gebhart/patrepeval huggingface dataset:
Mechanical Property of Hydrogels and the Presence of Adipose Stem Cells in Tumor Stroma Affect Spheroid Formation in the 3D Osteosarcoma Model (2019)

Osteosarcoma is one of the most common metastatic bone cancers, which results in significant morbidity and mortality. Unfolding of effectual therapeutic strategies against osteosarcoma is impeded because of the absence of adequate animal models, which can truly recapitulate disease biology of humans. Tissue engineering provides an opportunity to develop physiologically relevant, reproducible, and tunable in vitro platforms to investigate the interactions of osteosarcoma cells with its microenvironment. Adipose-derived stem cells (ASCs) are detected adjacent to osteosarcoma masses and are considered to have protumor effects. Hence, the present study focuses on investigating the role of reactive ASCs in formation of spheroids of osteosarcoma cells (Saos 2) within a three-dimensional (3D) niche, which is created using gellan gum (GG)-silk fibroin. By modifying the blending ratio of GG-silk, the optimum stiffness of the resultant hydrogels such as GG and GG75: S25 is obtained for cancer spheroid formation. This work indicates that the co-existence of cancer and stem cells can form a spheroid, the hallmark of cancer, only in particular microenvironment stiffness. The incorporation of fibrillar silk fibroin within the hydrophilic network of GG in GG75: S25 spongy-like hydrogels closely mimics the stiffness of commercially established cancer biomaterials (e.g., Matrigel, HyStem). The GG75: S25 hydrogel maintains the metabolically active construct for a longer time with elevated expression of osteopontin, osteocalcin, RUNX 2, and bone sialoprotein genes, the biomarkers of osteosarcoma, compared to GG. The GG75: S25 construct also exhibits intense alkaline phosphatase expression in immunohistochemistry compared to GG, indicating itspotentiality to serve as biomimetic niche to model osteosarcoma. Taken together, the GG-silk fibroin-blended spongy-like hydrogel is envisioned as an alternative low-cost platform for 3D cancer modeling.
Prevention of fatigue cracks in ultrahigh molecular weight polyethylene joint components by the addition of vitamin E (1999)

Flaking-type wear, so-called delamination, is often observed in polyethylene joint components. This is thought to occur partly due to crack formation and propagation at grain boundaries. This study examined the effect of vitamin E on the crack formation and/or propagation in UHMWPE by using 2-dimensional sliding fatigue testing and micro indenter testing. An in vitro sliding fatigue test was performed under two simplified articulating movements, and the cracks produced were observed by scanning acoustic tomography (SAT). Gamma-irradiated ultrahigh molecular weight polyethylene (UHMWPE) specimens demonstrated a smaller area of accumulated cracks as compared to virgin specimens, when the loading movement was reciprocated on a single linear locus. However, four out of five gamma-irradiated UHMWPE specimens exhibited severe flaking-like destruction under the complicated sliding condition, suggesting that gamma irradiation accelerated crack propagation under multidirectional loading. All the gamma-irradiated vitamin-E-containing specimens demonstrated no subsurface crack formation and no flaking-like destruction. Results using micro indenter testing showed that the dynamic hardness at grain boundary was higher than that in grain, and was increased by gamma irradiation. This hardening at grain boundary was reduced by adding vitamin E. It is possible that the presence of vitamin E prevents crack propagation partly due to reduced hardness at grain boundaries. The gamma-irradiated vitamin-E-containing UHMWPE is a promising material to prevent flaking-like destruction of polyethylene joint components.
Characterization of the Surface Layer on a Strained Si Wafer by Electrochemical Methods (2008)

To assess the surface reactivity of strained Si wafers, open circuit potential (ocp) measurement and scanning surface potential microscopy (SPoM) were carried out. Surface conditions of the wafers were varied by changing the structure of the wafers, i.e., the Ge content of the SiGe underlayer and the thickness of the strained Si layer. The ocp value of the strained Si was negative compared with that of nonstrained Si, and it shifted in the negative direction with an increase in Ge content of the SiGe layer and/or in the thickness of the strained Si layer, indicating that the degree of strain and/or the density of defects at the Si wafer surface affect its reactivity. In addition, the ocp value shifted in the positive direction to reach the value of the nonstrained Si, possibility due to stress relaxation, when the thickness of strained Si exceeds a certain value, which is expected to be the “critical” thickness. The SPoM analysis confirmed that the negative potential shift takes place locally at the surface, whose contrast was associated with the crosshatchlike surface morphology, suggesting that there is nanoscopic difference in strain at the strained surface.
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update (2009)

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows 'on-the-fly' prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.
Reduced-dimension blind space-time 2-D RAKE receivers for DS-CDMA communication systems (2000)

Blind space-time RAKE receivers for classical DS-CDMA that cancel strong multiuser access interference while optimally combining the desired user's multipath are presented. The delay spread is assumed to be fraction of a symbol interval as in the IS-95 CDMA standard. The post-correlation symbol interval is segmented into that which encompasses the RAKE fingers and that away from the RAKE fingers. The signal-plus-interference and interference alone space-time correlation matrices are estimated during the former and latter, respectively. Reduced-dimension space-time RAKE receivers are investigated for alleviation of the computational burden of computing the largest generalized eigenvector of the resulting matrix pencil. Theoretical analysis and supporting simulations reveal that if the space and time compressing transformations are designed judiciously, reduced-dimension two-dimensional (2-D) RAKE receivers offer faster convergence at the expense of only a slight loss in asymptotic signal-to-interference-plus-noise ratio (SINR) relative to the full-dimension space-time RAKE receiver. Applications to the IS-95 uplink are also presented along with supporting simulations.
Controllable polarization splitting in liquid crystal infiltrated photonic crystals (2006)

Large and controllable polarization splitting effects are demonstrated based on liquid crystal infiltrated two-dimensional photonic crystals with silicon as a background material. Due to the strong birefringence of the liquid crystal, the dispersion curves of the two polarizations are distinctly different, resulting in large splitting between the two polarizations. Extremely large splitting, as large as 90 degree, can be obtained. Moreover, the splitting can be substantially tuned upon re-orienting the optic axis of liquid crystal. The influence of incident angle and the birefringence of the LC to the polarization splitting are also analyzed.
The Active Site of Cellobiohydrolase Cel6A fromTrichoderma reesei:  The Roles of Aspartic Acids D221 and D175 (2002)

Trichoderma reesei cellobiohydrolase Cel6A is an inverting glycosidase. Structural studies have established that the tunnel-shaped active site of Cel6A contains two aspartic acids, D221 and D175, that are close to the glycosidic oxygen of the scissile bond and at hydrogen-bonding distance from each other. Here, site-directed mutagenesis, X-ray crystallography, and enzyme kinetic studies have been used to confirm the role of residue D221 as the catalytic acid. D175 is shown to affect protonation of D221 and to contribute to the electrostatic stabilization of the partial positive charge in the transition state. Structural and modeling studies suggest that the single-displacement mechanism of Cel6A may not directly involve a catalytic base. The value of (D2O)(V) of 1.16 +/- 0.14 for hydrolysis of cellotriose suggests that the large direct effect expected for proton transfer from the nucleophilic water through a water chain (Grotthus mechanism) is offset by an inverse effect arising from reversibly breaking the short, tight hydrogen bond between D221 and D175 before catalysis.
Directional Emission from Dye-Functionalized Plasmonic DNA Superlattice Microcavities* (2020)

Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as atestbedto studydirectional light 1288emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal body-centered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space. At the micrometer scale, the anisotropic rhombic dodecahedron crystal habit couples with photonic modes to give directional light emission. At the nanoscale, the interaction between the dye dipoles and surface plasmons can be finely tuned by coupling the dye molecules to specific sites of the DNA particle-linker strands, thereby modulating dye-nanoparticle distance (three different positions are studied). The ability to control dye position with subnanometer precision allows one to systematically tune plasmon-excition interaction strength and decay lifetime, the results of which have been supported by electrodynamics calculations that span length scales from nanometers to micrometers. The unique ability to control surface plasmon/exciton interactions within such superlattice microcavities will catalyze studies involving quantum optics, plasmon laser physics, strong coupling, and nonlinear phenomena.
ChemInform Abstract: Bis(N,N‐diisopropylamino)trimethylsiloxyphosphane: A Versatile Phosphite‐Transferring Reagent; Application for Synthesis of P‐Modified Nucleotides. (1990)

Abstract The synthesized title phosphane (IV) may be used for transfer of the phosphite group with retention of the siloxy group.
Driven geometric phase gates with trapped ions (2013)

Abstract We describe a hybrid laser–microwave scheme to implement two-qubit geometric phase gates in crystals of trapped ions. The proposed gates can attain errors below the fault-tolerance threshold in the presence of thermal, dephasing, laser-phase and microwave-intensity noise. Moreover, our proposal is technically less demanding than previous schemes, since it does not require a laser arrangement with interferometric stability. The laser beams are tuned close to a single vibrational sideband to entangle the qubits, while strong microwave drivings provide the geometric character to the gate, and thus protect the qubits from these different sources of noise. A thorough analytic and numerical study of the performance of these gates in realistic noisy regimes is presented.
Bending Durability of Ni-Mo pre-alloyed Sintered Steel Case-Carburizing Gears with Different Densities and Tooth Root Bending Stress Analysis Using FEM Model Considering Voids (2016)

Single tooth bending fatigue tests were first carried out using Ni-Mo pre-alloyed sintered steel (46F4H) spur gears with different densities in the range of 7.30~7.54 Mg/m3. The sintered gears specimens were machined from sintered steel packs made from the single-press single-sinter route and some were surface-rolled using CNC form rolling machine. All test gears were case-carburized. The experimental results showed that the surface-rolled sintered gears with a density of 7.40 Mg/m3 or more had sufficiently high bending fatigue strength to replace gears made of typical Cr-Mo case-carburized wrought steel. Then, the stress analysis in the root fillet area of gear teeth was performed using a FEM simulation model considering a void distribution. The peak value of the maximum principal stress in the surface near the most critical stressed point was increased with the increase of porosity for un-surface rolled gears and was decreased as the amount of surface fully densified depth was increased. These simulation results can explain well the experimental results and show the appropriate material initial density and the surface densification level.
ChemInform Abstract: A NOVEL SYNTHESIS OF 1‐BENZOTHIOPHENES FROM 2‐(PHENYLTHIO) ALDEHYDES (1985)

Abstract (V ‐′ 12 lderivate A Novel Synthesis of 1‐Benzothiophenes from Z‐(Phenylthiomldehydes.
High‐Purity Discrete PEG‐Oligomer Crystals Allow Structural Insight (2009)

Abstract Über kurz oder lang : Eine verbesserte Methode zur Synthese von Ethylenglycol (EG)‐Oligomeren eröffnet den Zugang zu 16‐ und 32‐meren, die rein genug für einen mehrfachen Einbau sind, sowie zum bisher längsten (48‐meren) einzelnen EG‐Oligomer. Die hohe Reinheit ermöglichte die ersten Kristallisationen und damit die ersten Einblicke in sekundäre 3 10 ‐helicale PEG‐Strukturen. magnified image
Site-Specific DNA Photocleavage by Rhodium Intercalators Analyzed by MALDI-TOF Mass Spectrometry (2006)

The DNA photocleavage reaction of mismatch-selective Rh complexes has been analyzed by MALDI-TOF mass spectrometry as well as gel electrophoresis analysis of radioactively tagged oligonucleotides. Analogous results are obtained with these two techniques showing site-specific cleavage neighboring the mismatch to yield primarily 5'- and 3'-phosphate termini. Additional intermediates and products are observed, however, using MALDI-TOF analysis. MALDI-TOF mass spectrometry is seen to be particularly powerful in the analysis of DNA cleavage by site-specific molecules. The method requires no radioactive labeling, only little material, and analysis can be accomplished within minutes. Moreover, this mass spectral analysis of DNA cleavage yields direct information regarding products rather than simply the base pair site of cleavage.
Spin‐Coating Preparation of Highly Ordered Photoluminescent Films of Layered PbI2‐Aminoalkyloxysilane Perovskites (2004)

Abstract By utilising 3‐aminopropyltrimethoxysilane (APTMOS) cations and PbI 2 as the organic and inorganic precursors, respectively, a spin‐coated film of a layered perovskite‐type organic/inorganic derivative of APTMOS‐PbI 4 was prepared. The structure of APTMOS‐PbI 4 was characterised by X‐ray diffraction (XRD), UV/Vis absorption and infrared red spectroscopy (IR). The film showed green emission from the excitons of the inorganic layers and a weak blue emission related to the small amount of gel of adjacent APTMOS cations. Furthermore, the significant effect of the size of the inorganic framework on the cross‐linking degree of APTMOS molecules is discussed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Robust Aeroservoelastic Stability Of Helicopters: Application To The Air/Ground Resonance (2011)

Aeroelastic stability is a key issue that drives the design of modern rotorcraft. Rotary wing vehicles may present significant parameter variability and uncertainty related to environment, operating conditions, wear. The robustness of stability analysis is fundamental to determine the amount of freedom a designer has in defining the key properties in specific rotorcraft problems dominated by stability. This paper discusses robust stability analysis, focusing on the generalization of the computation of frequency dependent stability margins for MIMO systems. The proposed method is applied to the air/ground resonance problem, cast in a form that isolates a closed loop containing the lead-lag damper, which is considered the uncertain component. The problem is solved considering linear and nonlinear models of the damper, illustrating how stability requirements can be used to determine uncertainty bounds on the stiffness and damping properties of the damper.
Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion (2008)

Our results suggest that the power of genome-wide quantitative shRNA screens can be significantly increased when analyzed using a systems biology-based approach to identify functional gene networks.
Tissue-equivalent solar particle dosimeter using CMOS SSPMs (2009)

A dosimeter-on-a-chip (DoseChip) comprised of a tissue-equivalent scintillator coupled to a solid-state photomultiplier (SSPM) built using CMOS technology represents an ideal technology for a space-worthy, real-time solar-particle monitor for astronauts. It provides a tissue-equivalent response to the relevant energies and types of radiation for low-Earth orbit and interplanetary space flight to the moon or Mars. The DoseChip will complement the existing Crew Passive Dosimeters by providing real-time dosimetry and as an alarming monitor for solar particle events (SPEs). A prototype of the DoseChip was exposed to protons at three incident energies at the NASA space radiation laboratory at Brookhaven National Laboratory. The prototype provides an unambiguous, proportional response for 200, 500, and 1000 MeV protons. The measured response produced a detector response function that was used to model the behavior of an improved instrument. The data presented here indicate that a 3 times 3 times 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> piece of BC-430 plastic scintillator coupled to a 2000-pixel SSPM can accommodate the needed dynamic range for protons with an incident energy of 20 MeV and greater.
The ecological, economic and public health impacts of nuisance chironomids and their potential as aquatic invaders (2015)

This review examines the ecological, economical, and public health significance of chironomids and provides examples of chironomid invasions via international shipping and the subsequent local and regional impacts. Dispersal and adaptation mechanisms as facilitators of chironomid invasions are presented, and control methods are discussed. Impacts ranged from increased nuisance occurrences to agricultural disruption. Anthropogenic activities including pollution-related decimation of aquatic benthic communities might allow introduction of invasive chironomids. Chironomids can inhabit many environments, including eutrophic lakes and wastewater treatment areas, and may accumulate contaminants in high concentrations. Health concerns include the association of chironomid egg masses with Vibrio cholerae, roles of chironomids as vectors for avian botulism, and effects of chironomid chemicals as human allergens. Therefore, the presence of new chironomid species in an environment may present threats to public health and local ecosystems.
Infection causes childhood leukemia (2015)

This is an open-access article distributed under the terms of the Creative Commons Attribution License.-- Editorial.
Incremental Few-Shot Object Detection for Robotics (2020)

Incremental few-shot learning is highly expected for practical robotics applications. On one hand, robot is desired to learn new tasks quickly and flexibly using only few annotated training samples; on the other hand, such new additional tasks should be learned in a continuous and incremental manner without forgetting the previous learned knowledge dramatically. In this work, we propose a novel Class-Incremental Few-Shot Object Detection (CI-FSOD) framework that enables deep object detection network to perform effective continual learning from just few-shot samples without re-accessing the previous training data. We achieve this by equipping the widely-used Faster-RCNN detector with three elegant components. Firstly, to best preserve performance on the pre-trained base classes, we propose a novel Dual-Embedding-Space (DES) architecture which decouples the representation learning of base and novel categories into different spaces. Secondly, to mitigate the catastrophic forgetting on the accumulated novel classes, we propose a Sequential Model Fusion (SMF) method, which is able to achieve long-term memory without additional storage cost. Thirdly, to promote inter-task class separation in feature space, we propose a novel regularization technique that extends the classification boundary further away from the previous classes to avoid misclassification. Overall, our framework is simple yet effective and outperforms the previous SOTA with a significant margin of 2.4 points in AP performance.
Opposing Neuroendocrine Actions of the Natriuretic Peptides: C‐Type and A‐Type Natriuretic Peptides do not Interact with the same Hypothalamic Cells Controlling Prolactin Secretion (1995)

Abstract The two major members of the family of natriuretic peptides (NPs) in brain, A‐type natriuretic peptide (ANP) and C‐type natriuretic peptide (CNP) exert opposing actions on the neuroendocrine regulation of prolactin (PRL) secretion. We have targeted for compromise and destruction cells within the diencephalon which bear receptors for ANP (NPR‐A receptors), CNP (NPR‐B receptors), or both peptides (NPR‐C receptors) using novel cytotoxin cell targeting methodology in order to determine if the neuroendocrine effects of these two peptides are exerted on similar cell systems. In animals pretreated with ANP conjugated to the cytotoxic A chain of ricin, central administration of a dose of ANP which is known to inhibit PRL secretion did not alter PRL levels in plasma; however, subsequent administration of CNP elicited the stimulation of PRL secretion. In rats pretreated with CNP‐ricin A chain conjugate, a treatment we hypothesize targets for destruction CNP responsive cells, ANP injection did inhibit PRL secretion, while the stimulatory effect of CNP was absent. These results suggest that the neuroendocrine effects of these two natriuretic peptides on PRL secretion are expressed on different cellular elements of the hypothalamo‐pituitary axis. Furthermore, they reveal that neither peptide acts directly on the tuberoinfundibular dopamine system since pretreatment with either cytotoxin conjugate failed to alter basal PRL levels. Thus ANP and CNP do not appear to express opposing actions on the same cell systems, suggesting the recruitment of each peptide individually by differing, unique stimuli for PRL release.
Metabolic consequences of a high-fat diet on mouse models of GH action (2014)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)