gebhart/patrepeval huggingface dataset:
Deciphering the conformations and dynamics of FG-nucleoporins <i>in situ</i> (2022)

Abstract The ∼120 MDa nuclear pore complex (NPC) acts as a gatekeeper for the molecular traffic between the nucleus and the cytosol. Small cargo readily passes through the transport channel, yet large cargo requires specialized nuclear transport receptors. While the scaffold structure that anchors the NPC in the double-layered nuclear envelope has been resolved to remarkable details, the spatial organization of intrinsically disordered nucleoporins (NUPs) within the central channel remains enigmatic. These so-called FG-NUPs account for about one-third of the total mass of the NPC and form the actual transport barrier. Here we combined site-specific fluorescent labeling in non-fixed cells and fluorescent lifetime imaging microscopy (FLIM) to directly decipher the conformations of an essential constituent of the permeability barrier, NUP98, inside the functioning NPCs using Fluorescence resonance energy transfer (FRET). With detailed measurements of the distance distribution of eighteen NUP98 segments combined with coarse-grained modeling, we mapped the uncharted biochemical environment inside the nanosized transport channel. We found that ‘good-solvent’ conditions for a polymer dominate the inside of the nanosized NPC, expand the FG-domain in situ and facilitate nuclear transport, in sharp contrast to the collapsed NUP98 FG-chain in aqueous solution. The combination of fluorescence microscopy, high-resolution electron tomography, and molecular simulation opens a window into the so-far unresolved organization of the FG-NUPs at the center of NPC function, allowing us to reconcile scientific models of nuclear transport.
Lithium‐Ion Desolvation Induced by Nitrate Additives Reveals New Insights into High Performance Lithium Batteries (2021)

Abstract Electrolyte additives have been widely used to address critical issues in current metal (ion) battery technologies. While their functions as solid electrolyte interface forming agents are reasonably well‐understood, their interactions in the liquid electrolyte environment remain rather elusive. This lack of knowledge represents a significant bottleneck that hinders the development of improved electrolyte systems. Here, the key role of additives in promoting cation (e.g., Li + ) desolvation is unraveled. In particular, nitrate anions (NO 3 − ) are found to incorporate into the solvation shells, change the local environment of cations (e.g., Li + ) as well as their coordination in the electrolytes. The combination of these effects leads to effective Li + desolvation and enhanced battery performance. Remarkably, the inexpensive NaNO 3 can successfully substitute the widely used LiNO 3 offering superior long‐term stability of Li + (de‐)intercalation at the graphite anode and suppressed polysulfide shuttle effect at the sulfur cathode, while enhancing the performance of lithium–sulfur full batteries (initial capacity of 1153 mAh g −1 at 0.25C) with Coulombic efficiency of ≈100% over 300 cycles. This work provides important new insights into the unexplored effects of additives and paves the way to developing improved electrolytes for electrochemical energy storage applications.
Suppression of self-pulsations in dual-clad, ytterbium-doped fiber lasers (2008)

Regimes of self-pulsing in fiber lasers have been characterized. Experiments show that the addition of a long section of passive fiber in the laser cavity can stabilize the laser and largely suppress the self-pulsations.
Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from <i>Mytilus edulis</i> (1996)

Iron(III) binding to the DOPA-containing Mytilus edulis adhesive protein (Mefp1) has been studied by spectrophotometric titrations, electron paramagnetic resonance (EPR), and resonance Raman spectroscopies. At pH 7.0, two different forms of the iron−protein complex exist: one purple (λmax = 548 nm) and one pink (λmax = 500 nm). The pink form is favored at high DOPA:Fe ratios and the purple at low DOPA:Fe ratios. Resonance Raman spectroscopy of both forms demonstrates that the chromophores are ferric catecholate complexes. EPR spectra of both forms of the protein measured at the same iron concentration reveal a g ≈ 4.3 resonance of approximately 4 times the intensity in the spectrum of the pink complex compared with that of the purple form. On the basis of the collective evidence obtained here, a model for the purple form of the ferric Mefp1 involving bis(catecholato) coordination of ferric ions with most of the iron(III) complexed as EPR-silent μ-oxo- or μ-hydroxo-bridged binuclear clusters is suggested. In the pink form, in contrast, the ferric iron is EPR-active, mononuclear, and present in high-spin tris(catecholato) complexes. The biological implications of these complexes are discussed.
X-ray imaging glass micro-pore optics (2007)

Glass micro-pore optics technology, developed over the last years for planetary X-ray imagers, has been used to assemble optical modules in approximation of a Wolter-I configuration. These tandems of glass sectors consist of hundreds of square, millimetre sized, multi-fibres that each contain more than a thousand, 3 &mu;m thin, X-ray mirrors with a surface roughness suitable for application at medium X-ray energies. The performance of the tandems can be traced back to the quality of the individual fibres. Extensive X-ray testing has been done on all constituents, from several fibres up to tandem level, using pencil beam and, for the first time, full beam illumination at PANTER. The results of these campaigns and of reflectometry measurements are discussed in this paper and have been used throughout the technology development program to monitor the X-ray performance. It will be shown that the quality of focussing micro-pore X-ray optics is now high enough to achieve an angular resolution of several arc minutes and that the multi-fibres are as good as 20 arc seconds, demonstrating the potential of this technology. The tandems can be combined and assembled into larger geometries, hence forming a very light and compact X-ray lens of ~200 mm diameter and a focal length of 1 m. This is part of an ESA breadboard program discussed elsewhere in this conference.
Unbiased Screening of Kawasaki Disease Sera for Viral Antigen Exposure (2017)

Kawasaki disease(KD) is a medium-vessel vasculitis with a predilection for coronary arteries and is of unknown etiology. KD is responsible for the majority of acquired pediatric cardiovascular disease in the industrialized world, and is associated with development of coronary artery aneurysms in approximately 25% of untreated patients. Epidemiologic, pathologic, and clinical characteristics of KD display notable overlap with common pediatric viral illnesses, leading some to hypothesize that a viral infection is the inciting agent for KD. We investigated viral exposure history in KD patients by utilizing a recently developed technique to profile sera against the known human virome in an unbiased manner. We collected sera during the acute (pretreatment) and subacute phases of illness from 35 patients meeting clinical diagnostic criteria for KD, preferentially selecting patients with coronary involvement and/or late presentation. Control samples included healthy children and patients with known viral infections. Using phage immunoprecipitation sequencing(PhIP-seq), the sera were screened against a phage display library expressing epitopes that cover the complete reference protein sequences of the known 206 viruses with human tropism. The mean patient age was 4.6 years(range 0.4–16.9) and mean day of illness at acute sample collection was 14.5 days(range 5 to 32). A majority of patients demonstrated coronary artery changes during the course of their illness(22/35, 62%). Sera from patients with KD demonstrated patterns of viral infection to common pediatric viruses with similar signal intensity and distribution to healthy control children. Interestingly, one patient demonstrated a strong signal to parvovirus B19. She presented on Illness Day 29 with periungual peeling and severe hip arthritis, and her initial KD course with 14 days of fever and 4/5 clinical criteria was missed. Although sera obtained early in the disease course could have missed a titer rise, we conclude that patients with KD do not exhibit unique serologic evidence of infection to known viruses or a viral exposure history that differs from age-similar healthy children. All authors: No reported disclosures.
Sub-Daily Earth Rotation During Epoch '92 (1994)

Earth rotation data were obtained with GPS during the EPOCH '92 campaign in the summer of 1992. About 10 days of data were acquired from 25 globally distributed stations and a constellation of 17 GPS satellites.
The development of a potent, tumour-specific heptamethine cyanine dye-crizotinib conjugate for the treatment of glioblastoma (2022)

Cancer cells show higher energy and biomolecules requirements than healthy cells, making the targeting of cancer metabolic dysfunctions an appealing therapeutic approach.Unfortunately, tackling the tumor metabolism is a daunting task, due to the ability of cancer cells to re-organize their metabolism switching between glycolysis and oxidative phosphorylation.Cancer metabolic plasticity and re-programming is partially supported by altered ionic channels expression and activity, our laboratory has described Chloride Intracellular Channel 1 (CLIC1) as a marker of malignancy in tumor cells and a possible therapeutic target.CLIC1 is a metamorphic protein able to switch between cytoplasmic and transmembrane forms (tmCLIC1), the latter characterized by chloride conductance.TmCLIC1 was found to be overexpressed in several solid tumors where supports cancer proliferation and growth, while it is mainly absent in healthy cells.Recently, it has been demonstrated that tmCLIC1 activity is affected by biguanide compounds, in particular metformin.Metformin was recently repurposed as an anticancer drug with unclear mechanisms.We demonstrated that in hypoglycemia, metformin displays increased toxic effect on cancer cells, inducing apoptosis.Metformin inhibits Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A), and hypoglycemia upregulates PP2A subunit B56δ targeting the Glycogen Synthase Kinase 3 Beta (GSK3b).Metformin treatment in combination with hypoglycemia leads to de-phosphorylation of GSK3b protein resulting in degradation of induced myeloid leukemia cell differentiation protein (MCL-1), a pro-survival protein, and cell death.In primary glioblastoma cell lines enriched in tumor-initiating-cells (GSCs), metformin has proven to be effective in reducing cell growth without affecting viability.Here, we are going to show studies trying to establish whether CLIC1 is a component of the established PP2A-mediated signaling network.Our work aims to clarify metformin molecular mechanism of action and to assess a new potential therapeutic approach for solid tumors in which tmCLIC1 is found to be overexpressed.
A Left Ventricle Model to Predict Post-Revascularization Ejection Fraction Based on Cine Magnetic Resonance Images (2001)

The left ventricular ejection fraction (LVEF) is an important clinical indicator of the cardiac function and long-term outcome for patients with coronary artery disease. A biomechanical model of the left ventricle was developed to quantitatively predict post-revascularization LVEF based on noninvasive magnetic resonance imaging. The myocardium was categorized into normal, hibernating, and infarcted regions from the ventricular short-axis images. Assuming that hibernating tissue would potentially regain contractility after revascularization, the expected maximum post-revascularization LVEF was calculated for four patients with chronic left ventricular dysfunction. The predictions were within three ejection fraction points of the follow-up LVEFs. This model may be useful to estimate the outcome and efficacy of revascularization plans.
Diagnostic techniques in thermal plasma processing (Part II). Volume 2 (1986)

Techniques for diagnostics for thermal plasmas are discussed. These include both optical techniques and in-flight measurements of particulate matter. In the core of the plasma, collisional excitation of the various chemical species is so strong that the population of the corresponding quantum levels becomes high enough for net emission from the plasma. In that case, the classical methods of emission spectroscopy may be applied. But in the regions where the temperatures are below 4000/sup 0/K (these regions are of primary importance for plasma processing), the emission from the plasma is no longer sufficient for emission spectroscopy. In this situation, the population of excited levels must be increased by the absorption of the light from an external source. Such sources, as for example pulsed tunable dye lasers, are now commercially available. The use of such new devices leads to various techniques such as laser induced fluorescence (LIF) or Coherent Anti Stockes Raman Spectroscopy (CARS) that can be used for analyzing plasmas. Particle velocity measurements can be achieved by photography and laser Doppler anemometry. Particle flux measurements are typically achieved by collecting particles on a substrate. Particle size measurements are based on intensity of scattered light. (WRF)
ChemInform Abstract: Facile Synthesis of Enantiopure trans‐2,3‐Diphenyl‐1,4‐diazabicyclo(2. 2.2)octane. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Allylic hydroxy fatty compounds with Δ5‐, Δ7‐, Δ8‐, and Δ10‐Unsaturation (1995)

Abstract Several novel allylic mono‐ and dihydroxy fatty compounds were synthesized from Δ5, Δ7‐, Δ8‐, and Δ10‐monounsaturated fatty acids with the selenium dioxide/ tert ‐butyl‐hydroperoxide. Chainlengths were C 19 for Δ7 and Δ10, and C 20 for Δ5 and Δ8 compounds. With a full range of Δ5‐ to Δ11‐unsaturated allylic monohydroxy fatty compounds available, position‐dependent effects in the 13 C‐nuclear magnetic resonance spectra of these compounds are discussed. The olefinic carbon shift differences in monohydroxy compounds, where the OH group is located between the double bond and the terminal methyl group, were plotted as a function of double‐bond distance from C 1 . This plot is presumably a rational function. During SeO 2 ‐based hydroxylation, lactonization of the hydroxy groups, located between the double‐bond and the carboxyl group, also occurs for Δ5 unsaturation.
El modelo transteórico del comportamiento en salud (2000)

El modelo transteorico del cambio del comportamiento en salud MT se origino en la decada de los 70 gracias a un analisis comparativo de teorias relevantes para explicar cambios en el comportamiento de dependientes de drogas; su nombre se derivo de la integracion de los principios y componentes teoricos de los sistemas terapeuticos analizados. Hoy el MT explica el cambio del comportamiento segun 5 variables: etapas y procesos del cambio, balance decisorio, auto eficacia y tentacion. El articulo describe antecedentes historicos, componentes actuales, asi como la representacion esquematica, la conceptualizacion y operacionalizacion de las variables del MT tal como fueron aplicadas en una investigacion referida a la promocion de la salud basada en modelos.
Atmospheric Cold Plasma Treatment of Soybean Oil with Hydrogen Gas (2020)

High voltage atmospheric cold plasma (HVACP) treatment generates reactive gas species that induce inter and intramolecular reactions in soybean oil. The goal of this study is to analyze the effect of HVACP treatment on the chemical structure of soybean oil in a hydrogen gas environment at atmospheric pressure. HVACP was used to treat soybean oil (15g), for up to 6h by triplicate. Plasma generated reactive gas species interact with the sample producing three distinct fractions identified as a liquid, gel, and solid. Fatty acid profile, FTIR, 1H-NMR/13C-NMR, GPC, thermal properties and peroxide value, were used to characterize the chemical structure. Results indicated a lower content of polyunsaturated fatty acids, increased content of saturated fatty acids, and the presence of isomers. An insoluble portion was observed in the solid fraction and increase with treatment time up to 42% in the 6h treated samples. Plasma species may cause two main reactions: polymerization and hydrogenation.
Analysis of Screech Phenomena in a Mach 1.0 Jet with Linear Array Focused Laser Differential Interferometry (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-1798.vid In this work, an underexpanded Mach 1.0 jet will be analyzed using an expansion of the traditional focused laser differential interferometer (FLDI). This expansion is known as linear array FLDI (LA-FLDI), and permits simultaneous probing of multiple spatial locations by means of a diffractive optical element. An array of six points is used to probe the jet in several spatial locations both inside and outside of the flowfield. The jet flowfield is measured in six distinct locations, oriented parallel with the nozzle axis, leading to a total of 36 distinct measurement points. Spectral analysis is used to determine that two screech modes---the flapping B mode and helical C mode---are present in the jet across broad spectrum of supply pressures. Four nozzle pressure ratios of interest were selected. The spectral content at these pressure ratios indicate there are several instances where these modes undergo mode-staging, as well as exist simultaneously. In general, this work is an extension of an earlier work on single-point FLDI applied to a Mach 1.5 jet, and it is expected that this work will demonstrate the utility and power of multi-point FLDI for making spatially-resolved, high-speed jet measurements---particularly for jet screech measurements.
Philip Saffman and viscous flow theory (2000)

Philip Saffman made valuable theoretical contributions to different areas of low-Reynolds-number hydrodynamics. Three themes are selected for discussion here: (i) the lift force on a sphere in a shear flow at small, but finite Reynolds number, (ii) Brownian motion in thin liquid films, and (iii) particle motion in rapidly rotating flows. In addition, brief descriptions are given of some of Saffman's other contributions including dispersion in porous media, the average velocity of sedimenting suspensions, and compressible low-Reynolds-number flows.
Uncertainty management for on-line optimisation of a POMDP-based large-scale spoken dialogue system (2011)

The optimization of dialogue policies using reinforcement learning (RL) is now an accepted part of the state of the art in spoken dialogue systems (SDS). Yet, it is still the case that the commonly used training algorithms for SDS require a large number of dialogues and hence most systems still rely on artificial data generated by a user simulator. Optimization is therefore performed off-line before releasing the system to real users. Gaussian Processes (GP) for RL have recently been applied to dialogue systems. One advantage of GP is that they compute an explicit measure of uncertainty in the value function estimates computed during learning. In this paper, a class of novel learning strategies is described which use uncertainty to control exploration on-line. Comparisons between several exploration schemes show that significant improvements to learning speed can be obtained and that rapid and safe online optimisation is possible, even on a complex task.
Data from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine (2023)

&lt;div&gt;Abstract&lt;p&gt;The H3K4 demethylase &lt;i&gt;KDM5B&lt;/i&gt; is amplified and overexpressed in luminal breast cancer, suggesting it might constitute a potential cancer therapy target. Here, we characterize, in breast cancer cells, the molecular effects of a recently developed small-molecule inhibitor of the KDM5 family of proteins (KDM5i), either alone or in combination with the DNA-demethylating agent 5-aza-2′-deoxycytidine (DAC). KDM5i treatment alone increased expression of a small number of genes, whereas combined treatment with DAC enhanced the effects of the latter for increasing expression of hundreds of DAC-responsive genes. ChIP-seq studies revealed that KDM5i resulted in the broadening of existing H3K4me3 peaks. Furthermore, cells treated with the drug combination exhibited increased promoter and gene body H3K4me3 occupancy at DAC-responsive genes compared with DAC alone. Importantly, treatment with either DAC or DAC+KDM5i induced a dramatic increase in H3K27ac at enhancers with an associated significant increase in target gene expression, suggesting a previously unappreciated effect of DAC on transcriptional regulation. KDM5i synergized with DAC to reduce the viability of luminal breast cancer cells in &lt;i&gt;in vitro&lt;/i&gt; assays. Our study provides the first look into the molecular effects of a novel KDM5i compound and suggests that combinatorial inhibition along with DAC represents a new area to explore in translational epigenetics.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; This study offers a first look into the molecular effects of a novel KDM5 inhibitory compound, suggesting how its use in combination with DNA methylation inhibitors presents new opportunities to explore in translational cancer epigenetics. &lt;i&gt;Cancer Res; 78(5); 1127–39. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Biofilm development and computational screening for new putative inhibitors of a homolog of the regulatory protein BrpA in Streptococcus dysgalactiae subsp. dysgalactiae (2019)

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD), a Lancefield group C streptococci (GCS), is a frequent cause of bovine mastitis. This highly prevalent disease is the costliest in dairy industry. Adherence and biofilm production are important factors in streptoccocal pathogenesis. We have previously described the adhesion and internalization of SDSD isolates in human cells and now we describe the biofilm production capability of this bacterium. In this work we integrated microbiology, imaging and computational methods to evaluate the biofilm production capability of SDSD isolates; to assess the presence of biofilm regulatory protein BrpA homolog in the biofilm producers; and to predict a structural model of BrpA-like protein and its binding to putative inhibitors. Our results show that SDSD isolates form biofilms on abiotic surface such as glass (hydrophilic) and polystyrene (hydrophobic), with the strongest biofilm formation observed in glass. This ability was mainly associated with a proteinaceous extracellular matrix, confirmed by the dispersion of the biofilms after proteinase K and trypsin treatment. The biofilm formation in SDSD isolates was also confirmed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). Under SEM observation, VSD16 isolate formed cell aggregates during biofilm growth while VSD9 and VSD10 formed smooth and filmy layers. We show that brpA-like gene is present and expressed in SDSD biofilm-producing isolates and its expression levels correlated with the biofilm production capability, being more expressed in the late exponential phase of planktonic growth compared to biofilm growth. Fisetin, a known biofilm inhibitor and a putative BrpA binding molecule, dramatically inhibited biofilm formation by the SDSD isolates but did not affect planktonic growth, at the tested concentrations. Homology modeling was used to predict the 3D structure of BrpA-like protein. Using high throughput virtual screening and molecular docking, we selected five ligand molecules with strong binding affinity to the hydrophobic cleft of the protein, making them potential inhibitor candidates of the SDSD BrpA-like protein. These results warrant further investigations for developing novel strategies for SDSD anti-biofilm therapy.