gebhart/patrepeval huggingface dataset:
Candida albicans Cell Wall Glycosylation May Be Indirectly Required for Activation of Epithelial Cell Proinflammatory Responses (2011)

Oral epithelial cells discriminate between the yeast and hyphal forms of Candida albicans via the mitogen-activated protein kinase (MAPK) signaling pathway. This occurs through phosphorylation of the MAPK phosphatase MKP1 and activation of the c-Fos transcription factor by the hyphal form. Given that fungal cell wall polysaccharides are critical in host recognition and immune activation in myeloid cells, we sought to determine whether β-glucan and N- or O-glycosylation was important in activating the MAPK/MKP1/c-Fos hypha-mediated response mechanism and proinflammatory cytokines in oral epithelial cells. Using a series of β-glucan and N- and O-mannan mutants, we found that N-mannosylation (via Δoch1 and Δpmr1 mutants) and O-mannosylation (via Δpmt1 and Δmnt1 Δmnt2 mutants), but not phosphomannan (via a Δmnn4 mutant) or β-1,2 mannosylation (via Δbmt1 to Δbmt6 mutants), were required for MKP1/c-Fos activation, proinflammatory cytokine production, and cell damage induction. However, the N- and O-mannan mutants showed reduced adhesion or lack of initial hypha formation at 2 h, resulting in little MKP1/c-Fos activation, or restricted hypha formation/pseudohyphal formation at 24 h, resulting in minimal proinflammatory cytokine production and cell damage. Further, the α-1,6-mannose backbone of the N-linked outer chain (corresponding to a Δmnn9 mutant) may be required for epithelial adhesion, while the α-1,2-mannose component of phospholipomannan (corresponding to a Δmit1 mutant) may contribute to epithelial cell damage. β-Glucan appeared to play no role in adhesion, epithelial activation, or cell damage. In summary, N- and O-mannosylation defects affect the ability of C. albicans to induce proinflammatory cytokines and damage in oral epithelial cells, but this may be due to indirect effects on fungal pathogenicity rather than mannose residues being direct activators of the MAPK/MKP1/c-Fos hypha-mediated immune response.
Determination of the Encapsulation Efficiency of Individual Vesicles Using Single-Vesicle Photolysis and Confocal Single-Molecule Detection (2005)

This paper describes a new method to measure the encapsulation efficiency of individual lipid vesicles. Single vesicles were first optically trapped (with a CW Nd:YAG laser at 1064 nm) and then photolyzed with a single 3-ns UV laser pulse (from a N(2) laser at 337 nm) to release the molecules encapsulated within the vesicle; confocal detection with single-molecule sensitivity (laser excitation at 488 nm from a CW Ar(+) laser) was used to measure the number of released molecules. By placing the confocal probe volume a few micrometers from the vesicle and by monitoring the transit times and the number of released molecules that crossed this probe volume, we could calculate the total number of molecules released from the vesicle using a three-dimensional diffusion equation. Unlike traditional definitions of encapsulation efficiencies based on bulk assays, because we can measure the contents of and release from individual vesicles, we can define the encapsulation efficiency by dividing the concentration of molecules encapsulated in each vesicle over the original concentration of the molecules present in the loading solution. We characterized the encapsulation efficiency of carboxyfluorescein for vesicles prepared by rotary evaporation and found oligolamellar vesicles have an encapsulation efficiency of 36.3 +/- 18.9%, while multilamellar vesicles have an encapsulation efficiency of 17.5 +/- 8.9%.
Retracted: 3D Printing of Bilineage Constructive Biomaterials for Bone and Cartilage Regeneration (2017)

Owing to the different biological properties of articular cartilage and subchondral bone, it remains significant challenge to construct a bi‐lineage constructive scaffold. In this study, manganese (Mn)‐doped β‐TCP (Mn‐TCP) scaffolds with varied Mn contents are prepared by a 3D‐printing technology. The effects of Mn on the physicochemical properties, bioactivity, and corresponding mechanism for stimulating osteochondral regeneration are systematically investigated. The incorporation of Mn into β‐TCP lowers the lattices parameters and crystallization temperatures, but improves the scaffold density and compressive strength. The ionic products from Mn‐TCP significantly improve the proliferation of both rabbit chondrocytes and mesenchymal stem cells (rBMSCs), as well as promote the differentiation of chondrocytes and rBMSCs. The in vivo study shows that Mn‐TCP scaffolds distinctly improve the regeneration of subchondral bone and cartilage tissues as compared to TCP scaffolds, upon transplantation in rabbit osteochondral defects for 8 and 12 weeks. The mechanism is closely related to the Mn 2+ ions significantly stimulated the proliferation and differentiation of chondrocytes through activating HIF pathway and protected chondrocytes from the inflammatory osteoarthritis environment by activating autophagy. These findings suggest that 3D‐printing of Mn‐containing scaffolds with improved physicochemical properties and bilineage bioactivities represents an intelligent strategy for regenerating osteochondral defects.
On calibration of modern neural networks (2017)

Confidence calibration -- the problem of predicting probability estimates representative of the true correctness likelihood -- is important for classification models in many applications. We discover that modern neural networks, unlike those from a decade ago, are poorly calibrated. Through extensive experiments, we observe that depth, width, weight decay, and Batch Normalization are important factors influencing calibration. We evaluate the performance of various post-processing calibration methods on state-of-the-art architectures with image and document classification datasets. Our analysis and experiments not only offer insights into neural network learning, but also provide a simple and straightforward recipe for practical settings: on most datasets, temperature scaling -- a single-parameter variant of Platt Scaling -- is surprisingly effective at calibrating predictions.
Volumetric breast density estimation from full-field digital mammograms (2006)

A method is presented for estimation of dense breast tissue volume from mammograms obtained with full-field digital mammography (FFDM). The thickness of dense tissue mapping to a pixel is determined by using a physical model of image acquisition. This model is based on the assumption that the breast is composed of two types of tissue, fat and parenchyma. Effective linear attenuation coefficients of these tissues are derived from empirical data as a function of tube voltage (kVp), anode material, filtration, and compressed breast thickness. By employing these, tissue composition at a given pixel is computed after performing breast thickness compensation, using a reference value for fatty tissue determined by the maximum pixel value in the breast tissue projection. Validation has been performed using 22 FFDM cases acquired with a GE Senographe 2000D by comparing the volume estimates with volumes obtained by semi-automatic segmentation of breast magnetic resonance imaging (MRI) data. The correlation between MRI and mammography volumes was 0.94 on a per image basis and 0.97 on a per patient basis. Using the dense tissue volumes from MRI data as the gold standard, the average relative error of the volume estimates was 13.6%.
Adhesive-free adhesion between polytetrafluoroethylene (PTFE) and isobutylene–isoprene rubber (IIR) via heat-assisted plasma treatment (2017)

A polytetrafluoroethylene (PTFE) surface was modified using atmospheric pressure plasma treatment under heating (heat-assisted plasma treatment) to promote its direct adhesion to isobutylene–isoprene rubber (IIR) without any adhesives.
VERTICAL DIAMAGNETIC LEVITATION ARRAY WITH EXTENDED STABILITY AREA (2006)

Stable static levitation of one permanent magnet by another with no energy input and without superconductors is forbidden by Earnshaw's theorem. Adding a diamagnetic material nearby the suspended magnet the intrinsically unstable equilibrium can be stabilized. For a vertical symmetric configuration this paper establishes the equilibrium and stability equation using an analytical procedure of magnetic field computation and suggests methods of enlarging the stability area by alternating the geometry of magnetic fields sources. The applications of these levitation devices concern the designing of ultra-sensitive measurement instruments used where sensitivity to minor variation of the gravitational field is required.
Ultra-fast and calibration-free temperature sensing in the intrapulse mode (2014)

A simultaneously time-resolved and calibration-free sensor has been demonstrated to measure temperature at the nanosecond timescale at repetition rates of 1.0 MHz. The sensor benefits from relying on a single laser, is intuitive and straightforward to implement, and can sweep across spectral ranges in excess of 1 cm⁻¹. The sensor can fully resolve rovibrational features of the CO molecule, native to combustion environments, in the mid-infrared range near λ=4.85 μm at typical combustion temperatures (800-2500 K) and pressures (1-3 atm). All of this is possible through the exploitation of chirp in a quantum cascade laser, operating at a duty cycle of 50%, and by using high bandwidth (500 MHz) photodetection. Here, we showcase uncluttered, spectrally-pure Voigt profile fitting with accompanying peak SNRs of 150, resulting in a typical temperature precision of 0.9% (1σ) at an effective time-resolution of 1.0 MHz. Our sensor is applicable to other species, and can be integrated into commercial technologies.
Brain Region‐Specific Histopathological Effects of Varying Trajectories of Controlled Cortical Impact Injury Model of Traumatic Brain Injury (2016)

These results indicate a trajectory-dependent injury characterized by exacerbation of inflammation and different levels of impaired cell proliferation and neurogenesis. Such multiple brain areas showing varying levels of cell death after region-specific CCI model may closely mimic the clinical manifestations of TBI.
Assessment of left ventricular and aortic valve function after aortic balloon valvuloplasty in adult patients with critical aortic stenosis. (1987)

Preliminary reports have documented the utility of balloon aortic valvuloplasty as a palliative treatment for high-risk patients with critical aortic stenosis, but the effect of this procedure on cardiac performance has not been studied in detail. Accordingly, 32 patients (mean age 79 years) with long-standing, calcific aortic stenosis were treated at the time of cardiac catheterization with balloon dilatation of the aortic valve, and serial changes in left ventricular and valvular function were followed before and after valvuloplasty by radionuclide ventriculography, determination of systolic time intervals, and Doppler echocardiography. Prevalvuloplasty examination revealed heavily calcified aortic valves in all patients, a mean peak-to-peak aortic valve gradient of 77 +/- 27 mm Hg, a mean Fick cardiac output of 4.6 +/- 1.4 liters/min, and a mean calculated aortic valve area of 0.6 +/- 0.2 cm2. Subsequent balloon dilatation with 12 to 23 mm valvuloplasty balloons resulted in a fall in aortic valve gradient to 39 +/- 15 mm Hg, an increase in cardiac output to 5.2 +/- 1.8 liters/min, and an increase in calculated aortic valve area to 0.9 +/- 0.3 cm2. Individual hemodynamic responses varied considerably, with some patients showing major increases in valve area, while others demonstrated only small increases. In no case was balloon dilatation accompanied by evidence of embolic phenomena. Supravalvular aortography obtained in 13 patients demonstrated no or a mild (less than or equal to 1+) increase in aortic insufficiency. Serial radionuclide ventriculography in patients with a depressed left ventricular ejection fraction (i.e., that less than or equal to 55%) revealed a small increase in ejection fraction from 40 +/- 13% to 46 +/- 12% (p less than .03). In addition, for the study group as a whole there was a decrease in left ventricular end-diastolic volume index (113 +/- 38 to 101 +/- 37 ml/m2, p less than .003), a fall in stroke-volume ratio (1.49 +/- 0.44 to 1.35 +/- 0.33, p less than .04), and no immediate change in left ventricular peak filling rate (2.05 +/- 0.77 to 2.21 +/- 0.65 end-diastolic counts/sec, p = NS). Serial M mode echocardiography and phonocardiography showed an increase in aortic valve excursion (0.5 +/- 0.2 to 0.8 +/- 0.2 cm, p less than .001), a decrease in time to one-half carotid upstroke (80 +/- 30 to 60 +/- 10 msec, p less than .001), and a small decrease in left ventricular ejection time (0.44 +/- 0.03 to 0.42 +/- 0.02 sec, p less than .001).(ABSTRACT TRUNCATED AT 400 WORDS)
An initial validation of Landsat 5 and 7 derived surface water temperature for U.S. lakes, reservoirs, and estuaries (2018)

The United States Harmful Algal Bloom and Hypoxia Research Control Act of 2014 identified the need for forecasting and monitoring harmful algal blooms (HAB) in lakes, reservoirs, and estuaries across the nation. Temperature is a driver in HAB forecasting models that affects both HAB growth rates and toxin production. Therefore, temperature data derived from the U.S. Geological Survey Landsat 5 Thematic Mapper and Landsat 7 Enhanced Thematic Mapper Plus thermal band products were validated across 35 lakes and reservoirs, and 24 estuaries. <i>In situ</i> data from the Water Quality Portal (WQP) were used for validation. The WQP serves data collected by state, federal, and tribal groups. Discrete <i>in situ</i> temperature data included measurements at 11,910 U.S. lakes and reservoirs from 1980 through 2015. Landsat temperature measurements could include 170,240 lakes and reservoirs once an operational product is achieved. The Landsat-derived temperature mean absolute error was 1.34°C in lake pixels >180 m from land, 4.89°C at the land-water boundary, and 1.11°C in estuaries based on comparison against discrete surface <i>in situ</i> measurements. This is the first study to quantify Landsat resolvable U.S. lakes and reservoirs, and large-scale validation of an operational satellite provisional temperature climate data record algorithm. Due to the high performance of open water pixels, Landsat satellite data may supplement traditional <i>in situ</i> sampling by providing data for most U.S. lakes, reservoirs, and estuaries over consistent seasonal intervals (even with cloud cover) for an extended period of record of more than 35 years.
Direct Manufacturing of Metal Prototypes and Prototype Tools (2018)

Due to the limited mechanical characteristics of the materials which can currently be\nprocessed using industrially available Rapid Prototyping machines, a lot of research is focused on\nthe development of techniques which allow a direct manufacturing of metallic parts. These\ninclude Selective Laser Sintering and Controlled Metal Build Up. Both methods produce the\nworkpiece not by removal of material but by a layerwise deposition and local melting or sintering\nof a powder material without part-specific tooling.\nControlled Metal Build Up is a new Rapid Prototyping technique similar to Fused\nDeposition Modeling combining laser generating/welding with conventional 2Y2 dimensional\nmilling. Due to the excellent surface quality and high dimensional and form accuracy achievable\nwith Controlled Metal Build Up, this technology offers an interesting alternative to the\nconventional time consuming processes for the manufacture of prototype tools required for\nlimited production runs.\nWith respect to Selective Laser Sintering, a test facility was developed for experimental\ninvestigations into the direct sintering of low and high melting metallic powders without the use\nof a polymer binder as well as ceramic powders. Great potential is expected from Selective Laser\nSintering concerning the prototyping of molds and dies.\nThis paper will discuss current developments for these two techniques as well as point out\npossible applications and future developments.
Microfabrication and Characterization of Diaphorase-Patterned Surfaces by Scanning Electrochemical Microscopy (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrofabrication and Characterization of Diaphorase-Patterned Surfaces by Scanning Electrochemical MicroscopyHitoshi. Shiku, Toshihiro. Takeda, Hiroshi. Yamada, Tomokazu. Matsue, and Isamu. UchidaCite this: Anal. Chem. 1995, 67, 2, 312–317Publication Date (Print):January 15, 1995Publication History Published online1 May 2002Published inissue 15 January 1995https://pubs.acs.org/doi/10.1021/ac00098a014https://doi.org/10.1021/ac00098a014research-articleACS PublicationsRequest reuse permissionsArticle Views468Altmetric-Citations122LEARN 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
Preparation, properties and thermal control applications of silica aerogel infiltrated with solid–liquid phase change materials (2011)

In this study, silica aerogel saturated with erythritol as phase change materials (PCMs) was prepared by melt infiltration. The properties of the composite were determined by scanning electronic microscope (SEM), Fourier transformation-infrared spectroscope (FT-IR) and differential scanning calorimeter (DSC). In the novel composite, erythritol with high latent heat of fusion was used as PCM for thermal control, whereas nanoporous silica aerogel was prepared as the phase change matrix to provide structural strength and prevent leakage of the melted erythritol. Nitrogen gas adsorption curves and SEM analysis indicate that the pore structure of silica aerogel was porous and connected with each other. FT-IR analysis showed that the composite formation of silica aerogel and erythritol were physical, whereas DSC analysis showed that the melting point and heat storage capacity of the composite were 123.8°C and 289.92 kJ/kg, respectively. The thermal protection properties of phase change composites were designed under laboratory conditions using a thermal measurement setup of a simulated thermal environment of an aircraft. The phase change composite produced by the study can be used for thermal protection applications. Compared with the paraffin–silica aerogel composite, the erythritol–silica aerogel composite could rapidly control the rising temperature by absorbing heat under high thermal environments.
MR image reconstruction using deep learning: evaluation of network structure and loss functions (2019)

CNN image reconstruction using Resnet yields comparable image quality to Unet with 10X the number of parameters. This has implications for training with significantly lower data requirements. Network training using the perceptual loss function was found to better agree with radiologist scoring compared to L1, L2 or Dssim loss functions.
Minimal inhibitory concentrations of various antimicrobial agents for human oral anaerobic bacteria (1983)

The minimal inhibitory concentrations of a series of antimicrobial agents for human oral organisms were determined under anaerobic growth conditions by an agar dilution assay. With the exception of black-pigmented Bacteroides spp., minimal inhibitory concentrations for oral isolates were similar to those for non-oral isolates of organisms of the same or closely related species.
Normal pattern and physiological significance of mitral valve flow velocity recorded using transseptal directional Doppler ultrasound catheterization. (1975)

In 10 cardiac patients in whom an organic lesion of the mitral valve was exluded by standard investigation procedures during which a diagnostic transseptal catheterization for pressure measurements in the left heart was performed, the authors placed a directional Doppler ultrasonic catheter tip velocimeter at the site of the mitral ring and recorded the mitral flow velocity traces. The pattern of these normal curves is presented and a physiological interpretation proposed. The relation between the mitral flow velocity and low volume curves is discussed in the light of present experimental data on mitral valve flow velocity profiles and variations in size of the mitral orifice. The authors concluded that the flow velocity curves obtained by the Doppler technique constitute a valid physiological reference system for the study of the mitral valve flow velocity tracings that can be recorded in the various forms of mitral valve disease.
Two Tree-Based Algorithms for Network Spare Capacity Design (2007)

Survivable network design has become increasingly important due to the need for reliable communication service. Its main purpose is to provide cost-efficient spare capacity reservation at certain survivability level. In this paper, we introduce two pre-planned path restoration algorithms for spare capacity design in mesh-like networks. First one is a spanning tree based algorithm, which needs less spare capacity than the well known hierarchical tree algorithm while keeping the same level of restorability. The second algorithm is a cycle based tree algorithm with backup parents and extra cycle edges, which forms cycles with the original spanning tree edges. Simulation results show that this algorithm works much better than the other two algorithms on restorability. Both algorithms have time complexity O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) and space complexity O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), where n is the total number of nodes in the network.
Polarization Characteristics of Single-Mode Fiber Couplers (1982)

The polarization characteristics of fiber couplers made of birefringent single-mode fibers are studied. The effect of anisotropic interfiber coupling, fiber birefringence, angular misalignment of fibers, and twisting on the coupler characteristics are identified. The polarization characteristics of the couplers are compared with that of isolated uncoupled fibers of the same birefringence and length. The equivalent lumped element representations for three classes of fiber couplers are also presented.
Fluorescence quenching: A tool for single-molecule protein-folding study (2000)

By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The unfolded titin molecules with multiple dye molecules attached are able to fold to the native state. In the native folded state, the fluorescence from dye molecules is quenched due to the close proximity between the dye molecules. Unfolding of the titin leads to a dramatic increase in the fluorescence intensity. Such a change makes the folded and unfolded states of a single titin molecule clearly distinguishable and allows us to measure the folding dynamics of individual titin molecules in real time. We have also shown that fluorescence quenching can signal folding and unfolding of a small protein with only one immunoglobulin domain.