gebhart/patrepeval huggingface dataset:
Multiomics to investigate the mechanisms contributing to repression of PTPRC and SOCS2 in pediatric T-ALL: focus on miR-363-3p and promoter methylation (2022)

T-cell acute lymphoblastic leukemia (T-ALL) is a heterogeneous and aggressive malignancy arising from T cell precursors. MiRNAs are implicated in negative regulation of gene expression and when aberrantly expressed contribute to various cancer types, including T-ALL. Previously we demonstrated the oncogenic potential of miR-363-3p overexpression in a subgroup of T-ALL patients. Here, using combined proteomic and transcriptomic approaches, we show that miR-363-3p enhances cell growth of T-ALL <em>in vitro</em> via inhibition of <em>PTPRC </em>and <em>SOCS2</em>, which are implicated in repression of the JAK-STAT pathway. We propose that overexpression of miR-363-3p is a novel mechanism potentially contributing to overactivation of JAK-STAT pathway. Additionally, by combining the transcriptomic and methylation data of T-ALL patients, we show that promoter methylation may also contribute to downregulation of <em>SOCS2</em> expression and thus potentially to JAK-STAT activation. In conclusion, we highlight aberrant miRNA expression and aberrant promoter methylation as mechanisms, alternative to mutations of JAK-STAT related genes, which might lead to the upregulation of JAK-dependent signaling in T-ALL.
Table S1 from Targeting Adenosine with Adenosine Deaminase 2 to Inhibit Growth of Solid Tumors (2023)

&lt;p&gt;Supplementary Table S1&lt;/p&gt;
Empirical Bayes based relative impulse response estimation (2018)

Relative impulse responses (ReIRs) have several applications in speech enhancement, noise suppression and source localization for multi-channel speech processing in reverberant environments. Estimating the ReIRs can be reduced to a system identification problem. A system identification method using an empirical Bayes framework is proposed and its application for spatial source subtraction in audio signal processing is evaluated. The proposed estimator allows for incorporating prior structure information of the system into the estimation procedure, leading to an improved performance especially in the presence of noise. The estimator utilizes the sparse Bayesian learning algorithm with appropriate priors to characterize both the early reflections and reverberant tails. The mean squared error of the proposed estimator is studied and an extensive experimental study with real-world recordings is conducted to show the efficacy of the proposed approach over other competing approaches.
The Role of Periadventitial Fat in Atherosclerosis (2007)

Abstract Context.—It has become increasingly evident that adipose tissue is a multifunctional organ that produces and secretes multiple paracrine and endocrine factors. Research into obesity, insulin resistance, and diabetes has identified a proinflammatory state associated with obesity. Substantial differences between subcutaneous and omental fat have been noted, including the fact that omental fat produces relatively more inflammatory cytokines. Periadventitial fat, as a specific adipose tissue subset, has been overlooked in the field of atherosclerosis despite its potential diagnostic and therapeutic implications. Objective.—To review (1) evidence for the role of adventitial and periadventitial fat in vessel remodeling after injury, (2) the relationship between adventitial inflammation and atherosclerosis, (3) the association between periadventitial fat and plaque inflammation, and (4) the diagnostic and therapeutic implications of these roles and relationships for the progression of atherosclerosis. Data Sources.—We present new data showing greater uptake of iron, administered in the form of superparamagnetic iron oxide, in the periadventitial fat of atherosclerotic mice than in control mice. In addition, macrophage density in the periadventitial fat of lipid-rich plaques is increased compared with fibrocalcific plaques. Conclusions.—There is a striking paucity of data on the relationship between the periadventitial fat of coronary arteries and atherosclerosis. Greater insight into this relationship might be instrumental in making strides into the pathophysiology, diagnosis, and treatment of coronary artery disease.
Calculation of the Vibronic Intensities in the Emission Spectra of Manganese(V) in Oxide Lattices (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalculation of the Vibronic Intensities in the Emission Spectra of Manganese(V) in Oxide LatticesDavid Wexler and Jeffrey I. ZinkCite this: Inorg. Chem. 1995, 34, 6, 1500–1506Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ic00110a031https://doi.org/10.1021/ic00110a031research-articleACS PublicationsRequest reuse permissionsArticle Views136Altmetric-Citations11LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Thin Film of Silica Nanoparticles with Highly Ordered Hemispherical Macropores (2007)

A thin film of silica nanoparticles with highly ordered hemispherical macropores and an ordering factor, ØVP6, of 98% was proved to be obtained by the Voronoi polygon analysis. Firstly, a monolayer of submicron polystyrene latex particles (PSL) with silica nanoparticles is obtained by coating a binary suspension of PSL particles and silica nanoparticles on a glass substrate using a spin coater. Secondly, the PSL particles are completely decomposed by calcining the coated films at 400°C for 10 min, affording a thin film of silica nanoparticles with hemispherical macropores. The size of the hemispherical macropores can be controlled from 136 to 506 nm by choosing PSL particles as a template. Although the monolayer of PSL particles without silica nanoparticles has several point and line defects, the PSL particle monolayer with silica nanoparticles has few defects. The small size of the silica nanoparticles is preferable for highly ordered hemispherical macropores. We propose a model that explains the ordering mechanism of particles during drying. The thin film of highly ordered hemispherical macropores can be used as a template for microcontact printing due to its hemispherical shape, or as an anti-reflective film due to its optical properties.
Supplementary Data from Patient-Specific Tumor Growth Trajectories Determine Persistent and Resistant Cancer Cell Populations during Treatment with Targeted Therapies (2023)

&lt;p&gt;This file contains supplemental figures 1-3. SF1: detailed description of sequential fitting process with example; SF2: relative uncertainties of the pre-existing resistant and persistent fractions; SF3: robustness analysis - results of the combined model for different mutation induction probabilities&lt;/p&gt;
Interobserver Variability in Target Definition for Stereotactic Arrhythmia Radioablation (2023)

ABSTRACT Background Stereotactic arrhythmia radioablation (STAR) is emerging as a potential new therapy for patients with refractory ventricular tachycardia (VT). The arrhythmogenic substrate (target) is synthesized from clinical and electro-anatomical information. This study was designed to evaluate the baseline interobserver variability in target delineation for STAR. Methods Delineation software designed for research purposes was used. The study was split into three phases. Firstly, electrophysiologists (observers) delineated a well-defined structure in three patients (spinal canal). Secondly, observers delineated the arrhythmogenic cardiac VT target in three patients previously treated with STAR based on case descriptions. To evaluate baseline performance, a basic workflow approach was used, no advanced techniques were allowed (e.g. image integration). Thirdly, observers delineated three predefined segments from the cardiac 17-segment model. Interobserver variability was evaluated by assessing volumes, variation in distance to the median volume as expressed by the root-mean-square of the observer standard deviation (RMS SD) over the target volume, and the Dice coefficient. Results Ten electrophysiologists completed the study. For the first phase (spinal canal delineation), interobserver variability was low as indicated by low variation in distance to the median volume (RMS SD range: 0.02-0.02cm) and high Dice coefficients (mean: 0.97±0.01). In the second phase (VT-target delineation), distance to the median volume was large (RMS SD range: 0.52-1.02cm) and the Dice coefficients low (mean: 0.40±0.15). In the third phase (segment delineation), similar results were observed (RMS SD range: 0.51-1.55cm, Dice coefficient mean: 0.31±0.21) Conclusions Interobserver variability is high for manual delineation of the VT-target and ventricular segments. Difficulties in cardiac anatomical orientation on traditional radiation oncology CT scans appear to be an important driver of variability. This evaluation of the baseline observer variation shows that there is a need for methods and tools to improve variability and allows for future comparison of interventions aiming to reduce observer variation.
Metallic resistivity in crystalline ropes of single-wall carbon nanotubes (1997)

Laser ablation of (Co,Ni)-doped graphite yields \ensuremath{\sim} 70% single-wall nanotubes, predominantly (10,10) armchair tubes which self-organize into crystalline ``ropes''&gt;100 \AA{} in diameter and&gt;10 \ensuremath{\mu}m long. We find ${\mathrm{\ensuremath{\rho}}}_{\mathrm{\ensuremath{\Vert}}}$=0.03-0.10m\ensuremath{\Omega} cm at 300 K, with positive (negative) d\ensuremath{\rho}/dT above (below) T = 35 K. Unoriented bulk samples exhibit similar behavior, with higher (directionally averaged) resistivities and ${\mathrm{T}}^{\mathrm{*}}$'s. The high-T behavior is consistent with the predicted intrinsic metallic state for this structure.
Characterization of regular Diophantine quadruples (2001)

A set S of positive integers is said to have a Diophantine property, and called a Diophantine set, if xy + 1 is a perfect square for any x = y ∈ S. The task of finding integer Diophantine quadruples {a, b, c, d}, where a < b < c < d, involves several open problems. An integer Diophantine quadruple {a, b, c, d} is called regular if (a + b − c − d)2 = 4(ab + 1)(cd + 1). No non-regular Diophantine quadruple has been found, and it has been conjectured that all Diophantine quadruples are regular.
Double-Directional Channel Measurements for Urban THz Microcellular Communications in a Street Canyon (2022)

THz communication has attracted a great deal of attention due to the large bandwidth available in this band. However, system development and deployment requires detailed knowledge of the wireless channel, which must be provided by measurements (channel sounding) and subsequent modeling in key scenarios of interest. One important scenario in this regard is the urban outdoor microcellular scenario where the Transmitter (Tx) and the Receiver (Rx) have a significant height difference. In this paper, we present ultra-wideband double-directional channel measurements in a microcellular scenario for the band between 145-146 GHz in a street canyon with Tx-Rx of distances up to 67 m. The results are analyzed in the delay and angular domain, and the impact of the street canyon on the power delay profiles and angular power spectra is detailed. These measurements thus contribute towards the creation of a more realistic and detailed THz channel model in these scenarios.
Structural Changes in the Cervical Spine: A Study on Autopsy Specimens in Different Age Groups (1967)

(1967). Structural Changes in the Cervical Spine: A Study on Autopsy Specimens in Different Age Groups. Acta Orthopaedica Scandinavica: Vol. 38, No. sup109, pp. 1-77.
Biodistribution and Trafficking of Hydrogel Nanoparticles in Adult Mosquitoes (2020)

BackgroundNanotechnology offers great potential for molecular genetic investigations and potential control of medically important arthropods. Major advances have been made in mammalian systems to define nanoparticle (NP) characteristics that condition trafficking and biodistribution of NPs in the host. Such information is critical for effective delivery of therapeutics and molecules to cells and organs, but little is known about biodistribution of NPs in mosquitoes.Methodology/Principal FindingsPRINT technology was used to construct a library of fluorescently labeled hydrogel NPs of defined size, shape, and surface charge. The biodistribution (organ, tissue, and cell tropisms and trafficking kinetics) of positively and negatively charged 200 nm x 200 nm, 80 nm x 320 nm, and 80 nm x 5000 nm NPs was determined in adult Anopheles gambiae mosquitoes as a function of the route of challenge (ingestion, injection or contact) using whole body imaging and fluorescence microscopy. Mosquitoes readily ingested NPs in sugar solution. Whole body fluorescence imaging revealed substantial NP accumulation (load) in the alimentary tracts of the adult mosquitoes, with the greatest loads in the diverticula, cardia and foregut. Positively and negatively charged NPs differed in their biodistribution and trafficking. Following oral challenge, negatively charged NPs transited the alimentary tract more rapidly than positively charged NPs. Following contact challenge, negatively charged NPs trafficked more efficiently in alimentary tract tissues. Following parenteral challenge, positively and negatively charged NPs differed in tissue tropisms and trafficking in the hemocoel. Injected NPs were also detected in cardia/foregut, suggesting trafficking of NPs from the hemocoel into the alimentary tract.Conclusions/SignificanceHerein we have developed a tool box of NPs with the biodistribution and tissue tropism characteristics for gene structure/function studies and for delivery of vector lethal cargoes for mosquito control.Author SummaryEmerging insecticide resistance in disease vectors is of great public health concern. Discovery of new targets and novel strategies for insecticidal interventions to control vector borne diseases is a public health imperative. Nanotechnology offers great potential for molecular genetic investigations and for delivery of effector molecules for control of disease vectors. We have developed a tool box of hydrogel nanoparticles (NPs) with the biodistribution and tissue tropism characteristics for gene structure/function studies and for delivery of vector lethal cargoes to adult mosquitoes. Nanotechnology will likely be useful for molecular investigations and potential control of the arthropod vectors of other neglected tropical diseases.
Evaluation of neurotoxicity of TIQ and MPTP and of parkinsonism‐preventing effect of 1‐MeTIQ by in vivo measurement of pre‐synaptic dopamine transporters and post‐synaptic dopamine D2 receptors in the mouse striatum (2001)

Parkinsonism-inducing neurotoxicity of 1,2,3,4-tetrahydroisoquinoline (TIQ), as contrasted to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), and parkinsonism-preventing effect of 1-methyl-1,2,3,4-tetrahydroisoquinoline (1-MeTIQ) have been investigated in mice by measuring their effects on the in vivo binding of radioligand to pre-synaptic dopamine transporters (DATs) or to dopamine D(2) receptors (D2R) in the striatum. A significant reduction of the ligand-DATs binding was found in the mice treated with MPTP, but not with TIQ, under the dosage inducing behavioral abnormality and loss of tyrosine hydroxylase-positive cells in the substantia nigra. A slight decrease in the ligand-DATs binding was observed in the mice given a larger dose of TIQ. Compensatory up-regulation in the post-synaptic D2Rs was found in the MPTP-treated mice. Pre-treatment with (S)-enantiomer, but not (R)-enantiomer, of 1-MeTIQ prevented the degeneration of DATs to some extent. We concluded that the TIQ-induced parkinsonism model is different from the MPTP-induced model as evaluated by the radioligand-DATs binding and that (S)-1-MeTIQ has a preventing effect for the degeneration of the DATs to a certain extent.
Progress on Covalent Inhibition of KRASG12C (2016)

Recent reports of small-molecule approaches to directly inhibit oncogenic KRAS(G12C) have invigorated the RAS research community by raising the possibility of drugging a protein that was long considered "undruggable." A new iteration of covalent compounds targeting the allosteric switch II pocket of KRAS(G12C) showed improved potency and selectivity and enabled studies demonstrating that KRAS(G12C) rapidly cycles its nucleotide substrate. This report illustrates the value of chemical probes in dissecting RAS biology and raises additional hope for development of viable pharmacologic strategies for directly targeting KRAS(G12C).
RETINAL LEAKAGE INDEX DYNAMICS ON ULTRA-WIDEFIELD FLUORESCEIN ANGIOGRAPHY IN EYES TREATED WITH INTRAVITREAL AFLIBERCEPT FOR PROLIFERATIVE DIABETIC RETINOPATHY IN THE RECOVERY STUDY (2020)

RECOVERY study (NCT02863354); https://clinicaltrials.gov/ct2/show/NCT02863354.
Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold (2014)

Interfering with LPS binding by the co-receptor protein myeloid differentiation factor 2 (MD-2) represents a useful approach for down-regulation of MD-2·TLR4-mediated innate immune signaling, which is implicated in the pathogenesis of a variety of human diseases, including sepsis syndrome. The antagonistic activity of a series of novel synthetic tetraacylated bis-phosphorylated glycolipids based on the βGlcN(1↔1)αGlcN scaffold was assessed in human monocytic macrophage-like cell line THP-1, dendritic cells and human epithelial cells. Two compounds were shown to inhibit efficiently the LPS-induced inflammatory signaling by down-regulation of the expression of TNF-α, IL-6, IL-8, IL-10 and IL-12 to background levels. The binding of the tetraacylated by (R)-3-hydroxy-fatty acids (2 × C12, 2 × C14), 4,4'-bisphosphorylated βGlcN(1↔1)αGlcN-based lipid A mimetic DA193 to human MD-2 was calculated to be 20-fold stronger than that of Escherichia coli lipid A. Potent antagonistic activity was related to a specific molecular shape induced by the β,α(1↔1)-diglucosamine backbone. 'Co-planar' relative arrangement of the GlcN rings was inflicted by the double exo-anomeric conformation around both glycosidic torsions in the rigid β,α(1↔1) linkage, which was ascertained using NOESY NMR experiments and confirmed by molecular dynamics simulation. In contrast to the native lipid A ligands, the binding affinity of βGlcN(1↔1)αGlcN-based lipid A mimetics to human MD-2 was independent on the orientation of the diglucosamine backbone of the synthetic antagonist within the binding pocket of hMD-2 (rotation by 180°) allowing for two equally efficient binding modes as shown by molecular dynamics simulation.
Lentivirus-Mediated RNA Interference in Mammalian Neurons (2008)

The ability to manipulate RNAi in cultured mammalian cells has provided scientists with a very powerful tool to influence gene expression. Neurons represent a cell type that initially displayed resistance to transduction by siRNAs or shRNA, when attempting to silence expression of endogenous genes. However, the development of lentiviral systems with that goal has facilitated the exogenous manipulation of RNAi in these postmitotic cells. Lentiviral-mediated RNAi experiments in cultured mammalian neurons can be designed to address a wide variety of biological questions or to test potential therapeutic hairpins before moving to treatment trials in vivo. We provide a practical approach to accomplish siRNA-mediated silencing of the disease-linked protein torsinA in primary neuronal cultures through the generation of lentiviral vectors expressing shRNAs.
Leukocyte-Dependent Responses of the Microvasculature to Chronic Angiotensin II Exposure (2012)

Angiotensin II (Ang II) contributes to the pathogenesis of hypertension and other cardiovascular diseases. Ang II induces a pro-oxidative, proinflammatory, and prothrombogenic phenotype in vascular endothelial cells. Although the peptide promotes the recruitment of leukocytes and platelets and induces oxidative stress in the microvasculature, it remains unclear whether and how the blood cell recruitment is linked to the production of reactive oxygen species. In this study, we addressed the contributions of Ang II type 1 receptors (AT 1 r) and gp91 phox to the recruitment of leukocytes and platelets and reactive oxygen species production in venules during chronic (2-week) infusion of Ang II in wild-type (WT) and mutant mice. Intravital video microscopy was used to measure the adhesion and emigration of leukocytes, the adhesion of fluorescently labeled platelets, and dihydrorhodamine oxidation (a measure of oxidative stress) in cremaster muscle postcapillary venules. In WT mice, Ang II infusion induced a time-dependent increase in the adhesion of leukocytes and platelets and enhanced reactive oxygen species production in venules. These changes in blood cell adhesion and reactive oxygen species production were not observed in AT 1 r −/− mice, AT 1 r −/− bone marrow chimeras (blood cells deficient in AT 1 r), gp91 phox−/− mice, gp91 phox−/− chimeras (blood cells or endothelial cells deficient in gp91 phox ), and in WT mice rendered granulocytopenic via intraperitoneal injection of antimouse granulocyte receptor 1 antibody. Thrombocytopenic WT mice (platelets depleted by intraperitoneal injection of rabbit antimouse thrombocyte antiserum) responded similar to WT mice. These findings implicate leukocyte-associated AT 1 r and gp91 phox in the induction of the pro-oxidative, proinflammatory, and prothrombogenic phenotype assumed by microvessels that is chronically exposed to elevated Ang II.
Hydrodynamic studies of laser fusion using plasma block ignition driven by nonlinear ponderomotive forces (2010)

In contrast to laser fusion with spherical plasma compression to very high densities, the alternative was studied with side-on ignition of solid state (or modestly higher) deuterium-tritium, based on hydrodynamic theory. The extremely difficult conditions may be overcome using petawatt-picosecond (PW-ps) laser pulses, however, only by applying the advantages of a discovered anomaly of plane geometry interaction without relativistic self-focusing using very high contrast ratios of the laser. The conditions of this side-on ignition could be further relaxed by inclusion of interaction effects. Ignition of solid state density or modestly compressed deuterium-tritium (DT) and of proton-boron11 (HB11) seems to be possible with laser pulses of several PW power and ps duration.