ions. UV spectra and viscometry data suggest that the actin-bound Th4+ has an ionic radius of about 110 pm. Th4+ also contributes to the formation of crystalline actin tubes under appropriate conditions. The factors governing whether tubes form appear to be cationic radius and total charge on the actin monomer, rather than the valency of the ion per se.
Hardware support for object-oriented systems (abstract) (1992)

When the performance penalty of object-oriented systems is mentioned, a common response is to blame antiquated hardware designs for not supporting object-oriented languages as they deserve, To what extent can the performance gap between conventional languages and object-oriented languages be closed using hardware? What architectural changes benefit object-oriented systems, and by how much?
Geometric optimization and mechanical risk mmitigation in 2.5D flip-chip packages using parametric finite element analysis (FEA) simulations (2016)

This study is focused on geometric optimization of a 2.5D interposer based single die flip-chip package. Parametric analyses using the well-established global-local finite element method (FEM) technique have been conducted on the package at both the pre and post encapsulation (or underfill) stages. At the pre and post encapsulation phases, effects of geometric parameters which included variations in silicon die dimensions, interposer dimensions and substrate dimensions were analyzed to determine the corresponding mechanical risks associated during the die bonding and capping process. The geometric optimization at the macro-scale was focused on reducing die-underfill shear stresses and strains in the thermal interface material (TIM). At the local level, studies were geared towards understanding the impact of geometric variables on the solder inelastic strain and stresses within the back end of the line layers within the chip. The results presented from both these modeling analyses will provide configurations that reduce the overall mechanical risks in 2.5D packages and provide guidelines for geometric optimization of such packages.
One-Pot Synthesis of Tetrahydroquinolines by an Imino-Diels-Alder Reaction (2008)

Reported is a synthesis of 1,2,3,4-tetrahydroquinolines by the Diels-Alder reaction of alkenes with iminium salts formed in situ from N-methylaniline and different sources of formaldehyde. The influence of the source of formaldehyde, Lewis acid and alkene structure on yield and stereochemistry of the products obtained was moderately investigated. The formation of both syn and anti products suggests the competition of pericyclic [4+2] cycloaddition with a stepwise mechanism involving cationic species.
An Acoustothermal Microheater with Omni-temperature Controllability (2015)

Abstract Here we report the first observation of rapid volumetric heating of polydimethylsiloxane (PDMS) under cyclic loadings at a range of high (∼MHz) frequencies. Based on the finding, we developed a microheater which utilizes the vibration damping of PDMS, the most commonly used material in microfluidics, induced by sound waves generated and precisely controlled by a surface acoustic wave (SAW) microfluidic system. An omni-temperature controllability of the microheater enabled us to perform two-step continuous flow polymerase chain reaction for a billion-fold amplification of 134 bp DNA amplicon in less than 45 sec.
PIKM 2010 (2010)

The PIKM workshop focuses on papers consisting mainly of the Ph.D. dissertation proposals of doctoral students. A wide range of topics on any area in databases, information retrieval and knowledge management are presented at this workshop. The areas of interest are similar to those at the CIKM main conference in the three respective tracks. Interdisciplinary work across these tracks is encouraged.
Calculation of electric fields and currents induced in a millimeter-resolution human model at 60 Hz using the FDTD method with a novel time-to-frequency-domain conversion (2002)

The finite-difference time-domain (FDTD) method has previously been used to calculate induced currents in anatomically based models of the human body at frequencies ranging from 20 to 915 MHz and resolutions down to 1.31 cm. Calculations at lower frequencies and higher resolutions have been precluded by the huge number of time steps which would be needed to run these simulations in the traditional way. This paper describes a new method used to overcome this problem and calculate the induced currents in a MRI-based 6-mm-resolution human model at 60 Hz. A new algorithm based on solving two equations with two unknowns is used for calculating magnitude and phase from the CW FDTD simulation. This allows magnitude and phase calculations to be made as soon as steady-state is reached, which is within a fraction of a cycle. For incident electric fields of 10 kV/m, local induced current densities above 16 mA/m/sup 2/ have been calculated in the torso, with even higher values up to 45 mA/m/sup 2/ for the legs. These are considerably higher than the 4 or even 10 mA/m/sup 2/ that have been suggested in the safety guidelines.
Observation of dust particles ejected from the tungsten surface by transient heat flux with small-angle scattering of cw laser light (2017)

A new test facility for experimental simulation of transient heat load expected in the ITER divertor during unmitigated events is developed. Application of a long-pulse (0.1–0.3ms) wide-aperture (up to 2cm2) electron beam as a heating device provides powerful energy loads at a tungsten target with FHF> 250MJm−2s−0.5. Dynamics of tungsten particles in the ablation plume is investigated with a novel for PSI experiments small-angle laser light scattering technique. The threshold of intense droplet generation and dynamics of particles sizes are estimated.