gebhart/patrepeval huggingface dataset:
Amplification and over‐expression of MAP3K3 gene in human breast cancer promotes formation and survival of breast cancer cells (2013)

Gene amplifications in the 17q chromosomal region are observed frequently in breast cancers. An integrative bioinformatics analysis of this region nominated the MAP3K3 gene as a potential therapeutic target in breast cancer. This gene encodes mitogen-activated protein kinase kinase kinase 3 (MAP3K3/MEKK3), which has not yet been reported to be associated with cancer-causing genetic aberrations. We found that MAP3K3 was amplified in approximately 8-20% of breast cancers. Knockdown of MAP3K3 expression significantly inhibited cell proliferation and colony formation in MAP3K3-amplified breast cancer cell lines MCF-7 and MDA-MB-361 but not in MAP3K3 non-amplified breast cancer cells. Knockdown of MAP3K3 expression in MAP3K3-amplified breast cancer cells sensitized breast cancer cells to apoptotic induction by TNFα and TRAIL, as well as doxorubicin, VP-16 and fluorouracil, three commonly used chemotherapeutic drugs for treating breast cancer. In addition, ectopic expression of MAP3K3, in collaboration with Ras, induced colony formation in both primary mouse embryonic fibroblasts and immortalized human breast epithelial cells (MCF-10A). Combined, these results suggest that MAP3K3 contributes to breast carcinogenesis and may endow resistance of breast cancer cells to cytotoxic chemotherapy. Therefore, MAP3K3 may be a valuable therapeutic target in patients with MAP3K3-amplified breast cancers, and blocking MAP3K3 kinase activity with a small molecule inhibitor may sensitize MAP3K3-amplified breast cancer cells to chemotherapy.
Characterization of post translational modifications of histones by electrospray ionization mass spectrometry (1994)

Histones, which together with other specialized protein and DNA, form the complex structure of chromatin in the nucleus, are post-translationally modified. In the case of histone proteins, such post-translational modifications include acetylation, methylation, and phosphorylation. These modifications are known to be associated with the alteration in chromatin structure which occurs through the cell cycle or in response to chemical or radiation induced damage and repair to the cell nucleus. Such modifications effect of the protein-protein and protein-DNA associations of chromatin through ionic, H-bonds and hydrophobic interactions. The authors hypothesize that the distinct temporal and spatial patterns of these modifications, although complex, are non-random and predictably related to cellular responses to physical or chemical insult. Electrospray ionization mass spectrometry permits the direct analysis of the intact modified protein with precise mass measurement unambiguous evaluation of the nature and extent of posttranslational modification. Preliminary experiments of HPLC-purified histones from chick erythrocyte cells revealed protein species, which have mass values which closely correlate to the mass values predicted from the gene sequence. The mass spectra of all the proteins were found to contain additional species which appear to correspond to sequence varients and/or post translational modifications to the proteins. Histones H2B and H3more » were examined more closely by mass spectrometry on a linear triple quadrupole mass spectrometer as well as a Fourier transform ion cyclotron resonance mass spectrometer.« less
Pole-zero modeling and principal component analysis of head-related transfer functions. (1995)

Synthesizing over headphones the free-field to eardrum transfer functions, or head-related transfer functions (HRTFs), of the human auditory system poses several difficulties from both signal processing and psychoacoustic perspectives. Viewed as a system approximation problem, an experiment and two analytic approaches are considered for designing digital filter implementations of HRTFs. Compared to an all-zero model of HRTFs, a pole-zero model would seem to promise fewer parameters and, consequently, a lower computational complexity associated with synthesizing 3-D acoustic fields. The number of parameters might be further reduced by using an appropriate error criterion in the design of these HRTF approximations. In order to identify approximation design criteria, results are presented from a psychophysical experiment that measured the ability of listeners to discriminate between measured HRTFs and their pole-zero model approximations. While a significant reduction in the number of parameters is achieved using a pole-zero, model, a least-squares error criterion may not be the most appropriate in designing the HRTF approximations. Instead, error criteria that are sensitive to log-magnitude spectrum differences between the measured and approximated HRTFs are likely to be more subjectively relevant. A pole-zero model design algorithm is presented, incorporating gradient search techniques to minimize both log-magnitude and phase response errors. Application of the algorithm to approximating HRTFs results in smaller pole-zero model orders than those required when using a least-squares error criterion. Moreover, the gradient search techniques provide a means to interpolate pole-zero models. In comparing two proposed interpolation methods to a standard all-zero model interpolation method, one of the proposed methods shows relatively poor performance, and the other shows performance similar to the all-zero model interpolation method. In a separate analysis, principal component analysis (PCA) is used to investigate the common and directional transfer function representation of HRTFs. Based on alternative assumptions from those made previously, results from PCA applied to measured HRTFs show that a common transfer function does not exist. Consequently, an alternative representation of HRTFs is proposed, and comparisons are made to the directional transfer function model.
Thermo-hydraulic instability due to a blockage of flow by vapor in a boiling two-phase flow system. (Experimental results concerning the mechanism) (1987)

Thermo-hydraulic instability has been investigated experimentally in a boiling two-phase flow system composed of a vertical N-shaped boiling channel and an adiabatic bypass between an inlet plenum and an outlet plenum, using Freon 113. Instability caused by the blockage of flow by vapor, which cannot be found in Boure's classification of two-phase flow instabilities, has been observed. The flow maps in each section, static characteristics, stable flow limits and characteristics of this instability have been studied under various conditions to clarify the mechanism. The inlet velocity decreases when a vapor slug combining in the inverted U-shpaed bend obstructs the flow. The vapor slug flowing into the downcomer increases the void fraction in the downcomer, resulting in increased gravitational loss. Consequently, flow instability is brought about.
Outgassing Properties and Microstructures of Ti-N Films. (1991)

Hydrogen evolution from Ti-N films and stainless steels (SUS 304) was investigated as a function of temperature .
Molecular mechanisms of McArdle's disease (muscle glycogen phosphorylase deficiency). RNA and DNA analysis. (1987)

Lack of muscle glycogen phosphorylase activity leads to McArdle's disease, a rare metabolic myopathy. To investigate its molecular basis at the nucleic acid level, we isolated muscle phosphorylase cDNA clones from a human cDNA library in Escherichia coli plasmid pBR 322. Subcloning of one insertion of M13 bacteriophage permitted its definite identification by sequencing. Northern blot experiments revealed one specific messenger RNA of 3.4 kilobases found uniquely in tissues expressing muscle phosphorylase. We show that McArdle's disease exhibits a molecular heterogeneity at the messenger RNA level. In eight unrelated cases of McArdle's disease in which no inactive proteins had been detected, we assayed muscle biopsies for phosphorylase mRNA by Northern blotting. In five cases, no muscle phosphorylase mRNA could be detected, while in three other cases, normal length mRNA was present in lower amounts. Moreover, Southern blot analysis of DNA isolated from white blood cells in four McArdle patients revealed no major deletion or rearrangements of the phosphorylase gene as compared with controls.
Multiaxial Mechanical Behavior of Biological Materials (2003)

For native and engineered biological tissues, there exist many physiological, surgical, and medical device applications where multiaxial material characterization and modeling is required. Because biological tissues and many biocompatible elastomers are incompressible, planar biaxial testing allows for a two-dimensional (2-D) stress-state that can be used to fully characterize their three-dimensional (3-D) mechanical properties. Biological tissues exhibit complex mechanical behaviors not easily accounted for in classic elastomeric constitutive models. Accounting for these behaviors by careful experimental evaluation and formulation of constitutive models continues to be a challenging area in biomechanical modeling and simulation. The focus of this review is to describe the application of multiaxial testing techniques to soft tissues and their relation to modern biomechanical constitutive theories.
Perfusion-Based Bioreactor for the Decellularization and Recellularization of Ferret Tracheas (2020)

Pai, Albert C. MD; Lynch, Thomas J. PhD; Ievlev, Vitaly BS; Ahlers, Bethany BS; Engelhardt, John F. PhD; Rajnikant Parekh, Kalpaj MBBS, FACS Author Information
High resolution laser Doppler holography of retinal blood flow by spatiotemporal eigenvalue filtering and rephasing (2020)

We improved image quality in retinal blood flow imaging by laser Doppler holography by several post-processing methods : decluttering by eigenvalue decomposition of digital holograms, digital aberration compensation by sub-aperture correlation measurements, and iterative optimization of the quality of image features.
The Conundrum of Systemic Arterial Pressure Management on Cardiopulmonary Bypass (2023)

The recently released EACTS/EACTA/EBCP guidelines on cardiopulmonary bypass (CPB) in adult cardiac surgery [...].
Low‐loss skimming waveguides with controllable mode leakage for on‐chip saturable absorbers (2023)

Emerging 3D photonic circuits would greatly benefit from the ability to integrate skimming waveguides with low loss and controllable inscription depth into photonic circuits. These waveguides allow for the interaction of guiding light directly with external modulation signals and enable programmable photonic circuits. Here, we report the fabrication of a novel photonic-lattice-like skimming waveguide (PLLSW) using femtosecond laser writing. Our method enables fine control of cross-sectional symmetry and writing depth of waveguides, achieving a minimum depth of 1 μm and a low insertion loss of 1 dB. Based on the PLLSW, we demonstrate on-chip light modulation by designing an evanescent-field-type saturable absorber through the coupling of a carbon nanotube film with the PLLSW, which exhibits saturation intensity from 20 to 200 MW/cm<sup>2</sup> through the balanced twin-detector measurement. The strong nonlinear optical response of the PLLSW-based saturable absorber is further exploited to drive a Q-switched pulse laser at 1550 nm based on a fiber laser cavity. Our work demonstrates an effective method to integrate nonlinear optical materials into a glass chip for all-optical switching based on 3D waveguides, which holds great potential for the construction of large-scale programmable photonic circuits in the future.
β4 Integrin signaling induces expansion of prostate tumor progenitors (2013)

The contextual signals that regulate the expansion of prostate tumor progenitor cells are poorly defined. We found that a significant fraction of advanced human prostate cancers and castration-resistant metastases express high levels of the β4 integrin, which binds to laminin-5. Targeted deletion of the signaling domain of β4 inhibited prostate tumor growth and progression in response to loss of p53 and Rb function in a mouse model of prostate cancer (PB-TAg mice). Additionally, it suppressed Pten loss-driven prostate tumorigenesis in tissue recombination experiments. We traced this defect back to an inability of signaling-defective β4 to sustain self-renewal of putative cancer stem cells in vitro and proliferation of transit-amplifying cells in vivo. Mechanistic studies indicated that mutant β4 fails to promote transactivation of ErbB2 and c-Met in prostate tumor progenitor cells and human cancer cell lines. Pharmacological inhibition of ErbB2 and c-Met reduced the ability of prostate tumor progenitor cells to undergo self-renewal in vitro. Finally, we found that β4 is often coexpressed with c-Met and ErbB2 in human prostate cancers and that combined pharmacological inhibition of these receptor tyrosine kinases exerts antitumor activity in a mouse xenograft model. These findings indicate that the β4 integrin promotes prostate tumorigenesis by amplifying ErbB2 and c-Met signaling in tumor progenitor cells.
Laser Performance and Optical Properties of LiSrGaF6:Cr3+ (1991)

The laser-pumped laser performance of the new material LiSrGaF<sub>6</sub>:Cr<sup>3+</sup> has been characterized. The laser results indicate that the material operates with a high slope efficiency of 50% due to the low passive, and pump-induced, loss levels. The optical and laser properties of Cr<sup>3+</sup>-doped LiSrGaF<sub>6</sub> are similar to those of the LiSrAlF<sub>6</sub> host previously investigated, although the magnitude of the expansion coefficients of the gallium analog are more favorable.
Modulation speed of an efficient porous silicon light emitting device (1999)

Trends in the efficiency and small signal modulation behavior of porous silicon light emitting diodes (LEDs) are reported for devices formed by the anodization of bulk silicon p–n junctions. As the average size of the silicon skeleton is decreased, the external electroluminescence (EL) efficiency increases from 0.001% to 0.18% and there is a corresponding blue shift in the EL peak from 776 to 633 nm. An associated tenfold increase is observed in the photoluminescence efficiency while the diode resistance, at 2 V, increases from 3×103 to 1×106 Ω. Under small signal pulsed operation, the voltage dependence of the rising edge of the EL is well described by a carrier mobility of 3×10−4 cm2 s−1 V−1 which is independent of the average size of the luminescent regions of the silicon nanostructure. The falling edge of the EL transient is dominated by radiative recombination of quantum confined excitons. The modulation speed is found to be limited by a combination of carrier mobility in the silicon wires and radiative recombination processes. Evidence of charge trapping and discharge is found in an EL overshoot phenomenon. The major application of this type of porous silicon LED, with modulation speeds below 1 MHz, appears to be for displays integrated with circuitry rather than for optical interconnection.
Stretchable Inductor Design (2015)

High-quality inductors are difficult to realize in stretchable electronics, since the thick parallel traces needed to minimize resistance also result in a highly rigid structure. Adding periodic waves or kinks to the traces of an inductor coil has been found to result in a more compliant structure that will not permanently deform or break after stretching by tens of percent. In this paper, the effects on electrical performance of creating inductor coils from stretchable wavy traces are investigated. Eight different tortuous trace designs were modeled and experimentally tested in one- and three-turn inductors, as well as an electrical transformer design. Incorporating waves into an inductor was found to result in a negative mutual coupling along the traces, degrading the inductor performance. The incremental self-inductance per resistance of the added length due to the waviness, ~1.2 nH/Q, was similar for all interconnect types tested. This value is less than a third that of using a longer straight conductor of similar cross section (4.4 nH/Q), resulting in a drop in ratio of inductance to resistance and resulting peak quality factor in the measured inductors by as much as a factor of two.
Dependence of diatomic photofragment fluorescence polarization on triatomic predissociation lifetime (1981)

When a triatomic molecule, ABC, is dissociated by a beam of light to yield an electronically excited diatomic molecule, AB*, the degree of linear polarization of the AB* photofragment flourescence depends in general on the lifetime of the excited parent molecule, ABC*. Analytical expressions are developed for the polarization of diatomic flourescence as a function of predissociation lifetime. These calculations are carried out under the assumptions that: (a) the absorption and emission transition dipole moments can be replaced by classical hertzian dipole oscillators; (b) the AB* fragment rotates in the plane of the ABC* parent at the time of dissociation; and (c) the motion of the ABC* parent can be approximated by the classical motion of a prolate or oblate symmetric top.
Short-Term Metabolome Dynamics and Carbon, Electron, and ATP Balances in Chemostat-Grown Saccharomyces cerevisiae CEN.PK 113-7D following a Glucose Pulse (2006)

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O(2) uptake and CO(2) evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO(2) evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.
Experiments on Cloud-RAN Wireless Handover using Optical Switching in a Dense Urban Testbed (2020)

We investigate dynamic network resource allocation using software-defined networking optical controller with software-defined radios on the COSMOS testbed. 10 Gb/s capacity, deterministic low latency are maintained through user equipment wireless handover via optical switching.
Home Video Editing Made Easy : Balancing Automation and User Control (2001)

Hitchcock is a system to simplify the process of editing video. Its key features are the use of automatic analysis to find the best quality video clips, an algorithm to cluster those clips into meaningful piles, and an intuitive user interface for combining the desired clips into a final video. We conducted a user study to determine how the automatic clip creation and pile navigation support users in the editing process. The study showed that users liked the ease-of-use afforded by automation, but occasionally had problems navigating and overriding the automated editing decisions. These findings demonstrate the need for a proper balance between automation and user control. Thus, we built a new version of Hitchcock that retains the automatic editing features, but provides additional controls for navigation and for allowing users to modify the system decisions.
Humoral and Cellular Cross-Reactivity between Amb a 1, the Major Ragweed Pollen Allergen, and Its Mugwort Homolog Art v 6 (2011)

Ragweed and mugwort are closely related weeds that represent the major cause of pollen allergy in late summer. Concomitant sensitization and clinical cross-reactivity frequently occur in subjects who are coexposed to both pollen species, and have implications for diagnosis and specific immunotherapy. Molecules involved in this cross-reactivity might be Amb a 1, the major ragweed pollen allergen, and Art v 6, a highly homologous allergen from mugwort. Therefore, we investigated the IgE and T cell response to Art v 6 of 60 weed pollen-allergic patients and assessed its immunological cross-reactivity with Amb a 1. Results of ELISA inhibition experiments suggested that both allergens are largely cross-reactive, but Amb a 1 possesses more IgE epitopes than Art v 6. In patients with IgE to both allergens, Amb a 1-induced T cell lines and clones responded weakly to Art v 6. Moreover, Art v 6-induced T cell lines responded stronger to Amb a 1. T cell epitope mapping of Art v 6 revealed that it contains only a few cross-reactive epitopes, which is opposed to the multiple T cell-activating regions present in Amb a 1. In summary, Amb a 1 can elicit more diverse allergen-specific IgE and T cell responses than Art v 6 and dominates the cross-reactivity with its homolog. Nevertheless, Art v 6 can act as a primary sensitizing allergen in areas with high mugwort pollen exposure, and consequently may facilitate sensitization to Amb a 1 by epitope cross-recognition of T and B cells.
ChemInform Abstract: TfNH2 as Achiral Hydrogen‐Bond Donor Additive to Enhance the Selectivity of a Transition Metal Catalyzed Reaction. Highly Enantio‐ and Diastereoselective Rhodium‐Catalyzed Cyclopropanation of Alkenes Using α‐Cyano Diazoacetamide. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
First-Principles Calculation of Dielectric Response in Molecule-Based Materials (2013)

The dielectric properties of materials are of fundamental significance to many chemical processes and the functioning of numerous solid-state device technologies. While experimental methods for measuring bulk dielectric constants are well-established, far less is known, either experimentally or theoretically, about the origin of dielectric response at the molecular/multimolecular scale. In this contribution we report the implementation of an accurate first-principles approach to calculating the dielectric response of molecular systems. We assess the accuracy of the method by reproducing the experimental dielectric constants of several bulk π-electron materials and demonstrating the ability of the method to capture dielectric properties as a function of frequency and molecular orientation in representative arrays of substituted aromatic derivatives. The role of molecular alignment and packing density on dielectric response is also examined, showing that the local dielectric behavior of molecular assemblies can diverge significantly from that of the bulk material.