gebhart/patrepeval huggingface dataset:
Changes in starch physical characteristics following digestion of foods in the human small intestine (2010)

Factors controlling the concentration of resistant starch (RS) in foods are of considerable interest on account of the potential for this type of fibre to deliver health benefits to consumers. The present study was aimed at establishing changes in starch granule morphology as a result of human small-intestinal digestion. Volunteers with ileostomy consumed six selected foods: breakfast cereal (muesli), white bread, oven-baked French fries, canned mixed beans and a custard containing either a low-amylose maize starch (LAMS) or a high-amylose maize starch (HAMS). Analysis showed that digesta total RS (as a fraction of ingested starch) was: muesli, 8·9 %; bread, 4·8 %; fries, 4·2 %; bean mix, 35·9 %; LAMS custard, 4·0 %; HAMS custard, 29·1 %. Chromatographic analysis showed that undigested food contained three major starch fractions. These had average molecular weights (MW) of 43 500 kDa, 420 kDa and 8·5 kDa and were rich in amylopectin, higher-MW amylose and low-MW amylose, respectively. The low-MW amylose fraction became enriched preferentially in the stomal effluent while the medium-MW starch fraction showed the greatest loss. Fourier transform IR spectroscopy showed that absorbance at 1022 per cm decreased after digestion while the absorbance band at 1047 per cm became greater. Such changes have been suggested to indicate shifts from less ordered to more ordered granule structures. Further analysis of amylose composition by scanning iodine spectra indicated that the MW of amylose in ileal digesta was lower than that of undigested amylose. It appears that high-MW amylose is preferentially digested and that MW, rather than amylose content alone, is associated with resistance of starch to digestion in the upper gut of humans.
Applications of sonic waves in the estimation of petrophysical, geophysical and geomechanical properties of subsurface rocks (2008)

Sonic waves play an important role in estimating rock properties that are crucial in an efficient and safe production of oil and gas wells. An acoustic source in a fluid-filled borehole can generate both nondispersive headwaves as well as relatively stronger borehole guided modes. Processing of waveforms recorded with adequate spatial sampling yields sonic velocities in the surrounding formation over the receiver aperture. These velocities are then transformed into elastic moduli of the propagating medium. Elastic moduli of the formation provide many useful petrophysical, geophysical and geomechanical attributes of porous rocks that constitute hydrocarbon bearing formations. Petrophysical attributes of hydrocarbon bearing formations include porosity, pore pressure, and fluid mobility. Geophysical attributes of the formation deal with anisotropy characterization of formations on a seismic scale. Geomechanical properties of rock consists of estimating in-situ formation stresses and strengths as a function of radial position away from the borehole surface. Compressional velocity through a porous rock has been used to estimate porosity using Wyllie time-average equation whereby an interval transit time is decomposed into transit times in the solid and fluid components of the composite structure. Rock porosity can then be estimated using compressional velocity of the rock matrix and pore fluid in conjunction with measured velocity in the composite structure. There are well established correlations that help identify formation lithology in terms of the compressional to shear velocity ratio or the Poisson's ratio of the material. Plots of compressional to shear velocity ratio against compressional transit time help identify intervals containing limestone, dolomite, salt and quartz. Recent applications of elastic moduli of rocks in a reasonably uniform lithology are in the estimation of fluid mobility in porous rocks; formation stresses; and fracture characterization. The presence of a fluid-filled borehole in a tectonically stressed formation causes both radial and azimuthal heterogeneities in rock stresses. Formation stresses are estimated using an acoustoelastic model based on nonlinear continuum mechanics. This model predicts crossing dipole dispersions to be an indicator of stress differential in the borehole cross-sectional plane. In-situ rock strength can be estimated using radial variations of shear velocities obtained from the inversion of borehole dispersions. Estimates of rock stresses and strength help maintain wellbore stability during drilling and production.
Near-Field Radiative Transfer Between Heavily Doped SiGe at Elevated Temperatures (2011)

SiGe alloys represent an important type of high-temperature semiconductor material for solid-state energy conversion. In the present study, the near-field radiative heat transfer between heavily doped SiGe plates is investigated. A dielectric function model is formulated based on the previously reported room-temperature mobility and temperature-dependent electric resistivity of several silicon-rich alloys with different doping type and concentration. The fluctuational electrodynamics is used to evaluate the near-field noncontact heat transfer coefficient. The variation of the heat transfer coefficient with doping concentration and temperature is explained according to the change in the optical constants and in the spectral distribution of the near-field heat flux.
The Role of Mobility in the Substrate Binding and Catalytic Machinery of Enzymes (1983)

Recent theoretical and experimental studies have demonstrated that proteins are fluctuating systems capable of large, seemingly random, excursions from the equilibrium conformation. Attention is now focusing on the functional consequences of these motions. X-ray diffraction is a powerful tool for mapping the spatial distribution of protein dynamics; studies on the temperature dependence of the apparent Debye-Waller factors of crystalline myoglobin demonstrate that proteins are flexible in the solid state. Crystallographic studies of a Michaelis complex of ribonuclease A show that a mobile lysine adapts its conformation to the changes in stereochemistry and charge distribution in the substrate during catalysis. The structure of the triose phosphate isomerase-substrate complex shows that a mobile region of 10 amino acids becomes ordered when ligand binds. These studies suggest several roles for protein mobility in enzymic catalysis: providing access to internal sites, allowing changes in substrate structure during the reaction, and reducing the observed binding constant of substrate and product to the enzyme by decreasing entropy. A flexible enzyme also does not need a communication system to signal binding or transformation, since a pre-existing equilibrium can be used. More speculative ideas, such as the guiding of thermal vibrations along the reaction coordinate, can only be tested when more detailed data are available.
Obstructive thrombosis of an aortic root homograft (2005)

1010-7940/$ see front matter Q 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.ejcts.2005.02.021 * Corresponding author. Tel.: C32 16 344260; fax: C32 16 344616. E-mail address: steven.laga@uz.kuleuven.ac.be (S. Laga). revealed a large thrombus lodged in the right coronary cusp, causing right coronary ostium occlusion and partial left main stem stenosis (Figs. 1 and 2). European Journal of Cardio-thoracic Surgery 27 (2005) 1115 www.elsevier.com/locate/ejcts
Detection and Identification of Yeasts from Formalin-Fixed, Paraffin-Embedded Tissue by Use of PCR-Electrospray Ionization Mass Spectrometry (2013)

Diagnosis of yeast infection is typically accomplished by fungal smear and culture, histopathologic examination, and/or serologic studies. Newer assays based on mass spectrometry may be useful for yeast identification when histologic examination is inconclusive, fungal cultures are not ordered, or cultures fail to yield a causative agent. The purpose of this study was to evaluate the ability of the PLEX-ID broad fungal assay to accurately detect and identify yeasts in formalin-fixed paraffin-embedded (FFPE) tissues. Tissue samples from 78 FFPE specimens with both histopathology and corresponding culture results for a variety of yeasts were tested using the PLEX-ID broad fungal assay. A 40-μm FFPE tissue section from each specimen was digested with proteinase K followed by nucleic acid extraction and PCR using broad-range fungal primers. Yeast DNA in amplified products was identified using electrospray ionization mass spectrometry. Discordant results were resolved by D2 rRNA gene sequencing. PLEX-ID analysis detected yeast DNA in 78.2% (61/78) of the cases, of which 91.8% (56/61) were concordant with culture results. Of the 5 discordant positive results, 4 PLEX-ID results were considered to result from environmental contaminants, while 1 clinically important discrepancy was observed (Blastomyces dermatitidis by culture and Cryptococcus neoformans by PLEX-ID). Sequencing of the discordant sample was unsuccessful. The majority of histopathology results (89.7% [70/78]) correlated with culture results. The PLEX-ID broad fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional culture and histopathology tests.
Measurement of modal gain in 1.1 µm <i>p</i> -doped tunnel injection InGaAs/GaAs quantum dot laser heterostructures (2005)

Single-pass optical gain of self-assembled InGaAs/GaAs p-doped tunnel injection quantum dot laser heterostructures emitting at 1.1 µm is measured by the multisection device technique. The heterostructures, consisting of three layers of quantum dots in the active region, demonstrate net modal gain as high as 57 cm−1.
A phase lb, open-label, multicenter, dose-escalation study of the oral pan-PI3K inhibitor BKM120 in combination with the oral MEK1/2 inhibitor GSK1120212 in patients (pts) with selected advanced solid tumors. (2012)

3003 Background: MAPK and PI3K/AKT signaling pathways regulate proliferation, differentiation and cell death in human cancers. Known interaction between the 2 pathways provides the rationale for combining both inhibitors in a phase I study. Methods: The objective is to determine the maximum tolerated dose (MTD) and/or recommended phase II dose (RP2D) for oral, daily administered, BKM120 + GSK1120212, mainly in pts with tumors with RAS/RAF mutations (mt). A Bayesian logistic regression model with overdose control guides the dose escalation of the treatment. Secondary objectives include safety, tolerability, PK and efficacy. Results: As of 22.09.11, 49 pts were treated with BKM120 + GSK1120212 as follows: 30mg + 0.5mg, 60mg + 0.5mg, 60mg + 1.0mg, 60mg + 1.5mg, 60mg + 2.0mg, 70mg + 1.5mg, 80mg + 1.0mg, 80mg + 1.5mg. 6 pts had dose-limiting toxicities (DLTs); all were reversible. Grade 3 DLTs were: 3 x stomatitis, 1 x dysphagia, 1 x LVEF decrease, 1 x CK increase, 1 x nausea, 1 x anorexia, 1 x decreased oral intake. MTD and/or RP2D for the combination have not been reached. Most common adverse events (AEs) (&gt;25%), all grades and causality, were dermatitis acneiform, diarrhea (51% each); nausea (41%); vomiting (37%); rash (33%); asthenia (31%); CK increase, decreased appetite, pyrexia or stomatitis (29% each) and hyperglycemia (27%). There were 4 on-treatment deaths unrelated to treatment. AEs led to treatment discontinuation, 17 pts (35%) and interruptions/dose reductions, 25 pts (51%). Apparent steady-states of BKM120 and GSK1120212 were reached by day 28. Plasma concentrations of BKM120 in combination with GSK1120212 were lower than for monotherapy. Exposure to GSK1120212 with BKM120 was similar to that observed in monotherapy studies. 3 confirmed partial responses have been observed in pts with KRAS mt ovarian cancer; 2 lasting &gt;9 months. 2 patients with BRAF mt melanoma, who had previously progressed on BRAF inhibitors, had stable disease, for 1 of whom treatment is still ongoing in cycle 6. Conclusions: BKM120 and GSK1120212 can be safely combined. Signs of clinical activity have been seen in pts with RAS/RAF mt tumors.
Visual search in noise: Revealing the influence of structural cues by gaze-contingent classification image analysis (2006)

Visual search experiments have usually involved the detection of a salient target in the presence of distracters against a blank background. In such high signal-to-noise scenarios, observers have been shown to use visual cues such as color, size, and shape of the target to program their saccades during visual search. The degree to which these features affect search performance is usually measured using reaction times and detection accuracy. We asked whether human observers are able to use target features to succeed in visual search tasks in stimuli with very low signal-to-noise ratios. Using the classification image analysis technique, we investigated whether observers used structural cues to direct their fixations as they searched for simple geometric targets embedded at very low signal-to-noise ratios in noise stimuli that had the spectral characteristics of natural images. By analyzing properties of the noise stimulus at observers' fixations, we were able to reveal idiosyncratic, target-dependent features used by observers in our visual search task. We demonstrate that even in very noisy displays, observers do not search randomly, but in many cases they deploy their fixations to regions in the stimulus that resemble some aspect of the target in their local image features.
Improving the transient performance of a high penetration of LV connected microgeneration (2009)

This paper widens the knowledge about the microgeneration transient response under faulted conditions. The paper provides the following significant contributions: Firstly, a range of microgeneration transient models have been developed in PSCAD/EMTDC and tested on a typical distribution network. Two types of technologies are considered: a small diesel engine driving a three-phase synchronous machine connected within commercial premises; and a small microwind turbine interfaced directly within residential dwellings by a single-phase induction generator. Secondly, a valuable insight into the transient behavioral of this range of technologies during and after the clearing of remote faults at a medium voltage (MV) distribution system is provided, and their resilience levels are quantified. Thirdly, for reliable microgeneration operating in parallel with the distribution networks, the paper includes a discussion on some of remedial measures by which the transient stability of a large penetration of microgeneration may be improved. Also in this paper the inclusion of resistive superconducting fault current limiters into medium voltage distribution systems has been proposed as one of the practical solutions that can enhance the transient performance of large numbers of low voltage connected microgeneration. The effectiveness of fault current limiters on the grid-connected microgeneration transient stability enhancement has also been evaluated.
Engineering the Loop Region of a Homeodomain-Leucine Zipper Protein Promotes Efficient Binding to a Monomeric DNA Binding Site (2004)

Plant homeodomain-leucine zipper (HD-Zip) proteins, unlike many animal homeodomains (HDs), are unable to bind DNA as monomers. To investigate the molecular basis of their different behavior, we have constructed chimeras between the HD of the sunflower HD-Zip protein Hahb-4 and that of Drosophila engrailed (EN). Analysis of the interaction of these proteins with the pseudopalindromic Hahb-4 binding site and the monomeric EN binding site suggests that the loop located between helix I and helix II (amino acids 21-28) of EN is enough to confer efficient DNA binding activity to the Hahb-4 HD. Accordingly, the combined mutation of residues 24 and 25 of Hahb-4 to those present in EN (S24R/R25Y) originated an HD able to interact with the EN binding site, while single mutations were ineffective. We have also determined that a protein with the leucine zipper and helix III of Hahb-4 fused to the rest of the EN HD binds to the Hahb-4 pseudopalindomic binding site with increased affinity and shows extended contacts with DNA respective to Hahb-4. We conclude that the loop located between helix I and helix II of the HD must be regarded as one of the segments that contribute to the present-day diversity in the properties of different HDs.
Micromovements (2017)

Computer simulations of spike trains generated by brain neurons have been a useful tool to generate questions in the field of computational neuroscience. There is, however, a paucity of such methods in the study of complex behaviors, including analyses of kinematics parameters from movement trajectories embedded in natural purposeful behaviors. This chapter explores new data types and computational techniques leading to the simulation of patterns present in actual empirical data, along with synthetic patterns generated by computational models. We discuss their utility in setting normative bounds to compare modeled data with actual data obtained from individuals with the pathology of the developing nervous systems leading to a diagnosis of autism spectrum disorder (ASD).
Induced CD45 Proximity Potentiates Natural Killer Cell Receptor Antagonism (2022)

Abstract Natural Killer (NK) cells are a major subset of innate immune cells that are essential for host defense against pathogens and cancer. Two main classes of inhibitory NK receptors (NKR), KIR and CD94/NKG2A, play a key role in suppressing NK activity upon engagement with tumor cells or virus infected cells, limiting their antitumor and antiviral activity. Here, we find that single-chain mouse NKR antagonists linked to a VHH that binds the cell surface phosphatase CD45 potentiate NK and T activity to a greater extent than NKR blocking antibodies alone in vitro . We also uncovered crosstalk between mouse NKG2A and Ly49 that collectively inhibit NK cell activation, such that CD45-NKG2A and CD45-Ly49 bispecific molecules show synergistic effects in their ability to enhance NK cell activation. The basis of the activity enhancement by CD45 ligation may reflect greater antagonism of inhibitory signaling from engagement of MHC I on target cells, combined with other mechanisms, including avidity effects, tonic signaling, antagonism of weak inhibition from engagement of MHC I on non-target cells and possibly CD45 segregation within the NK cell-target cell synapse. These engineered ligands uncover a mechanism for enhancing the activity of mouse NK and T cells that merits evaluation in the context of human NKR antagonist cancer immunotherapies.
Impact of arterial input function selection on the accuracy of dynamic contrast‐enhanced MRI quantitative analysis for the diagnosis of clinically significant prostate cancer (2015)

W-AIF yielded a higher performance than FH-AIF and a similar or higher performance than Ind-AIF in distinguishing PCa from benign tissue.
Spontaneous and stimulated Raman scattering in silica-cladded silicon photonic crystal waveguides (2015)

We report the observation of spontaneous and stimulated Raman scattering in a silica-cladded silicon photonic crystal (PhC) waveguide (WG) with modified holes. Spontaneous Raman scattering in the WG was enhanced when the Stokes wavelength was approached to the bandedge of a WG mode. A maximum enhancement up to ∼5 times was obtained in the present work. At a Stokes wavelength in the lower group velocity region, nonlinear increase of the Stokes power as the pump power, a clear indication of the onset of stimulated Raman scattering, was observed. Moreover, Raman amplification with an external signal beam was also demonstrated. On–off gain becomes small as the Stokes wavelength gets away from the bandedge of the WG mode. These are the first observations of Raman scattering effects in silica-cladded silicon PhC structures.
Study of Nitrogen Effect on the Boron Diffusion during Heat Treatment in Polycrystalline Silicon/Nitrogen-Doped Silicon Thin Films (2011)

The present paper studies the boron (B) diffusion in nitrogen (N) doped amorphous silicon (a-Si) layer in original bi-layer B-doped polycrystalline silicon (poly-Si)/ in-situ N-doped Si layers (NIDOS) thin films deposited by low pressure chemical vapor deposition (LPCVD) technique. The B diffusion in the NIDOS layer was investigated by secondary ion mass spectrometry (SIMS) and Fourier transform infrared spectroscopy (FTIR) analysis. A new extended diffusion model is proposed to fit the SIMS profile of the bi-layer films. This model introduces new terms which take into account the effect of N concentration on the complex diffusion phenomena of B atoms in bi-layer films. SIMS results show that B diffusion does not exceed one third of NIDOS layer thickness after annealing. The reduction of the B diffusion in the NIDOS layer is due to the formation of complex B–N as shown by infrared absorption measurements. Electrical measurements using four-probe and Hall effect techniques show the good conductivity of the B-doped poly-Si layer after annealing treatment.
&lt;title&gt;Core-based boundary claiming&lt;/title&gt; (1994)

The core (defined in the accompanying paper by Morse) provides a means for characterizing the middle/width behavior of a figure, that is, an object or component thereof, directly from the image intensities and in a way insensitive to detail. The figures in question are either complete objects, contained subobjects, object protrusions, or object intrusions. The core provides the ability to claim regions of the image as including either the boundary information of an object or its protrusion or intrusion cores. The angulation in scale space, spatial position, and scale of a figure's core allows one to move from the core to a boundary at the scale of the figure. The core of protrusion and intrusion subfigures of the figure in question will intersect this boundary at the scale of the core. Moreover, if each point on the boundary at the scale of the core is blurred in proportion to the scale of the corresponding point on the core, a collar is formed within which the boundary of the figure can be found. We show how to find the collar and how stably to find the boundary, given the collar, even in noisy or blurred objects. This ability leads to an accurate, robust, automatic method of object area computation, and the generalization of this approach to 3D also provides the basis for efficient surface rendering and volume rendering.
Evidence of CD8 <sup>+</sup> T-Cell-Mediated Selective Pressure on Human Immunodeficiency Virus Type 1 <i>nef</i> in HLA-B*57 <sup>+</sup> Elite Suppressors (2008)

Elite suppressors (ES) are human immunodeficiency virus type 1 (HIV-1)-infected patients who maintain viral loads of <50 copies/ml without treatment. The observation that the HLA-B*57 allele is overrepresented in these patients implies that HIV-1-specific CD8(+) T cells play a key role in suppressing viral replication. We have previously shown that while CD8(+) T-cell escape mutations are rarely seen in proviral Gag sequences in resting CD4(+) T cells from peripheral blood, they are present in every clone amplified from the low levels of free virus in the plasma of HLA-B*57(+) ES. In this study, we compared the pattern of mutations in Nef sequences amplified from peripheral blood CD4(+) T cells and from plasma virus. We show that Nef mutations are present in plasma virus but are rare in the cellular sequences and provide evidence that these plasma Nef variants represent novel escape mutants. The results provide further evidence of CD8(+) T-cell-mediated selective pressure on plasma virus in ES and suggest that there must be ongoing HIV-1 replication in spite of the very low viral loads seen for these patients.