gebhart/patrepeval huggingface dataset:
Hyperpolarized NMR Probes for Biological Assays (2014)

During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized) molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.
Humanization and Expression of IgG and IgM Antibodies in Plants as Potential Diagnostic Reagents for Valley Fever (2022)

Abstract Monoclonal antibodies (mAbs) are important proteins used in many life science applications, from diagnostics to therapeutics. High demand for mAbs for different applications urges the development of rapid and reliable recombinant production platforms. Plants provide a quick and inexpensive system for producing recombinant mAbs. Moreover, when paired with an established platform for mAb discovery, plants can easily be tailored to produce mAbs of different isotypes against the same target. Here, we demonstrate that a hybridoma-generated mouse mAb against chitinase 1 (CTS1), an antigen from Coccidioides spp., can be biologically engineered for use with serologic diagnostic test kits for coccidioidomycosis (Valley Fever) using plant expression. The original mouse IgG was modified and recombinantly produced in plants as IgG and IgM isotypes with human kappa, gamma, and mu constant regions. The two mAb isotypes produced in plants were shown to maintain target antigen recognition to CTS1 using similar reagents as the Food and Drug Administration (FDA)-approved Valley Fever diagnostic kits. As none of the currently approved kits provide antibody dilution controls, humanization of antibodies that bind to CTS1, a major component of the diagnostic antigen preparation, may provide a solution to the lack of consistently reactive antibody controls for Valley Fever diagnosis. Furthermore, our work provides a foundation for reproducible and consistent production of recombinant mAbs engineered to have a specific isotype for use in diagnostic assays.
Voiceless speech recognition using dynamic visual speech features (2006)

This paper describes a voiceless speech recognition technique that utilizes dynamic visual features to represent the facial movements during phonation. The dynamic features extracted from the mouth video are used to classify utterances without using the acoustic data. The audio signals of consonants are more confusing than vowels and the facial movements involved in pronunciation of consonants are more discernible. Thus, this paper focuses on identifying consonants using visual information. This paper adopts a visual speech model that categorizes utterances into sequences of smallest visually distinguishable units known as visemes. The viseme model used is based on the viseme model of Moving Picture Experts Group 4 (MPEG-4) standard. The facial movements are segmented from the video data using motion history images (MHI). MHI is a spatio-temporal template (grayscale image) generated from the video data using accumulative image subtraction technique. The proposed approach combines discrete stationary wavelet transform (SWT) and Zernike moments to extract rotation invariant features from the MHI. A feed forward multilayer perceptron (MLP) neural network is used to classify the features based on the patterns of visible facial movements. The preliminary experimental results indicate that the proposed technique is suitable for recognition of English consonants.
Basic Characteristics of New Developed Higher-Voltage Direct-Current Power-Feeding Prototype System (2010)

High efficiency power feeding systems are effective solutions for reducing the ICT power consumption with reducing power consumption of the ICT equipment and cooling systems. A higher voltage direct current (HVDC) power feeding system prototype was produced. This system is composed of a rectifier equipment, power distribution unit, batteries, and the ICT equipment. The configuration is similar to a -48V DC power supply system. The output of the rectifier equipment is 100kW, and the output voltage is 401.4V. This paper present the configuration of the HVDC power feeding system and discuss its basic characteristics in the prototype system.
Isolated MPTL reconstruction fails to restore lateral patellar stability when compared to MPFL reconstruction (2020)

MPTL-R and both techniques for MPFL-R did not increase patellofemoral contact pressures; however, MPTL-R failed to provide a sufficient restraint against lateral patellar translation lateral translation in 30° of flexion. It, therefore, cannot be recommended as an isolated procedure for the treatment of patellar instability.
Lucerastat, an iminosugar with potential as substrate reduction therapy for glycolipid storage disorders: safety, tolerability, and pharmacokinetics in healthy subjects (2017)

Lucerastat, an inhibitor of glucosylceramide synthase, has the potential to restore the balance between synthesis and degradation of glycosphingolipids in glycolipid storage disorders such as Gaucher disease and Fabry disease. The safety, tolerability, and pharmacokinetics of oral lucerastat were evaluated in two separate randomized, double-blind, placebo-controlled, single- and multiple-ascending dose studies (SAD and MAD, respectively) in healthy male subjects. In the SAD study, 31 subjects received placebo or a single oral dose of 100, 300, 500, or 1000 mg lucerastat. Eight additional subjects received two doses of 1000 mg lucerastat or placebo separated by 12 h. In the MAD study, 37 subjects received placebo or 200, 500, or 1000 mg b.i.d. lucerastat for 7 consecutive days. Six subjects in the 500 mg cohort received lucerastat in both absence and presence of food. In the SAD study, 15 adverse events (AEs) were reported in ten subjects. Eighteen AEs were reported in 15 subjects in the MAD study, in which the 500 mg dose cohort was repeated because of elevated alanine aminotransferase (ALT) values in 4 subjects, not observed in other dose cohorts. No severe or serious AE was observed. No clinically relevant abnormalities regarding vital signs and 12–lead electrocardiograms were observed. Lucerastat Cmax values were comparable between studies, with geometric mean Cmax 10.5 (95% CI: 7.5, 14.7) and 11.1 (95% CI: 8.7, 14.2) μg/mL in the SAD and MAD study, respectively, after 1000 mg lucerastat b.i.d. tmax (0.5 – 4 h) and t1/2 (3.6 – 8.1 h) were also within the same range across dose groups in both studies. Using the Gough power model, dose proportionality was confirmed in the SAD study for Cmax and AUC0–∞, and for AUC0–12 in the MAD study. Fed-to-fasted geometric mean ratio for AUC0–12 was 0.93 (90% CI: 0.80, 1.07) and tmax was the same with or without food, indicating no food effect. Incidence of drug-related AEs did not increase with dose. No serious AEs were reported for any subject. Overall, lucerastat was well tolerated. These results warrant further investigation of substrate reduction therapy with lucerastat in patients with glycolipid storage disorders. SAD study was registered on clinicaltrials.gov under the identifier NCT02944487 on the 24th of October 2016 (retrospectively registered). MAD study was registered on clinicaltrials.gov under the identifier NCT02944474 on the 25th of October 2016 (retrospectively registered). A Study to Assess the Safety and Tolerability of Lucerastat in Subjects With Fabry Disease. Clinicaltrials.gov: NCT02930655 .
<i>In vitro</i> characterization of macrophage interaction with mesenchymal stromal cell‐hyaluronan hydrogel constructs (2013)

Macrophages play a critical role in mediating not only normal tissue healing, but also the host reaction against biomaterial scaffolds. There is increasing interest in regenerative medicine to combine mesenchymal stromal/stem cells (MSCs) with biomaterial scaffolds to modulate inflammatory response while restoring tissue architecture. The objective of the current study was to investigate the interaction between MSCs (derived from bone marrow, adipose or vocal fold tissue) encapsulated in hyaluronan-based hydrogel and differentiating macrophages as measured by extracellular matrix (ECM) gene expression and cytokine, chemokine, and growth factor concentrations. Gene expression was analyzed using real-time polymerase chain reaction from MSCs embedded in Carbylan-GSX after 7 days of coculture with or without CD14+ cells. Protein concentrations were measured using a Bio-plex assay from cell culture supernatants on days 3 and 7 for all conditions. Following 7 days, we identified upregulation of collagen-I, collagen-III, procollagen, and matrix metalloproteinase-9 genes compared to control conditions. We demonstrate increased concentrations of immunoregulatory cytokines [interleukin (IL)-1β, tumor necrosis factor-α, macrophage inflammatory protein-1α, IFN-γ, IL-12, and IL-10] and remodeling growth factors (vascular endothelial growth factor, hepatocyte growth factor) in MSC-3D constructs cocultured with macrophages compared to control conditions, with some temporal variation. Our results indicate an alteration of expression of ECM proteins important to tissue regeneration and cytokines critical to the inflammatory cascade when 3D constructs were cultured with differentiating macrophages.
Enzyme function in organic solvents (1992)

Enzyme catalysis in organic solvents is being increasingly used for a variety of applications. Of special interest are the cases in which the medium is predominantly non-aqueous and contains little water. A display of enzyme activity, even in anhydrous solvents (water less than 0.02% by vol.), perhaps reflects that the minimum necessity for water is for forming bonds with polar amino acids on the enzyme surface. The rigidity of enzyme structure at such low water content results in novel substrate specificities, pH memory and the possibility of techniques such as molecular imprinting. Limited data indicates that, while enhanced thermal stability invariably results, the optimum temperature for catalysis may not change. If true in general, this enhanced thermostability would have extremely limited benefits. Medium engineering and biocatalyst engineering are relevant techniques to improve the efficiency and stability of enzymes in such low water systems. Most promising, as part of the latter, is the technique of protein engineering. Finally, this review provides illustrations of applications of such systems in the diverse areas of organic synthesis, analysis and polymer chemistry.
Figure S1 from Radiotherapy Followed by Aurora Kinase Inhibition Targets Tumor-Propagating Cells in Human Glioblastoma (2023)

&lt;p&gt;Figure S1. A chemical screen of multi-targeted kinase inhibitors identify compounds that induce apoptosis in human glioblastoma cultures.&lt;/p&gt;
Resveratrol impairs the 3D aggregation of MDA-MB-231 through a ceramide-mediated mechanism (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

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Resveratrol, a polyphenol present in grapes and wine, exerts a drastic growth -inhibitory effect on the human breast cancer MDA-MB-231 cell line grown in 2D-culture. We recently described the mechanistic relationship between growth inhibitory/proapoptotic effect of resveratrol and de novo synthesis of ceramide (Scarlatti et al FASEB J, 2003). Here we report that ceramide mediates the growth inhibitory effects of resveratrol in MDA-MB-231 cells grown in three-dimensional (3D) cultures. MDA-MB-231 when grown in 3D-cultures can form multicellular spheroids (MCSs). First we treated fully grown MCSs with resveratrol (32 μ M, 48 hours) and observed an accumulation of ceramide in the MCSs, in concomitance with the disruption of the most external spheroid cell layer(s) and loss of the clonogenic potential. Second, we observed that treatment of MDA-MB-231 cells with 32 μ M resveratrol significantly impaired the formation (number and size) of 3D-MCSs. This effect correlated with a time-dependent accumulation of endogenous ceramide. In addition, cells disaggregated from the few MCSs that were able to form MCSs after resveratrol treatment lost their clonogenic potential. Thus, resveratrol can both reduce full-grown MCSs and prevent the formation of MCSs by triggering ceramide-dependent pathways. These results indicate that resveratrol-ceramide signaling is independent of the culture substrate. Acknowledgements: This work was supported by CISI, Cancer Drug Targeting Work Package; Cofin 2001.
ChemInform Abstract: Sulfur Imidations by Light‐Induced Ruthenium‐Catalyzed Nitrene Transfer Reactions. (2015)

Abstract A wide range of N‐substituted sulfimides and sulfoximines is prepared from dioxazolones.
Semantics for Robotic Mapping, Perception and Interaction: A Survey (2020)

For robots to navigate and interact more richly with the world around them, they will likely require a deeper understanding of the world in which they operate. In robotics and related research fields, the study of understanding is often referred to as semantics, which dictates what does the world ‘mean’ to a robot, and is strongly tied to the question of how to represent that meaning. With humans and robots increasingly operating in the same world, the prospects of human-robot interaction also bring semantics and ontology of natural language into the picture. Driven by need, as well as by enablers like increasing availability of training data and computational resources, semantics is a rapidly growing research area in robotics. The field has received significant attention in the research literature to date, but most reviews and surveys have focused on particular aspects of the topic: the technical research issues regarding its use in specific robotic topics like mapping or segmentation, or its relevance to one particular application domain like autonomous driving. A new treatment is therefore required, and is also timely because so much relevant research has occurred since many of the key surveys were published. This survey provides an overarching snapshot of where semantics in robotics stands today. We establish a taxonomy for semantics research in or relevant to robotics, split into four broad categories of activity in which semantics are extracted, used, or both. Within these broad categories, we survey dozens of major topics including fundamentals from the computer vision field and key robotics research areas utilizing semantics such as mapping, navigation and interaction with the world. The survey also covers key practical considerations, including enablers like increased data availability and improved computational hardware, and major application areas where semantics is or is likely to play a key role. In creating this survey, we hope to provide researchers across academia and industry with a comprehensive reference that helps facilitate future research in this exciting field.
A Shape Grammar to Generate Loggia Rucellai (2013)

This article shows the result of generating a 3d model of Loggia Rucellai in Florence using a shape grammar from Leon Batista AlbertiÂs treatise De Re Aedificatoria and it is a test bed for further generations of buildings using AlbertiÂs rules. It shows the accuracy of such grammar to help tracing the degree of influence of AlbertiÂs treatise in Renaissence Portuguese architecture. Rucellai palace facade ornaments and its interior loggia where used to analyze and compare the Loggia generation accuracy. A Grasshopper script is used for the automation of the rules derivation. An evaluation process is presented and its use aims to better understand the deviations between the treatise and the Loggia grammars.Â Â
PX3-induced migratory insertion reactions of half-sandwich-type carbenerhodium(I) complexes (2001)

The carbenerhodium(I) complexes trans-[RhCl(CPh2)(L)2] (L = PPri3, 1a; SbPri3, 1b) react with PF3 by cleavage of the rhodium–carbene bond to give the corresponding PF3 derivatives trans-[RhCl(PF3)(L)2] 5a,b, in good yield. In contrast, treatment of the half-sandwich-type compound [(η5-C5H5)Rh(CPh2)(PPri3)], 2a, with both PF3 and P(OPh)3 leads to the migratory insertion of the CPh2 unit into one of the cyclopentadienyl C–H bonds to form the ring-substituted products [{η5-C5H4(CHPh2)}Rh(PX3)(PPri3)] (X = F, 6a; OPh, 6b). The molecular structures of 6a and 6b have been determined by X-ray crystallography. The reaction of the stibine complex [(η5-C5H5)Rh(CPh2)(SbPri3)], 2b, with PF3 proceeds by ligand displacement to afford the new carbenerhodium(I) compound [(η5-C5H5)Rh(CPh2)(PF3)], 7. The mechanism of the migratory insertion reaction is discussed.
Slow release glucose in small intestine via dietary approach slows gastric emptying in vivo in a dose response fashion (2011)

Ileal infusion of carbohydrates has been shown to inhibit gastric emptying. However, such effect via dietary delivery of glucose has not been demonstrated. Aim Examine the effect of materials with varying degrees of slow glucose release on gastric emptying and glucose/insulin levels. Methods Alginate-entrapped starch microspheres (M) with different slow digesting rates were fabricated. Sprague Dawley rats were assigned to 5 test groups: 1) blank control (n=7); 2) Polycose (n=5); 3) slow digesting M (n=8); 4) slower digesting M (n=8); and 5) slowest digesting M (n=8). Animals were fasted 24 hr prior to oral gavaging of respective test material. Blood insulin, glucose, and starch content from the segments of the GI tract were measured. Results Glucose response profiles to the 3 slowly digesting microspheres showed an incrementally lower and more sustained glucose release compared with Polycose. Insulin response showed a similar trend. Among the microsphere groups, the amount of starch retained in the stomach increased (P<0.05) between slow and slowest digesting microspheres 2 hr after gavaging, and all microsphere treatments were higher than Polycose that showed no remaining stomach starch. Conclusion Gastric emptying is positively correlated to dietary glucose delivery to the small intestine in a dose response fashion and conceivably could be a practical dietary approach to controlling gastric emptying. Grant Funding Source: USDA
Neuronal avalanches and the cortico-striatal network (2012)

Neuronal avalanches are spontaneous activity cascades observed in superficial cortical layers with statistical properties expected from the network operating near a critical point [1]. In such a network, neuronal activity on one active site triggers, on average, similar activity at other site and therefore the overall activity does not increase or die out over time. Neuronal avalanches have been found in vitro [1] and in vivo [2], and display long-term stability, diversity, and fast propagation of local synchrony. They characterize networks that have a maximum dynamic range [3] and might play a central role in information transmission [1] and storage [4]. Their activity is characterized by brief bursts lasting tens of milliseconds, separated by periods of quiescence lasting several seconds and when observed with multi-electrode arrays, the number of electrodes activated is well described by a power law with exponent close to -1.5 [5].

Here we study neuronal avalanches in an open-loop system of cortex and striatum. The striatum is the main input structure of the basal ganglia and plays an important role in motor and cognitive functions. Understanding how the striatum responds to cortical inputs has crucial importance for clarifying the overall functions of the basal ganglia. The projection neurons of the striatum have a high threshold for activation and receive excitatory input from different regions of the cerebral cortex. Although the striatum contains several distinct cell types, 90-95% are GABAergic medium spiny projection neurons (MSNs). These cells are major targets of cortical inputs, the recurrent connection among them mediate weak feedback inhibition and neighboring MSNs are not likely to share cortical inputs [6]. Fast-spiking interneurons are relatively sparse elements of striatal networks. They project extensively to nearby MSNs and provide strong feedforward inhibition and seem to be critical nodes governing striatal output [7].

Preliminary experiments indicate that activity bursts in the striatum do not follow a power law with characteristic exponent of -1.5. Here we developed an abstract model of the cortico-striatal network that reproduces statistics observed in experimental data. We discuss which kind of connectivity between cortex and striatum, as well as connectivity and strength of inhibition within striatum can lead to results that are in line with experimental data.
&lt;title&gt;Supporting IP multicast integrated services in ATM networks&lt;/title&gt; (1997)

This paper presents an integrated, server-based mechanism for the efficient support of the IP integrated services (IIS) model in ATM networks, namely the multicast integration server (MIS) architecture. Instead of viewing IP-ATM multicast address resolution and QoS support separately, the approach in this paper is to consider such issues in an integrated manner. The multicast integration server is capable of IP multicast to ATM NSAP address resolution using the easy multicast routing through ATM clouds (EARTH) protocol, as well as of QoS management using the resource reservation protocol (RSVP). With the use of EARTH, several ATM point-to-multipoint connections with different QoS parameters can be associated to a single IP multicast address. AN RSVP server within the MIS is used to distribute RSVP messages inside the ATM cloud and to set the corresponding QoS state in the address resolution table of EARTH. In addition, this paper defines a quantized heterogeneity model which supports, together with the MIS, advanced IIS features as QoS heterogeneity and dynamic QoS changes in IP-ATM networks.
Temporal Frame Interpolation With Motion-Divergence-Guided Occlusion Handling (2018)

We present a high-quality temporal frame interpolation (TFI) method that employs piecewise-smooth motion and handles disoccluded regions using the observation that motion discontinuities travel with the foreground object. We derive a “motion discontinuity” likelihood map from the divergence of a motion field between the input frames. Motion which is modeled at the reference frame is mapped to the target frame using a cellular-affine mapping strategy - a process during which regions of disocclusion are readily observed. This information is then used to guide the occlusion-aware, bidirectional FI process. Furthermore, we propose two computationally inexpensive texture optimizations that selectively improve the quality of the interpolated frames in regions around moving objects. The scheme produces very high-quality interpolated frames and outperforms current high-quality state-of-the-art TFI schemes by 2-2.5 dB; the method works with a very low-complexity motion estimation scheme and runs orders of magnitudes faster than its competitors.