gebhart/patrepeval huggingface dataset:
Dynamic interactions and intracellular fate of label-free, thin graphene oxide sheets within mammalian cells: role of lateral sheet size (2019)

Abstract Graphene oxide (GO) holds great potential for biomedical applications, however fundamental understanding of the way it interacts with biological systems is still lacking even though it is essential for successful clinical translation. In this study, we exploit intrinsic fluorescent properties of thin GO sheets to establish the relationship between lateral dimensions of the material, its cellular uptake mechanisms and intracellular fate over time. Label-free GO with distinct lateral dimensions, small (s-GO) and ultra-small (us-GO) were thoroughly characterised both in water and in biologically relevant cell culture medium. Interactions of the material with a range of non-phagocytic mammalian cell lines (BEAS-2B, NIH/3T3, HaCaT, 293T) were studied using a combination of complementary analytical techniques (confocal microscopy, flow cytometry and TEM). The uptake mechanism was initially interrogated using a range of pharmaceutical inhibitors and validated using polystyrene beads of different diameters (0.1 and 1 μm). Subsequently, RNA-Seq was used to follow the changes in the uptake mechanism used to internalize s-GO flakes over time. Regardless of lateral dimensions, both types of GO were found to interact with the plasma membrane and to be internalized by a panel of cell lines studied. However, s-GO was internalized mainly via macropinocytosis while us-GO was mainly internalized via clathrin- and caveolae-mediated endocytosis. Importantly, we report the shift from macropinocytosis to clathrin-dependent endocytosis in the uptake of s-GO at 24 h, mediated by upregulation of mTORC1/2 pathway. Finally, we show that both s-GO and us-GO terminate in lysosomal compartments for up to 48 h. Our results offer an insight into the mechanism of interaction of GO with non-phagocytic cell lines over time that can be exploited for the design of biomedically-applicable 2D transport systems.
Abstract 15312: Automatic Left Atrial Volume and Sphericity Index Calculation From Cardiac CT Using Computer Graphics Imaging and Deep Learning (2022)

Introduction: Left atrial (LA) volume and sphericity index are important for atrial fibrillation (AF) recurrence prediction after ablation and AF-associated atrial remodeling analysis. However, calculating these indexes from computed tomography (CT) requires manual outlining, which is subjective and difficult to scale. Hypothesis: We hypothesized LA body can be "virtually" dissected from electroanatomic shells using computer graphics imaging (CGI). We further hypothesized that the results of virtual dissection can be used to train a deep learning (DL) model for automatic LA volume and sphericity index calculation. Methods: First, by encoding the anatomic knowledge with geometric modeling, we developed a mathematical method (termed "virtual dissection") based on CGI techniques to isolate the LA body from electroanatomic shells (Fig A). Second, we used virtual dissection to train a DL model to segment CTs in N=20 patient atria (Fig B-C). Finally, we used this pipeline to segment raw CTs in a test cohort of N=100 patients (30.0% women, 66.0±10.3Y; Fig D). Results: In the independent test cohort (N=100), the LA volume and sphericity index were automatically calculated from DL-based segmentation, with the agreement within 4.04 ml (95% CI: -11.48 to 19.55; r=0.98; p &lt; 0.0001; Fig E-F) and 2.75% (95% CI: -5.71 to 11.22; r=0.88; p &lt; 0.0001; Fig G-H), compared to expert annotation. Conclusions: Encoded anatomical knowledge combined with deep learning in small datasets can accurately extract 3D cardiac models from raw CT scans in large populations, yielding automatic calculation of indexes such as volume and sphericity. This computational pipeline may simplify the outcome analysis and prediction using geometric indexes as predictors.
Radiofrequency renal nerve denervation decreases blood pressure, sympathetic activity and renal norepinephrine content in spontaneously hypertensive rats (72.1) (2014)

Radiofrequency renal denervation (RF‐RDN) decreases blood pressure (BP) in patients with drug‐resistant hypertension. This study investigated the effects of RF‐RDN on sympathetic activity and BP (Systolic, SBP; Diastolic, DBP) in SHR. Methods Nineteen‐week old male SHR were instrumented with telemetry probes for chronic measurement of BP and BP variability (BPV). After 1‐week, control BP was measured in rats for 3 days. The next day SHR (n=6/group) were anesthetized and randomly received either bilateral Sham‐RDN or RF‐RDN of the renal arteries (Biosense Webster Stockert 70 generator and RF‐probe). BP was then measured in SHR for 8 weeks. Results Following RF‐RDN, SBP/DBP was significantly decreased the day after (153±8/102±4 mmHg) and throughout the post‐RDN study (4‐week SBP/DBP, 173±7/120±5; 8‐weeks, 171±6/116±4 mmHg) compared to pre‐RDN control levels (SBP/DBP, 187±9/130±5 mmHg). RF‐RDN significantly decreased the low frequency component of BPV in SHR with the peak attenuation observed at 8 weeks (LF/HF 2.2±0.2 vs 0.9±0.2); this correlated with a blunting of the hypotensive response to i.p. chlorisondamine in RF‐RDN rats. Finally, at the end of week 8, kidney norepinephrine (NE) levels in RF‐RDN rats (left, 10±10; right, 0.0±0.0 ng/g kidney) were dramatically decreased compared with levels from sham SHR (left, 130±10; right, 110±10 ng/g kidney). Conclusions These data demonstrate that in hypertensive SHR, bilateral RF‐RDN of the renal arteries decreases BP in part by chronic inhibition of sympathetic neural pathways and a decrease in renal tissue NE levels. Grant Funding Source : Biosense Webster grant IIS‐175 to DRK and FS; NIH NIGMS P20 GM103514 to DK
Inhibition of IL-10 expression by IFN-γ up-regulates transcription of TNF-α in human monocytes (1995)

Stimulation of human monocytes with LPS induces expression of multiple cytokines, including TNF-alpha, IL-1 beta, IL-6, and IL-10, IL-10 expression is delayed relative to that of TNF-alpha, IL-1 beta, and IL-6. Furthermore, IL-10 feedback inhibits expression of TNF-alpha, IL-1 beta, and IL-6, thus providing an efficient autocrine mechanism for controlling proinflammatory cytokine production in monocytes. The Th1-type lymphokine, IFN-gamma, markedly up-regulates TNF-alpha production in monocytes. However, the precise mechanism by which IFN-gamma mediates this effect is unknown. We examined the effects of IFN-gamma on IL-10 expression in LPS-stimulated monocytes, and the relationship between IL-10 and TNF-alpha production in these cells. LPS stimulation induced rapid, ordered expression of multiple cytokines. Steady-state mRNA levels for TNF-alpha increased rapidly, reached maximal levels by 2 to 3 h poststimulation, and then declined sharply. IL-1 beta and IL-6 mRNA levels also increased markedly following stimulation with LPS, but decreased more slowly than did TNF-alpha. Down-regulation of mRNA for TNF-alpha, IL-1 beta, and IL-6 coincided with a delayed and more gradual increase in IL-10 mRNA levels. Furthermore, neutralization of IL-10 with anti-IL-10 Abs prolonged TNF-alpha mRNA expression, and significantly increased net TNF-alpha production. IFN-gamma suppressed expression of IL-10 mRNA and protein in a dose-dependent manner. Moreover, inhibition of IL-10 production correlated with a marked increase in both the magnitude and duration of TNF-alpha expression. Thus, potentiation of TNF-alpha production by IFN-gamma in monocytes is coupled to inhibition of endogenous IL-10 expression.
Low-Temperature Activation of Mg-Doped GaN with Pd Thin Films (2001)

The activation of metalorganic chemical vapor deposition (MOCVD)-grown Mg-doped GaN by N2 annealing with thin Pd films has been investigated. p-type GaN with a hole concentration of 7 × 1016 cm—3 has been obtained at an annealing temperature as low as 200 °C using this technique. Thermal desorption spectroscopy (TDS) measurements have revealed that hydrogen is effectively removed from the Mg-doped GaN layer by the use of the Pd film.
A Serum Protein Classifier Identifying Patients with Advanced Non–Small Cell Lung Cancer Who Derive Clinical Benefit from Treatment with Immune Checkpoint Inhibitors (2020)

This serum-derived protein signature successfully stratified outcomes in cohorts of patients with advanced NSCLC treated with second-line PD-1 CPIs and deserves further prospective study.
#668 Use of low molecular weight heparin (LMWH) for the management of venous thromboembolic disease (VTE) in children undergoing bone marrow transplant (BMT) (1998)

Dix, D.; Marzinotto, V.; Monagle, P.; Freedman, M.; Saunders, E. F.; Doyle, J.; Calderwood, S.; Massicotte, M. P. Author Information
Breathing Signature as Vitality Score Index Created by Exercises of Qigong: Implications of Artificial Intelligence Tools Used in Traditional Chinese Medicine (2019)

Rising concerns about the short- and long-term detrimental consequences of administration of conventional pharmacopeia are fueling the search for alternative, complementary, personalized, and comprehensive approaches to human healthcare. Qigong, a form of Traditional Chinese Medicine, represents a viable alternative approach. Here, we started with the practical, philosophical, and psychological background of Ki (in Japanese) or Qi (in Chinese) and their relationship to Qigong theory and clinical application. Noting the drawbacks of the current state of Qigong clinic, herein we propose that to manage the unique aspects of the Eastern 'non-linearity' and 'holistic' approach, it needs to be integrated with the Western "linearity" "one-direction" approach. This is done through developing the concepts of "Qigong breathing signatures," which can define our life breathing patterns associated with diseases using machine learning technology. We predict that this can be achieved by establishing an artificial intelligence (AI)-Medicine training camp of databases, which will integrate Qigong-like breathing patterns with different pathologies unique to individuals. Such an integrated connection will allow the AI-Medicine algorithm to identify breathing patterns and guide medical intervention. This unique view of potentially connecting Eastern Medicine and Western Technology can further add a novel insight to our current understanding of both Western and Eastern medicine, thereby establishing a vitality score index (VSI) that can predict the outcomes of lifestyle behaviors and medical conditions.
Serotonin inhibits the peptide FMRFamide response through a cyclic AMP-independent pathway in Aplysia (1991)

1. The S-K+ conductance was isolated by voltage-clamping near the resting potential pleural mechanosensory neurons of Aplysia in culture. This background conductance is modulated in opposite directions by two distinct, transmitter-controlled second-messenger cascades: it is enhanced by the peptide FMRFamide through the 12-lipoxygenase pathway of arachidonic acid, and it is decreased by serotonin (5-HT) through adenosine 3',5'-cyclic monophosphate (cAMP)-dependent phosphorylation. 2. The dose-dependent activating effect of FMRFamide (0.01-500 microM) on the S-K+ conductance was measured in the presence and the absence either of 1-100 microM 8-bromo-cAMP (8b-cAMP, a membrane-permeable and hydrolysis-resistant analogue of cAMP), or of 0.01-0.1 microM 5-HT. 3. When 8b-cAMP was applied, it produced a slow inward current response due to closure of the S-K+ conductance. This response was antagonized by FMRFamide in a dose-dependent mode. Application of 100 microM FMRFamide, in the presence of 1-10 microM 8b-cAMP, produced an outward current response larger than the control FMRFa response and equal to the sum of the responses to FMRFamide alone and to 8b-cAMP alone. Similarly, at 500 microM, FMRFamide completely antagonized the closing action of maximal 8b-cAMP levels (100 microM). This observation confirms previous work that indicated that FMRFamide can reopen S-K+ channels closed by FMRFamide. 4. In contrast, in the presence of moderate concentrations of 5-HT (0.01 microM), which produce a slow inward current due to the closing of the S-K+ conductance, FMRFamide elicited a response that only partially antagonized this 5-HT action. Under maximal 5-HT concentrations (0.1 microM), the 5-HT response was not antagonized by any FMRFamide concentration: instead, the FMRFamide response was smaller than the control response without 5-HT. This experiment suggests that 5-HT, with an action independent from cAMP, inhibits the effect of FMRFamide on the S-K+ channel. 5. The dose-dependent inhibitory effect of 5-HT (0.001-10 microM) on the S-K+ conductance was measured in the presence and the absence either of FMRFamide (1-50 microM), which stimulates the release and metabolism of arachidonic acid in Aplysia sensory neurons or of arachidonic acid (25 microM). 6. Under these conditions, supramaximal concentrations of 5-HT could not completely suppress the slow outward current evoked by FMRFamide or by arachidonic acid, indicating that a component of the arachidonic-mediated response to FMRFamide is resistant to actions that maximally increase the S-K+ channel phosphorylation.(ABSTRACT TRUNCATED AT 400 WORDS)
PBR, StAR, AND PKA: PARTNERS IN CHOLESTEROL TRANSPORT IN STEROIDOGENIC CELLS (2002)

Acute stimulation of cholesterol transport into mitochondria involves the cAMP-dependent protein kinase (PKA), peripheral-type benzodiazepine receptor (PBR), and the steroidogenesis acute regulatory (StAR) proteins. We investigated the respective role of these proteins in hormone-induced steroidogenesis. Oligonucleotides antisense, but not sense, to PBR and StAR reduced their respective levels in steroidogenic cells and inhibited hormone-stimulated steroid formation in MA-10 mouse Leydig tumor cells. In search of the proteins regulating PBR we identified a protein, PAP7, which interacts with PBR and the PKA regulatory subunit RIalpha, is present in adrenal and gonadal cells and is found in mitochondria. Overexpression of the full length PAP7 increased the hormone-induced steroid production. However, inhibition of PAP7 expression reduced the gonadotropin-induced steroid formation. In search of a PBR functional antagonist that would facilitate the studies on the biological function of PBR, we screened a phage display library. A 7-mer competitive PBR peptide antagonist was identified, which when transduced into Leydig cells inhibited the benzodiazepine and hormone-stimulated steroid production suggesting that the endogenous PBR agonist/receptor interaction is critical for the hormone-dependent steroidogenesis. These data indicate that hormone-induced cholesterol transport and the subsequent steroid formation is a dynamic multistep process involving protein-protein interactions.
Synthetic A beta prion strains producing distinct amyloid deposits in the brains of transgenic mice (2014)

Author(s): Stoehr, Jan; Condello, Carlo; Watts, Joel C; Bloch, Lillian; Oehler, Abby; Nick, Mimi; Bhate, Manasi; DeArmond, Stephen J; Giles, Kurt; DeGrado, William F; Prusiner, Stanley B
Supplemental Figure 6 from Cytoplasmic Cyclin E Mediates Resistance to Aromatase Inhibitors in Breast Cancer (2023)

&lt;p&gt;Low molecular weight cyclin E (LMW-E) does not affect estrogen receptor gene transcription or aromatase activity.&lt;/p&gt;
Hybrid Belief Pruning with Guarantees for Viewpoint-Dependent Semantic SLAM (2022)

Semantic simultaneous localization and mapping is a subject of increasing interest in robotics and AI that directly influences the autonomous vehicles industry, the army industries, and more. One of the challenges in this field is to obtain object classification jointly with robot trajectory estimation. Considering view-dependent semantic measurements, there is a coupling between different classes, resulting in a combinatorial number of hypotheses. A common solution is to prune hypotheses that have a sufficiently low probability and to retain only a limited number of hypotheses. However, after pruning and renormalization, the updated probability is overconfident with respect to the original probability. This is especially problematic for systems that require high accuracy. If the prior probability of the classes is independent, the original normalization factor can be computed efficiently without pruning hypotheses. To the best of our knowledge, this is the first work to present these results. If the prior probability of the classes is dependent, we propose a lower bound on the normalization factor that ensures cautious results. The bound is calculated incrementally and with similar efficiency as in the independent case. After pruning and updating based on the bound, this belief is shown empirically to be close to the original belief.
Molecular epidemiology of adenoviruses isolated from hospitalized children with severe lower acute respiratory infection in Santiago, Chile (1990)

Genome analysis was performed on 69 adenovirus isolates from pharyngeal secretions of young children hospitalized with severe lower acute respiratory disease in Santiago, Chile, between 1984 and 1986. As expected, most isolated strains belonged to subgenus B (68.1%). Among the isolates of 1984, Ad7c was the dominant genotype (12 out of 23). The majority of isolates of 1986 were of the recently described genomic variant 3f.
New 4-Aminoquinoline Mannich Base Antimalarials. 1. Effect of an Alkyl Substituent in the 5‘-Position of the 4‘-Hydroxyanilino Side Chain (1999)

A new series of 4-aminoquinoline Mannich base derivatives have been synthesized, in which the 3'-diethylamino function of amodiaquine (AQ) is replaced by a 3'-tert-butylamino group and an aliphatic hydrocarbon entity is incorporated into the 5'-position of the 4'-hydroxyanilino side chain. Seven alkyl Mannich base derivatives were screened and found to be active against both chloroquine-sensitive and -resistant strains of Plasmodium falciparum in vitro. The propyl and isopropyl alkyl derivatives were found to be the most active; consequently these derivatives were tested against a nonsensitive strain of Plasmodium berghi in vivo and found to be 3-fold more active than AQ, irrespective of the route of administration (oral or intraperitoneal).
Identification of the epidermal growth factor–TM7 receptor EMR2 and its ligand dermatan sulfate in rheumatoid synovial tissue (2005)

The EGF-TM7 receptors EMR2 and CD97 are abundantly expressed on myeloid cells in ST of RA patients where their cognate ligands dermatan sulfate and CD55 are detected. These results suggest that these interactions may facilitate the retention of activated macrophages in the synovium.
Multi-Channel RF Supervision Module for Thermal Magnetic Resonance Based Cancer Therapy (2021)

Glioblastoma multiforme (GBM) is the most lethal and common brain tumor. Combining hyperthermia with chemotherapy and/or radiotherapy improves the survival of GBM patients. Thermal magnetic resonance (ThermalMR) is a hyperthermia variant that exploits radio frequency (RF)-induced heating to examine the role of temperature in biological systems and disease. The RF signals' power and phase need to be supervised to manage the formation of the energy focal point, accurate thermal dose control, and safety. Patient position during treatment also needs to be monitored to ensure the efficacy of the treatment and avoid damages to healthy tissue. This work reports on a multi-channel RF signal supervision module that is capable of monitoring and regulating RF signals and detecting patient motion. System characterization was performed for a broad range of frequencies. Monte-Carlo simulations were performed to examine the impact of power and phase errors on hyperthermia performance. The supervision module's utility was demonstrated in characterizing RF power amplifiers and being a key part of a feedback control loop regulating RF signals in heating experiments. Electromagnetic field simulations were conducted to calculate the impact of patient displacement during treatment. The supervision module was experimentally tested for detecting patient motion to a submillimeter level. To conclude, this work presents a cost-effective RF supervision module that is a key component for a hyperthermia hardware system and forms a technological basis for future ThermalMR applications.
Composition Control of Barium Strontium Titanate Thin Films Prepared by Chemical Vapor Deposition (1998)

Composition control of barium strontium titanate thin films prepared by chemical vapor deposition using Ba(THD) 2 , Sr(THD) 2 , and Ti(THD) 2 ( i -OC 3 H 7 ) 2 (THD: 2,2,6,6-tetramethyl-3,5-heptanedionate) has been studied by investigating the effects of deposition temperature and the supply rates of metal sources. Although there were complicated correlations among the deposition rates of Ba, Sr, and Ti under kinetically limited conditions, the deposition rate ratio of Ba/Sr was linearly related to the partial pressure ratio of Ba(THD) 2 /Sr(THD) 2 , and the ratio of Ti/(Ba+Sr) spontaneously approaches unity. In order to explain these characteristics, we proposed a model wherein the THD complex of Ba or Sr reacts with the THD complex of Ti and generates a dimer such as (THD) 2 Ba–O–Ti(THD) 2 , and this dimer becomes the dominant precursor for chemical vapor deposition (CVD) under kinetically limited conditions.
Next‐Generation Solid‐State‐Lighting Technology (2010)

Inorganic light‐emitting diodes (LEDs) and organic light‐emitting diodes (OLEDs) have the potential to revolutionize the lighting industry due to high efficiency, long lifetime, and unique form factors that will enable creative lighting designs not possible with conventional light sources. This article will provide an overview of inorganic and organic light‐emitting‐diode technology as it applies to solid‐state lighting, with an emphasis on OLEDs.
Anomalous indirect carrier relaxation in direct band gap atomically thin gallium telluride (2023)

We report ultrafast studies on atomically thin Gallium telluride, a 2D metal monochalcogenide that has appeared to display superior photodetection properties in visible frequencies. Pump photon energy-dependent spectroscopic studies reveal that photoinduced carriers in this direct band-gap material undergo indirect relaxation within $\ensuremath{\sim}30$ ps of photoexcitation, which is at least an order slower than that of most 2D materials. Despite the direct band-gap nature, slow and indirect carrier relaxation places this layered material as a prime candidate in the multitude of atomically thin semiconductor-based photodetectors and highlights the potential for prospective optoelectronic applications.
Format-compliant encryption techniques for high efficiency video coding (2013)

When middlebox devices should be able to adapt an encrypted video stream in the network without having the decryption key, format-compliant partial encryption schemes should be applied. In this paper, we propose such encryption schemes for the recently standardized High Efficiency Video Coding (HEVC) standard. By encrypting specific syntax elements like the sign of the residual information, the sign of the motion vector (MV) difference, the MV prediction index, and the MV reference index, format compliance and the possibility for adaptation are offered. Scrambling performance gradually increases when shifting from encrypting the motion information to encrypting the residual sign and finally to the combination thereof. Applying all these techniques has a negligible impact on the compression efficiency.
Cover Image, Volume 95, Number 6, June 2023 (2023)

Front Cover Caption: The cover image is based on the Research Article Comparative spatial transcriptomic profiling of severe acute respiratory syndrome coronavirus 2 Delta and Omicron variants infections in the lungs of cynomolgus macaques by Taehwan Oh et al., https://doi.org/10.1002/jmv.28847.
Study of Impact of Photonic Switch Speed on Transport Networks (2007)

Impact of photonic switch speed on performance of transport networks is studied with a new variable switch speed test set. The results of the study generate the requirements for new "maintenance friendly" optical networks.