gebhart/patrepeval huggingface dataset:
Optofluidic time-stretch quantitative phase microscopy for high-throughput label-free single-cell analysis (Conference Presentation) (2017)

The ability to sift through a large heterogeneous population of cells is of paramount importance in a diverse range of biomedical and green applications. Furthermore, the capability of identifying various features of cells in a label-free manner is useful for high-throughput screening. Here we present optofluidic time-stretch quantitative phase microscopy for high-throughput label-free single-cell screening. This method is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch microscope for high-speed imaging with a spatial resolution of ~800 nm at a frame rate of ~10 million frames per second, and a digital image processor for image-based characterization, classification, and statistical analysis of biological cells such as blood cells and microalgae. It provides both the opacity (amplitude) and thickness (phase) content of every cell at a high throughput of ~10,000 cells per second. This method is expected to be effective for a diverse range of applications such as cancer detection and biofuel production.
Retention behavior of resorcinarene‐based cavitands on C8 and C18 stationary phases (2015)

The understanding of the retention behavior of large molecules is an area of interest in liquid chromatography. Resorcinarene-based cavitands are cavity-shaped cyclic oligomers that can create host-guest interactions. We have investigated the chromatographic behavior of two types of cyclic tetramers as analytes in high-performance liquid chromatography. The experiments were performed at four different temperatures (15, 25, 35, 45°C) on two types of reversed stationary phases (C8 and C18 ) from two different manufacturers. We have found a huge difference between the retention of resorcinarenes and cavitands. In some cases, the retention factor of cavitands was even a hundred times larger than the retention factor of resorcinarenes. The retention of methylated derivates was two to four times larger compared to that of demethylated compounds on every column. The opposite retention behavior of the resorcinarenes and cavitands on the two types of stationary phases showed well the difference of the selectivity of the XTerra and BDS Hypersil columns. The retention mechanism was studied by the thermodynamic parameters calculated from the van't Hoff equation.
Surveillance System with Object-Aware Video Transcoder (2005)

This paper presents an object-aware video surveillance system that is not only smart and friendly for users, but allows for transmission of the scene over limited bandwidth networks. The proposed system stores high-quality video data and associated object metadata, which includes ROI (region-of-interest) information. To satisfy bandwidth constraints and display important parts of the images fast and precisely, the stored images are efficiently transcoded in the compressed-domain based on the ROI information. At the receiver, effective display methods such as a mosaic style allow for an intuitive understanding of the important objects in the scene, as well as their movement over time
Indole-2-carboxamide-based MmpL3 Inhibitors Show Exceptional Antitubercular Activity in an Animal Model of Tuberculosis Infection (2016)

Our team had previously identified certain indolecarboxamides that represented a new chemical scaffold that showed promising anti-TB activity at both an in vitro and in vivo level. Based on mutational analysis using bacteria found resistant to one of these indolecarboxamides, we identified the trehalose monomycolate transporter MmpL3 as the likely target of these compounds. In the present work, we now further elaborate on the SAR of these compounds, which has led in turn to the identification of a new analog, 4,6-difluoro-N-((1R,2R,3R,5S)-2,6,6-trimethylbicyclo[3.1.1]heptan-3-yl)-1H-indole-2-carboxamide (26), that shows excellent activity against drug-sensitive (MIC = 0.012 μM; SI ≥ 16000), multidrug-resistant (MDR), and extensively drug-resistant (XDR) Mycobacterium tuberculosis strains, has superior ADMET properties, and shows excellent activity in the TB aerosol lung infection model. Compound 26 is also shown to work in synergy with rifampin. Because of these properties, we believe that indolecarboxamide 26 is a possible candidate for advancement to human clinical trials.
Virtual framework for testing the reliability of system software on embedded systems (2007)

System software development and testing on embedded systems can be quite difficult and time consuming. In this paper, we propose a cost effective method, namely virtual testing framework that can be used easily to test the reliability of system software. The framework consists of three layers; virtual platform layer, system software layer, and test environment layer. The virtual platform layer emulates a variety of embedded hardware on which any system software can be run and is used to verify its capability in handling faults injected by the test environment layer. We use the framework to verify the reliability of the file system and FTL (flash translation layer) by injecting faults that may be found in Flash memory. We discuss experimental results that we gained using this framework to gather post-fault behavior of the system software of interest.
Clarification and extension of the optical reciprocity theorem (2009)

Clarifications on the optical reciprocity theorem are provided by explicitly proving the equivalence between the Lorentz lemma and the symmetry of the Green dyadic for the electromagnetic wave equation. This is achieved by explicitly including the surface term in the former so that different boundary conditions can be considered as required in the formulation of the latter. In addition, we shall also extend the theorem to include anisotropic magnetic materials with a nonlocal response, leading to a result which will be useful for the study of materials possessing such properties such as certain types of metamaterials.
A Simple and Effective Method for the Thionation of Amides to Thioamides Using Al2O3-Supported P4S10 (2005)

A simple and effective method for the thionation of amides to thioamides using Al2O3-supported P4S10 was developed and applied to a series of amides including some heterocyclic examples. The reaction was best performed in anhydrous dioxane at reflux temperature. Yields ranging from 62 - 93% are comparable to, or superior to those obtained with Lawessons reagent. The method uses inexpensive reagents and has the advantage that reagent-derived byproducts may be removed by a simple hydrolytic workup rather than by chromatography, as required for Lawessons reagent. Keywords: thioamide, thionation, heterocycles, lawessons reagent, supported reagents
In vitro effects of interferon-alpha subtypes on the Th1/Th2 balance in the peripheral blood mononuclear cells from patients with hepatitis C virus infection (2004)

Enhanced T helper 1 (Th1)-type immunity was observed in patients with hepatitis C virus (HCV) infection during investigations on the efficiency of interferon (IFN) therapy. The mechanism for the shift to Th1-type immunity is, however, obscure in HCV infection. In this study, we examined the in vitro effect of IFN-α subtypes (IFN-α1, -α2, -α5, -α8 and -α10) on the Th1/Th2 balance in the peripheral blood mononuclear cells (PBMC) obtained from healthy control volunteers and HCV-infected patients. A two-day incubation without IFN stimulation did raise the Th1-type cell percentage but not the Th2-type cell percentage in the PBMC of the control group. The Th1-type cell percentage and Th1/Th2 ratio were significantly larger in the PBMC of patients when compared to controls both before and after treatment with the IFNs. IFN-α5 treatment induced an increase of the Th2-type cell percentage in both control and patient PBMC but did not show any significant changes in the Th1/Th2 ratio. Furthermore, IFN-α8 treatment slightly promoted an increase in the Th1/Th2 ratio only in patient PBMC. Statistical analysis revealed that effects of the IFN-α subtypes on the Th1/Th2 balance differed between two patient groups with severe liver damage (alanine aminotransferase; ALT: ≥ 80 IU/ml) and mild liver damage (ALT: 〈 80 IU/ml). IFN-α5 treatment lowered the Th1/Th2 ratio in patients with mild liver damage, whereas IFN- α 8 treatment raised the Th1/Th2 ratio in patients with severe liver damage without IFN-α5-induced decrease in the ratio. These findings imply that HCV infection and its disease status modify the effects of IFN-α subtypes on Th1 and Th2 immune balance in patients. Our findings should help to elucidate the mechanisms underlying IFN therapy for HCV infection.
Bolus arrival time and its effect on tissue characterization with dynamic contrast-enhanced magnetic resonance imaging (2016)

Matching the bolus arrival time (BAT) of the arterial input function (AIF) and tissue residue function (TRF) is necessary for accurate pharmacokinetic (PK) modeling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). We investigated the sensitivity of volume transfer constant ([Formula: see text]) and extravascular extracellular volume fraction ([Formula: see text]) to BAT and compared the results of four automatic BAT measurement methods in characterization of prostate and breast cancers. Variation in delay between AIF and TRF resulted in a monotonous change trend of [Formula: see text] and [Formula: see text] values. The results of automatic BAT estimators for clinical data were all comparable except for one BAT estimation method. Our results indicate that inaccuracies in BAT measurement can lead to variability among DCE-MRI PK model parameters, diminish the quality of model fit, and produce fewer valid voxels in a region of interest. Although the selection of the BAT method did not affect the direction of change in the treatment assessment cohort, we suggest that BAT measurement methods must be used consistently in the course of longitudinal studies to control measurement variability.
Illuminating trap density trends in amorphous oxide semiconductors with ultrabroadband photoconduction (2023)

Under varying growth and device processing conditions, ultrabroadband photoconduction (UBPC) reveals strongly evolving trends in the defect density of states (DoS) for amorphous oxide semiconductor thin-film transistors (TFTs). Spanning the wide bandgap of amorphous InGaZnO$_x$ (a-IGZO), UBPC identifies seven oxygen-deep donor vacancy peaks that are independently confirmed by energetically matching to photoluminescence emission peaks. The sub-gap DoS from 15 different types of a-IGZO TFTs all yield similar DoS, except only back-channel etch TFTs can have a deep acceptor peak seen at 2.2 eV below the conduction band mobility edge. This deep acceptor is likely a zinc vacancy, evidenced by trap density which becomes 5-6x larger when TFT wet-etch methods are employed. Certain DoS peaks are strongly enhanced for TFTs with active channel processing damage caused by plasma exposure. While Ar implantation and He plasma processing damage are similar, Ar plasma yields more disorder showing a 2x larger valence-band Urbach energy and two orders of magnitude increase in the deep oxygen vacancy trap density. Changing the growth conditions of a-IGZO also impacts the DoS, with zinc-rich TFTs showing much poorer electrical performance compared to 1:1:1 molar ratio a-IGZO TFTs owing to the former having a ~10xlarger oxygen vacancy trap density. Finally, hydrogen is found to behave as a donor in amorphous indium tin gallium zinc oxide TFTs.
253GB recorded in two-photon 3D disk (2007)

253GB have been recorded in one of our two-photon 3-d disks. Experiments indicate a roadmap of full disk recordings from 0.5 to 1TB utilizing our very stable and efficient materials and new high-performance objective lens.
5-Aminolevulinic acid bypasses mitochondrial complex I deficiency and corrects physiological dysfunctions in Drosophila (2023)

Complex I (CI) deficiency in mitochondrial oxidative phosphorylation (OXPHOS) is the most common cause of mitochondrial diseases, and limited evidence-based treatment options exist. Although CI provides the most electrons to OXPHOS, complex II (CII) is another entry point of electrons. Enhancement of this pathway may compensate for a loss of CI; however, the effects of boosting CII activity on CI deficiency are unclear at the animal level. 5-Aminolevulinic acid (5-ALA) is a crucial precursor of heme, which is essential for CII, complex III, complex IV (CIV) and cytochrome c activities. Here, we show that feeding a combination of 5-ALA hydrochloride and sodium ferrous citrate (5-ALA-HCl + SFC) increases ATP production and suppresses defective phenotypes in Drosophila with CI deficiency. Knockdown of sicily, a Drosophila homolog of the critical CI assembly protein NDUFAF6, caused CI deficiency, accumulation of lactate and pyruvate and detrimental phenotypes such as abnormal neuromuscular junction development, locomotor dysfunctions and premature death. 5-ALA-HCl + SFC feeding increased ATP levels without recovery of CI activity. The activities of CII and CIV were upregulated, and accumulation of lactate and pyruvate was suppressed. 5-ALA-HCl + SFC feeding improved neuromuscular junction development and locomotor functions in sicily-knockdown flies. These results suggest that 5-ALA-HCl + SFC shifts metabolic programs to cope with CI deficiency. Bullet outline 5-Aminolevulinic acid (5-ALA-HCl + SFC) increases ATP production in flies with complex I deficiency.5-ALA-HCl + SFC increases the activities of complexes II and IV.5-ALA-HCl + SFC corrects metabolic abnormalities and suppresses the detrimental phenotypes caused by complex I deficiency.
A Novel High‐Pressure Tin Oxynitride Sn2N2O (2019)

We report the first oxynitride of tin, Sn<sub>2</sub> N<sub>2</sub> O (SNO), exhibiting a Rh<sub>2</sub> S<sub>3</sub> -type crystal structure with space group Pbcn. All Sn atoms are in six-fold coordination, in contrast to Si in silicon oxynitride (Si<sub>2</sub> N<sub>2</sub> O) and Ge in the isostructural germanium oxynitride (Ge<sub>2</sub> N<sub>2</sub> O), which appear in four-fold coordination. SNO was synthesized at 20 GPa and 1200-1500 °C in a large volume press. The recovered samples were characterized by synchrotron powder X-ray diffraction and single-crystal electron diffraction in the TEM using the automated diffraction tomography (ADT) technique. The isothermal bulk modulus was determined as B<sub>o</sub> =193(5) GPa by using in-situ synchrotron X-ray diffraction in a diamond anvil cell. The structure model is supported by DFT calculations. The enthalpy of formation, the bulk modulus, and the band structure have been calculated.
Sensitive Detection of Norovirus Using Phage Nanoparticle Reporters in Lateral-Flow Assay (2015)

Noroviruses are recognized worldwide as the principal cause of acute, non-bacterial gastroenteritis, resulting in 19-21 million cases of disease every year in the United States. Noroviruses have a very low infectious dose, a short incubation period, high resistance to traditional disinfection techniques and multiple modes of transmission, making early, point-of-care detection essential for controlling the spread of the disease. The traditional diagnostic tools, electron microscopy, RT-PCR and ELISA require sophisticated and expensive instrumentation, and are considered too laborious and slow to be useful during severe outbreaks. In this paper we describe the development of a new, rapid and sensitive lateral-flow assay using labeled phage particles for the detection of the prototypical norovirus GI.1 (Norwalk), with a limit of detection of 107 virus-like particles per mL, one hundred-fold lower than a conventional gold nanoparticle lateral-flow assay using the same antibody pair.
Model-Based Optimization: Accurate and Consistent Site Modeling (1996)

Keywords: Snakes ; Active Contours Reference CVLAB-CONF-1996-001 Record created on 2006-02-03, modified on 2017-05-12
The Newtonian gravitational constant on the feasibility of an oceanic measurement (1988)

The Newtonian gravitational constant G is a fundamental parameter of physics relating the gravitational force to the product of body masses by an inverse square of the separation. G has been measured with an accuracy of about 7 parts in 10 5 in individual laboratory experiments [e.g., Luther and Towler , 1982], but the consistency of all modern laboratory measurements is only about 7 parts in 10 4 (Figure 1), making it one of the most poorly determined physical constants of nature [cf. Cohen and Taylor , 1986; Gillies , 1987]. For the past century, virtually all experiments to measure G have been conducted on a scale (i.e., separation between test masses) of 50 cm or less, using a modification of the Cavendish balance. In recent years there has been increasing interest in determinations of G over larger scales than can be achieved in the laboratory. Some theoretical attempts to combine gravity with the other forces of nature predict the existence of a fifth force in addition to the classical gravitational, electromagnetic, weak, and strong forces. The fifth force would produce departures from Newtonian or inverse square law gravity at mass separations of tens of meters to tens of kilometers. Geophysical experiments are uniquely suited to measure the gravitational constant at these scales, and in this paper we outline the advantages of conducting such an experiment in the ocean.
Determination of Ruthenium Tetroxide (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of Ruthenium TetroxideC. J. Anderson, Richard. Del Grosso, and M. H. OrtnerCite this: Anal. Chem. 1961, 33, 4, 646–647Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://pubs.acs.org/doi/10.1021/ac60172a052https://doi.org/10.1021/ac60172a052research-articleACS PublicationsRequest reuse permissionsArticle Views66Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Molecular and Biological Characterization of Human Monoclonal Antibodies Binding to the Spike and Nucleocapsid Proteins of Severe Acute Respiratory Syndrome Coronavirus (2005)

Human monoclonal antibodies (MAbs) were selected from semisynthetic antibody phage display libraries by using whole irradiated severe acute respiratory syndrome (SARS) coronavirus (CoV) virions as target. We identified eight human MAbs binding to virus and infected cells, six of which could be mapped to two SARS-CoV structural proteins: the nucleocapsid (N) and spike (S) proteins. Two MAbs reacted with N protein. One of the N protein MAbs recognized a linear epitope conserved between all published human and animal SARS-CoV isolates, and the other bound to a nonlinear N epitope. These two N MAbs did not compete for binding to SARS-CoV. Four MAbs reacted with the S glycoprotein, and three of these MAbs neutralized SARS-CoV in vitro. All three neutralizing anti-S MAbs bound a recombinant S1 fragment comprising residues 318 to 510, a region previously identified as the SARS-CoV S receptor binding domain; the nonneutralizing MAb did not. Two strongly neutralizing anti-S1 MAbs blocked the binding of a recombinant S fragment (residues 1 to 565) to SARS-CoV-susceptible Vero cells completely, whereas a poorly neutralizing S1 MAb blocked binding only partially. The MAb ability to block S1-receptor binding and the level of neutralization of the two strongly neutralizing S1 MAbs correlated with the binding affinity to the S1 domain. Finally, epitope mapping, using recombinant S fragments (residues 318 to 510) containing naturally occurring mutations, revealed the importance of residue N479 for the binding of the most potent neutralizing MAb, CR3014. The complete set of SARS-CoV MAbs described here may be useful for diagnosis, chemoprophylaxis, and therapy of SARS-CoV infection and disease.
Sol–gel transition behavior of biodegradable three‐arm and four‐arm star‐shaped PLGA–PEG block copolymer aqueous solution (2005)

Abstract Two types of temperature‐sensitive biodegradable three‐arm and four‐arm star‐shaped poly( DL ‐lactic acid‐ co ‐glycolic acid‐ b ‐ethylene glycol) (3‐arm and 4‐arm PLGA–PEG) were successfully synthesized via the coupling reaction of 3‐arm and 4‐arm PLGA and α‐monocarboxyl‐ω‐monomethoxypoly(ethylene glycol) (CMPEG). In dilute aqueous solutions, star PLGA–PEGs showed the temperature‐ and concentration‐dependent formation and aggregation of micelles over specific concentration and specific temperature. With increasing the molecular weight and the relative hydrophobicity of hydrophobic PLGA block, critical micelle temperature (CMT) decreased. Aqueous solution of 4‐arm PLGA–PEG started to form micelles at lower temperature and showed sharper temperature‐dependent growth in micelle size. These results are due to the enhanced hydrophobicity of PLGA block. On the other hand, at high concentration, two types of 3‐arm and 4‐arm PLGA–PEG showed sol–gel–sol transition behavior as the temperature was increased. The 3‐arm and 4‐arm PLGA–PEG showed sol–gel transition at higher polymer concentrations (above 24 wt %) than the PEG–PLGA–PEG triblock copolymer. As the molecular weight and the relative hydrophobicity of PLGA block increased, the critical gel concentration (CGC) decreased. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 888–899, 2006
THE STRESS RESPONSE OF CRITICAL ILLNESS (1999)

The integrated stress response to tissue trauma is crucial for the maintenance of homeostasis. An exaggerated or prolonged response may be detrimental in compromised patients. Knowledge of the involved afferent pathways will suggest therapeutic interventions that may modulate the intensity of the stress response. Described are these concepts as they relate to perioperative medicine.
Effects of the intestinal microbiota on prostate cancer treatment by androgen deprivation therapy (2022)

Prostate cancer (PC) can be kept in check by androgen deprivation therapy (ADT, usually with the androgen synthesis inhibitor abiraterone acetate or the androgen receptor antagonist such as enzalutamide) until the tumor evolves to castration-resistant prostate cancer (CRPC). The transition of hormone-sensitive PC (HSPC) to CPRC has been explained by cancer cell-intrinsic resistance mechanisms. Recent data indicate that this transition is also marked by cancer cell-extrinsic mechanisms such as the failure of ADT-induced PC immunosurveillance, which depends on the presence of immunostimulatory bacteria in the gut. Moreover, intestinal bacteria that degrade drugs used for ADT, as well as bacteria that produce androgens, can interfere with the efficacy of ADT. Thus, specific bacteria in the gut serve as a source of testosterone, which accelerates prostate cancer progression, and men with CRPC exhibit an increased abundance of such bacteria with androgenic functions. In conclusion, the response of PC to ADT is profoundly influenced by the composition of the microbiota with its immunostimulatory, immunosuppressive and directly ADT-subversive elements.