gebhart/patrepeval huggingface dataset:
Gold Nanoparticle Effects in Polymerase Chain Reaction: Favoring of Smaller Products by Polymerase Adsorption (2008)

Gold nanoparticles were recently reported to reduce the formation of nonspecific products in polymerase chain reaction (PCR) at remarkably low temperatures, with hypothesized mechanisms including adsorption of DNA and heat-transfer enhancement. In contrast to these reports, we report that gold nanoparticles do not enhance the specificity of PCR but rather suppress the amplification of longer products while favoring amplification of shorter products, independent of specificity. Gold nanoparticles bearing a self-assembled monolayer of hexadecanethiol did not affect PCR, suggesting that surface interactions play an essential role. This role was further confirmed by experiments in which a similar effect on PCR was observed for the same total surface area of particles over a 100-fold range of per-particle surface area. The effect was seen with Taq and Tfl polymerases but not with Vent polymerase, and the effects of nanoparticles can be reversed by increasing the polymerase concentration or by adding bovine serum albumin (BSA). Transient high-temperature nanoparticle pre-exposure of PCR mix containing polymerase but not template or primers, followed by nanoparticle removal, modified subsequent nanoparticle-free PCR. Interaction between polymerase and gold nanoparticles was confirmed by changes in nanoparticle absorption spectrum and electrophoretic mobility in the presence of polymerase. Taken together, these results suggest that the nanoparticles nonspecifically adsorb polymerase, thus effectively reducing polymerase concentration.
Machine Learning-Based Hyperspectral and RGB Discrimination of Three Polyphagous Fungi Species Grown on Culture Media (2022)

In this study, three fungi species (Botrytis cinerea, Rhizoctonia solani, Sclerotinia sclerotiorum) were discriminated using hyperspectral and red-green-blue (RGB) data and machine learning methods. The fungi were incubated at 25 °C for 10 days on potato dextrose agar in Petri dishes. The Hyperspectral data were acquired using an ASD spectroradiometer, which measures reflectance with 3 and 10 nm bandwidths over the range 350–1000 nm and the range 1000–2500 nm, respectively. The RGB images were collected using a digital Canon 450D camera equipped with the DIGIC 3 processor. The research showed the possibility of distinguishing the analysed fungi species based on hyperspectral curves and RGB images and assessing this differentiation using machine learning statistical methods (extreme boosting machine with bootstrap simulation). The best results in analysed fungi discrimination based on hyperspectral data were achieved using the Principal Component Analysis method, in which the average values of recognition and accuracy for all three species were 0.96 and 0.93, respectively. The wavelengths of the shortwave infrared (SWIR) wavelength region appeared to be the most effective in distinguishing B. cinerea-R. solani and B. cinerea-S. sclerotiorum, while of the visible range (VIS) of electromagnetic spectrum in discrimination of R. solani-S. sclerotiorum. The hyperspectral reflectance data were strongly correlated with the intensity of the pixels in the visible range (R2 = 0.894–0.984). The RGB images proved to be successfully used primarily for the identification of R. solani (recognition = 0.90, accuracy = 0.79) and S. sclerotiorum (recognition = 0.84, accuracy = 0.76). The greatest differences in the intensity of the pixels between B. cinerea and R. solani as well as R. solani and S. sclerotiorum occurred in the blue band and in distinguishing B. cinerea and S. sclerotiorum in the red band.
Abstract 4400: Anti-tumor activity of liposomal docetaxel prodrug MNK-010 on PC3 human prostate xenografts in mice (2015)

Abstract The anti-mitotic taxanes are one of the most important families of anticancer drugs that have broad anti-tumor activity and are widely used for a variety of human cancer types. However, the taxanes are limited by a number of serious pharmacological and toxicological effects, including dose limiting myelosuppression, neurotoxicity and serious hypersensitivity reactions. We are developing a unique delivery system for docetaxel, comprised of a PEGylated liposomal nanoparticle containing a prodrug of docetaxel to improve solubility, tolerability and increase efficacy through improved pharmacokinetics and biodistribution. In this study we evaluated the antitumor activity of MNK-010 on the growth of established human PC3 xenografts in male immunodeficient mice. This study tested the hypothesis that MNK-010 can provide greater efficacy than Taxotere (docetaxel) at equivalent maximum tolerated doses (MTD) in mice implanted with human PC3 tumor cells. Male nude mice bearing PC3 human prostate xenografts were given two or four intravenous (IV) doses of MNK-010, Taxotere or saline. Dosing intervals were twenty-one days for two cycles or every four days for four cycles. The doses of Taxotere and MNK-010 were based on maximum tolerated dose (MTD) or highest dose tested for a given dose interval. Tumor volume was measured twice per week using the Biopticon tumor imaging system and tumor volume data was analyzed to determine tumor growth delay and partial tumor regression. Survival analysis was conducted and median survival time determined. MNK-010 significantly (p &amp;lt;0.05) inhibited PC3 human tumor growth in nude mice at all dose regimens evaluated compared to saline and Taxotere treatment. MNK-010 delayed tumor growth up to 145 days, which was 59 days longer than Taxotere at its MTD. MNK-010 also partially regressed 90% - 100% of tumors in all dose groups. This antitumor activity contributed to achieving median survival of 177 days, which was 150 days longer than saline control and 80 days longer than Taxotere at its MTD. This study demonstrated that Mallinckrodt Pharmaceuticals’ PEGylated liposomal docetaxel prodrug nanoparticle MNK-010 is an active antitumor agent in the PC3 prostate xenograft and possess significantly greater antitumor activity compared to the standard of care Taxotere. Citation Format: Richard M. Fitch, Jolette K. Wojdyla, James A. Blackledge, William D. McGhee. Anti-tumor activity of liposomal docetaxel prodrug MNK-010 on PC3 human prostate xenografts in mice. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4400. doi:10.1158/1538-7445.AM2015-4400
Integrated Stefan–Maxwell, Mean Field, and Single-Event Microkinetic Methodology for Simultaneous Diffusion and Reaction inside Microporous Materials (2014)

The assessment of intrinsic reaction kinetics in the presence of diffusion limitations within a porous material remains one of the key challenges within the field of catalysis. The model-guided design of medium-pore zeolite catalysts which typically give rise to mass transport limitations would offer a feasible alternative to conventional trial-and-error procedures. Intracrystalline diffusion limitations during n-hexane hydroconversion on Pt/H-ZSM5 were assessed using an integrated Stefan–Maxwell, mean field, and Single-Event MicroKinetic (SEMK) methodology. The former theory quantifies multicomponent diffusion through a microporous substituent from pure component properties, while framework parameters inherent to the ZSM5 topology are incorporated via a mean field approximation. The complex chemistry involved in n-hexane hydroconversion was described by an SEMK model which is based upon the reaction family concept. Model regression against experimental data resulted in excellent agreement between the model and experiment. In addition, the estimated values for, among others, the component diffusion coefficients were physically meaningful. A sensitivity analysis of the catalyst descriptors demonstrated that especially the total acid site concentration and the crystallite geometry impact the catalyst activity and product distribution, establishing them as critical catalyst design parameters.
Recognizing interaction between human performers using 'key pose doublet' (2011)

In this paper, we propose a graph theoretic approach for recognizing interactions between two human performers present in a video clip. We watch primarily the human poses of each performer and derive descriptors that capture the motion patterns of the poses. From an initial dictionary of poses (visual words), we extract key poses (or key words) by ranking the poses on the centrality measure of graph connectivity. We argue that the key poses are graph nodes which share a close semantic relationship (in terms of some suitable edge weight function) with all other pose nodes and hence are said to be the central part of the graph. We apply the same centrality measure on all possible combinations of the key poses of the two performers to select the set of 'key pose doublets' that best represent the corresponding action. The results on standard interaction recognition dataset show the robustness of our approach when compared to the present state of the art method.
Premio EITP'98 para las Antenas Fractales (1999)

Peer Reviewed
Accelerated healing of diabetic wounds by NorLeu3-angiotensin (1-7) (2011)

Research to date has shown that NorLeu(3)-A(1-7) is highly effective in the closure of diabetic wounds and is superior to Regranex in animal studies. Further clinical development of this product as a topical agent for the healing of chronic wounds and investigation into the mechanisms by which this product accelerates healing are warranted.
Mechanistic involvement of the calpain‐calpastatin system in Alzheimer neuropathology (2011)

The mechanism by which amyloid-β peptide (Aβ) accumulation causes neurodegeneration in Alzheimer's disease (AD) remains unresolved. Given that Aβ perturbs calcium homeostasis in neurons, we investigated the possible involvement of calpain, a calcium-activated neutral protease. We first demonstrated close postsynaptic association of calpain activation with Aβ plaque formation in brains from both patients with AD and transgenic (Tg) mice overexpressing amyloid precursor protein (APP). Using a viral vector-based tracer, we then showed that axonal termini were dynamically misdirected to calpain activation-positive Aβ plaques. Consistently, cerebrospinal fluid from patients with AD contained a higher level of calpain-cleaved spectrin than that of controls. Genetic deficiency of calpastatin (CS), a calpain-specific inhibitor protein, augmented Aβ amyloidosis, tau phosphorylation, microgliosis, and somatodendritic dystrophy, and increased mortality in APP-Tg mice. In contrast, brain-specific CS overexpression had the opposite effect. These findings implicate that calpain activation plays a pivotal role in the Aβ-triggered pathological cascade, highlighting a target for pharmacological intervention in the treatment of AD.
Uniaxial Tensile Properties of AS4 3D Woven Composites with Four Different Resin Systems: Experimental Results and Analysis-Property Computations (2019)

As a part of the NASA Composite Technology for Exploration project, eight different AS4 3D orthogonal woven composite panels were manufactured and were subjected to mechanical testing including uniaxial tension along the weaves' warp direction. Each set, with four different resin systems (KCR-IR6070, EP2400, RTM6, and RS-50), included weave architectures designed using 12K and 6K AS4 carbon fiber yarns. For the tension testing conducted at Room Temperature Ambient (RTA) conditions, the elastic modulus and strength of these eight panels (as-processed and thermally-cycled) were measured and compared while the potential evolution of micro-cracking before and after thermal cycling were monitored via optical microscopy and X-Ray Computed Tomography. The data set also included test results of the as-processed materials at Elevated Temperature Wet (ETW) conditions. In the second part of this study, efforts were made to compute elastic constants for AS4 6K/RTM6 and AS4 12K/RTM6 materials by implementing a finite element approach and the Multiscale Generalized Method of Cells (MSGMC) technique developed at NASA Glenn Research Center. Digimat-FE was used to model the weave architectures, assign properties, calculate yarn properties, create the finite element mesh, and compute the elastic properties by applying periodic boundary conditions to finite element models of each repeating unit cell. The required input data for MSGMC was generated using Matlab from Digimat exported weave information. Experimental and computational results were compared, and the differences and limitations in correlating to the test data were briefly discussed.
LightGlue: Local Feature Matching at Light Speed (2023)

We introduce LightGlue, a deep neural network that learns to match local features across images. We revisit multiple design decisions of SuperGlue, the state of the art in sparse matching, and derive simple but effective improvements. Cumulatively, they make LightGlue more efficient - in terms of both memory and computation, more accurate, and much easier to train. One key property is that LightGlue is adaptive to the difficulty of the problem: the inference is much faster on image pairs that are intuitively easy to match, for example because of a larger visual overlap or limited appearance change. This opens up exciting prospects for deploying deep matchers in latency-sensitive applications like 3D reconstruction. The code and trained models are publicly available at https://github.com/cvg/LightGlue.
Magnetic resonance elastography in the liver at 3 Tesla using a second harmonic approach (2009)

Magnetic resonance elastography (MRE) using mechanical stimulation has demonstrated diagnostic value and clinical promise in breast, liver, and kidney at 1.5 Tesla (T). However, MRE at 1.5T suffers from long imaging times and would benefit from greater signal-to-noise for more robust postprocessing. We present an MRE sequence modified for liver imaging at 3.0T. To avoid artifacts in the phase images, the sequence maintains a short TE by using a second harmonic approach, including stronger motion encoding gradients, shorter radio frequency pulses and an echo-planar readout. Scan time was decreased by a factor of approximately 2 relative to 1.5T by using an EPI readout and a higher density sampling of the phase waveform was used to calculate shear stiffness and viscosity. Localized (small region of interest) and global (whole-liver region of interest) measurements in normal healthy subjects compared very favorably with previously published results at 1.5T. There was no significant difference between global and localized measures.
Prediction and exposure of delays from a base station perspective in 5G and beyond networks (2022)

The inherent flexibility of 5G networks come with a high degree of configuration and management complexity. This makes the performance outcome for UEs, more than ever, dependent on intricate configurations and interplay between algorithms at various network components. In this paper, we take initial steps towards a performance exposure system at the base station using a data-driven approach for predicting performance violations in terms of RTT, as observed by the UE, in a 5G mmWave network. We present ML models to predict RTT using low-level and high-frequency base station metrics from a 5G mmWave testbed based on commercially available equipment. Predicting UE performance from a base station perspective, and exposing this knowledge, is valuable for applications to proactively address performance violations. We also compare several methods for feature reduction, which have a significant impact on monitoring load. We demonstrate our model's ability to identify RTT violations, paving the way for network providers towards an intelligent performance exposure system.
Caffeic acid phenethyl ester reduces the secretion of vascular endothelial growth factor through the inhibition of the ROS, PI3K and HIF-1α signaling pathways in human retinal pigment epithelial cells under hypoxic conditions (2015)

Choroidal neovascularization (CNV) can lead to progressive and severe visual loss. Vascular endothelial growth factor (VEGF) promotes the development of CNV. Caffeic acid phenethyl ester (CAPE), a biologically active component of the honeybee (Apis mellifera) propolis, has been demonstrated to have several interesting biological regulatory properties. The objective of this study was to determine whether treatment with CAPE results in the inhibition of the production of vascular endothelial growth factor (VEGF) in retinal pigment epithelial cells (RPE cells) under hypoxic conditions and to explore the possible underlying mechanisms. An in vitro experimental model of hypoxia was used to mimic an ischemic microenvironment for the RPE cells. Human RPE cells (ARPE-19) were exposed to hypoxia with or without CAPE pre-treatment. ARPE-19 cells were used to investigate the pathway involved in the regulation of VEGF production under hypoxic conditions, based on western blot analysis, enzyme-linked immunosorbent assay (ELISA) and electrophoretic mobility shift assay (EMSA). The amount of VEGF released from the hypoxia-exposed cells was significantly higher than that of the normoxic controls. Pre-treatment with CAPE suppressed the hypoxia-induced production of VEGF in the ARPE-19 cells, and this effect was inhibited through the attenuation of reactive oxygen species (ROS) production, and the inhibition of phosphoinositide 3-kinase (PI3K)/AKT and hypoxia-inducible factor-1α (HIF-1α) expression. These in vitro findings suggest that CAPE may prove to be a novel anti-angiogenic agent for the treatment of diseases associated with CNV.
Data from Involvement of the TGF-β and β-Catenin Pathways in Pelvic Lymph Node Metastasis in Early-Stage Cervical Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Presence of pelvic lymph node metastases is the main prognostic factor in early-stage cervical cancer patients, primarily treated with surgery. Aim of this study was to identify cellular tumor pathways associated with pelvic lymph node metastasis in early-stage cervical cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Gene expression profiles (Affymetrix U133 plus 2.0) of 20 patients with negative (N&lt;sub&gt;0&lt;/sub&gt;) and 19 with positive lymph nodes (N&lt;sub&gt;+&lt;/sub&gt;), were compared with gene sets that represent all 285 presently available pathway signatures. Validation immunostaining of tumors of 274 consecutive early-stage cervical cancer patients was performed for representatives of the identified pathways.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Analysis of 285 pathways resulted in identification of five pathways (TGF-β, NFAT, ALK, BAD, and PAR1) that were dysregulated in the N&lt;sub&gt;0&lt;/sub&gt;, and two pathways (β-catenin and Glycosphingolipid Biosynthesis Neo Lactoseries) in the N&lt;sub&gt;+&lt;/sub&gt; group. Class comparison analysis revealed that five of 149 genes that were most significantly differentially expressed between N&lt;sub&gt;0&lt;/sub&gt; and N&lt;sub&gt;+&lt;/sub&gt; tumors (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) were involved in β-catenin signaling (TCF4, CTNNAL1, CTNND1/p120, DKK3, and WNT5a). Immunohistochemical validation of two well-known cellular tumor pathways (TGF-β and β-catenin) confirmed that the TGF-β pathway (positivity of Smad4) was related to N&lt;sub&gt;0&lt;/sub&gt; (OR: 0.20, 95% CI: 0.06–0.66) and the β-catenin pathway (p120 positivity) to N&lt;sub&gt;+&lt;/sub&gt; (OR: 1.79, 95%CI: 1.05–3.05).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our study provides new, validated insights in the molecular mechanism of lymph node metastasis in cervical cancer. Pathway analysis of the microarray expression profile suggested that the TGF-β and p120-associated noncanonical β-catenin pathways are important in pelvic lymph node metastasis in early-stage cervical cancer. &lt;i&gt;Clin Cancer Res; 17(6); 1317–30. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Integration of On-Line Protein Digestion, Peptide Separation, and Protein Identification Using Pepsin-Coated Photopolymerized Sol−Gel Columns and Capillary Electrophoresis/Mass Spectrometry (2004)

A miniaturized pepsin reactor was prepared inside a fused-silica capillary (i.d. 75 microm) by coating a pepsin-containing gel on a photopolymerized porous silica monolith. The pepsin-encapsulated film was prepared by a sol-gel method. The sol-gel reaction was optimized so that the sol solution containing pepsin forms a thin film on the photopolymerized sol-gel (PSG) monolith that was initially fabricated at the inlet of the capillary. Pepsin was encapsulated into the gel matrix without losing its activity. The large surface area of the PSG monolith enabled the immobilized pepsin to achieve a high catalytic turnover rate, and the porous nature of the PSG promotes penetration of large molecular proteins into the column. The immobilized pepsin-digested peptides and proteins, and the resulting mixture of peptide fragments, could be directly separated in the portion of the capillary where no PSG monolith exists. The durability and repeatability of the fabricated pepsin-coated column was tested and found to be satisfactory. An acidic solution consisting of 0.5 M formic acid was used as the running buffer, because it suppresses the adsorption of proteins or peptides on the inner surface of the capillary as well as enables direct connection of the output of the capillary electrophoresis column to a mass spectrometer. The on-line digestion of insulin chain beta and lysozyme provides identification of the proteolytic peptides. Recovery was achieved for 100% of the insulin chain beta amino acid sequence and 73% of the lysozyme amino acid sequence.
Treatment-focused Ebola trials, supportive care and future of filovirus care (2017)

During the 2014-2016 Ebolavirus (EBOV) outbreak, several candidate therapeutics were used in EBOV-infected patients in clinical trials and under expanded access for emergency use. This review will focus briefly on medications used during the outbreak. We will discuss current therapeutic candidates and their status and will then turn to a related and essential topic: supportive care and the standard of care for filovirus infected patients. Potential benefits and pitfalls of combination therapies for filoviruses will be discussed. Areas covered: Clinical trials of therapeutics targeting EBOV; clinical usage of therapeutics during recent EBOV outbreak; potential need for combination therapy; role of supportive care in treatment of Ebola virus disease (EVD). Expert commentary: In the absence of another large scale EBOV outbreak, the path to therapeutic product licensure in the United States of America (USA) would need to be via the FDA Animal Rule. However, human data may be needed to supplement animal data. The future of filovirus therapeutics may therefore benefit by establishing the ability to implement clinical trials in an outbreak setting in a timely fashion. Supportive care guidelines for filovirus infection should be defined and established as standard of care for treatment of EVD.
Epithelial endoplasmic reticulum stress orchestrates a protective IgA response (2019)

Immunoglobulin A (IgA) is the major secretory immunoglobulin isotype found at mucosal surfaces, where it regulates microbial commensalism and excludes luminal factors from contacting intestinal epithelial cells (IECs). IgA is induced by both T cell-dependent and -independent (TI) pathways. However, little is known about TI regulation. We report that IEC endoplasmic reticulum (ER) stress induces a polyreactive IgA response, which is protective against enteric inflammation. IEC ER stress causes TI and microbiota-independent expansion and activation of peritoneal B1b cells, which culminates in increased lamina propria and luminal IgA. Increased numbers of IgA-producing plasma cells were observed in healthy humans with defective autophagy, who are known to exhibit IEC ER stress. Upon ER stress, IECs communicate signals to the peritoneum that induce a barrier-protective TI IgA response.