gebhart/patrepeval huggingface dataset:
<i>Asaia</i> , a versatile acetic acid bacterial symbiont, capable of cross‐colonizing insects of phylogenetically distant genera and orders (2009)

Bacterial symbionts of insects have been proposed for blocking transmission of vector-borne pathogens. However, in many vector models the ecology of symbionts and their capability of cross-colonizing different hosts, an important feature in the symbiotic control approach, is poorly known. Here we show that the acetic acid bacterium Asaia, previously found in the malaria mosquito vector Anopheles stephensi, is also present in, and capable of cross-colonizing other sugar-feeding insects of phylogenetically distant genera and orders. PCR, real-time PCR and in situ hybridization experiments showed Asaia in the body of the mosquito Aedes aegypti and the leafhopper Scaphoideus titanus, vectors of human viruses and a grapevine phytoplasma respectively. Cross-colonization patterns of the body of Ae. aegypti, An. stephensi and S. titanus have been documented with Asaia strains isolated from An. stephensi or Ae. aegypti, and labelled with plasmid- or chromosome-encoded fluorescent proteins (Gfp and DsRed respectively). Fluorescence and confocal microscopy showed that Asaia, administered with the sugar meal, efficiently colonized guts, male and female reproductive systems and the salivary glands. The ability in cross-colonizing insects of phylogenetically distant orders indicated that Asaia adopts body invasion mechanisms independent from host-specific biological characteristics. This versatility is an important property for the development of symbiont-based control of different vector-borne diseases.
Measurement of the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mi>D</mml:mi><mml:mo>*</mml:mo></mml:msup><mml:mo stretchy="false">(</mml:mo><mml:mn>2010</mml:mn><mml:msup><mml:mo stretchy="false">)</mml:mo><mml:mo mathvariant="bold">+</mml:mo></mml:msup></mml:math>natural linewidth and the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mi>D</mml:mi><mml:mo>*</mml:mo></mml:msup><mml:mo stretchy="false">(</mml:mo><mml:mn>2010</mml:mn><mml:msup><mml:mo stretchy="false">)</mml:mo><mml:mo mathvariant="bold">+</mml:mo></mml:msup><mml:mo mathvariant="bold">−</mml:mo><mml:msup><mml:mi>D</mml:mi><mml:mn>0</mml:mn></mml:msup></mml:math>mass difference (2013)

We measure the mass difference, $\ensuremath{\Delta}{m}_{0}$, between the ${D}^{*}(2010{)}^{+}$ and the ${D}^{0}$ and the natural linewidth, $\ensuremath{\Gamma}$, of the transition ${D}^{*}(2010{)}^{+}\ensuremath{\rightarrow}{D}^{0}{\ensuremath{\pi}}^{+}$. The data were recorded with the BABAR detector at center-of-mass energies at and near the $\ensuremath{\Upsilon}(4S)$ resonance, and correspond to an integrated luminosity of approximately $477\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. The ${D}^{0}$ is reconstructed in the decay modes ${D}^{0}\ensuremath{\rightarrow}{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ and ${D}^{0}\ensuremath{\rightarrow}{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$. For the decay mode ${D}^{0}\ensuremath{\rightarrow}{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ we obtain $\ensuremath{\Gamma}=(83.4\ifmmode\pm\else\textpm\fi{}1.7\ifmmode\pm\else\textpm\fi{}1.5)\text{ }\text{ }\mathrm{keV}$ and $\ensuremath{\Delta}{m}_{0}=(145425.6\ifmmode\pm\else\textpm\fi{}0.6\ifmmode\pm\else\textpm\fi{}1.8)\text{ }\text{ }\mathrm{keV}$, where the quoted errors are statistical and systematic, respectively. For the ${D}^{0}\ensuremath{\rightarrow}{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ mode we obtain $\ensuremath{\Gamma}=(83.2\ifmmode\pm\else\textpm\fi{}1.5\ifmmode\pm\else\textpm\fi{}2.6)\text{ }\text{ }\mathrm{keV}$ and $\ensuremath{\Delta}{m}_{0}=(145426.6\ifmmode\pm\else\textpm\fi{}0.5\ifmmode\pm\else\textpm\fi{}2.0)\text{ }\text{ }\mathrm{keV}$. The combined measurements yield $\ensuremath{\Gamma}=(83.3\ifmmode\pm\else\textpm\fi{}1.2\ifmmode\pm\else\textpm\fi{}1.4)\text{ }\text{ }\mathrm{keV}$ and $\ensuremath{\Delta}{m}_{0}=(145425.9\ifmmode\pm\else\textpm\fi{}0.4\ifmmode\pm\else\textpm\fi{}1.7)\text{ }\text{ }\mathrm{keV}$; the width is a factor of approximately 12 times more precise than the previous value, while the mass difference is a factor of approximately 6 times more precise.
Figure S3 from The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas (2023)

&lt;p&gt;Figure S3 shows mutation signatures identified.&lt;/p&gt;
Cells Isolated from Cadaveric Bone Marrow are Safe for Use in Bone Healing and Effective at Promoting Osteogenic Re-construction (2017)

The efficacy and immune-modulation of mesenchymal stem cells is well documented. The issue of obtaining mesenchymal stem cells without patient risk, extensive intra-operative procedure, cell manipulation or exposure of cells to harmful reagents remains an issue. This study was designed to test the viability, composition and osteogenic potential of cells derived from cadaveric bone marrow by a new process. Vertebral bone from cadavers was collected within 24 hours of death, processed by a new procedure of tumbling and collection, and evaluated for viability, marker expression, cell composition, and inflammatory properties at various stages of the isolation process and following cryopreservation. Viability was excellent in all fractions and at all stages of the study. Cell staining and microscopic observation showed increased erythrocyte content in the first tumble of bone for marrow extraction, as well as gross observation of debris. Cryopreservation favored the preservation of CD45-/CD105+ and GlycoA-/STRO-1+ mesenchymal stem cells at the expense of platelets, red blood cells, white blood cells and neutrophils. The resulting cell solution contains a percentage of mesenchymal stem cells far above that required for immune modulation. A mixed lymphocyte reaction assay showed no inflammatory response to this cell composition. The cells produced and preserved in this manner are viable, should elicit no immune response, suppress recipient immune responses and osteogenically differentiate.
Long-Term Results following Cranial Hydroxyapatite Prosthesis Implantation in a Large Skull Defect Model (2011)

The hydroxyapatite prosthesis showed its osteoconductivity and good biocompatibility. A low rate of fibrous tissue formation and a high rate of bony regeneration were found.
A Spectral Approach to Gradient Estimation for Implicit Distributions. (2018)

Recently there have been increasing interests in learning and inference with implicit distributions (i.e., distributions without tractable densities). To this end, we develop a gradient estimator for implicit distributions based on Stein's identity and a spectral decomposition of kernel operators, where the eigenfunctions are approximated by the Nystrom method. Unlike the previous works that only provide estimates at the sample points, our approach directly estimates the gradient function, thus allows for a simple and principled out-of-sample extension. We provide theoretical results on the error bound of the estimator and discuss the bias-variance tradeoff in practice. The effectiveness of our method is demonstrated by applications to gradient-free Hamiltonian Monte Carlo and variational inference with implicit distributions. Finally, we discuss the intuition behind the estimator by drawing connections between the Nystrom method and kernel PCA, which indicates that the estimator can automatically adapt to the geometry of the underlying distribution.
Regression Tree Fields &amp;#x2014; An efficient, non-parametric approach to image labeling problems (2012)

We introduce Regression Tree Fields (RTFs), a fully conditional random field model for image labeling problems. RTFs gain their expressive power from the use of non-parametric regression trees that specify a tractable Gaussian random field, thereby ensuring globally consistent predictions. Our approach improves on the recently introduced decision tree field (DTF) model [14] in three key ways: (i) RTFs have tractable test-time inference, making efficient optimal predictions feasible and orders of magnitude faster than for DTFs, (ii) RTFs can be applied to both discrete and continuous vector-valued labeling tasks, and (Hi) the entire model, including the structure of the regression trees and energy function parameters, can be efficiently and jointly learned from training data. We demonstrate the expressive power and flexibility of the RTF model on a wide variety of tasks, including inpainting, colorization, denoising, and joint detection and registration. We achieve excellent predictive performance which is on par with, or even surpassing, DTFs on all tasks where a comparison is possible.
Polarization Capabilities and Status of TERRASAR-X (2009)

TerraSAR-X is the first German Radar satellite for scientific and commercial applications. The project is a public-private partnership between DLR and EADS Astrium GmbH. TerraSAR-X consists of a high resolution Synthetic Aperture Radar at X-Band. The radar antenna is based on active phased array technology that allows the control of many different instrument parameters and operational modes (Stripmap, ScanSAR and Spotlight) with various polarizations. The TerraSAR-X launch was the 15 June 2007. Only 4 days later the first image was delivered. The variety of TerraSAR-X polarization modes is reviewed and validation results of each mode are presented. The polarization modes include operational modes like dual-pol in Stripmap and Spotlight. Additionally there are experimental modes like twin polarization mode which is similar to the ASAR alternating polarization mode, or the full polarimetric mode which is realized in the TerraSAR-X Dual Receive Antenna configuration. The Dual Receiving Antenna Mode (DRA) of TerraSAR-X offers a high variety of interesting applications and experiments, e.g. along track interferometry, geometric resolution enhancement and especially the full polarimetric mode. In the DRA mode of TerraSAR-X, the complete antenna is used for transmission but in receive, the antenna is divided into two separate partitions in along track. The signals of both receiving antennas are recorded separately by exploiting the redundant receiver chain of the instrument. Both signals are not recorded separately but as sum and difference signal. This demands for special calibration in the reconstruction of fore and aft channel before SAR processing and has influence on the polarimetric performance. The paper provides a selection of TS-X images acquired in different polarization modes and thus demonstrates the polarimetric capabilities of TerraSAR-X. 

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DeepHeme: A generalizable, bone marrow classifier with hematopathologist-level performance (2023)

Morphology-based classification of cells in the bone marrow aspirate (BMA) is a key step in the diagnosis and management of hematologic malignancies. However, it is time-intensive and must be performed by expert hematopathologists and laboratory professionals. We curated a large, high-quality dataset of 41,595 hematopathologist consensus-annotated single-cell images extracted from BMA whole slide images (WSIs) containing 23 morphologic classes from the clinical archives of the University of California, San Francisco. We trained a convolutional neural network, DeepHeme, to classify images in this dataset, achieving a mean area under the curve (AUC) of 0.99. DeepHeme was then externally validated on WSIs from Memorial Sloan Kettering Cancer Center, with a similar AUC of 0.98, demonstrating robust generalization. When compared to individual hematopathologists from three different top academic medical centers, the algorithm outperformed all three. Finally, DeepHeme reliably identified cell states such as mitosis, paving the way for image-based quantification of mitotic index in a cell-specific manner, which may have important clinical applications.
Maximizing loop squareness by minimizing gradients in the microstructure (1999)

Enhanced energy product and higher operating fields can be achieved by improving the squareness of the demagnetization loop. In isotropic materials, increasing loop squareness can be achieved by minimizing microstructural gradients and maximizing homogeneity. Achieving homogeneity by melt spinning can be difficult due to localized changes in cooling conditions from extrinsic factors such as gas entrapment between the melt and the chill surface and intrinsic effects resulting from the stochastic nature of nucleation on a surface. These localized variations are reduced by altering the solidification kinetics of the alloy, thus reducing its sensitivity to localized changes in cooling conditions. This was achieved through development of a nine-element modified Nd–Fe–B alloy which solidified with a uniform glass structure at much lower cooling rates. After crystallization, enhanced microstructural homogeneity was verified by electron microscopy and described by parameters based on the loop shape. The nine-element alloy had squarer loops and uniformly high hard magnetic properties (&amp;gt;12 MG Oe) for cooling rates over 10 m/s.
Applications Of Neural Networks To Ocean Acoustic Tomography (2005)

Ocean acoustic tomography differs from medical ultrasound tomography and seismic tomography in that one must first understand the forward problem, that is, how the sound channel and the mesoscale feature refracts sound in three dimensions and how such refraction alters the pulse-arrival sequence. The parabolic equation (PE) model is used in the forward problem. A neural network is used to perform the inversion of tomography data. The author uses the feedforward neural network to implement the filtered back projection algorithm. The advantages are that one does not need to assume weak scattering and the instability problem of the frequency domain interpolation algorithm does not exist. >
Storage of Pure Hydrogen in Different States (2012)

This chapter contains sections titled: Purification of Hydrogen Compressed Hydrogen Liquid/Slush Hydrogen Metal Hydrides References
Elevated intracellular chloride level in albino visual cortex neurons is mediated by Na-K-Cl co-transporter (2008)

Our findings suggest that blocking of NKCC1 in albino visual cortex neurons could improve processing in visual cortex and therefore might be beneficial for vision in albinos.
Stereoselective synthesis of a 4-⍺-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S (2021)

Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identification of new classes of therapeutics. In these studies, we identified a 4-⍺-glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1-V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose-response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1-V279S by 65%. The synthetic route to 8 and a closely related 4-⍺-glucoside of validamine (7) was achieved starting from readily available D-maltose. A key step in the synthesis was a chelation-controlled addition of vinylmagnesium bromide to a maltose-derived enone intermediate. X-ray structures of both 7 and 8 in complex with Sco GlgE1-V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E<sub>2</sub> conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen-bonding contact from the pseudo-diaxial C(3)-OH to the catalytic nucleophile Asp 394 at the enzyme active site. Asp 394, in fact, forms a bidentate interaction with both the C(3)-OH and C(7)-OH of the inhibitor. In contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via steric interactions resulting in a conformation change in Asp 394. These findings will have implications for the design other aminocarbasugar-based GH13-inhibitors and will be useful for identifying more potent and selective inhibitors.
Effect ofglucose onplasma concentrations ofindividual non-esterified fatty acids ofnon-diabetic andinsulin-independent diabetic men (1981)

Summary Thecomposition ofplasma non-esterified fatty acids wasinvestigated during glucose tolerance tests to determine changes inindividual fatty acidconcentrations after glucose administration andtodetermine whether differences existed between theindividual fatty acidconcentrations ofmaturity-onset diabetic andnon-diabetic men.Themeanfasting total nonesterified fatty acidconcentration ofthe9diabetics wasgreater thanthatofthe12non-diabetics studied. After glucose ingestion, themeantotal non-esterified fatty acidconcentrations ofbothgroups decreased. Gaschromatographic analysis oftheplasmanonesterified fatty acids of6diabetic and6non-diabetic menrevealed thattheconcentrations ofpalmitic, stearic andoleic acids weresignificantly higher inthe diabetic meninthefasting state. Withthesole exception ofstearic acidinthenon-diabetic patients, themeanconcentration ofeachofthe6plasma nonesterified fatty acids determined decreased inboth groups after glucose ingestion. At1,2and3hrafter glucose ingestion, there werenolonger anysignificant differences betweenthemeanconcentrations of individual plasmanon-esterified fatty acidsofthe non-diabetic anddiabetic men.
Reactivity and Spectroscopy of the {Ru(DMAP)<sub>5</sub>} Fragment: An {Ru(NH<sub>3</sub>)<sub>5</sub>} Analogue (2008)

Reaction of trans-Ru(DMSO)4Cl2 with DMAP (DMAP = 4-dimethylaminopyridine) yields the yellow [Ru(DMAP)6](2+) cation in good yield. The crystal and molecular structure of [Ru(DMAP)6]Cl2.6CH3CH2OH was determined by X-ray diffraction methods. The complex crystallizes in the trigonal R3 space group with a = b = 16.373(1), c = 20.311(1) A, gamma = 120 degrees , and Z = 3 molecules per unit cell. The reaction of [Ru(DMAP)6](2+) in aerobic water gives the red [Ru(III)(DMAP)5(OH)](2+) cation. This complex shows a chemical behavior similar to [Ru(III)(NH3)5Cl](2+) and allows the preparation of a family of [Ru(DMAP)5L](n+) complexes. Their electronic properties indicate that the {Ru(II)(DMAP)5} fragment is a weaker pi-donor than {Ru(II)(NH 3)5}. Our density functional theory (DFT) calculations show that in {Ru(II)(DMAP)5} the DMAP ligands can compete for the pi electron density of the ruthenium making the fragment a weaker pi-donor.
Dexamethasone-Mediated Changes in Adipose Triacylglycerol Metabolism Are Exaggerated, Not Diminished, in the Absence of a Functional GR Dimerization Domain (2013)

The glucocorticoid (GC) receptor (GR) has multiple effector mechanisms, including dimerization-mediated transactivation of target genes via DNA binding and transcriptional repression mediated by protein-protein interactions. Much attention has been focused on developing selective GR modulators that would dissociate adverse effects from therapeutic anti-inflammatory effects. The GR(dim/dim) mouse has a mutation in the dimerization domain of GR and has been shown to have attenuated transactivation with intact repression. To understand the role of GR dimerization-dependent targets in multiple tissues, we measured metabolic fluxes through several disease-relevant GC target pathways using heavy water labeling and mass spectrometry in wild-type and GR(dim/dim) mice administered the potent GC dexamethasone (DEX). Absolute triglyceride synthesis was increased in both wild-type and GR(dim/dim) mice by DEX in the inguinal and epididymal fat depots. GR(dim/dim) mice showed an exaggerated response to DEX in both depots. De novo lipogenesis was also greatly increased in both depots in response to DEX in GR(dim/dim), but not wild-type mice. In contrast, the inhibitory effect of DEX on bone and skin collagen synthesis rates was greater in wild-type compared with GR(dim/dim) mice. Wild-type mice were more sensitive to DEX-dependent decreases in insulin sensitivity than GR(dim/dim) mice. Wild-type and GR(dim/dim) mice were equally sensitive to DEX-dependent decreases in muscle protein synthesis. Chronic elevation of GCs in GR(dim/dim) mice results in severe runting and lethality. In conclusion, some metabolic effects of GC treatment are exaggerated in adipose tissue of GR(dim/dim) mice, suggesting that selective GR modulators based on dissociating GR transactivation from repression should be evaluated carefully.
Regulation of in vivo Expression of Fc Receptors for IgE (FcεR) on Murine Lymphocytes (1990)

Homologous monomeric IgE was employed in a flow cytometric assay for the detection of IgE Fc receptors (Fc epsilon R) on mouse lymphocytes. The expression of Fc epsilon R in normal BALB/c mice was detected on splenic and circulating lymphocytes, but not on bone marrow cells. The Fc epsilon R expression was observed in B cells with B220, surface IgM, and IgD, but not in T cells. Infection of mice with Nippostrongylus brasiliensis resulted in a marked increase in the expression of Fc epsilon R on splenic B cells. T cells, however, did not express Fc epsilon R even after N. brasiliensis infection. On the other hand, the Fc epsilon R expression on normal B cells decreased after a simple incubation at 37 degrees C for 24 h, while in the presence of IgE this decrease was inhibited. In contrast, B cells stimulated with interleukin 4 display Fc epsilon R with high densities. Interestingly, IgE enhanced the Fc epsilon R expression induced by interleukin 4, suggesting that both interleukin 4 and IgE may be responsible for an increase in the expression of Fc epsilon R on B cells of N. brasiliensis infected mice.
Production of Highly Active Recombinant Dermonecrotic Toxin of Bordetella Pertussis (2020)

Pathogenic <i>Bordetella</i> bacteria release a neurotropic dermonecrotic toxin (DNT) that is endocytosed into animal cells and permanently activates the Rho family GTPases by polyamination or deamidation of the glutamine residues in their switch II regions (e.g., Gln63 of RhoA). DNT was found to enable high level colonization of the nasal cavity of pigs by <i>B. bronchiseptica</i> and the capacity of DNT to inhibit differentiation of nasal turbinate bone osteoblasts causes atrophic rhinitis in infected pigs. However, it remains unknown whether DNT plays any role also in virulence of the human pathogen <i>B. pertussis</i> and in pathogenesis of the whooping cough disease. We report a procedure for purification of large amounts of LPS-free recombinant DNT that exhibits a high biological activity on cells expressing the DNT receptors Cav3.1 and Cav3.2. Electron microscopy and single particle image analysis of negatively stained preparations revealed that the DNT molecule adopts a V-shaped structure with well-resolved protein domains. These results open the way to structure-function studies on DNT and its interactions with airway epithelial layers.