gebhart/patrepeval huggingface dataset:
Apoptosis of tail muscle during amphibian metamorphosis involves a caspase 9‐dependent mechanism (2005)

The climax of amphibian metamorphosis is marked by thyroid hormone-dependent tadpole tail resorption, implicating apoptosis of multiple cell types, including epidermal cells, fibroblasts, nerve cells, and muscles. The molecular cascades leading to and coordinating the death of different cell types are not fully elucidated. It is known that the mitochondrial pathway, and in particular the Bax and XR11 genes, regulates the balance between apoptosis and survival in muscle. However, the down-stream factors modulated by changes in mitochondrial permeability have not been studied in a functional context. To investigate further the mitochondrial-dependent pathway, we analyzed the regulation and the role of caspase 9 in Xenopus tadpoles. We report that caspase 9 mRNA is expressed in the tail before metamorphosis and increases before and during climax. Similarly, at the protein level, the production of active forms of caspase 9 increases in muscle tissue as metamorphosis progresses. To assess the functional role of caspase 9, we designed a dominant-negative protein. Overexpression of this dominant-negative abrogates both Bax-induced cell death in vitro and muscle apoptosis in vivo during natural metamorphosis. These findings consolidate a model of metamorphic muscle death that directly implicates the mitochondrial pathway and the apoptosome.
Optically controlled silicon microactuators (1990)

Four novel schemes are introduced for controlling the motion of a Si mu -actuator directly using a low-power optical signal: (i) photoelectric leakage current, (ii) electric field screening in a semi-insulating layer, (iii) modulating the leakage current of a p-n junction and (iv) modulating the permittivity of a dielectric gas. All use a parallel-plate capacitor with a flexible Si cantilever as one plate. Experiments with the photoelectric device demonstrate for the first time light-controlled actuation, over a distance approximately 0.1 mu m in a time <0.5 s. A figure of merit, defined as a product of useful force and displacement over the product of required power and actuation duration, is introduced for evaluating and comparing different mechanisms that are used to achieve mu -actuation. The figure of merit for direct optical mechanisms are: mu approximately=0.34 for the photoelectric actuator, mu approximately=1 for the electric field screening controlled actuator, mu approximately=1 for the p-n junction leakage current controlled actuator, and mu approximately=2.5*10-6 for the permittivity modulated actuator. Direct optical mechanisms are faster and use less power than thermal techniques ( mu approximately=10-5) and purely electrostatic actuators ( mu approximately=0.1).
Wideband true-time-delay beam former that employs a tunable chirped fiber grating prism (2003)

A fiber grating prism that consists of four tunable chirped-grating delay lines for wideband true-time-delay beam forming is proposed and demonstrated. The chirped gratings are produced by use of the grating bending technique in which a uniform grating is surface mounted on a simply supported beam. We obtained chirped gratings with different chirp rates by bending the uniform gratings with different beam deflections. Four linear chirped fiber gratings with identical spectral width but linearly increased grating length are fabricated. The spectra and time-delay responses of the tunable chirped gratings are measured. A chirped-grating prism for wideband true-time-delay beam forming by use of four chirped gratings is constructed and tested experimentally. We obtained different time delays by tuning the wavelength of the optical carrier. The proposed true-time-delay beam former with a four-element phased-array steerer is suitable for continuous beam forming at microwave frequencies up to 20 GHz.
Enzymic degradation of heme. Oxygenative cleavage requiring cytochrome P-450 (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic degradation of heme. Oxygenative cleavage requiring cytochrome P-450R. Tenhunen, H. Marver, N. R. Pinstone, W. F. Trager, David Y. Cooper, and R. SchmidCite this: Biochemistry 1972, 11, 9, 1716–1720Publication Date (Print):April 1, 1972Publication History Published online1 May 2002Published inissue 1 April 1972https://pubs.acs.org/doi/10.1021/bi00759a029https://doi.org/10.1021/bi00759a029research-articleACS PublicationsRequest reuse permissionsArticle Views176Altmetric-Citations97LEARN 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
Homophilic adhesion of E-cadherin occurs by a co-operative two-step interaction of N-terminal domains. (1996)

Cluster formation of E-cadherin on the cell surface is believed to be of major importance for cell-cell adhesion. To mimic this process the extracellular part of mouse E-cadherin (ECAD) was recombinantly fused to the assembly domain of rat cartilage oligomeric matrix protein (COMP), resulting in the chimeric protein ECAD-COMP. The COMP domain formed a five-stranded alpha-helical coiled-coil. This enabled the formation of a pentameric ECAD with bundled C-termini and free N-termini. The pentameric protein construct ECAD-COMP and the monomeric ECAD were expressed in human embryonal kidney 293 cells. Electron microscopy, analytical ultracentrifugation, solid phase binding and cell attachment assays revealed that pentamers showed strong self-association and cell attachment, whereas monomers exhibited no activity. At the high internal concentration in the pentamer the N-terminal EC1 domains of two E-cadherin arms interact to form a ring-like structure. Then the paired domains interact with a corresponding pair from another pentamer. None of the four other extracellular domains of E-cadherin is involved in this interaction. Based on these results, an in vivo mechanism is proposed whereby two N-terminal domains of neighbouring E-cadherins at the cell surface first form a pair, which binds with high affinity to a similar complex on another cell. The strong dependence of homophilic interactions on C-terminal clustering points towards a regulation of E-cadherin mediated cell-cell adhesion via lateral association.
A high‐repetition rate attosecond light source for time‐resolved coincidence spectroscopy (2020)

Abstract Attosecond pulses, produced through high‐order harmonic generation in gases, have been successfully used for observing ultrafast, subfemtosecond electron dynamics in atoms, molecules and solid state systems. Today’s typical attosecond sources, however, are often impaired by their low repetition rate and the resulting insufficient statistics, especially when the number of detectable events per shot is limited. This is the case for experiments, where several reaction products must be detected in coincidence, and for surface science applications where space charge effects compromise spectral and spatial resolution. In this work, we present an attosecond light source operating at 200 kHz, which opens up the exploration of phenomena previously inaccessible to attosecond interferometric and spectroscopic techniques. Key to our approach is the combination of a high‐repetition rate, few‐cycle laser source, a specially designed gas target for efficient high harmonic generation, a passively and actively stabilized pump‐probe interferometer and an advanced 3D photoelectron/ion momentum detector. While most experiments in the field of attosecond science so far have been performed with either single attosecond pulses or long trains of pulses, we explore the hitherto mostly overlooked intermediate regime with short trains consisting of only a few attosecond pulses. We also present the first coincidence measurement of single‐photon double‐ionization of helium with full angular resolution, using an attosecond source. This opens up for future studies of the dynamic evolution of strongly correlated electrons.
Changes in visibility as a function of spatial frequency and microsaccade occurrence (2016)

Fixational eye movements (FEMs), including microsaccades, drift, and tremor, shift our eye position during ocular fixation, producing retinal motion that is thought to help visibility by counteracting neural adaptation to unchanging stimulation. Yet, how each FEM type influences this process is still debated. Recent studies found little to no relationship between microsaccades and visual perception of spatial frequencies (SF). However, these conclusions were based on coarse analyses that make it hard to appreciate the actual effects of microsaccades on target visibility as a function of SF. Thus, how microsaccades contribute to the visibility of stimuli of different SFs remains unclear. Here, we asked how the visibility of targets of various SFs changed over time, in relationship with concurrent microsaccade production. Participants continuously reported on changes in target visibility, allowing us to time-lock ongoing changes in microsaccade parameters to perceptual transitions in visibility. Microsaccades restored/increased the visibility of low SF targets more efficiently than that of high SF targets. Yet, microsaccade rates rose before periods of increased visibility, and dropped before periods of diminished visibility, for all the SFs tested, suggesting that microsaccades boosted target visibility across a wide range of SFs. Our data also indicate that visual stimuli fade/become harder to see less often in the presence of microsaccades. In addition, larger microsaccades restored/increased target visibility more effectively than smaller microsaccades. These combined results support the proposal that microsaccades enhance visibility across a broad variety of SFs.
Multistatic radar imaging from sparse measurements (2010)

We consider the problem of multistatic radar imaging in the case when the sources and receivers are sparse and irregularly spaced. The key to handling sparse sources and receivers is the development of a data-weighting scheme that compensates for nonuniform sampling. To determine the appropriate weights, we formulate a criterion for measuring the optimality of the point-spread function, and solve the resulting optimization problem using regularized least-squares. Once the weights are determined, they can be used to compute the point-spread function and thus determine resolution, and they can also be applied to the measured data to form an image. Tests of our minimization scheme with different regularization parameters show that, with appropriate weighting, individual scatterers can be resolved at sub-wavelength scales even when the data are noisy and the locations of both sources and receivers are uncertain. The example shows that the weights determined by our method improve the resolution relative to reconstructions with constant weights.
Increased lungkine and chitinase levels in allergic airway inflammation: A proteomics approach (2005)

Asthma is a chronic inflammatory disease characterized by pulmonary eosinophilia and airway hyperresponsiveness. Mechanisms underlying the pathogenesis of asthma are still not fully understood. The present study investigated alterations in global protein expression in bronchoalveolar lavage fluid in allergic airway inflammation using a proteomics approach. BALB/c mice sensitized and challenged with ovalbumin developed airway eosinophilia, mucus hypersecretion, elevation of immunoglobulin E, and airway hyperresponsiveness. Lavage fluid proteins from normal and asthmatic mice were resolved by two-dimensional gel electrophoresis, and identified by peptide mass fingerprinting matrix-assisted laser desorption/ionization-time of flight mass spectrometry. A total of 28 protein spots were significantly altered. Several of these proteins were undetectable or at very low levels in normal mice but were significantly increased in airway inflammation. These include lungkine, a recently described chemokine, a family of chitinases including Ym1, Ym2, and acidic mammalian chitinase, gob-5, a protein that mediates mucus secretion, and surfactant protein-D, a C-type lectin capable of modulating inflammatory responses. Overall, proteomics is a powerful tool in unraveling protein expression changes in allergic airway inflammation. The proteins identified in this study may be associated with the pathogenesis of allergic airway inflammation and may also be found useful as surrogate biomarkers for asthma.
Serological Diagnosis of Parelaphostrongylus tenuis Infection in White-Tailed Deer and Identification of a Potentially Unique Parasite Antigen (1999)

Serological diagnosis of Parelaphostrongylus tenuis infection should offer many advantages over the currently used method of fecal analysis that relies on a patent infection. Toward this end, we investigated the presence of P. tenuis-specific antibodies in experimentally infected white-tailed deer (WTD) and of unique P. tenuis antigens that may be exploited for serodiagnosis. WTD infected with 6, 20 or 100-150 P. tenuis third-stage larvae (L3) had anti-parasite antibodies from as early as 21 days postinoculation (dpi) until the end of the experiment (147 dpi). Peak anti-P. tenuis enzyme-linked immunosorbent assay (ELISA) titers in individual animals ranged from 1:70 to 1:5,700. Serum from infected WTD reacted with 5 distinct P. tenuis L3 antigens (105, 45, 37, 32, and 19 kDa) as detected by the immunoblotting technique. Serum from caribou infected with Parelaphostrongylus andersoni or Elaphostrongylus rangiferi reacted with all antigens except the 37-kDa antigen of L3, indicating that it may be unique to P. tenuis and can serve as a serodiagnostic antigen. The 37-kDa antigen appears to be present in the adult P. tenuis but not adult E. rangiferi or E. cervi. The development of an ELISA utilizing the unique antigen of P. tenuis should lead to a reliable diagnostic assay for P. tenuis infection in WTD.
Negligible water surface charge determined using Kelvin probe and total reflection X-ray fluorescence techniques (2013)

The water surface charge has been extensively debated in recent decades. Electrophoretic mobilities of air bubbles in water and disjoining pressures between the surfaces of aqueous films suggest that the surface of water exhibits a significant negative charge. This is commonly attributed to a strong adsorption of hydroxide ions at the interface, though spectroscopic measurements and simulation studies suggest surface depletion of hydroxide ions. Alternatively, the negative surface charge could arise from surface contamination with trace charged surfactants. We have probed the variation in the surface charge of water with pH by measuring surface potentials using the Kelvin probe technique. Independently, the abundance in the interfacial layer of "reporter ions" (Rb(+) and Br(-)), which must be affected by a charged surface, has been monitored using the total reflection X-ray fluorescence (TRXF) technique. Special care was taken to prove the high sensitivity of this technique as well as to avoid surface contaminants. The magnitude of the surface charge was found to be below 1 e per 500 nm(2) (TRXF). No evidence of variations in the surface potential between pH 2-3 and pH 9-12 was detected within the accuracies of the methods (5 mV for Kelvin probe and 2 mV for TRXF). Hence, our findings suggest that the clean water surface exhibits negligible charge in a wide pH range.
Development of an Advanced Automated Knowledge Based Combustor Preliminary Design Process Suitable for Low NOx Combustion Systems Optimization (2015)

Within the current combustor design process, the combustor performance and sizing is mainly estimated using Prelim Design Tools, which are based on empirical correlations. In order to investigate these preliminary designs in more detail, the application of CFD within the preliminary combustor design process has steadily increased. However, the generation of CFD solutions is a time consuming process, since it requires adapted CAD models and the generation of meshes before the actual CFD computations can be performed. Moreover, it has to be assured that the meshes are suitable for the computational code, which may require several iterations within the grid generation process. Next the manual setting of the boundary conditions for CFD is also prone to errors and the post-processing of the CFD results is generally time consuming. Therefore, an advanced approach of an automated preliminary combustor design process has been developed within the 7th framework of the European research project IMPACT-AE, based on the knowledge obtained in the 6th framework of the European research project INTELLECT D.M. The processes developed are based on improved and robust knowledge-based-engineering tools for modern low NOx combustor geometries. The advanced approach comprises a KBE preliminary design tool with improved Rolls-Royce in-house design rules for modern low NOx high efficiency combustors. It is based on fully featured 3-D parametric combustor models, including the pre-diffuser, the injector, the flame tube and the casing parts. An unstructured automatable meshing-tool CFS BOXERMesh is used to generate high quality meshes. Subsequent CFD analyses are performed using an unstructured Rolls-Royce in-house combustion CFD code PRECISE-UNS and the post-processing is performed using the open source tool ParaView. The choice of these tools is based on their ability to be fully automated using appropriate scripts and information. To create a strong linkage between these tools a KBE interface-tool and a database were implemented. These tools manage the individual processes fully automatically, including e.g. the transfer of geometry parameters to the CAD models; the gathering of the combustion chamber dependent boundary conditions and numerical parameters for the CFD analysis; or the generation of tool-internal automation scripts, using interface-tool input and database information. Several grid refinement studies were performed to define an automated mesh refinement strategy, using scaled cell sizes for each combustor feature. Furthermore, a mixing port diameter scaling and a detailed post-processing procedure are described.
Physicobiochemical Synergism Through Gene Therapy and Functional Tissue Engineering for In Vitro Chondrogenesis (2009)

Mechanical and chemical stimulation have been shown to enhance in vitro chondrogenesis. The aim of this study was to analyze and compare combined physicobiochemical effects. Bovine articular chondrocytes were retrovirally transduced to express bone morphogenetic protein-2 (BMP-2) or left as naïve controls. Cells were seeded in three-dimensional polyurethane scaffolds and further cultured under static conditions or exposed to dynamic compression and shear in a joint-specific bioreactor. Four groups: control (A), load (B), BMP-2-infected (C), and BMP-2-infected plus load (D) were analyzed for DNA and glycosaminoglycan (GAG) content; collagen I, II, and X; aggrecan, (cartilage oligomeric protein (COMP), superficial zone protein, matrix metalloproteinase (MMP)-3; MMP-13 mRNA; histology; and immunohistochemistry at 7, 21, and 35 days post-seeding. Synergistic effects (D) were higher than the sum of the individual treatments (B and C) for GAG/DNA, collagen II, and COMP. Histology revealed a functional organization in D including an intense safranin O staining in C and D superior to that in A and B. Immunostaining for collagen II and aggrecan was detected in C and D and was strongest in D. The results show that both stimuli augment in vitro chondrogenesis better than in controls. Biochemical manipulation proved to be predominantly more effective than load, and synergistic effects were demonstrated.
Control of Laser Ablation Plasma with Longitudinal Magnetic Field (2012)

We investigated the interaction of a laser ablation plasma with a longitudinal magnetic field, intending to create a directional moving plasma for laser ion source. To study the plasma dynamics, time-of-flight measurements of ion flux were made as a function of laser intensity and the magnetic field. The results indicate that the ion current density in the forward direction is strongly affected by a moderate (∼0.2 T) magnetic field. Results also indicate that the longitudinal magnetic field can control the ion flux as well as degree of ionization of the moving plasma by reducing the transverse expansion and setting on the recombination process during the interaction.
Crystal structure of N,N'-bis(diphenylphosphino)- 2,6-diaminopyridine-iodo-nickel(II) iodide, (C5NH3)(P(C6H5)2(NH))2(INi)I (1990)

Article Crystal structure of N,N'-bis(diphenylphosphino)- 2,6-diaminopyridine-iodo-nickel(II) iodide, (C5NH3)(P(C6H5)2(NH))2(INi)I was published on October 1, 1990 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 191, issue 1-4).
Enhancing Akt Imaging through Targeted Reporter Expression (2008)

The serine/threonine kinase PKB/Akt is a key mediator of survival and resistance to cancer therapy. Pharmacologic inhibition of Akt and its biologic sequelae may significantly impact the treatment of cancer. The use of molecular imaging technologies has contributed significantly to drug discovery research with an emphasis on drug efficacy, the mechanism of action, and target validation studies. We constructed a genetically engineered hybrid bioluminescent Akt reporter (BAR) molecule that reports on Akt serine/threonine kinase activity. Based on the fact that Akt is recruited to the plasma membrane on activation, we here describe a modified version of this reporter molecule (myristoylated and palmitoylated bioluminescent Akt reporter [MyrPalm-BAR]), which is membrane bound and whose bioluminescence activity can be used to monitor Akt activity at the cell membrane. Using changes in Akt activation status with small molecule inhibitors of Akt, we demonstrated that the membrane-targeted Akt reporter was more sensitive and quantitative. In addition, inhibition of upstream signaling kinases such as epidermal growth factor receptor and phosphatidylinositol 3-kinase activity resulted in changes in Akt activity that were quantitatively monitored by bioluminescence imaging. Based on these results, we propose that the membrane-associated Akt reporter may be better suited for identification of novel compounds that modulate the Akt pathway by high-throughput screening.
Supplementary Figure 6 from Identification of Luminal Breast Cancers That Establish a Tumor-Supportive Macroenvironment Defined by Proangiogenic Platelets and Bone Marrow–Derived Cells (2023)

&lt;p&gt;PDF file - 319K, Tumor specimens from women with luminal breast cancer used to identify instigators, non-instigators, or responders in the systemic instigation xenograft model&lt;/p&gt;
Fundamental science behind today’s important medicines (2018)

Today's most transformative medicines exist because of fundamental discoveries that were made without regard to practical outcome and with their relevance to therapeutics only appearing decades later.