gebhart/patrepeval huggingface dataset:
Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience (2018)

Abstract Background Clinical genome and exome sequencing ( CGES ) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X‐linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed. Methods Representatives from 11 projects in the clinical sequencing exploratory research ( CSER ) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project‐specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects. Results The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results. Conclusion Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.
Estimating diffusion coefficients of dense fluids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEstimating diffusion coefficients of dense fluidsMohammad R. Riazi and Curtis H. WhitsonCite this: Ind. Eng. Chem. Res. 1993, 32, 12, 3081–3088Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/ie00024a018https://doi.org/10.1021/ie00024a018research-articleACS PublicationsRequest reuse permissionsArticle Views1190Altmetric-Citations117LEARN 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
Rate of Glutamate Synthesis from Leucine in Rat Brain Measured In Vivo by 15N NMR (1998)

The rate of glutamate synthesis from leucine by the branched-chain aminotransferase was measured in rat brain in vivo at steady state. The rats were fed exclusively by intravenous infusion of a nutrient solution containing [15N]leucine. The rate of glutamate synthesis from leucine, determined from the rate of increase of brain [15N]glutamate measured by 15N NMR and the 15N enrichments of brain and blood leucine analyzed by gas chromatography-mass spectrometry, was 0.7-1.8 micromol/g/h at a steady-state brain leucine concentration of 0.25 micromol/g. A comparison of the observed fractional 15N enrichments of brain leucine (0.42 +/- 0.03) and glutamate (0.21 +/- 0.015) showed that leucine provides approximately 50% of glutamate nitrogen under our experimental condition. From the observed rate (0.7-1.8 micromol/g) and the known Km of the branched-chain aminotransferase for leucine (1.2 mM), the rate of glutamate synthesis from leucine at physiological brain leucine concentration (0.11 micromol/g) was estimated to be 0.35-0.9 micromol/g/h, with leucine providing approximately 25% of glutamate nitrogen. The results strongly suggest that plasma leucine from dietary source, transported into the brain, is an important external source of nitrogen for replenishment of brain glutamate in vivo. Implications of the results for treatment of maple-syrup urine disease patients with leucine-restricted diet are discussed.
First and Second Law Analyses of a Naturally-Aspirated, Miller Cycle, SI Engine with Late Intake Valve Closure (1998)

&lt;div class="htmlview paragraph"&gt;A naturally-aspirated, Miller cycle, Spark-Ignition (SI) engine that controls output with variable intake valve closure is compared to a conventionally-throttled engine using computer simulation. Based on First and Second Law analyses, the two load control strategies are compared in detail through one thermodynamic cycle at light load conditions and over a wide range of loads at 2000 rpm. The Miller Cycle engine can use late intake valve closure (LIVC) to control indicated output down to 35% of the maximum, but requires supplemental throttling at lighter loads. The First Law analysis shows that the Miller cycle increases indicated thermal efficiency at light loads by as much as 6.3%, primarily due to reductions in pumping and compression work while heat transfer losses are comparable. The Second Law analysis shows that the throttling process in the conventional engine destroys up to 3% of the available energy in the fuel, and that the phasing of the heat transfer losses is more costly to its work producing potential. Overall, the availability analysis recognizes that the higher pressure in the LIVC intake manifold leads to a notable thermomechanical advantage, which the throttled engine has to overcome by consuming more chemical availability to achieve the same load.&lt;/div&gt;
Volar Rim Fractures of the Distal Radius: Can We Reduce the Complications and Need for Revision Surgery? (2022)

Over the last couple of years there has been an increasing focus on the importance of volar rim fractures, and a better understanding of the poor clinical outcomes, due to associated instabilities, failure of fixation, and the need for revision surgery.[1]
Measurements of the Higgs boson inclusive and differential fiducial cross sections in the 4$$\ell $$ decay channel at $$\sqrt{s}$$ = 13 TeV (2020)

Abstract Inclusive and differential fiducial cross sections of the Higgs boson are measured in the $$H \rightarrow ZZ^{*} \rightarrow 4\ell $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>H</mml:mi> <mml:mo>→</mml:mo> <mml:mi>Z</mml:mi> <mml:msup> <mml:mi>Z</mml:mi> <mml:mrow> <mml:mrow/> <mml:mo>∗</mml:mo> </mml:mrow> </mml:msup> <mml:mo>→</mml:mo> <mml:mn>4</mml:mn> <mml:mi>ℓ</mml:mi> </mml:mrow> </mml:math> ( $$\ell = e,\mu $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>ℓ</mml:mi> <mml:mo>=</mml:mo> <mml:mi>e</mml:mi> <mml:mo>,</mml:mo> <mml:mi>μ</mml:mi> </mml:mrow> </mml:math> ) decay channel. The results are based on proton-proton collision data produced at the Large Hadron Collider at a centre-of-mass energy of 13 TeV and recorded by the ATLAS detector from 2015 to 2018, equivalent to an integrated luminosity of 139 $$\hbox {fb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mtext>fb</mml:mtext> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:math> . The inclusive fiducial cross section for the $$H \rightarrow ZZ^{*} \rightarrow 4\ell $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>H</mml:mi> <mml:mo>→</mml:mo> <mml:mi>Z</mml:mi> <mml:msup> <mml:mi>Z</mml:mi> <mml:mrow> <mml:mrow/> <mml:mo>∗</mml:mo> </mml:mrow> </mml:msup> <mml:mo>→</mml:mo> <mml:mn>4</mml:mn> <mml:mi>ℓ</mml:mi> </mml:mrow> </mml:math> process is measured to be $$\sigma _\mathrm {fid} = 3.28 \,{\pm }\, 0.32$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>σ</mml:mi> <mml:mi>fid</mml:mi> </mml:msub> <mml:mo>=</mml:mo> <mml:mn>3.28</mml:mn> <mml:mspace/> <mml:mo>±</mml:mo> <mml:mspace/> <mml:mn>0.32</mml:mn> </mml:mrow> </mml:math> fb, in agreement with the Standard Model prediction of $$\sigma _\mathrm {fid, SM} = 3.41 \pm 0.18 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>σ</mml:mi> <mml:mrow> <mml:mi>fid</mml:mi> <mml:mo>,</mml:mo> <mml:mi>SM</mml:mi> </mml:mrow> </mml:msub> <mml:mo>=</mml:mo> <mml:mn>3.41</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.18</mml:mn> </mml:mrow> </mml:math> fb. Differential fiducial cross sections are measured for a variety of observables which are sensitive to the production and decay of the Higgs boson. All measurements are in agreement with the Standard Model predictions. The results are used to constrain anomalous Higgs boson interactions with Standard Model particles.
Endoscopic ultrasound-assisted endoscopic submucosal dissection of a gastric subepithelial tumor (2013)

The malignant potential of subepithelial lesions is difficult to establish before resection. Concerns regarding endoscopic submucosal dissection (ESD) of subepithelial lesions arising from the muscularis propria include adequacy of oncologic resection and perforation risk [1] [2] [3] [4] [5]. We describe a case where precise endoscopic ultrasound (EUS)-guided injection into the muscularis propria allowed complete endoscopic resection of a gastric subepithelial lesion otherwise deemed inappropriate for ESD due to the extent of involvement of the muscularis propria.
X-ray and vacuum ultraviolet imaging for electron cyclotron resonance processing plasmas (1993)

Electron cyclotron resonance (ECR) plasma systems are currently being investigated for plasma etching and plasma enhanced chemical vapor deposition. ECR generates high charged-particle densities at lower operating pressures which permits a higher degree of directionality for plasma etching, but produces low-energy x rays and vacuum ultraviolet radiation (VUV). Both types of radiation may cause damage to the wafer being processed. To reduce or shield the radiation damage, one would need to determine the spectrum and locations where the radiation is produced. The regions of radiation production can be determined by the image obtained from a pinhole camera placed along and across the center line of the dc magnetic field. The location of x-ray production could be changed by altering the shape of the dc magnetic field. The results verify that x rays are produced whenever hot electrons that travel along magnetic field lines strike the chamber walls. Similar methods were used to image the VUV radiation. The images show that the VUV is produced over the entire bulk plasma in addition to locations of wall bremsstrahlung where the x rays were produced.
Formation of lanthanum strontium cobalt thin films by metalorganic decomposition (1994)

Electrically conductive films of La0.5Sr0.5CoO3, 1 μm thick, were formed on a variety of substrates by metalorganic decomposition. The lowest resistivity films (1.2×10−3 Ω cm) were obtained on c-axis sapphire by annealing in oxygen at 800 °C. The film conductivity was limited by the diffusion of strontium into the substrate.
Registration of 2D x-ray images to 3D MRI by generating pseudo-CT data (2011)

Spatial and soft tissue information provided by magnetic resonance imaging can be very valuable during image-guided procedures, where usually only real-time two-dimensional (2D) x-ray images are available. Registration of 2D x-ray images to three-dimensional (3D) magnetic resonance imaging (MRI) data, acquired prior to the procedure, can provide optimal information to guide the procedure. However, registering x-ray images to MRI data is not a trivial task because of their fundamental difference in tissue contrast. This paper presents a technique that generates pseudo-computed tomography (CT) data from multi-spectral MRI acquisitions which is sufficiently similar to real CT data to enable registration of x-ray to MRI with comparable accuracy as registration of x-ray to CT. The method is based on a k-nearest-neighbors (kNN)-regression strategy which labels voxels of MRI data with CT Hounsfield Units. The regression method uses multi-spectral MRI intensities and intensity gradients as features to discriminate between various tissue types. The efficacy of using pseudo-CT data for registration of x-ray to MRI was tested on ex vivo animal data. 2D-3D registration experiments using CT and pseudo-CT data of multiple subjects were performed with a commonly used 2D-3D registration algorithm. On average, the median target registration error for registration of two x-ray images to MRI data was approximately 1 mm larger than for x-ray to CT registration. The authors have shown that pseudo-CT data generated from multi-spectral MRI facilitate registration of MRI to x-ray images. From the experiments it could be concluded that the accuracy achieved was comparable to that of registering x-ray images to CT data.
Parathyroid hormone-related peptide incrases urinary phosphate excretion in fetal lambs (1992)

International audience
CT of the solitary pulmonary nodule (1980)

Computed tomography (CT) with thin sections (2-5 mm) was used to assess tissue density in 91 apparently noncalcified pulmonary nodules in 88 patients. The study included 45 primary lung malignancies and 13 metastases proven by subsequent lung biopsy or thoracotomy. There were 33 benign lesions of which 13 were biopsy proven. The other 20 nodules were presumed benign on the basis of serial radiography showing no growth. A representative CT number based on the 32 most dense voxels was calculated for each lesion. For the primary malignancies, the mean representative CT number was 92 H, with a standard deviation of 18 H. The highest representative CT number for any malignant lesion was 147 H. Of the 33 benign lesions, 20 had a representative CT number of 164 H or greater. It is presumed that nodules with representative CT numbers of 164 H are benign, and that diffuse calcification likely accounts for the higher CT number of some benign lesions. CT has proven to be more objective and more sensitive than standard tomography in assessing the density of pulmonary nodules.
High Frequency Thermoacoustic Modulation Mechanisms in Swirl-Stabilized Gas Turbine Combustors: Part One — Experimental Investigation of Local Flame Response (2016)

This paper presents the experimental approach for determination and validation of non-compact flame transfer functions of high frequency, transverse combustion instabilities observed in a generic lean premixed gas turbine combustor. The established non-compact transfer functions describe the interaction of the flame’s heat release with the acoustics locally, which is necessary due to the respective length scales being of the same order of magnitude. Spatio-temporal dynamics of the flame are measured by imaging the OH* chemiluminescence signal, phase-locked to the dynamic pressure at the combustor’s front plate. Radon transforms provide a local insight into the flame’s modulated reaction zone. Applied to different burner configurations, the impact of the unsteady heat release distribution on the thermoacoustic driving potential, as well as distinct flame regions that exhibit high modulation intensity are revealed. Utilizing these spatially distributed transfer functions within thermoacoustic analysis tools (addressed in this joint publication’s part two) allows then to predict transverse linear stability of gas turbine combustors.
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting (2006)

The signal recognition particle (SRP) cotranslationally targets proteins to cell membranes by coordinated binding and release of ribosome-associated nascent polypeptides and a membrane-associated SRP receptor. GTP uptake and hydrolysis by the SRP-receptor complex govern this targeting cycle. Because no GTPase-activating proteins (GAPs) are known for the SRP and SRP receptor GTPases, however, it has been unclear whether and how GTP hydrolysis is stimulated during protein trafficking in vivo. Using both biochemical and genetic experiments, we show here that SRP RNA enhances GTPase activity of the SRP-receptor complex above a critical threshold required for cell viability. Furthermore, this stimulation is a property of the SRP RNA tetraloop. SRP RNA tetraloop mutants that confer defective growth phenotypes can assemble into SRP-receptor complexes, but fail to stimulate GTP hydrolysis in these complexes in vitro. Tethered hydroxyl radical probing data reveal that specific positioning of the RNA tetraloop within the SRP-receptor complex is required to stimulate GTPase activity to a level sufficient to support cell growth. These results explain why no external GAP is needed and why the phylogenetically conserved SRP RNA tetraloop is required in vivo.
Zeolite Synthesis Modelling with Support Vector Machines: A Combinatorial Approach (2007)

This work shows the application of support vector machines (SVM) for modelling and prediction of zeolite synthesis, when using the gel molar ratios as model input (synthesis descriptors). Experimental data includes the synthesis results of a multi-level factorial experimental design of the system TEA:SiO2:Na2O:Al2O3:H2O. The few parameters of the SVM model were studied and the fitting performance is compared with the ones obtained with other machine learning models such as neural networks and classification trees. SVM models show very good prediction performances and generalization capacity in zeolite synthesis prediction. They may overcome overfitting problems observed sometimes for neural networks. It is also studied the influence of the type of material descriptors used as model output.
Increased mutation rate and interlocus gene conversion within human segmental duplications (2022)

ABSTRACT Single-nucleotide variants (SNVs) within segmental duplications (SDs) have not been systematically assessed because of the difficulty in mapping short-read sequence data to virtually identical repetitive sequences. Using 102 phased human haplotypes, we constructed 1:1 unambiguous alignments spanning high-identity SDs and compared the pattern of SNVs between unique and SD regions. We find that human SNVs are elevated 60% in SDs compared to unique regions. We estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with &gt;7 Mbp of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of ~800 protein-coding genes. The latter includes 171 genes that have “relocated” on average 1.61 Mbp in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are evolutionarily older when compared to unique sequences with most of this signal originating from putative IGC loci. SNVs within SDs, however, also exhibit a distinct mutational spectrum where there is a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts. In addition, we observe a 7.6% reduction in the frequency of CpG associated mutations when compared to unique DNA. We hypothesize that these distinct mutational properties help to maintain an overall higher GC content of SD DNA when compared to unique DNA, and we show that these GC-favoring mutational events are likely driven by GC-biased conversion between paralogous sequences.
Peptide conformations. 28. Relayed heteronuclear correlation spectroscopy and conformational analysis of cyclic hexapeptides containing the active sequence of somatostatin (1983)

Homo- and heteronuclear 2-dimensional NMR techniques were used to assign the 1H and 13C NMR spectra of title cyclic peptides cyclo[Phe7-D-Trp-Lys(COCH2Ph)-Thr-X11-Pro6] [X = Gly (I), Phe (II)] in Me2SO. Unequivocal assignments of C resonances of Trp and Phe in II could only be obtained by heteronuclear relayed spectroscopy. II has a bII' turn at Phe7...Thr and a bVI turn at Thr...Phe7 including a cis peptide bond between Phe11 and Pro6. Substitution of Phe11 by Gly to give I results in a dramatic change in the conformation; 2 species of I exist in a slow equil. (70:30) in which the major isomer has a trans Gly-Pro bond. The technique of relayed heteronuclear correlation spectroscopy and an improved pulse sequence are described. [on SciFinder (R)]
Retinoic acid receptor-targeted drugs in neurodegenerative disease (2020)

New approaches to understanding retinoid's mechanisms of action, including non-genomic pathways, and how these mechanisms interact may prove vital in the development of future retinoid-based neurodegenerative disease treatments.