gebhart/patrepeval huggingface dataset:
Real-time quantitative analysis of metabolic flux in live cells using a hyperpolarized micromagnetic resonance spectrometer (2017)

Metabolic reprogramming is widely considered a hallmark of cancer, and understanding metabolic dynamics described by the conversion rates or "fluxes" of metabolites can shed light onto biological processes of tumorigenesis and response to therapy. For real-time analysis of metabolic flux in intact cells or organisms, magnetic resonance (MR) spectroscopy and imaging methods have been developed in conjunction with hyperpolarization of nuclear spins. These approaches enable noninvasive monitoring of tumor progression and treatment efficacy and are being tested in multiple clinical trials. However, because of their limited sensitivity, these methods require a larger number of cells, on the order of 10<sup>7</sup>, which is impractical for analyzing scant target cells or mass-limited samples. We present a new technology platform, a hyperpolarized micromagnetic resonance spectrometer (HMRS), that achieves real-time, 10<sup>3</sup>-fold more sensitive metabolic analysis on live cells. This platform enables quantification of the metabolic flux in a wide range of cell types, including leukemia stem cells, without significant changes in viability, which allows downstream molecular analyses in tandem. It also enables rapid assessment of metabolic changes by a given drug, which may direct therapeutic choices in patients. We further advanced this platform for high-throughput analysis of hyperpolarized molecules by integrating a three-dimensionally printed microfluidic system. The HMRS platform holds promise as a sensitive method for studying metabolic dynamics in mass-limited samples, including primary cancer cells, providing novel therapeutic targets and an enhanced understanding of cellular metabolism.
Current status and future prospects for a vaccine against American trypanosomiasis (2005)

The clinically relevant pathognomonic consequences of human infection by Trypanosoma cruzi are dilation and hypertrophy of the left ventricle walls and thinning of the apex. The major complications and debilitating evolutionary outcomes of chronic infection include ventricular fibrillation, thromboembolism and congestive heart failure. American trypanosomiasis (Chagas disease) poses serious public healthcare and budgetary concerns. The currently available drugs, although effective against acute infection, are highly toxic and ineffective in arresting or attenuating clinical disease symptoms in chronic patients. The development of an efficacious prophylactic vaccine faces many challenges, and progress is slow, despite several years of effort. Studies in animal models and human patients have revealed the pathogenic mechanisms during disease progression, pathology of disease and features of protective immunity. Accordingly, several antigens, antigen-delivery vehicles and adjuvants have been tested in animal models, and some efforts have been successful in controlling infection and disease. This review will summarize the accumulated knowledge about the parasite and disease, as well as pathogenesis and protective immunity. The authors will discuss the efforts to date, and the challenges faced in achieving an efficient prophylactic vaccine against human American trypanosomiasis, and present the future perspectives.
Algorithms for automatic placement of labels in drawings and maps (1998)

In this thesis we present a comprehensive study of the label (name) placement problem which has applications in many areas including cartography, geographic information systems, and graph drawing. We prove that the problem of assigning labels to a set of line segments (edges) is NP-Hard. For the first time we present efficient heuristics that solve the problem of assigning labels to a set of line segments. These techniques are more suitable for placing labels to edges of hierarchical drawings of graphs. Experimental results show that the techniques are effective for labeling many different drawing styles. Next, we introduce a unified approach for solving the general labeling problem where a graphical feature can be a node, edge, or area. Our approach does not favor the labeling of one type of graphical feature over another. Furthermore, labels are allowed to have arbitrary size and orientation. Next, we consider the problem of assigning multiple labels to each graphical feature of a drawing. We present a characterization of this problem along with techniques that solve it. Finally, we present techniques that minimally change a graph drawing to open-up space such that each graphical feature has a label assigned to it. We conclude with a discussion on design issues for a label placement software system.
CD4+ T cell clones obtained from <i>Plasmodium falciparum</i> sporozoite-immunized volunteers recognize polymorphic sequences of the circumsporozoite protein. (1993)

CD4+ T cell clones were derived from three volunteers who were protected against malaria after immunization with Plasmodium falciparum sporozoites. T cells specific for an epitope, Pf Th/Tc, contained in amino acids 326 to 345 of the circumsporozoite (CS) protein of P. falciparum (NF54) were derived from all three volunteers. DR1-, -4-, -7-, and -9-restricted T cell clones were found to recognize overlapping, but distinct, epitopes within a 20-mer peptide representing the amino acid 326 to 345 sequence. The Pf Th/Tc epitope contains part of the highly conserved region II as well as part of a polymorphic domain of the P. falciparum CS protein. All of the overlapping epitopes within peptide 326-345 contained at least three amino acids of the amino terminus of the conserved region II, in addition to a variable number of amino acids in the polymorphic region. The DR4-, -7-, and -9-restricted but not the DR1-restricted T cell clones recognized variant peptides representing this polymorphic region of the CS protein of P. falciparum isolates from Africa, Asia, and South America.
[Modernization of ophthalmoscopic techniques]. (1987)

The great principles of ophthalmoscopy have been known for many decades. This paper intends show the new possibilities allowed by modern technology, especially in two fields. First of all, it is possible, even in keeping basic principles, to improve previous machines with, for example, better magnification, new ophthalmoscopic lens, or to create new materials as telescopes for clinical practice or intra-ocular surgery, wide angle or high magnification fundus cameras for posterior pole examination. Secondary, by revolutionary principles, it is possible to introduce laser in the ophthalmoscopic field and to imagine new ophthalmoscopes: SLO i.e. Scanning Laser Ophthalmoscope or SLM i.e. Scanning Laser Microscope, which opens a window on the future.
Effect of Coinfection with GB Virus C on Survival among Patients with HIV Infection (2001)

GBV-C infection is common in people with HIV infection and is associated with significantly improved survival.
Extensions and enhancements for the DANNA neuromorphic architecture (2016)

Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic systems that have been developed for hardware implementation. They feature highly adaptive and programmable structural elements, which model artificial neural networks with spiking behavior. In this paper, we highlight the current hardware implementations of DANNA, including their features and functionalities. We conclude with future directions.
Affordable, ultra-broadband coherent detection of terahertz pulses via CMOS-compatible solid-state devices (2017)

We demonstrate the first fully solid-state technique for the coherent detection of ultra-broadband THz pulses (0.1-10 THz), relying on the electric-field-induced second-harmonic generation attained in integrated CMOS-compatible devices.
Identification and localization of minimal MHC-restricted CD8+ T cell epitopes within the Plasmodium falciparum AMA1 protein (2010)

This study predicted 14 and confirmed nine MHC class I-restricted CD8+ T cell epitopes on AMA1 recognized in the context of seven HLA alleles. These HLA alleles belong to four HLA supertypes that have a phenotypic frequency between 23% - 100% in different human populations.
Time-Resolved Stimulated-Emission Fluorescence Microscope (1996)

Time-resolved stimulated-emission fluorescence microscopy is a novel technique for obtaining super-diffraction limited spatial resolution and sub-nanosecond time resolution using a multi-photon process. This technique is inspired by traditional asynchronous stimulated-emission pump-probe spectroscopy. Fluorescence sample is first excited by a pump laser pulse, tuned to the molecular absorption band of the molecule. Within the chromophore lifetime, a second probe pulse, tuned to the emission band, stimulates fluorescence emission. The spatial resolution enhancement originates from the bilinear dependence of the stimulated emission efficiency on both the pump and probe beam intensities. At the objective focal point, the stimulated emission point spread function is the product of the point spread functions of the pump and probe beams. This situation is mathematically equivalent to both the confocal and the two-photon methods. 3-D depth discrimination and superior spatial resolution is expected.
Shack-Hartmann wavefront sensing using interferometric focusing of light onto guide-stars (2013)

Optical microscopy provides noninvasive imaging of biological tissues at subcellular level. The optical aberrations induced by the inhomogeneous refractive index of biological samples limits the resolution and can decrease the penetration depth. To compensate refractive aberrations, adaptive optics with Shack-Hartmann wavefront sensing has been used in microscopes. Wavefront measurement requires light from a guide-star inside of the sample. The scattering effect limits the intensity of the guide-star, hence reducing the signal to noise ratio of the wavefront measurement. In this paper, we demonstrate the use of interferometric focusing of excitation light onto a guide-star embedded deeply in tissue to increase its fluorescent intensity, thus overcoming the excitation signal loss caused by scattering. With interferometric focusing, we more than doubled the signal to noise ratio of the laser guide-star through scattering tissue as well as potentially extend the imaging depth through using AO microscopy.
A new family of neurotransmitter transporters: the high‐affinity glutamate transporters (1993)

An essential component of the transmission process at glutamatergic synapses is the removal of glutamate from the synaptic cleft. This is achieved by powerful transport systems which have a high affinity for glutamate and exhibit a novel coupling to inorganic ions. Transporters situated on presynaptic termini sequester glutamate directly from the synaptic cleft. In concert, transporters situated on glial cells maintain a low extracellular glutamate concentration, thereby establishing a diffusion gradient favoring movement of glutamate out of the synaptic cleft. Maintenance of a low extracellular glutamate concentration also serves to protect neurons from the excitotoxic action of glutamate. Despite the physiological importance of the glutamate transporters, little information has been available on their molecular structures. This gap, however, has begun to be bridged with the recent cloning of three species of eukaryotic glutamate transporters. The purpose of this review is to summarize the results of these three cloning successes, to compare and contrast the three novel transporters, and to reinterpret, in the light of these recent breakthroughs, information from previous studies.
Direct Measurement of Beam Angle in a High Current Ion Implanter (2006)

We report the first device results from a new method of direct measurement and real‐time control of the average angle of an ion beam in a high current ion implanter. The angle detector consists of an array of high aspect ratio slots that are mounted directly on the same process disk containing the wafers. Beam profiling is achieved by measuring the ion current through the slots versus angle as the disk is rotated perpendicular to the slots. From this profile we determine an angle offset relative to the nominal implant angle. This offset may be a result of beam steering, mechanical positioning uncertainty, or both. The disk is then reoriented if necessary to ensure that the desired beam angle with respect to the wafer is achieved. We implanted the NMOS and PMOS source/drain extension implants for several dozen lots of 90nm and 120nm NMOS and PMOS devices. We showed tightened distributions of both transistor drive currents and asymmetry of drive currents under reverse biasing for 90nm and 120nm devices manufactured on 300mm wafers after the installation of the angle detection hardware. We also observed a tightening of the yield distribution for the 120nm devices.
Overlapped parallel computations of scalar multiplication with resistance against Side Channel Attacks (2008)

This paper presents an efficient scheme for computing elliptic curve scalar multiplication that uses side-channel atomicity to resist against SPA attacks. The inherent parallelism within point operations is exploited to perform parallel computations of atomic blocks within the same point operation. The computations of atomic blocks of subsequent point operations are then overlapped to increase the performance. Randomising the scalar multiplier and the projective coordinates are applied together to immunise the scheme against DPA attacks. The results show that the proposed scheme is highly efficient in comparison with the pipelined scheme of Mishra (2006), which outperformed previous schemes.
Oils from Improved High Stearic Acid Sunflower Seeds (2005)

Seed oils from new recombinant high-stearic sunflower lines (Helianthus annuus L.) have been characterized. These new lines were generated by crossing high stearic acid lines between themselves or by crossing them with standard and high-oleic sunflower lines. Of the novel lines generated, the lines CAS-29 and CAS-30 are on a standard background and contain up to 34.5% of stearic acid. In contrast, CAS-15 and CAS-33 are on a high oleic acid background and contain only 24.9 and 17.4% of stearic acid, respectively. The stearic acid contents of lines CAS-19 and CAS-20 are 10.0 and 21.5%, respectively, and they have only one of the two genes that control the high stearic acid trait. In accordance with their vegetable origin, these lines have a low percentage of stearic acid in the sn-2 position of the TAGs, from 0.6 to 2.1%. The amount of disaturated TAGs increases with the stearic acid content, from 1.8% in the standard line to between 5.1% in CAS-20 and 38.5% in CAS-29. There was also a concomitant reduction in triunsaturated TAGs, which were reduced to levels as low as 8.4% in CAS-29, as opposed to the 67.9% that they constitute in the standard line RHA-274. The asymmetrical distribution of the saturated fatty acids between the sn-1 and sn-3 TAG positions ranges from 0.26 to 0.36, being lower in those lines with higher oleic acid content.
Abstract 18687: PARP9 and PARP14 are Novel Regulators of Macrophage Activation (2014)

Background: Pro-inflammatory “M1” macrophages may promote atherogenesis, while “M2” macrophages may favor an anti-inflammatory milieu. Our global proteomics of M1 and M2 cells identified ADP-ribosylation enzymes PARP9 and PARP14 as novel regulators of macrophage activation. The present study has examined the underlying mechanisms and explored in vivo evidence for their role in vascular disease. Methods and Results: IFN gamma (M1) stimulation induced and IL-4 (M2) decreased PARP9 and PARP14 in mouse and human macrophages. siRNA silencing of PARP14 enhanced expression of M1 genes (e.g. TNFα, iNOS) and activation (phosphorylation) of pro-inflammatory STAT1 while suppressing M2 markers (e.g., Arginase 1) and anti-inflammatory STAT6. Conversely, PARP9 silencing suppressed M1 polarization and STAT1 activation. These results suggest that PARP14 inhibits and PARP9 promotes a pro-inflammatory macrophage phenotype. Co-immunoprecipitation indicated that PARP14 and PARP9 physically interact. ADP-ribosylation assays revealed that PARP9 impairs PARP14-induced ribosylation (Figure A). Targeted proteomics via high-resolution mass spectrometry demonstrated that PARP14 ADP-ribosylates at least two sites in STAT1α, which PARP9 suppressed. Mechanically injured arteries of Parp14-/- mice had accelerated lesion formation and macrophage accumulation. Peritoneal and plaque macrophages of PARP14-/- mice showed increased STAT1 phosphorylation, decreased STAT6 phosphorylation, enhanced M1 gene expression, and reduced M2 responses (Figure B, laser capture microdissection). More macrophages[[Unable to Display Character: &#61472;]]were immunoreactive for PARP9 in human “unstable” plaques than in “stable” plaques (64.6±16.2% vs. 30.8±12.3%, p<0.01, n=5). Conclusions: PARP14 and PARP9 reciprocally regulate the mechanisms of macrophage activation, offering the potential for new therapies for cardiovascular diseases and other conditions, in which macrophage activity impacts outcomes.
Recent developments in superporous hydrogels (2007)

Superporous hydrogels (SPHs) were originally developed as a novel drug delivery system to retain drugs in the gastric medium. These systems should instantly swell in the stomach and maintain their integrity in the harsh stomach environment, while releasing the pharmaceutical active ingredient. For years, the synthetic features and properties of these SPH materials have been modified and improved to meet the requirements for gastric retention applications. Furthermore, an instant swelling hydrogel has also shown potential application for peroral intestinal peptide and protein absorption. This review discusses the formulation, characterization, properties and applications of these polymers.
Evaluation of Biodistribution of Sulforaphane after Administration of Oral Broccoli Sprout Extract in Melanoma Patients with Multiple Atypical Nevi (2018)

Broccoli sprout extract containing sulforaphane (BSE-SFN) has been shown to inhibit ultraviolet radiation-induced damage and tumor progression in skin. This study evaluated the toxicity and potential effects of oral BSE-SFN at three dosages. Seventeen patients who each had at least 2 atypical nevi and a prior history of melanoma were randomly allocated to 50, 100, or 200 μmol oral BSE-SFN daily for 28 days. Atypical nevi were photographed on days 1 and 28, and plasma and nevus samples were taken on days 1, 2, and 28. Endpoints assessed were safety, plasma and skin sulforaphane levels, gross and histologic changes, IHC for phospho-STAT3(Y705), Ki-67, Bcl-2, HMOX1, and TUNEL, plasma cytokine levels, and tissue proteomics. All 17 patients completed 28 days with no dose-limiting toxicities. Plasma sulforaphane levels pooled for days 1, 2, and 28 showed median postadministration increases of 120 ng/mL for 50 μmol, 206 ng/mL for 100 μmol, and 655 ng/mL for 200 μmol. Median skin sulforaphane levels on day 28 were 0.0, 3.1, and 34.1 ng/g for 50, 100, and 200 μmol, respectively. Plasma levels of proinflammatory cytokines decreased from day 1 to 28. The tumor suppressor decorin was increased from day 1 to 28. Oral BSE-SFN is well tolerated at daily doses up to 200 μmol and achieves dose-dependent levels in plasma and skin. A larger efficacy evaluation of 200 μmol daily for longer intervals is now reasonable to better characterize clinical and biological effects of BSE-SFN as chemoprevention for melanoma. <i>Cancer Prev Res; 11(7); 429-38. ©2018 AACR</i>.
Synthesis and Reaction Chemistry of Nanosize Monosodium Titanate (2016)

This paper describes the synthesis and peroxide-modification of nanosize monosodium titanate (nMST), along with an ion-exchange reaction to load the material with Au(III) ions. The synthesis method was derived from a sol-gel process used to produce micron-sized monosodium titanate (MST), with several key modifications, including altering reagent concentrations, omitting a particle seed step, and introducing a non-ionic surfactant to facilitate control of particle formation and growth. The resultant nMST material exhibits spherical-shaped particle morphology with a monodisperse distribution of particle diameters in the range from 100 to 150 nm. The nMST material was found to have a Brunauer-Emmett-Teller (BET) surface area of 285 m2g-1, which is more than an order of magnitude higher than the micron-sized MST. The isoelectric point of the nMST measured 3.34 pH units, which is a pH unit lower than that measured for the micron-size MST. The nMST material was found to serve as an effective ion exchanger under weakly acidic conditions for the preparation of an Au(III)-exchange nanotitanate. In addition, the formation of the corresponding peroxotitanate was demonstrated by reaction of the nMST with hydrogen peroxide.
Background identification based segmentation and multilayer tree representation of document images (2003)

We propose a segmentation algorithm for color document images called background identification based segmentation (BISeg). This algorithm efficiently locates and classifies objects in an image by identifying both the main background (paper background) and local backgrounds. In addition, BISeg generates a tree representation of document images, and the resulting segmentation can be used for many document processing applications including enhancement, rendering, editing and compression.
Resolution and Characterization of 2,2'-Bis(Diphenylphosphino)-1,1'-Bibenzimidazole (BIMIP): The First Chiral Atropisomeric Diphosphine Ligand with Hindered Rotation around a N-N Bond (1999)

2,2'-Bis(diphenylphosphino)-1,1'-bibenzimidazole BIMIP) was resolved in an enantiomerically pure state through a kinetic resolution process effected by complexation of the racemate with half of the stoichiometric amount of a chiral aminopalladium complex. The enantiopure diphosphine was fully characterized by X-ray diffractometric analysis.
Synthetic energy sensor AMPfret deciphers adenylate-dependent AMPK activation mechanism (2019)

AMP-activated protein kinase AMPK senses and regulates cellular energy state. AMPK activation by increasing AMP and ADP concentrations involves a conformational switch within the heterotrimeric complex. This is exploited here for the construction of a synthetic sensor of cellular energetics and allosteric AMPK activation, AMPfret. Based on engineered AMPK fused to fluorescent proteins, the sensor allows direct, real-time readout of the AMPK conformational state by fluorescence resonance energy transfer (FRET). AMPfret faithfully and dynamically reports the binding of AMP and ADP to AMPK γ-CBS sites, competed by Mg<sup>2+</sup>-free ATP. FRET signals correlate with activation of AMPK by allosteric mechanisms and protection from dephosphorylation, attributed here to specific CBS sites, but does not require activation loop phosphorylation. Moreover, AMPfret detects binding of pharmacological compounds to the AMPK α/β-ADaM site enabling activator screening. Cellular assays demonstrate that AMPfret is applicable in vivo for spatiotemporal analysis of energy state and allosteric AMPK activation.
Learning‐Based Animation of Clothing for Virtual Try‐On (2019)

Abstract This paper presents a learning‐based clothing animation method for highly efficient virtual try‐on simulation. Given a garment, we preprocess a rich database of physically‐based dressed character simulations, for multiple body shapes and animations. Then, using this database, we train a learning‐based model of cloth drape and wrinkles, as a function of body shape and dynamics. We propose a model that separates global garment fit, due to body shape, from local garment wrinkles, due to both pose dynamics and body shape. We use a recurrent neural network to regress garment wrinkles, and we achieve highly plausible nonlinear effects, in contrast to the blending artifacts suffered by previous methods. At runtime, dynamic virtual try‐on animations are produced in just a few milliseconds for garments with thousands of triangles. We show qualitative and quantitative analysis of results.