gebhart/patrepeval huggingface dataset:
Particle Separation in Microfluidic Channels Using Flow Rate Control (2004)

Microfluidic devices for particle recovery are successfully developed by controlling flow rate ratios of two daughter channels. Devices are prepared by using conventional Polydimethylsiloxane (PDMS) replica molding technique. The flow rate ratios of two daughter channels are controlled by changing the flow resistance through changing the geometry of the downstream channels. The particle recovery studies are conducted using 16 μm-diameter green fluorescent particles and using 8–10 μm-diameter human C8161 melanoma cells. For the fluorescent particles, the particle recovery efficiencies are 87.2%, 95.7%, 100%, and 100% for 2.5:1, 4:1, 6:1, and 8:1 flow rate ratios, respectively. Also, for the human C8161 melanoma cells, the cell recovery efficiencies are 88.7%, 98.9%, 100%, and 100% for 2.5:1, 4:1, 6:1, and 8:1 flow rate ratios, respectively.
Effect of Ponesimod, a Selective S1P1 Receptor Modulator, on the QT Interval in Healthy Individuals (2014)

Ponesimod is an orally active selective sphingosine-1-phosphate receptor 1 modulator under investigation for the treatment of multiple sclerosis. This was a single-centre, double-blind, randomized, placebo- and positive-controlled parallel-group study investigating the effects of ponesimod on the QTc interval in healthy individuals. A nested cross-over comparison between moxifloxacin and placebo was included in the combined moxifloxacin/placebo treatment group. Subjects in group A received multiple doses of 10-100 mg ponesimod according to an uptitration regimen on days 2-23 and moxifloxacin-matching placebo on days 1 and 24. Subjects in group B received ponesimod-matching placebo on days 2-23 and were randomized to receive either a single dose of 400 mg moxifloxacin or matching placebo on days 1 and 24. The primary end-point was the baseline-adjusted, placebo-corrected effect on the individually corrected QT interval (QTcI) on days 12 (after 5 days of 40 mg ponesimod) and 23 (after 5 days of 100 mg ponesimod). Ponesimod caused a mild QTcI prolongation with a largest effect of 6.9 ms (90% two-sided confidence interval (CI): 2.5-11.3) and 9.1 ms (90% CI: 4.1-14.0) for doses of 40 mg and 100 mg, respectively. A concentration-effect analysis confirmed the QTcI-prolonging effect of ponesimod with a shallow slope of 0.0053 ms per ng/mL. Using the concentration-effect analysis, the QTc prolongation caused by 20 mg ponesimod and the current highest therapeutic dose was predicted to be below the level of clinical concern (i.e. an upper bound of the two-sided 90% CI of ≥10 ms).
Generalized Performance Management of Multi-Class Real-Time Imprecise Data Services (2006)

The intricacy of real-time data service management increases mainly due to the emergence of applications operating in open and unpredictable environments, increases in software complexity, and need for performance guarantees. In this paper we propose an approach for managing the quality of service of real-time databases that provide imprecise and differentiated services, and that operate in unpredictable environments. Transactions are classified into service classes according to their level of importance. Transactions within each service class are further classified into subclasses based on their quality of service requirements. In this way transactions are explicitly differentiated according to their importance and quality of service requests. The performance evaluation shows that during overloads the most important transactions are guaranteed to meet their deadlines and that reliable quality of service is provided even in the face of varying load and execution time estimation errors.
Advanced assessment through intact glycopeptide analysis of Infliximab’s biologics and biosimilar (2022)

Characterization of therapeutic monoclonal antibodies (mAbs) represents a major challenge for analytical sciences due to their heterogeneity associated with post-translational modifications (PTMs). The protein glycosylation requires comprehensive identification, which could influence on the mAbs' structure and their function. Here, we demonstrated high-resolution tandem mass spectrometry with an ultra-high-performance liquid chromatography for characterization and comparison between biologics and biosimilar of infliximab at an advanced level. Comparing the N- and O-glycopeptides profiles, a total of 49 and 54 glycopeptides was identified for each product of the biologics and biosimilar, respectively. We also discovered one novel N-glycosylation site at the light chain from both biopharmaceuticals and one novel O-glycopeptide at the heavy chain from only biosimilar. Site-specific glycopeptide analysis process will be a robust and useful technique for evaluating therapeutic mAbs and complex glycoprotein products.
3′-Substituted Thymine α-L-nucleoside Derivatives as Potential Antiviral Agents: Synthesis and Biological Evaluation (1991)

Hitherto unknown 1-(3-deoxy-3-substituted-α-L-lyxofuranosyl)thymines and their 2-deoxy derivatives related to azidothymidine (AZT) and its congeners have been synthesized and their antiviral properties examined. They were prepared by nucleophilic substitution with inversion of configuration from 3′-O-trifluoromethanesulphonate α-L-arabinofuranonucleosides and their 2′-deoxy derivatives. All the prepared compounds were tested for their activity against a variety of RNA and DNA viruses, but they did not show significant antiviral activity.
A Systematic Review of Experimental Studies on Data Glyphs (2016)

We systematically reviewed 64 user-study papers on data glyphs to help researchers and practitioners gain an informed understanding of tradeoffs in the glyph design space. The glyphs we consider are individual representations of multi-dimensional data points, often meant to be shown in small-multiple settings. Over the past 60 years many different glyph designs were proposed and many of these designs have been subjected to perceptual or comparative evaluations. Yet, a systematic overview of the types of glyphs and design variations tested, the tasks under which they were analyzed, or even the study goals and results does not yet exist. In this paper we provide such an overview by systematically sampling and tabulating the literature on data glyph studies, listing their designs, questions, data, and tasks. In addition we present a concise overview of the types of glyphs and their design characteristics analyzed by researchers in the past, and a synthesis of the study results. Based on our meta analysis of all results we further contribute a set of design implications and a discussion on open research directions.
Epigenetic inactivation of VGF associated with Urothelial Cell Carcinoma and its potential as a non-invasive biomarker using urine (2014)

Selection of candidates from genome-wide screening approach in other solid tumors successfully identified UCC specific methylated genes.
Lignin Changes after Steam Explosion and Laccase-Mediator Treatment of Eucalyptus Wood Chips (2011)

Eucalyptus globulus chips were steam exploded followed by treatment with a laccase-mediator system (LMS) under different experimental conditions. Removal of hemicelluloses and, to a lesser extent, lignin was observed. Thermogravimetic analyses of whole meal obtained from chips before and after steam explosion indicated an increase in lignin degradation temperature due to lignin condensation. In contrast, application of LMS treatment caused a reduction in lignin and polysaccharide degradation temperatures. Lignins were isolated from wood samples before and after each treatment and analyzed by 2D NMR and (13)C NMR. An increase in carboxyl and phenolic hydroxyl groups and a significant decrease in β-O-4 structures were found in steam-exploded samples. The most relevant changes observed after laccase treatment were increased secondary OH and degree of condensation.
Models and algorithms for vision through the atmosphere (2004)

Current vision systems are designed to perform in clear weather. Needless to say, in any outdoor application, there is no escape from bad weather. Ultimately, computer vision systems must include mechanisms that enable them to function (even if somewhat less reliably) in the presence of haze, fog, rain, hail and snow. We begin by studying the visual manifestations of different weather conditions. For this, we draw on what is already known about atmospheric optics, and identify effects caused by bad weather that can be turned to our advantage; we are not only interested in what bad weather does to vision but also what it can do for vision. 
This thesis presents a novel and comprehensive set of models, algorithms and image datasets for better image understanding in bad weather. The models presented here can be broadly classified into single scattering and multiple scattering models. Existing single scattering models like attenuation and airlight form the basis of three new models viz., the contrast model, the dichromatic model and the polarization model. Each of these models is suited to different types of atmospheric and illumination conditions as well as different sensor types. Based on these models, we develop algorithms to recover pertinent scene properties, such as 3D structure, and clear day scene contrasts and colors, from one or more images taken under poor weather conditions. 
Next, we present an analytic model for multiple scattering of light in a scattering medium. From a single image of a light source immersed in a medium, interesting properties of the medium can be estimated. If the medium is the atmosphere, the weather condition and the visibility of the atmosphere can be estimated. These quantities can in turn be used to remove the glows around sources obtaining a clear picture of the scene. Based on these results, the camera serves as a “visual weather meter”. Our analytic model can be used to analyze scattering in virtually any scattering medium, including fluids and tissues. Therefore, in addition to vision in bad weather, our work has implications for real-time rendering of participating media in computer graphics, medical imaging and underwater imaging. 
Apart from the models and algorithms, we have acquired an extensive database of images of an outdoor scene almost every hour for 9 months. This dataset is the first of its kind and includes high quality calibrated images captured under a wide variety of weather and illumination conditions and all four seasons. Such a dataset could not only be used as a testbed for validating existing appearance models (including the ones presented in this work) but also inspire new data driven models. In addition to computer vision, this dataset could be useful for researchers in other fields like graphics, image processing, remote sensing and atmospheric sciences. The database is freely distributed for research purposes and can be requested through our web site http://www.cs.columbia.edu/∼wild. We believe that this thesis opens new research directions needed for computer vision to be successful in the outdoors.
Association between the HLA haplotype and the TCR‐Vβ repertoire of anti‐hCMV specific memory T‐cells in immunocompetent healthy adults (2007)

These results indicate that hCMV-specific memory T-cells are phenotypically heterogeneous, their TCR-Vbeta repertoire shaped through the interaction between hCMV epitopes and the HLA haplotype.
Protein Mapping of the Salivary Complex from a Hematophagous Leech (2005)

The salivary complex of leeches contains many components able to modulate physiological mechanisms, such as coagulation and fibrinolysis, and it is composed by the salivary glands and proboscis, encompassing two different proteomes. The bidimensional electrophoretic pattern of the salivary complex from the Haementeria depressa leech revealed a total of 352 spots, 103 in common with the muscular tissue and 249 exclusive from the salivary complex as detected by silver staining; these spots showed isoelectric points from 3.5 to 9.5 and covered an apparent molecular weight range from 10 to 105 kDa. The following isoforms of proteins were identified by mass spectrometry analysis: antiplatelet protein, myohemerythrin and carbonic anhydrase. Since the leeches were not fed for about 2-3 months to stimulate the secretion of proteins that facilitates the blood metabolism, these most abundant proteins in the salivary complex excised from leeches, are expected to play a role during feeding and might have some anti-hemostatic properties. Furthermore, by zymography, a gelatinolytic and a fibrinolytic protein were identified.
Towards a colony counting system using hyperspectral imaging (2012)

Colony counting is a procedure used in microbiology laboratories for food quality monitoring, environmental management, etc. Its purpose is to detect the level of contamination due to the presence and growth of bacteria, yeasts and molds in a given product. Current automated counters require a tedious training and setup procedure per product and bacteria type and do not cope well with diversity. This contrasts with the setting at microbiology laboratories, where a wide variety of food and bacteria types have to be screened on a daily basis. To overcome the limitations of current systems, we propose the use of hyperspectral imaging technology and examine the spectral variations induced by factors such as illumination, bacteria type, food source and age and type of the agar. To this end, we perform experiments making use of two alternative hyperspectral processing pipelines and compare our classification results to those yielded by color imagery. Our results show that colony counting may be automated through the automatic recovery of the illuminant power spectrum and reflectance. This is consistent with the notion that the recovery of the illuminant should minimize the variations in the spectra due to reflections, shadows and other photometric artifacts. We also illustrate how, with the reflectance at hand, the colonies can be counted making use of classical segmentation and classification algorithms.
Integrated Lithium Niobate Acousto-optic Frequency Shifter (2020)

We demonstrate a 3-GHz acousto-optic frequency shifter on a thin-film lithium niobate platform, featuring over 30 dB carrier suppression. The active frequency shifting loop generates a frequency comb with 200 lines over 5 nm optical bandwidth.
Selective oxidation of glycerol to glyceric acid using a gold catalyst in aqueous sodium hydroxide (2002)

Glycerol is oxidised to glyceric acid with 100% selectivity using either 1% Au/charcoal or 1% Au/graphite catalyst under mild reaction conditions (60 degrees C, 3 h, water as solvent).
Performance Analysis of Sleep Mode Operation for IEEE 802.16m Advanced WMAN (2009)

We mathematically analyze a sleep mode operation proposed by Samsung for IEEE 802.16 m. The sleep mode operation for downlink traffic is modeled as a 2-dimensional Markov chain. We obtain the power consumption of a mobile station. We show that the power consumption of a mobile station decreases as the sleep cycle increases and the analytical results also match with the simulation results very well.
Biomechanical Properties of the Lower Uterine Segment Above and Below the Reflection of the Urinary Bladder Flap (2007)

II.
Calibration of concomitant field offsets using phase contrast MRI for asymmetric gradient coils (2022)

The proposed implementation provides an accurate method for calibrating spatial offsets that can be used for real-time concomitant field compensation of zeroth and first-order terms, substantially reducing artifacts without retrospective correction or sequence specific waveform modifications.
Domain wall trajectory determined by its fractional topological edge defects (2013)

A domain wall (DW) in a ferromagnetic nanowire is composed of elementary topological bulk and edge defects with integer and fractional winding numbers, respectively, whose relative spatial arrangement determines the chirality of the DW. Here we show how we can understand and control the trajectory of DWs in magnetic branched networks, composed of connected nanowires, by considering their fractional elementary topological defects and how they interact with those innate to the network. We first develop a highly reliable mechanism for the injection of a DW of a given chirality into a nanowire and show that its chirality determines which branch the DW follows at a symmetric Y-shaped magnetic junction - the fundamental building block of the network. Using these concepts, we unravel the origin of the one-dimensional nature of magnetization reversal of connected artificial spin ice systems that have been observed in the form of Dirac strings.
Prediction of the Interaction of Coolant Ejection with the Main Stream at the Leading Edge of a Turbine Blade: Attached Grid Application (1994)

The flow field characteristics of film cooled turbine blades are strongly affected by the coolant ejection. In the present paper a qualitative study is performed which indicates that already the flow inside the coolant channel has a significant influence on the main flow field around the airfoil and, therefore, has to be considered in numerical predictions. To account for the flow inside the coolant channel an attached grid application technique is applied which is explained for general purpose. This technique allows the modelling of very complex but structured geometries by attaching grids of different sub-domains. The resulting numerical problem is solved efficiently with standard CFD-methods. A finite volume method is used for solving the time averaged two- or three-dimensional compressible Navier-Stokes equations in non-orthogonal coordinates. For discretization of the convective terms the Monotonized-Linear-Upwind-scheme (MLU) is used. The pressure-velocity coupling is achieved by the SIMPLEC-algorithm for compressible flows. The turbulent nature is taken into account with the standard k-ε-model.
Cost of Care in Open Cystectomy Patients Across Time and Space: Does it matter? (2021)

Significant differences in cost of ORC with ileal conduit exist with respect to patient sex, medical comorbidities, and discharge timing. These differences may relate to greater disease burden in female patients, patient complexity, and variation in postoperative care in academic programs.
Contrast-coding in amblyopia. I. Differences in the neural basis of human amblyopia (1983)

Abstract To shed light on the basis of normal contrast perception in general and its susceptibility during early visual development in particular the contrast-coding deficit of amblyopic eyes was investigated. This was accomplished by using two different but complementary paradigms, one involving equating the contrast sensations between the amblyopic and normal fellow eye and the other involving the assessment of incremental sensitivity at different contrast levels. Since human amblyopia is known to have three different forms, representatives of each were tested. These include strabismics, anisometropes and astigmats. The results of the contrast-matching approach suggest that (i) strabismic and anisometropic (including meridional) amblyopes show important differences in supra-threshold contrast matching (this difference, which occurs across different spatial frequencies, at different luminances and for different field sizes, suggests a different neural basis for the two main forms of human amblyopia); (ii) all forms of amblyopia share one common feature, that of large threshold losses relative to the extent of the suprathreshold anomaly; (iii) the accelerating growth in subjective contrast above the raised threshold shown by the matching procedure is not evident in the assessment of incremental contrast sensitivity. From these results it is argued that, although contrast perception (in the low contrast range) is disturbed in amblyopia, amblyopia cannot be adequately understood in these terms alone. This raises important questions for our understanding of the physiological basis of contrast-coding in normal vision and its perceptual importance.
Enhancement in wafer bow of free-standing GaN substrates due to high-dose hydrogen implantation: implications for GaN layer transfer applications (2007)

Two-inch free-standing GaN wafers were implanted by 100 keV H+2 ions with a dose of 1.3 × 1017 cm−2 at room temperature. The hydrogen implantation induced damage in GaN extends between 230 to 500 nm from the surface as measured by cross-sectional transmission electron microscopy (XTEM). The wafer bow of the free-standing GaN wafers was measured using a Tencor long range profilometer on a scan length of 48 mm before and after the hydrogen implantation. Before implantation the bow of two different free-standing GaN wafers (named A and B) with different thicknesses was 1.5 µm and 6 µm, respectively. Initially, both wafers were concave in shape. After implantation the bow changed to convex with a value of 36 µm for wafer A and a value of 32 µm for wafer B. High dose hydrogen implantation leads to an in-plane compressive stress in the top damaged layer of the GaN, which is responsible for the enhancement of wafer bow and change of bow direction. The high value of bow after implantation hinders the direct wafer bonding of the free-standing GaN wafers to sapphire or any other handle wafers. Tight bonding between hydrogen implanted GaN wafers and the handle wafers is a necessary requirement for the successful layer transfer of thin GaN layers onto other substrates based on wafer bonding and layer splitting (Smart-cut).
PSPN/GFRα4 has a significantly weaker capacity than GDNF/GFRα1 to recruit RET to rafts, but promotes neuronal survival and neurite outgrowth (2004)

Previously, it was shown that the recruitment of RET into lipid rafts by glial cell line-derived neurotrophic factor (GDNF)/GFRalpha1 is crucial for efficient signal transduction. Here, we show that the mouse GFRalpha4 is a functional, N-glycosylated, glycosylphosphatidylinositol (GPI)-anchored protein, which mediates persephin (PSPN)-induced phosphorylation of RET, but has an almost undetectable capacity to recruit RET into the 0.1% Triton X-100 insoluble membrane fraction. In spite of this, PSPN/mGFRalpha4 promotes neurite outgrowth in PC6-3 cells and survival of cerebellar granule neurons. As we show that also human PSPN/GFRalpha4 is unable to recruit RET into lipid rafts, we propose that the mammalian GFRalpha4 in this respect differs from GFRalpha1.
Elimination of Hepatic Rodent Plasmodium Parasites by Amino Acid Supplementation (2020)

<i>Plasmodium</i> parasites, causative agents of malaria, scavenge host nutrients to sustain their intracellular replication. Modulation of the host's nutritional status can potentially help control infection by limiting the parasite's access to nutrients, or by boosting the immune system. Here, we show that dietary supplementation of mice employing a combination of arginine (R) with two additional amino acids, lysine (K) and valine (V), termed RKV, significantly decreases <i>Plasmodium</i> liver infection. RKV supplementation results in the elimination of parasites at a late stage of their development in the liver. Our data employing genetic knockout mouse models and <i>in vivo</i> depletion of specific cell populations suggest that RKV supplementation boosts the host's overall innate immune response, and that parasite elimination is dependent on MyD88 signaling in immune cells. The immunostimulatory effect of RKV supplementation opens a potential role for dietary supplementation as an adjuvant for prophylaxis or immunization strategies against <i>Plasmodium</i> infection.
Omega-3 Fatty Acids for Depression in Multiple Sclerosis: A Randomized Pilot Study (2016)

ClinicalTrials.gov NCT00122954.