gebhart/patrepeval huggingface dataset:
Lipid bilayer stress in obesity-linked inflammatory and metabolic disorders (2018)

The maintenance of the characteristic lipid compositions and physicochemical properties of biological membranes is essential for their proper function. Mechanisms allowing to sense and restore membrane homeostasis have been identified in prokaryotes for a long time and more recently in eukaryotes. A membrane remodeling can result from aberrant metabolism as seen in obesity. In this review, we describe how such lipid bilayer stress can account for the modulation of membrane proteins involved in the pathogenesis of obesity-linked inflammatory and metabolic disorders. We address the case of the Toll-like receptor 4 that is implicated in the obesity-related low grade inflammation and insulin resistance. The lipid raft-mediated TLR4 activation is promoted by an enrichment of the plasma membrane with saturated lipids or cholesterol increasing the lipid phase order. We discuss of the plasma membrane Na, K-ATPase that illustrates a new concept according to which direct interactions between specific residues and particular lipids determine both stability and activity of the pump in parallel with indirect effects of the lipid bilayer. The closely related sarco(endo)-plasmic Ca-ATPase embedded in the more fluid ER membrane seems to be more sensitive to a lipid bilayer stress as demonstrated by its inactivation in cholesterol-loaded macrophages or its inhibition mediated by an increased PtdCho/PtdEtn ratio in obese mice hepatocytes. Finally, we describe the model recently proposed for the activation of the conserved IRE-1 protein through alterations in the ER membrane lipid packing and thickness. Such IRE-1 activation could occur in response to abnormal lipid synthesis and membrane remodeling as observed in hepatocytes exposed to excess nutrients. Since the IRE-1/XBP1 branch also stimulates the lipid synthesis, this pathway could create a vicious cycle "lipogenesis-ER lipid bilayer stress-lipogenesis" amplifying hepatic ER pathology and the obesity-linked systemic metabolic defects.
First-Principle Based Modeling of Electron and Hole Transfer in Amorphous Polyethylene Terephthalate Oligomer (2019)

Recently, we have proposed a first-principles based multi-scale modeling method for studying carrier transport properties in polymers with flexible backbones, and have successfully modeled hole transfer in polyethylene (PE). In this study, in order to see if we can model carrier transport in more complex polymers, we have utilized the multi-scale modeling method to simulate the time-of-flight carrier transients in polyethylene terephthalate (PET). When the electrostatic disorder was taken into account, the computed electron and hole mobilities were in reasonable agreement with experimental data, indicating that the multi-scale modeling technique can most likely be applied to other polymer dielectrics as well. Simulated current waveform was dispersive to a certain extent due to the disordered energetic landscape of the hopping site energies. Unlike the case for hole transfer in PE where the energetic disorder is dominated by the conformational disorder of the polymer chain, the energetic disorder for the electron and hole transfer in PET oligomer was dominated by the electrostatic disorder, which is caused by the local dipole of the PET molecule.
Ditopic boronic acid and imine-based naphthalimide fluorescence sensor for copper(<scp>ii</scp>) (2014)

Copper ions are essential for many biological processes. However, high concentrations of copper can be detrimental to the cell or organism. A novel naphthalimide derivative bearing a monoboronic acid group (BNP) was investigated as a Cu(2+) selective fluorescent sensor in living cells. This derivative is one of the rare examples of reversible fluorescent chemosensors for Cu(2+) which uses a boronic acid group for a binding site. Moreover, the adduct BNP-Cu(2+) displays a fluorescence enhancement with fructose. The uptake of this novel compound in HeLa cancer cells was imaged using confocal fluorescence microscopy techniques including two-photon fluorescence lifetime imaging microscopy.
Nicotine as a Marker for Environmental Tobacco Smoke: Implications of Sorption on Indoor Surface Materials (1998)

Recently developed models and data describing the interactions of gas-phase semi-volatile organic compounds with indoor surfaces are employed to examine the effects of sorption on nicotine's suitability as an environmental tobacco smoke (ETS) marker. Using parameters from our studies of nicotine sorption on carpet, painted wallboard, and stainless steel and previously published data on ETS particle deposition, the dynamic behavior of nicotine was modeled in two different indoor environments: a house and a stainless steel chamber. The results show that apparently contradictory observations of nicotine's behavior in indoor air can be understood by considering the effects of sorption under different experimental conditions. In indoor environments in which smoking has occurred regularly for an extended period, the sorbed mass of nicotine is very large relative to the mass emitted by a single cigarette. The importance of nicotine adsorption relative to ventilation as a gas-phase removal mechanism is reduced. Where smoking occurs less regularly or the indoor surfaces are cleaned prior to smoking (as in a laboratory chamber), nicotine deposition is more significant. Nicotine concentrations closely track the levels of other ETS constituents in environments with habitual smoking if the data are averaged over a period significantly longer than the period between cigarette combustion episodes. However, nicotine is not a suitable tracer for predicting ETS exposures at fine time scales or in settings where smoking occurs infrequently and irregularly.
Sensor applications of photosensitive capillary waveguides (2007)

We describe a photosensitive capillary waveguide sensor, composed of a capillary structure with a photosensitive cladding ring surrounding the bore. The bore is filled with a fluid having an index of refraction that is sensitive to a measurand of interest, and a grating is inscribed in the cladding ring. We measure the optical interaction between light propagating in the filled capillary waveguide and the grating to determine the parameter of interest. Methods for forming connections between the capillary and single mode optical fiber are also described. We demonstrate the performance of the capillary waveguide as a temperature sensor in which the sensitivity of the Bragg wavelength to temperature is -150 pm/°C. We also describe how to use the capillary waveguide sensor to discriminate between different measurands.
Neuronal population mechanisms of lightness perception (2018)

The way that humans and animals perceive the lightness of an object depends on its physical luminance as well as its surrounding context. While neuronal responses throughout the visual pathway are modulated by context, the relationship between neuronal responses and lightness perception is poorly understood. We searched for a neuronal mechanism of lightness by recording responses of neuronal populations in monkey primary visual cortex (V1) and area V4 to stimuli that produce a lightness illusion in humans, in which the lightness of a disk depends on the context in which it is embedded. We found that the way individual units encode the luminance (or equivalently for our stimuli, contrast) of the disk and its context is extremely heterogeneous. This motivated us to ask whether the population representation in either V1 or V4 satisfies three criteria: 1) disk luminance is represented with high fidelity, 2) the context surrounding the disk is also represented, and 3) the representations of disk luminance and context interact to create a representation of lightness that depends on these factors in a manner consistent with human psychophysical judgments of disk lightness. We found that populations of units in both V1 and V4 fulfill the first two criteria but that we cannot conclude that the two types of information in either area interact in a manner that clearly predicts human psychophysical measurements: the interpretation of our population measurements depends on how subsequent areas read out lightness from the population responses. NEW & NOTEWORTHY A core question in visual neuroscience is how the brain extracts stable representations of object properties from the retinal image. We searched for a neuronal mechanism of lightness perception by determining whether the responses of neuronal populations in primary visual cortex and area V4 could account for a lightness illusion measured using human psychophysics. Our results suggest that comparing psychophysics with population recordings will yield insight into neuronal mechanisms underlying a variety of perceptual phenomena.
&lt;title&gt;Spectral IR tissue diagnostics with photothermal detection&lt;/title&gt; (1999)

Photothermal (PT) and Photoacoustic (PA) Step-Scan FT-IR measurements are successful tools for thickness determination of layered samples. Aiming to separate optically between different layered tissues, we have been able to distinguish skin, liver and muscle tissues by means of PT and PA measurement techniques. Performing Step-Scan FT-IR measurements, the PT and PA phase and amplitude signals follow the tissue's absorption peaks which corresponds to the transmission spectra. These results are supported and confirmed by a simulation using the Finite- Difference-Method whereat the basic spectral data from transmission measurements and some assumed thermal properties of investigated tissues have been inserted.
PET/CT‐GUIDED BIOPSY FOR THE DIAGNOSIS OF LYMPHOMA (2017)

Introduction: Biopsy of affected tissue is required for lymphoma diagnosis at onset and relapse and to plan adequate treatment. Open incisional biopsy is traditionally the method of choice, with an accuracy of approximately 100%. Nevertheless, it requires hospitalization, availability of an operating room and sometimes general anesthesia and is associated with several drawbacks (morbidity, surgical complications, tumor contamination of surrounding tissues). The development of ultrasound and computed tomography (CT)-guided biopsies has almost overcome these disadvantages. However, a variable proportion of non-diagnostic procedures is reported, leading to an accuracy that ranges between 50% and 80%. Functional imaging, such as fluorodeoxyglucose (FDG) positron emission tomography (PET)/CT, is a procedure which can potentially be used to drive biopsy to the most metabolically active area within a lymph node (figure) or extranodal masses which sometimes show no morphologically detectable changes on CT scan. Methods: One hundred patients with suspect lymphoma at onset or relapse are expected to be enrolled in 3 years, provided they show FDG-avid findings. Patients are excluded if pregnant, breastfeeding or in case fine-needle PET/CT-guided biopsy is contraindicated. Diagnostic accuracy will be compared to published data concerning conventional imaging. Specimen adequacy will also be evaluated. The trial is supported by the Italian Association for Cancer Research (Progetto AIRC IG 2015 Id 17781). Results: Data are available for the first 32 patients. Thirty-four procedures have been performed: 3 (8.8%) were interrupted because of pain but could be successfully repeated in 2 cases. Biopsy target was lymph node in 19 cases and extranodal site in 13 (bone in 8 cases, soft tissue in 3, liver and kidney in 1 each). Median SUVmax of target lesions was 11.5 (4.9–37.7). Insufficient samples were obtained in 9.7% of cases (3 out of 31 successful procedures), whereas in all other instances the tissue was considered adequate to formulate a diagnosis (table). Table here Mean sample length was 10 mm (standard deviation ±6 mm). The mean amount of affected tissue in collected samples was 56% (±33%) and the mean proportion of fibrosis/bone was 37% (±32%). No severe adverse events were reported during or after each procedure. Keywords: positron emission tomography (PET).
Supramolecular chemistry anniversary (2007)

A graphical abstract is available for this content
Quantum Polaritonic (2017)

Abstract Microcavity polaritons have demonstrated their unique propensity to host macroscopic quantum phenomena. While they appear to be highly promising for applications in a classical realm, they are still far from competing even with decade old electronics. Another playground where polaritons could emerge as strong contenders is the microscopic quantum regime with single-particle effects and nonlinearities at the one-polariton level. Several theoretical proposals exist to explore polariton blockade mechanisms, realize sophisticated quantum phase transitions, implement quantum simulations and/or quantum information processing, thereby opening a new page of the polariton physics when such ideas will be implemented in the laboratory.
Error reporting from the da Vinci surgical system in robotic surgery: A Canadian multispecialty experience at a single academic centre (2017)

Robotic malfunction is not infrequent in the current era of robotic surgery in various surgical subspecialties, but rarely consequential. Their seldom occurrence does not seem to affect patient safety or surgical outcome.
Abstract 1408: Diffuse optical spectroscopic imaging reveals regimen-dependent changes in breast tumors throughout neoadjuvant chemotherapy (2019)

Abstract Diffuse Optical Spectroscopic Imaging (DOSI) is a non-invasive near-infrared imaging modality than can provide label-free functional and metabolic information about breast tumors, probing depths up to several centimeters. Previous work has shown that DOSI has prognostic value for pathological response at key timepoints during neoadjuvant (presurgical) chemotherapy (NAC), including baseline, 24 hours after the first infusion, week 1, and at the midpoint of therapy. To date there have been almost no reports on how specific NAC regimens affect the prognostic capability of DOSI. Here we present a large multi-center DOSI dataset consisting of 54 breast tumors and 313 unique measurements taken across three timepoints during NAC: Baseline, week 1, and midpoint of treatment. We will show for the first time that the manifestation of DOSI response parameters (oxyhemoglobin, de-oxyhemoglobin, water, and lipid) is highly dependent on the specific NAC regimen used. Subjects were treated with either a Maximum Tolerated Dose (MTD) regimen, in which a higher dose is administered less frequently, or a Metronomic (MET) regimen, in which a smaller dose is given more frequently. MTD regimen of cytotoxic agents has traditionally been the most effective method to treat breast cancer as it aims to kill the maximum amount of tumor cells before regrowth. MET administration of cytotoxic therapies has shown antiangiogenic properties aiming to limit toxic side effects and drug resistance, while potentially inducing tumor dormancy and immunomodulation. Subjects treated with MTD regimen and also responding to this treatment exhibited an oxyhemoglobin flare in the first day of NAC. In contrast, subjects treated with MET presented only small fluctuations in oxyhemoglobin throughout the first week of NAC. The oxyhemoglobin flare has been theorized to be induced by an inflammatory effect significant for cell death, which could be in response to specifically the MTD regimen and its higher dosing. This study indicates that the specific regimen must be considered when using DOSI for NAC monitoring. It also suggests DOSI may provide biological insight into the regimen-specific mechanisms of action. Citation Format: Anup Tank, Hannah Peterson, Vivian Pera, Syeda Tabassum, Naomi Ko, Anais Leproux, Bruce Tromberg, Darren Roblyer. Diffuse optical spectroscopic imaging reveals regimen-dependent changes in breast tumors throughout neoadjuvant chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1408.
Photoelectrochemical Reduction of Carbon Dioxide with a Copper Graphitic Carbon Nitride Photocathode (2021)

Research on the photoreduction of CO<sub>2</sub> often has been dominated by the use of sacrificial reducing agents. A pathway that avoids this problem would be the development of photocathodes for CO<sub>2</sub> reduction that could then be coupled to a photoanodic oxygen evolution reaction. Here, we present the use of copper-substituted graphitic carbon nitride (Cu-CN) on a fluorinated tin oxide (FTO) electrode for the photoelectrochemical two-electron reduction of CO<sub>2</sub> to CO as a major product (>95 %) and formic acid (<5 %). The results show that at a potential of -2.5 V versus Fc\Fc<sup>+</sup> the CO<sub>2</sub> reduction activity of Cu-CN on FTO electrode improves by 25 % upon illumination by visible light with a faradaic efficiency of nearly 100 %. Independently, X-ray photoelectron spectroscopy conclusively shows a pronounced increase in the electrical conductivity of the Cu-CN upon white light illumination under vacuum and a contactless measuring configuration. This photo-assisted charge mobility is shown to play a key role in the increased reactivity and faradaic efficiency for the reduction of CO<sub>2</sub> .
Experimental evaluation of apparent soot oxidation rates in diesel particulate filters (2004)

The rate expressions used by different researchers to model the oxidation of soot in diesel filters vary considerably, apparently due to different soot properties between different studies, as well as the inherent difficulties in sampling and measuring the reaction rate in a realistic way. In this work, an attempt is made to overcome the above-mentioned problems in real engine measurements with the combined use of mathematical modelling. The methodology relies on a calculation procedure for the on-line assessment of soot mass in the filter, based on pressure drop modelling. Specially designed experimental protocols are employed to study the reaction rate of soot under various operating conditions and filter loadings. Both uncatalysed and Ce-catalysed soot is tested. Moreover, the soot oxidation with NO2 facilitated by an upstream oxidation catalyst is also studied. The results are suitably processed towards deriving Arrhenius plots and assessing the respective kinetic parameters. The activation energies determined fall within the range of values reported in the literature.
Ligamentous injuries of the wrist in athletes. (1992)

The athlete's wrist is particularly prone to injury. Although many wrist injuries are dismissed as sprains or strains, a number of these injuries involve significant ligamentous damage that can lead to chronic carpal instability. A complete knowledge of the carpal ligamentous anatomy and classification of wrist instability patterns is necessary for the adequate diagnosis and treatment of these injuries.
Pigs Transgenic For Human Dominant Mutations Of The GUCY2D Gene (2011)

Purpose: Studies on large animal models are an important step to test new therapeutical strategies before human application. Considering the importance of cone function for human vision and the paucity of large animal models for cone dystrophies having an enriched cone region, we propose to develop a pig model for cone degeneration. With a lentiviral-directed transgenesis, we obtained pigs transgenic for a cone-dominant mutant gene described in a human cone dystrophy.Methods: Lentiviral vectors encoding the human double mutant GUCY2DE837D/R838S cDNA under the control of a region of the pig arrestin-3 promoter (Arr3) was produced and used for lentiviral-derived transgenesis in pigs. PCR-genotyping and southern blotting determined the genotype of pigs born after injection of the vector at the zygote stage. Retina function analysis was performed by ERG and behavioral tests at 11, 24 and 54 weeks of age. OCT and histological analyses were performed to describe the retina morphology.Results: The ratio of transgenic pigs born after lentiviral-directed transgenesis was close to 50%. Transgenic pigs with 3 to 5 transgene copies per cell clearly present a reduced photopic response from 3 months of age on. Except for one pig, which has 6 integrated transgene copies, no dramatic decrease in general mobility was observed even at 6 months of age. OCT examinations reveal no major changes in the ONL structure of the 6-months old pigs. The retina morphology was well conserved in the 2 pigs sacrificed (3 and 6 months old) except a noticeable displacement of some cone nuclei in the outer segment layer.Conclusions: Lentiviral-directed transgenesis is a rapid and straightforward method to engineer transgenic pigs. Some Arr3-GUCY2DE837D/R838S pigs show signs of retinal dysfunction but further work is needed to describe the progression of the disease in this model.
Surface Plasma Sources with Helicon Plasma Generators (2007)

A Surface Plasma Source (SPS) with plasma generation by a saddle type antenna is discussed. The following features of the helicon discharge with a saddle type antenna in magnetic field are identified: efficient plasma generation in resonant condition, low gas density, strong separation of plasma from the wall, possibility to control plasma flux distribution by magnetic field configuration. Applications of saddle type antenna in SPS for accelerators for Homeland Security and for Neutral Beam Injectors (NBI) are considered.
Supplementary Figure 1 from Endothelial Expression of TNF Receptor-1 Generates a Proapoptotic Signal Inhibited by Integrin α6β1 in Glioblastoma (2023)

&lt;p&gt;PDF file - 132K, Double-labeling of vWf and TNF�\, TNF-R1, or TNF-R2 in tumor-associated ECs of GBM.&lt;/p&gt;
Metagenomics Reveals Diet-Specific Specialization of Bacterial Communities in Fungus Gardens of Grass- and Dicot-Cutter Ants (2020)

Leaf-cutter ants in the genus <i>Atta</i> are dominant herbivores in the Neotropics. While most species of <i>Atta</i> cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 <i>Atta</i> fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Differences between community composition and functional capacity of the bacteria in the two types of fungus gardens reflect differences in the substrates that the ants incorporated. These results show that different substrate inputs matter for fungus garden bacteria and shed light on the potential role of bacteria in mediating the ants' transition to the use of a novel substrate.