gebhart/patrepeval huggingface dataset:
Small change – big consequence: The impact of C15-C16 double bond in a D‑ring of estrone on estrogen receptor activity (2023)

Estrogen receptor alpha (ER) is a key biomarker for breast cancer, and the presence or absence of ER in breast and other hormone-dependent cancers decides treatment regimens and patient prognosis. ER is activated after ligand binding - typically by steroid. 2682 steroid compounds were used in a molecular docking study to identify novel ligands for ER and to predict compounds that may show anticancer activity. The effect of the most promising compounds was determined by a novel luciferase reporter assay. Two compounds, 7 and 12, showing ER inhibitory activity comparable to clinical inhibitors such as tamoxifen or fulvestrant were selected. We propose that the inhibitory effect of compounds 7 and 12 on ER is related to the presence of a double bond in their D-ring, which may protect against ER activation by reducing the electron density of the keto group, or may undergo metabolism leading to an active compound. Western blotting revealed that compound 12 decreased the level of ER in the breast cancer cell line MCF7, which was associated with reduced expression of both isoforms of the progesterone receptor, a well-known downstream target of ER. However, compound 12 has a different mechanism of action from fulvestrant. Furthermore, we found that compound 12 interferes with mitochondrial functions, probably by disrupting the electron transport chain, leading to induction of the intrinsic apoptotic pathway even in ER-negative breast cancer cells. In conclusion, the combination of computational and experimental methods shown here represents a rapid approach to determine the activity of compounds towards ER. Our data will not only contribute to research focused on the regulation of ER activity but may also be useful for the further development of novel steroid receptor-targeted drugs applicable in clinical practice.
Dual scattering approximation for fast multiple scattering in hair (2008)

When rendering light colored hair, multiple fiber scattering is essential for the right perception of the overall hair color. In this context, we present a novel technique to efficiently approximate multiple fiber scattering for a full head of human hair or a similar fiber based geometry. In contrast to previous ad-hoc approaches, our method relies on the physically accurate concept of the Bidirectional Scattering Distribution Functions and gives physically plausible results with no need for parameter tweaking. We show that complex scattering effects can be approximated very well by using aggressive simplifications based on this theoretical model. When compared to unbiased Monte-Carlo path tracing, our approximations preserve photo-realism in most settings but with rendering times at least two-orders of magnitude lower. Time and space complexity are much lower compared to photon mapping-based techniques and we can even achieve realistic results in real-time on a standard PC with consumer graphics hardware.
Sub-Terahertz Channel Measurements and Characterization in a Factory Building (2022)

Sub-Terahertz (THz) frequencies between 100 GHz and 300 GHz are being considered as a key enabler for the sixth-generation (6G) wireless communications due to the vast amounts of unused spectrum. The 3rd Generation Partnership Project (3GPP) included the indoor industrial environments as a scenario of interest since Release 15. This paper presents recent sub-THz channel measurements using directional horn antennas of 27 dBi gain at 142 GHz in a factory building, which hosts equipment manufacturing startups. Directional measurements with co-polarized and cross-polarized antenna configurations were conducted over distances from 6 to 40 meters. Omnidirectional and directional path loss with two antenna polarization configurations produce the gross cross-polarization discrimination (XPD) with a mean of 27.7 dB, which suggests that dual-polarized antenna arrays can provide good multiplexing gain for sub-THz wireless systems. The measured power delay profile and power angular spectrum show the maximum root mean square (RMS) delay spread of 66.0 nanoseconds and the maximum RMS angular spread of 103.7 degrees using a 30 dB threshold, indicating the factory scenario is a rich-scattering environment due to a massive number of metal structures and objects. This work will facilitate emerging sub-THz applications such as super-resolution sensing and positioning for future smart factories.
2P-171 Angle Dependence of the Affinity for Nucleotides in Rotary Motor F_1-ATPase(The 46th Annual Meeting of the Biophysical Society of Japan) (2008)

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Structure and dielectric properties of amorphous tantalum pentoxide thin film capacitors (2007)

Amorphous tantalum pentoxide films are currently being studied as a high-k dielectric for high energy-density Metal-Insulator-Metal capacitors. Tantalum pentoxide thin films were prepared through pulsed-dc reactive magnetron sputtering at a high deposition rate (15 Å/s). The films were amorphous as determined by X-ray and electron diffraction through Transmission Electron Microscopy (TEM) at all sputtering conditions of both low and high ion bombardments unlike other oxides such as zirconium oxide. The structure was also confirmed by electron energy loss spectra using anodized Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> films as a benchmark. After annealing at 750 °C, the films crystallized to the β-Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> phase (x-ray analysis). The dielectric constant and loss of the 2μm-thick films are 21 and 0.3%, respectively, at 1 kHz at room temperature of 25 °C. The amorphous films have a Temperature Coefficient of dielectric constant (TCK) of 2.1×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−3</sup> °C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> , similar to crystalline forms of Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> namely, α-Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> and β-Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> . Electrical breakdown field of these amorphous tantalum pentoxide films is as high as 400 MV/m with a corresponding energy density of 14 J/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . Electrical breakdown is affected by material crystallinity, which is controlled by annealing. The crystallinity is studied both at bulk level through X-Ray diffraction and at the local atomic level through Fluctuation Electron Microscopy (FEM), which is an electron microscopy technique used to study Medium Range Order (MRO) on the length scale of 1–3 nm in apparently diffraction amorphous (TEM and X-ray) materials.
CD Spectra of Indolicidin Antimicrobial Peptides Suggest Turns, Not Polyproline Helix (1999)

Indolicidin is a 13-residue antimicrobial peptide-amide isolated from the cytoplasmic granules of bovine neutrophils that contains five Trp and three Pro residues. Falla et al. [(1996) J. Biol. Chem. 271, 19298] suggested that indolicidin forms a poly-L-proline II helix based upon the circular dichroism (CD) spectra of a closely related peptide (indolicidin methyl ester). In contrast, we found no evidence of poly-L-proline II helix formation in the CD spectra of native indolicidin in various solvents or when bound to micelles and membranes [Ladokhin et al. (1997) Biophys. J. 72, 794]. We interpreted the spectra as arising from unordered and/or beta-turn structures, but noted a sharp negative band at 227 nm arising from the tryptophan residues that would mask spectral features characteristic of poly-L-proline II helix. We have reexamined this issue by means of CD measurements of native indolicidin and several of its analogues. None of the features characteristic of a poly-L-proline helix (or alpha- or 3(10)-helix) were observed for any of the peptides studied. To eliminate artifacts associated with tryptophan, we synthesized indolicidin-L and indolicidin-F in which all five tryptophans were replaced with leucines or phenylalanines, respectively. The changes in CD spectra of these Trp-free peptides upon transfer into membrane-like environments were found to be consistent with the formation of beta-turns. For the native indolicidin in SDS micelles, temperature increases resulted in a coupled diminution of two sharp bands, a negative one at 227 nm and a positive one at 217 nm. This phenomenon, which is absent in indolicidin-L variants with single Leu-->Trp substitutions, is consistent with exciton splitting produced by the stacking of indole rings. Type VI turns in model peptides in aqueous solution are known to be promoted by stacking interactions between cis-proline and neighboring aromatic residues [Yao et al. (1994) J. Mol. Biol. 243, 754]. Molecular modeling of indolicidin with a -Trp(6)-cis-Pro(7)-Trp(8)- type VIa turn demonstrated the feasibility of this turn conformation and revealed the possibility of an accompanying amphipathic structure. We therefore suggest that turn conformations are the principal structural motif of indolicidin and that these turns greatly enhance membrane activity.
Purkinje cell-specific males absent on the first ( mMof ) gene deletion results in an ataxia-telangiectasia-like neurological phenotype and backward walking in mice (2011)

The brains of ataxia telangiectasia (AT) patients display an aberrant loss of Purkinje cells (PCs) that is postulated to contribute to the observed deficits in motor coordination as well as in learning and cognitive function. AT patients have mutations in the ataxia telangiectasia mutated (ATM) gene [Savitsky et al. (1995) Science 268:1749-1753]. However, in Atm-deficient mice, the neurological defects are limited, and the PCs are not deformed or lost as observed in AT patients [Barlow et al. (1996) Cell 86:159-171]. Here we report that PC-specific deletion of the mouse males absent on the first (mMof) gene (Cre(-)), which encodes a protein that specifically acetylates histone H4 at lysine 16 (H4K16ac) and influences ATM function, is critical for PC longevity. Mice deficient for PC-specific Mof display impaired motor coordination, ataxia, a backward-walking phenotype, and a reduced life span. Treatment of Mof(F/F)/Pcp2-Cre(+) mice with histone deacetylase inhibitors modestly prolongs PC survival and delays death. Therefore, Mof expression and H4K16 acetylation are essential for PC survival and function, and their absence leads to PC loss and cerebellar dysfunction similar to that observed in AT patients.
Processes and Limitations during Filament Formation and Dissolution in GeSx-based ReRAM Memory Cells (2015)

The SET and RESET switching kinetics of Ag–GeSx-based ECM memory cells are experimentally investigated. The results were qualitatively and quantitatively reproduced by our simulation model, accounting for a tunneling gap between the tip of the growing filament and the active electrode. Key processes are the nucleation, the electron transfer at the interfaces, and ionic hopping in the electrolyte. Current–voltage sweeps and pulse measurements were used to study the switching kinetics with respect to variety of factors like voltage, current, resistance, time, electrolyte thickness, and stoichiometry. Multilevel operations through the adjustability of the ON resistance by current compliance and sweep rate were confirmed. The SET kinetics for low voltages was limited by the nucleation process. SET time and SET voltage strongly depend on the Ag-ion normalized concentration in the electrolyte. The RESET behavior was mostly independent of the current compliance and the ON resistance. However, lower ON resistances require higher RESET currents but at the same time the RESET time was independent of the ON resistance for nearly 2 orders of magnitude. By pulsed measurements of the RESET kinetics two voltage ranges in the RESET time versus RESET voltage behavior were identified for the first time. Limiting factors in these two ranges were found to be the electron transfer and the ion migration for low and high voltages, respectively.
The Effect of Nanoscale Confinement on the Collective Electron Transport Behavior in Au Nanoparticles Self‐Assembled in a Nanostructured Polystyrene‐block‐poly(4‐vinylpyridine) Diblock Copolymer Ultra‐thin Film (2007)

Abstract This study involves the collective electron transport behavior of sequestered Au nanoparticles in a nanostructured polystyrene‐ block ‐poly(4‐vinylpyridine). The monolayer thin films (ca. 30 nm) consisting of Au nanoparticles self‐assembled in the 30‐nm spherical poly(4‐vinylpyridine) domains of an polystyrene‐ block ‐poly(4‐vinylpyridine) diblock copolymer were prepared. From the current‐voltage characteristics of these thin films, the collective electron transport behavior of Au nanoparticles sequestered in the spherical poly(4‐vinylpyridine) nanodomains was found to be dictated by Coulomb blockade and was quasi one‐dimensional, as opposed to the three‐dimensional behavior displayed by Au nanoparticles that had been dispersed randomly in homo‐poly(4‐vinylpyridine). The threshold voltage of these composite increased linearly upon increasing the inter‐nanoparticle distance. The electron tunneling rate constant in the case of Au nanoparticles confined in poly(4‐vinylpyridine) nanodomains is eight times larger than that in the randomly distributed case and it increases upon increasing the amount of Au nanoparticles. This phenomenon indicates that manipulating the spatial arrangement of metal nanoparticles by diblock copolymer can potentially create electronic devices with higher performance.
Optical control of neuronal excitation and inhibition using a single opsin protein, ChR2 (2013)

The effect of electrical stimulation on neuronal membrane potential is frequency dependent. Low frequency electrical stimulation can evoke action potentials, whereas high frequency stimulation can inhibit action potential transmission. Optical stimulation of channelrhodopsin-2 (ChR2) expressed in neuronal membranes can also excite action potentials. However, it is unknown whether optical stimulation of ChR2-expressing neurons produces a transition from excitation to inhibition with increasing light pulse frequencies. Here we report optical inhibition of motor neuron and muscle activity in vivo in the cooled sciatic nerves of Thy1-ChR2-EYFP mice. We also demonstrate all-optical single-wavelength control of neuronal excitation and inhibition without co-expression of inhibitory and excitatory opsins. This all-optical system is free from stimulation-induced electrical artifacts and thus provides a new approach to investigate mechanisms of high frequency inhibition in neuronal circuits in vivo and in vitro.
ATP-Sensitive K+ Channel Knockout Compromises the Metabolic Benefit of Exercise Training, Resulting in Cardiac Deficits (2004)

Exercise training elicits a metabolic and cardiovascular response that underlies fitness. The molecular mechanisms that orchestrate this adaptive response and secure the wide-ranging gains of a regimented exercise program are poorly understood. Formed through association of the Kir6.2 pore and the sulfonylurea receptor, the stress-responsive ATP-sensitive K(+) channels (K(ATP) channels), with their metabolic-sensing capability and broad tissue expression, are potential candidates for integrating the systemic adaptive response to repetitive exercise. Here, the responses of mice lacking functional Kir6.2-containing K(ATP) channels (Kir6.2-KO) were compared with wild-type controls following a 28-day endurance swimming protocol. While chronic aquatic training resulted in lighter, leaner, and fitter wild-type animals, the Kir6.2-KO manifested less augmentation in exercise capacity and lacked metabolic improvement in body fat composition and glycemic handling with myocellular defects. Moreover, the repetitive stress of swimming unmasked a survival disadvantage in the Kir6.2-KO, associated with pathologic calcium-dependent structural damage in the heart and impaired cardiac performance. Thus, Kir6.2-containing K(ATP) channel activity is required for attainment of the physiologic benefits of exercise training without injury.
Camera Pose Voting for Large-Scale Image-Based Localization (2015)

Image-based localization approaches aim to determine the camera pose from which an image was taken. Finding correct 2D-3D correspondences between query image features and 3D points in the scene model becomes harder as the size of the model increases. Current state-of-the-art methods therefore combine elaborate matching schemes with camera pose estimation techniques that are able to handle large fractions of wrong matches. In this work we study the benefits and limitations of spatial verification compared to appearance-based filtering. We propose a voting-based pose estimation strategy that exhibits O(n) complexity in the number of matches and thus facilitates to consider much more matches than previous approaches - whose complexity grows at least quadratically. This new outlier rejection formulation enables us to evaluate pose estimation for 1-to-many matches and to surpass the state-of-the-art. At the same time, we show that using more matches does not automatically lead to a better performance.
Heart Disease in Infancy and Childhood (1967)

An interval of eight years separates the first and second editions of this book. There are over 300 additional pages in the new edition, primarily a consequence of updating most chapters. There are five new chapters; several have been totally redone, and the illustrations are improved. The book is well organized; the format is that of the usual clinical textbook. The subject material is appropriate although a few minor sections are of debatable significance. The exposition is uniformly clear; the writing, multi-authored, is "modern medical" in style. The bibliography is comprehensive. The most notable additions are the chapters on dextrocardia, single ventricle and chamber localization by R. Van Praagh. These represent an attempt to clarify inversions, transpositions, and single ventricles. The result is the most understandable discussion of these topics presently available. The effort put into the clear presentation of these difficult topics is appreciated. The chapter with the greatest
Highly Efficient Micromachined Bragg Mirrors Using Advanced DRIE Process (2006)

A novel advanced deep reactive ion etching (DRIE) process technique is used to realize highly efficient vertical Bragg mirrors. The Bragg mirrors are realized by anisotropic etching of Si using DRIE, thus producing successive vertical interfaces between Si and air. The new etching technique is based on combining 2 steps of cryogenic and Bosch DRIE processes to obtain high quality Si walls in terms of both: high aspect ratio vertical walls as well as smooth surface. The realized Bragg mirrors, fabrication process, as well as measured optical performance showing the advantages of the new technique are presented
Small CD4 mimetics sensitize HIV-1-infected macrophages to antibody-dependent cellular cytotoxicity (2022)

Summary HIV-1 Envelope (Env) conformation determines the susceptibility of infected CD4 + T cells to Antibody Dependent Cellular Cytotoxicity (ADCC). Upon interaction with CD4, Env adopts more “open” conformations, exposing ADCC epitopes. HIV-1 limits Env-CD4 interaction and protects infected cells against ADCC by downregulating CD4 via Nef, Vpu and Env. Limited data exists however of the role of these proteins in downmodulating CD4 on infected macrophages and how this impacts Env conformation. While Nef, Vpu and Env are all required to efficiently downregulate CD4 on infected CD4 + T cells, we show here that any one of these proteins is sufficient to downmodulate most CD4 from the surface of infected macrophages. Consistent with this finding, Nef and Vpu have a lesser impact on Env conformation and ADCC sensitivity in infected macrophages compared to CD4 + T cells. However, treatment of infected macrophages with small CD4-mimetics expose vulnerable CD4-induced Env epitopes and sensitize them to ADCC.
Supplementary Legends for Figures 1-8, Tables 1-3, Methods from Fibroblast Growth Factor Receptor 4 Regulates Tumor Invasion by Coupling Fibroblast Growth Factor Signaling to Extracellular Matrix Degradation (2023)

Supplementary Legends for Figures 1-8, Tables 1-3, Methods from Fibroblast Growth Factor Receptor 4 Regulates Tumor Invasion by Coupling Fibroblast Growth Factor Signaling to Extracellular Matrix Degradation
Immunological Comparison of Native and Recombinant Hen’s Egg Yolk Allergen, Chicken Serum Albumin (Gal d 5), Produced in Kluveromyces lactis (2018)

Chicken serum albumin (CSA) is a hen's egg yolk allergen causing IgE-mediated allergy. The objective of this study was to produce a recombinant version of CSA and compare its IgE reactivity to natural CSA (nCSA). CSA was cloned and expressed as a soluble fraction in the yeast <i>Kluyveromyces lactis</i> (<i>K. lactis</i>) protein expression system. The gene encoding CSA was amplified with a <i>C</i>-terminal hemagglutinin epitope tag by polymerase chain reaction (PCR) and cloned into the pKLAC2 expression vector prior to transforming into <i>K. lactis</i>. Recombinant CSA (rCSA) was purified by immunoprecipitation. Twenty-one patients allergic to hen's egg white were examined for sensitisation against nCSA. 38% of patients were found to be sensitised to CSA based on Western immunoassay. Immunoglobulin E (IgE) binding capacity of rCSA and nCSA was analysed by ELISA using sera from patients sensitised to CSA. Levels of IgE-binding were similar for both the recombinant and the natural CSA, indicating the existence of similar epitopes. rCSA produced in this study is a potential candidate to be used in component-resolved diagnosis (CRD) of egg yolk allergy. The usefulness of rCSA in CRD of egg yolk allergy warrants further characterisation using sera from patients with allergy to hen's egg yolk in future studies.