gebhart/patrepeval huggingface dataset:
A Novel Role for Mixed-Lineage Kinase-Like Mitogen-Activated Protein Triple Kinase α in Neoplastic Cell Transformation and Tumor Development (2004)

Previously, no member of the mixed-lineage kinase (MLK) protein family was known to function as an oncogene. Here, we demonstrate that MLK-like mitogen-activated protein triple kinase (MLTK)-alpha, a member of the MLK family, induced neoplastic cell transformation and tumorigenesis in athymic nude mice. Introduction of small interference RNA (siRNA)-MLTK-alpha into MLTK-alpha-overexpressing cells dramatically suppressed cell transformation. Nuclear accumulation of the pHisG-MLTK-alpha fusion protein was observed after epidermal growth factor or 12-O-tetradecanoylphorbol-13-acetate treatment. Phosphorylation of downstream mitogen-activated protein kinase-targeted transcription factors including c-Myc, Elk-1, c-Jun, and activating transcription factor (ATF) 2 was also differentially enhanced in MLTK-alpha-overexpressing cells exposed to epidermal growth factor or 12-O-tetradecanoylphorbol-13-acetate stimulation compared with cells expressing mock vector or siRNA-MLTK-alpha. Very importantly, MLTK-alpha-overexpressing cells formed fibrosarcomas when injected s.c. into athymic nude mice, whereas almost no tumor formation was observed in mice that received injections of mock or siRNA-MLTK-alpha stably transfected cells. These results are the first to indicate that MLTK-alpha plays a key role in neoplastic cell transformation and cancer development.
Euphorbiae humifusae induces apoptosis in Hep3B hepatocarcinoma cells via simultaneous activation of the death receptor-mediated and mitochondrial pathways (2009)

In the present study, we investigated the effects of the water extract of Euphorbiae humifusae (WEEH), an oriental medicinal herb, on the growth of Hep3B human hepatocarcinoma cells. We found that WEEH treatment resulted in a significant decrease in the cell viability of Hep3B cells depending on dosage. This decrease was revealed to be apoptosis, evidenced by chromatin condensation, DNA fragmentation and an accumulation of apoptotic fraction. WEEH induced the expression of death receptor-related proteins such as Fas, tumor necrosis factor-related apoptosis-inducing ligand, death receptor (DR) 4 and DR5, which further triggered caspase-8 activation and truncated Bid cleavage. Mitochondrial dysfunction, the catalytic activation of caspase-9, down-regulation of anti-apoptotic Bcl-2 and Bcl-xL expression, and up-regulation of the pro-apoptotic Bax protein were also observed in WEEH-treated cells. In addition, the increase in apoptosis induced by WEEH was correlated with caspase-3 activation and the concomitant degradation of poly (ADP-ribose) polymerase. However, the cytotoxic effects and apoptotic characteristics induced by WEEH were significantly inhibited by z-DEVD-fmk, a caspase-3 inhibitor. This demonstrates the important role played by caspase-3 in the process. Collectively, our data indicate that WEEH induces Hep3B cell apoptosis through a signaling cascade of death receptor-mediated extrinsic and mitochondria-mediated intrinsic caspase pathways.
Volatile HRS asymmetry and subloops in resistive switching oxides (2017)

Current-voltage characteristics of oxide-based resistive switching memories often show a pronounced asymmetry with respect to the voltage polarity in the high resistive state (HRS), where the HRS after the RESET is more conducting than the one before the SET. Here, we report that most of this HRS asymmetry is a volatile effect as the HRS obtained from a read operation differs from the one taken from the switching cycle at identical polarity and voltages. Transitions between the relaxed and the volatile excited states can be achieved via voltage sweeps, which are named subloops. The excited states are stable over time as long as a voltage is applied to the device and have a higher conductance than the stable relaxed state. Experimental data on the time and voltage dependence of the excitation and decay are presented for Ta/TaO<sub>x</sub>/Pt and Ta/ZrO<sub>x</sub>/Pt devices. The effect is not limited to one oxide or electrode material but is observed with different magnitudes (up to 10× current change) in several oxide systems. These observations describe an additional state variable of the memristive system that is controlled in a highly polarity dependent manner.
4.2: Polymer‐Stabilized Blue‐Phase Material Driven at Low Voltage (2012)

Abstract We achieved low‐voltage driving of a blue‐phase liquid crystal display by employing liquid crystal with high dielectric anisotropy and a chiral material with high helical twisting power. A prototype of a 3.4‐inch polymer‐stabilized blue‐phase display was made, which includes a highly reliable crystalline oxide semiconductor and operates favorably.
Automatic Face Recognition System for Hidden Markov Model Techniques (2011)

Hidden Markov Models (HMMs) are a class of statistical models used to characterize the observable properties of a signal. HMMs consist of two interrelated processes: (i) an underlying, unobservable Markov chain with a finite number of states governed by a state transition probability matrix and an initial state probability distribution, and (ii) a set of
Computational Causal Reasoning Models of Mechanisms of Androgen Stimulation in Prostate Cancer (2006)

We describe the development of a very large-scale causal, computable model of biology and its specific application in the identification of molecular cause and effect hypotheses of mechanisms underlying the effects of androgen stimulation in the LNCaP prostate carcinoma cell line. In contrast to previous LNCaP studies in which genes have been hierarchically clustered by their pattern of response to androgen, our causal reasoning methodology identifies possible explanations in terms of discrete and testable molecular mechanisms. We have inferred changes in cell proliferation and fatty-acid synthesis transcriptional control mechanisms based on gene expression changes in transcriptional targets of proteins such as RBI, E2F1,2,3, and SREBF1,2. Further analysis has identified multiple causal pathways linking the activity of the androgen receptor (AR) to these processes, providing succinct, testable hypotheses for subsequent experimentation. This study identified new targets for RNAi-mediated gene knockdowns to study androgen control of cell proliferation in prostate cancer. Causal Reasoning and modeling provides a valuable tool for the analysis of molecular profiling data, can identify distinct mechanisms of action and can be used to design experiments to probe those mechanisms. Causal Reasoning is effective in the study of cellular models of prostate cancer, and this systems approach is broadly applicable to identifying the molecular mechanisms of cancer
IP over optical layer restoration: architecture, design, and analysis (2005)

Optical layer capacity and unit cost improvements are basic to the rapid growth of IP networks. However, the new rapid reconfiguration and restoration capabilities of the optical layer have been sparingly utilized by IP network operators. This is consistent with the economics: the widely deployed optical layer architecture based on a "discrete" optical crossconnect (DOXC - one not integrated into the WDM) incurs heavy interface costs. In addition, there are architectural and control issues which are roadblocks to IP exploitation of rapid optical layer agility. In the first part of the paper, we describe a next generation all-optical architecture based on OXCs integrated with the WDM ("IOXCs"), and one instantiation of this architecture using a class of reconfigurable degree-N optical add-drop multiplexer (OADM). A new shared mesh restoration mechanism based on hot standbys is designed to overcome slow convergence and transient behaviors that are typical in all-optical networks. A series of economic comparisons are made on both a 120-node hypothetical national network and a smaller express backbone network to demonstrate the cost effectiveness of the new IOXC-based restoration in comparison to the IP layer restoration after some optical layer failure that results in one or more IP link failures. In the IP over Optical architecture, the Optical Layer can provide its IP clients rapid and efficient restoration for IP link failures that are due to some optical layer failure; however its inability to protect against router and router interface failures erodes its attractiveness. In the second part of the paper, we propose a joint IP/Optical restoration mechanism to deal with this. It is suitable for IP offices with at least two backbone routers and an optical cross-connect. The OXC is used to re-terminate OC-48/OC-192 links from a failed backbone router to its mate. The entire interoffice portion of the re-terminated link is reused, thus minimizing the amount of additional inter-office capacity required to protect against router failures. The proposed scheme is also applicable to restoration for router interface failures as well as to cases with single backbone router office architecture.
Full-Duplex Transmission of Nyquist-SCM Signal over a Seamless Bidirectional Fiber–Wireless System in W-Band (2019)

We experimentally demonstrate a seamless full-duplex fiber-wireless system in the W-band for Nyquist-SCM signal transmission. Satisfactory performance is confirmed for 45-Gb/s and 20-Gb/s signal transmission over the downlink and uplink directions.
Review of bio-optical imaging systems with a high space-bandwidth product (2021)

Optical imaging has served as a primary method to collect information about biosystems across scales-from functionalities of tissues to morphological structures of cells and even at biomolecular levels. However, to adequately characterize a complex biosystem, an imaging system with a number of resolvable points, referred to as a space-bandwidth product (SBP), in excess of one billion is typically needed. Since a gigapixel-scale far exceeds the capacity of current optical imagers, compromises must be made to obtain either a low spatial resolution or a narrow field-of-view (FOV). The problem originates from constituent refractive optics-the larger the aperture, the more challenging the correction of lens aberrations. Therefore, it is impractical for a conventional optical imaging system to achieve an SBP over hundreds of millions. To address this unmet need, a variety of high-SBP imagers have emerged over the past decade, enabling an unprecedented resolution and FOV beyond the limit of conventional optics. We provide a comprehensive survey of high-SBP imaging techniques, exploring their underlying principles and applications in bioimaging.
Compaction of fiber reinforcements (2002)

Abstract In resin transfer molding, dry fiber reinforcements are compacted as the mold closes before injection of a curable resin matrix. This paper presents experimental data of compaction pressure as a function of fiber volume fraction. Data are presented for woven roving mats, random fiber mats, loose fiber rovings for pultrusion, and uniaxial or biaxial roving mats. These data are fit to a mathematical model derived in an Appendix. Experimental data are also given for six combinations of reinforcements. We use the compaction model of each constituent layer to predict the average volume fraction assuming that fiber layers do not interact. However, we see that most combinations of reinforcements have fiber volume fractions greater than expected at pressures under 50 psi, indicating a synergistic packing between the layers of different composition.
<title>Volume holography for 1550-nm digital databases</title> (2000)

A digital volume holographic database in iron-doped lithium niobate to be read out by a multi-wavelength signal in the near infrared is here successfully performed, thanks to so- called two-color technique. Three 4-bit digital words have been recorded via angle multiplexing at 488 nm and retrieved at 1550 nm by a 200 GHz-WDM (Wavelength Division Multiplexing) beam.
Mass transfer of water vapor in a hollow fiber for degassing processes (1999)

Abstract The mass‐transfer mechanisms of water vapor in hollow‐fiber membrane modules used to remove gases from water were studied experimentally and theoretically. Hollow‐fiber modules for degassing are widely used in various industries, including ultrapure water production. Although these modules perform extremely well, a general principle for the design has not been established. Recently, very highly efficient asymmetric hollow‐fiber modules were developed, that could reduce the dissolved oxygen to less than 1 μg/L (1 ppb). From our studies of the modules, it was found that the mass transfer of water vapor plays an extremely important role in the flow in the lumen side of the hollow fibers. The establishment of a theoretical design method for degassing modules can be expected from our studies.
Topics in biomedical optics—part I: introduction (2005)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Brian W. Pogue, Judith R. Mourant, and John George, "Topics in biomedical optics—part I: introduction," Appl. Opt. 44, 1784-1784 (2005) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Orientational epitaxy of a crystal-Eoverlayer on a hexatic-Bsubstrate (1991)

Thermal and structural experiments on thin free-standing liquid-crystal films of n-heptyl-4'-n-pentyloxybiphenyl-4-carboxylate have revealed the existence of a surface-freezing phenomenon, in which surface crystal-E layers coexist with a hexatic-B interior. The crystal-E surface is typically found by electron diffraction to exist in twin domains in which the orientation of the orthorhombic lattice is rotated by 2\ifmmode^\circ\else\textdegree\fi{}--3\ifmmode^\circ\else\textdegree\fi{} with respect to that of the underlying hexatic-B bond-orientational axes. It is shown theoretically that such a rotation minimizes the energy of the strain by the two incommensurate types of structural order, analogous to the Novaco-McTague theory, which applies to the orientational epitaxy of a crystalline overlayer on an incommensurate crystalline substrate.
Ladder Polyether Synthesis via Epoxide-Opening Cascades Using a Disappearing Directing Group (2006)

The combination of a trimethylsilyl group, a Brønsted base, a fluoride source, and a hydroxylic solvent enables the first construction of the tetrad of tetrahydropyran rings found in the majority of the ladder polyether natural products by way of a cascade of epoxide-opening events that emulates the final step of Nakanishi's proposed biosynthetic pathway. The trimethylsilyl group disappears during the course of the cascade, and thus these are the first epoxide ring-opening cascades that afford ladder polyether subunits containing no directing groups at the end of the cascade.
Investigating the Upper-Bound Performance of Sparse-Coding-Based Spectral Reconstruction from RGB Images (2021)

In Spectral Reconstruction (SR), we recover hyperspectral images from their RGB counterparts. Most of the recent approaches are based on Deep Neural Networks (DNN), where millions of parameters are trained mainly to extract and utilize the contextual features in large image patches as part of the SR process. On the other hand, the leading Sparse Coding method &#x2018;A+&#x2019;&#x2014;which is among the strongest point-based baselines against the DNNs&#x2014;seeks to divide the RGB space into neighborhoods, where locally a simple linear regression (comprised by roughly 102 parameters) suffices for SR. In this paper, we explore how the performance of Sparse Coding can be further advanced. We point out that in the original A+, the sparse dictionary used for neighborhood separations are optimized for the spectral data but used in the projected RGB space. In turn, we demonstrate that if the local linear mapping is trained for each spectral neighborhood instead of RGB neighborhood (and theoretically if we could recover each spectrum based on where it locates in the spectral space), the Sparse Coding algorithm can actually perform much better than the leading DNN method. In effect, our result defines one potential (and very appealing) upper-bound performance of point-based SR.
Antisense oligonucleotide therapy rescues disturbed brain rhythms and sleep in juvenile and adult mouse models of Angelman syndrome (2023)

<i>UBE3A</i> encodes ubiquitin protein ligase E3A, and in neurons its expression from the paternal allele is repressed by the <i>UBE3A</i> antisense transcript (<i>UBE3A-ATS</i>). This leaves neurons susceptible to loss-of-function of maternal <i>UBE3A</i>. Indeed, Angelman syndrome, a severe neurodevelopmental disorder, is caused by maternal <i>UBE3A</i> deficiency. A promising therapeutic approach to treating Angelman syndrome is to reactivate the intact paternal <i>UBE3A</i> by suppressing <i>UBE3A-ATS</i>. Prior studies show that many neurological phenotypes of maternal <i>Ube3a</i> knockout mice can only be rescued by reinstating <i>Ube3a</i> expression in early development, indicating a restricted therapeutic window for Angelman syndrome. Here, we report that reducing <i>Ube3a-ATS</i> by antisense oligonucleotides in juvenile or adult maternal <i>Ube3a</i> knockout mice rescues the abnormal electroencephalogram (EEG) rhythms and sleep disturbance, two prominent clinical features of Angelman syndrome. Importantly, the degree of phenotypic improvement correlates with the increase of Ube3a protein levels. These results indicate that the therapeutic window of genetic therapies for Angelman syndrome is broader than previously thought, and EEG power spectrum and sleep architecture should be used to evaluate the clinical efficacy of therapies.
Interaction, functional relations and evolution of large and small subunits in Rubisco from Prokaryota and Eukaryota (1986)

In early biological evolution anoxygenic photosynthetic bacteria may have been established through the acquisition of ribulose bisphosphate carboxylase-oxygenase (Rubisco). The establishment of cyanobacteria may have followed and led to the production of atmospheric oxygen. It has been postulated that a unicellular cyanobacterium evolved to cyanelles which were evolutionary precursors of chloroplasts of both green and non-green algae. The latter probably diverged from ancestors of green algae as evidenced by the occurrence of large (L) and small (S) subunit genes for Rubisco in the chloroplast genome of the chromophytic algae Olisthodiscus luteus. In contrast, the gene for the S subunit was integrated into the nucleus in the evolution of green algae and higher plants. The evolutionary advantages of this integration are uncertain because the function of S subunits is unknown. Recently, two forms of Rubisco (L8 and L8S8) of almost equivalent carboxylase and oxygenase activity have been isolated from the photosynthetic bacterium Chromatium vinosum. This observation perpetuates the enigma of S subunit function. Current breakthroughs are imminent, however, in our understanding of the function of catalytic L subunits because of the application of deoxyoligonucleotide-directed mutagenesis. Especially interesting mutated Rubisco molecules may have either enhanced carboxylase activity or higher carboxylase:oxygenase ratios. Tests of expression, however, must await the insertion of modified genes into the nucleus and chloroplasts. Methodology to accomplish chloroplast transformation is as yet unavailable. Recently, we have obtained the first transformation of cyanobacteria by a colE1 plasmid. We regard this transformation as an appropriate model for chloroplast transformation.
Interfacial Engineering of Perovskite Quantum-Dot Light-Emitting Devices Using Alkyl Ammonium Salt Layer (2018)

Herein, we demonstrated that alkyl ammonium salts containing the Br anion, oleylamine bromide (OAM-Br), was used as an interfacial engineering layer between the hole transport layer (HTL) and the perovskite QDs to passivate cation- and anion-defects in perovskite QDs. The OAM-Br interfacial layer enables a high PLQY due to the suppression of surface defects in perovskite QDs. Thus, the CsPbBr3 QD-LEDs with an OAM-Br layer exhibited a maximum power efficiency of 3.35 lm/W and an external quantum efficiency (EQE) of 2.08% that which are higher efficiencies than those of the LEDs without an OAM-Br layer.
Scatterometric Porosimetry for porous low-k patterns characterization (2011)

Porous low-k dielectrics integration in interconnects is required to keep improving Integrated Circuits performance. However, these materials are highly sensitive to plasma processes and may be damaged during the patterning steps. Characterizing the plasma induced modification is required on patterned structures to develop less damaging plasma processes. Scatterometric Porosimetry (SP) has recently been introduced to characterize the plasma-induced porous low-k modification on patterned structures. By discussing the sensitivity and correlations of the different optimization parameters on a simple dielectric stack, we will show in which manner the SP method is applicable to fundamental studies and to process optimization.
Efficiency Optimization for Burst-Mode Multilevel Radio Frequency Transmitters (2013)

The utilization of a burst-mode power amplifier (PA) together with pulse-width modulation (PWM) is a promising concept for achieving high efficiency in radio frequency (RF) transmitters. Nevertheless, such a transmitter architecture requires bandpass filtering to suppress side-band spectral components to retrieve the wanted signal, which reduces the transmit power and the transmitter efficiency. High efficiency can only be expected with the maximum transmit power and signals with low peak-to-average-power ratios (PAPRs). To boost efficiency for signals with high PAPRs and signals at variable transmit power levels, the burst-mode multilevel transmitter architecture has been widely discussed as a potential solution. This paper presents an efficiency optimization procedure of burst-mode multilevel transmitters for signals with high PAPRs and signals at variable transmit power levels. The impact of the threshold value on the transmitter efficiency is studied, where the optimum threshold value and the maximum transmitter efficiency can be obtained according to input magnitude statistics. In addition, the relation between the threshold value and the efficiency expression of burst-mode multilevel transmitters and those of Doherty PAs is investigated. It is shown that the obtained optimum threshold value, although originally designed for burst-mode transmitters, can also be applied to Doherty and multistage Doherty PAs to achieve maximum transmitter efficiency. Simulations are used to validate the efficiency improvement of the optimized burst-mode multilevel transmitters compared to two-level and non-optimized multilevel transmitters.
Exploring parallelizations of applications for MPSoC platforms using MPA (2009)

This paper presents a tool for exploring different parallelization options for an application. It can be used to quickly find a high-quality match between an application and a multi-processor platform architecture. By specifying the parallelization at a high abstraction level, and leaving the actual source code transformations to the tool, a designer can try out many parallelizations in a short time. A parallelization may use either functional or data-level splits, or a combination of both. An accompanying high-level simulator provides rapid feedback about the expected performance of a parallelization, based on platform parameters and profiling data of the sequential application on the target processor. The use of the tool and simulator are demonstrated on an MPEG-4 video encoder application and two different platform architectures.
Carbon nanotube bearings in theory and practice (2011)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2011.