gebhart/patrepeval huggingface dataset:
The Interface Between ER and Mitochondria: Molecular Compositions and Functions. (2018)

Mitochondria and endoplasmic reticulum (ER) are essential organelles in eukaryotic cells, which play key roles in various biological pathways. Mitochondria are responsible for ATP production, maintenance of Ca<sup>2+</sup> homeostasis and regulation of apoptosis, while ER is involved in protein folding, lipid metabolism as well as Ca<sup>2+</sup> homeostasis. These organelles have their own functions, but they also communicate via mitochondrial-associated ER membrane (MAM) to provide another level of regulations in energy production, lipid process, Ca<sup>2+</sup> buffering, and apoptosis. Hence, defects in MAM alter cell survival and death. Here, we review components forming the molecular junctions of MAM and how MAM regulates cellular functions. Furthermore, we discuss the effects of impaired ER-mitochondrial communication in various neurodegenerative diseases.
A 3-V CMOS differential bandpass amplifier for GSM receivers (2002)

A 3V CMOS differential bandpass amplifier to be integrated in a GSM RF front-end is presented. With a center frequency tuning circuit, the center frequency can be varied from 877 to 962 MHz, and with a Q-compensation circuit, the Q-value can be tuned from 3 to 230. Detailed analysis of the noise figure including the resistive losses in on-chip inductors is given. With a 3V supply and a Q of 32, the amplifier achieves a noise figure of 5.2 dB, a power gain of 25 dB and consumes 45 mW. The IIP/sub 3/ and Po/sub -1 dB/ are -32.5 dBm and -44 dBm respectively.
Immunodominant epitopes defined by a yeast-expressed library of random fragments of the rabies glycoprotein map outside major antigenic sites (1996)

International audience
Compressed mode techniques for inter-frequency measurements in a wide-band DS-CDMA system (2002)

We discuss inter-frequency hand-over (IFHO) in third generation cellular systems based on wide-band DS-CDMA. In order to provide maximum flexibility for future radio network design, it is important to develop a technique allowing reliable IFHO in the system. The compressed mode (CM) scheme first presented by Baier et. al (see IEEE JSAC, vol.12, no.4, p.733-43, 1994) facilitates the use of the mobile-assisted hand-over (MAHO) technique commonly used in all second generation systems, also for IFHO in a CDMA system. We present and analyze four different ways of achieving a CM mechanism in a CDMA system. It is found that methods based on a variable spreading factor and coding-rate increment may be of most interest for practical use.
Metformin Inhibits Skin Tumor Promotion in Overweight and Obese Mice (2013)

In the present study, the ability of metformin to inhibit skin tumor promotion by 12-O-tetradecanoylphorbol-13-acetate (TPA) was analyzed in mice maintained on either an overweight control diet or an obesity-inducing diet. Rapamycin was included for comparison, and a combination of metformin and rapamycin was also evaluated. Metformin (given in the drinking water) and rapamycin (given topically) inhibited development of both papillomas and squamous cell carcinomas in overweight and obese mice in a dose-dependent manner. A low-dose combination of these two compounds displayed an additive inhibitory effect on tumor development. Metformin treatment also reduced the size of papillomas. Interestingly, all treatments seemed to be at least as effective for inhibiting tumor formation in obese mice, and both metformin and rapamycin were more effective at reducing tumor size in obese mice compared with overweight control mice. The effect of metformin on skin tumor development was associated with a significant reduction in TPA-induced epidermal hyperproliferation. Furthermore, treatment with metformin led to activation of epidermal AMP-activated protein kinase (AMPK) and attenuated signaling through mTOR complex (mTORC)-1 and p70S6K. Combinations of metformin and rapamycin were more effective at blocking epidermal mTORC1 signaling induced by TPA consistent with the greater inhibitory effect on skin tumor promotion. Collectively, the current data demonstrate that metformin given in the drinking water effectively inhibited skin tumor promotion in both overweight and obese mice and that the mechanism involves activation of epidermal AMPK and attenuated signaling downstream of mTORC1.
Outcome of critically ill patients with acute kidney injury using the Acute Kidney Injury Network criteria* (2011)

More than 50% of our critically ill patients developed some stage of acute kidney injury resulting in a stagewise increased mortality risk. However, the mortality risk associated with acute kidney injury stages 1 and 2 does not differ significantly. In light of these findings, re-evaluation of the Acute Kidney Injury Network staging criteria should be considered.
M-AODV+: An extension of AODV+ routing protocol for supporting vehicle-to-vehicle communication in vehicular ad hoc networks (2014)

The unique characteristics of vehicular ad hoc network (VANET) such as highly dynamic mobility and constrained mobility pattern along predetermined road have made the existing routing protocols designed for traditional mobile adhoc network (MANET) cannot be directly applied to support the reliability of vehicle-to-vehicle (V2V) communication in VANET. AODV+ protocol was proposed to support the internet connectivity for MANETs by utilizing a gateway to communicate between mobile network and infrastructure network. However, AODV+ only considers that the destination node lies on the infrastructure network (Internet). When a link breaks, reliable transmission from source to destination cannot be maintained. In the present paper, an extension of AODV+ routing protocol for VANETs called M-AODV+ (Modified AODV+) is proposed. The proposed M-AODV+ routing protocol supports the reliability of vehicle-to-vehicle communication in VANETs by enabling vehicleto- infrastructure (V2I) and infrastructure-to-infrastructure (I2I) communications as alternative communication links among vehicles when single hop or multi-hop communication in the mobile network is not possible. M-AODV+ consists of three parts: communication channel selection, gateway discovery, and I2I communication routing. The simulation results show that the proposed protocol improves the performance in terms of packet delivery fraction in the given simulation scenarios compared to that of AODV+ routing protocol with a slight loss on the average end-to-end delay.
Impression Management using Typeface Design (2004)

This article develops empirically based guidelines to help managers select typefaces that affect strategically valued impressions. The authors discuss the potential trade-offs among the impressions created by typeface (e.g., pleasing, engaging, reassuring, prominent). The selection of typeface can be simplified with the use of six underlying design dimensions: elaborate, harmony, natural, flourish, weight, and compressed.
Modulation codes and data processing for seismic apparition of towed-streamer seismic data (2018)

Seismic apparition uses regular periodic codes for blended acquisitions with airgun source arrays, in contrast with the more commonly used natural or artificial random dithers. The periodic codes act as modulation functions and facilitate isolation of the coded sources. This paper discusses modulation codes and an approach for their optimisation, as well as issues related with processing the data in preparation for apparition de-blending. Presentation Date: Tuesday, October 16, 2018 Start Time: 1:50:00 PM Location: Poster Station 20 Presentation Type: Poster
The Induced Magnetic Field (2011)

Aromaticity is indispensable for explaining a variety of chemical behaviors, including reactivity, structural features, relative energetic stabilities, and spectroscopic properties. When interpreted as the spatial delocalization of π-electrons, it represents the driving force for the stabilization of many planar molecular structures. A delocalized electron system is sensitive to an external magnetic field; it responds with an induced magnetic field having a particularly long range. The shape of the induced magnetic field reflects the size and strength of the system of delocalized electrons and can have a large influence on neighboring molecules. In 2004, we proposed using the induced magnetic field as a means of estimating the degree of electron delocalization and aromaticity in planar as well as in nonplanar molecules. We have since tested the method on aromatic, antiaromatic, and nonaromatic compounds, and a refinement now allows the individual treatment of core-, σ-, and π-electrons. In this Account, we describe the use of the induced magnetic field as an analytical probe for electron delocalization and its application to a large series of uncommon molecules. The compounds include borazine; all-metal aromatic systems Al(4)(n-); molecular stars Si(5)Li(n)(6-n); electronically stabilized planar tetracoordinate carbon; planar hypercoordinate atoms inside boron wheels; and planar boron wheels with fluxional internal boron cluster moieties. In all cases, we have observed that planar structures show a high degree of electron delocalization in the π-electrons and, in some examples, also in the σ-framework. Quantitatively, the induced magnetic field has contributions from the entire electronic system of a molecule, but at long range the contributions arising from the delocalized electronic π-system dominate. The induced magnetic field can only indirectly be confirmed by experiment, for example, through intermolecular contributions to NMR chemical shifts. We show that calculating the induced field is a useful method for understanding any planar organic or inorganic system, as it corresponds to the intuitive Pople model for explaining the anomalous proton chemical shifts in aromatic molecules. Indeed, aromatic, antiaromatic, and nonaromatic molecules show differing responses to an external field; that is, they reduce, augment, or do not affect the external field at long range. The induced field can be dissected into different orbital contributions, in the same way that the nucleus-independent chemical shift or the shielding function can be separated into component contributions. The result is a versatile tool that is particularly useful in the analysis of planar, densely packed systems with strong orbital contributions directly atop individual atoms.
Single-mode tapered quantum cascade lasers (2013)

We demonstrate tapered quantum cascade lasers monolithically integrated with a distributed Bragg reflector acting as both a wavelength-selective back mirror and a transverse mode filter. Each of the 14 devices operates at a different wavelength between 9.2 and 9.7 μm, where nine devices feature single-mode operation at peak powers between 0.3 and 1.6 W at room temperature. High output power and excellent beam quality with peak brightness values up to 1.6 MW cm−2 sr−1 render these two-terminal devices highly suitable for stand-off spectroscopy applications.
High Bulk Spin Scattering Asymmetry in CPP Spin Valves With Alternated Monatomic $[\hbox{Fe/Co}]_{\rm n}$ Superlattice (2009)

We confirmed the structural properties of trilayered epitaxial films with AML [Fe/Co] <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> and Au spacer on Au electrode by RHEED and TEM. A considerably large DeltaRA (2.61 mOmegamum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) resistance area product was observed in all metallic current perpendicular-to-plane giant magneto-resistance (CPP-GMR) spin-valve elements by using alternate monatomic epitaxial [Fe/Co] <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ferromagnetic layer with IrMn layer on the top. The estimated spin scattering asymmetry coefficient beta and interface asymmetry coefficient gamma was 0.81 and 0.43 plusmn 0.05, respectively. This value of beta is higher than that of Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50</sub> /Cu laminated with Cu spacer or Heusler alloy which is largest value ever reported at room temperature.
Two-Step Approach to the Formation of Organic Monolayers on the Silicon Oxide Surface (2001)

A new synthetic strategy has been developed for the formation of densely packed monolayers on oxide surfaces. This technique involves a simple two-step procedure in which the oxide surface is initially chlorinated and then exposed to alcohol molecules for monolayer formation via Si−O linkages. We demonstrate this approach with the formation of octadecanol (C18) monolayers on the oxide-terminated Si(111) surface. Characterization of the resulting C18H37O− monolayer by a combination of techniques reveals a densely packed film with partial disorder. At the highest surface coverage, the thickness of the film is determined to be 24 Å. Kinetics of monolayer growth is characterized by a fast initial step at low coverage; the rate constant decreases by 3 orders of magnitude when surface coverage approaches saturation.
Effect of Pressure on Emission Characteristics in LBG-Fueled 1500°C-Class Gas Turbine (1998)

Developing integrated coal gasification combined cycle (IGCC) systems ensures cost-effective and environmentally sound options for supplying future power generation needs. In order to enhance thermal efficiency of IGCC and to reduce NOx emission, a 1500°C-class gas turbine combustor for IGCC was designed, tested, and the performance of the combustor was evaluated under pressurized conditions. The designed combustor had the following three characteristics: (1) in order to assure the stable combustion burning low-Btu gas (LBG), an auxiliary combustion chamber was installed at the entrance of the combustor; (2) to reduce fuel NOx emission that was produced from the ammonia (NH3) in the fuel, the rich-lean combustion method was introduced; and (3) to compensate for the declined cooling-air associated with the higher temperature of the gas turbine, the tested combustor was equipped with a dual-structure transition piece so that the cooling air in the transition piece can be recycled to cool down the combustor liner wall. As a result of combustor tests, it is confirmed that CO emission is less than 20 ppm, the conversion rate of NH3 which contains about 1000 ppm in the coal gasified fuel to NOx shows 40 percent or below, and the liner wall temperature remained below almost 850°C under high pressure (1.4 MPa), rated load condition.
Graph-based joint clustering of fixations and visual entities (2013)

We present a method that extracts groups of fixations and image regions for the purpose of gaze analysis and image understanding. Since the attentional relationship between visual entities conveys rich information, automatically determining the relationship provides us a semantic representation of images. We show that, by jointly clustering human gaze and visual entities, it is possible to build meaningful and comprehensive metadata that offer an interpretation about how people see images. To achieve this, we developed a clustering method that uses a joint graph structure between fixation points and over-segmented image regions to ensure a cross-domain smoothness constraint. We show that the proposed clustering method achieves better performance in relating attention to visual entities in comparison with standard clustering techniques.
Implementation of Low Power Multi-hop Wireless Sensor Network (2016)

In this paper, the multi-hop wireless sensor network is created, which is realized by Micaz and Mib520 Board using TinyOS and Cygwin. The mote transmission mode is engaged and off-the-shelf protocols and algorithm, RSSI and PDR, are applied in this wireless network and the performance is improved. Several experiments are proposed to set standard RSSI threshold value to allow the user to send packet with efficient power level.
Joint demosaicing and denoising of noisy bayer images with ADMM (2017)

Image demosaicing and denoising are import steps of image signal processing. Sequential executions of demosaicing and denoising have essential drawbacks that they degrade the results of each other. Joint demosaicing and denoising overcomes the difficulties by solving the two problems in one model. This paper introduces a unified object function with hidden priors and a variant of ADMM to recover a full-resolution color image with a noisy Bayer input. Experimental results demonstrate that our method performs better than state-of-the-art methods in both PSNR comparison and human vision. In addition, our method is much more robust to variations of noise level.
Identification of a natural product-like STAT3 dimerization inhibitor by structure-based virtual screening (2014)

STAT3 regulates a variety of genes involved with cell proliferation, differentiation, apoptosis, angiogenesis, metastasis, inflammation, and immunity. The purpose of this study was to apply molecular docking techniques to identify STAT3 inhibitors from a database of over 90000 natural product and natural product-like compounds. The virtual screening campaign furnished 14 hit compounds, from which compound 1 emerged as a top candidate. Compound 1 inhibited STAT3 DNA-binding activity in vitro and attenuated STAT3-directed transcription in cellulo with selectivity over STAT1 and with comparable potency to the well-known STAT3 inhibitor S3I-201. Furthermore, compound 1 inhibited STAT3 dimerization and decreased STAT3 phosphorylation in cells without affecting STAT1 dimerization and phosphorylation. Compound 1 also exhibited selective anti-proliferative activity against cancer cells over normal cells in vitro. Molecular docking analysis suggested that compound 1 might putatively function as an inhibitor of STAT3 dimerization by binding to the SH2 domain. This study also validates the use of in silico techniques to identify inhibitors of protein-protein interactions, which are typically considered difficult to target with small molecules.
Protein tyrosine phosphorylation induced by lysophosphatidic acid in Rat-1 fibroblasts. Evidence that phosphorylation of map kinase is mediated by the Gi-p21ras pathway. (1994)

Lysophosphatidic acid (LPA) is a platelet-derived phospholipid that serves as a mitogen for fibroblasts. LPA activates its own G protein-coupled receptor(s) leading to stimulation of phospholipase C and inhibition of adenylate cyclase. Furthermore, LPA rapidly activates p21ras through a pertussis toxin-sensitive pathway. In this study, we have examined LPA-induced protein tyrosine phosphorylation in Rat-1 fibroblasts. LPA action was compared with that of endothelin, which is a stronger activator of phospholipase C than LPA but fails to activate p21ras and to stimulate DNA synthesis in these cells. LPA and, more effectively, endothelin rapidly stimulate tyrosine phosphorylation of proteins of 110-130, 95, and 65-75 kDa. The effect of LPA is dose- and time-dependent, being half-maximal at 3-30 nM and peaking after 2-5 min. Among the 110-130-kDa group of phosphotyrosyl proteins is the 125-kDa "focal adhesion kinase" (p125FAK) but not the 120-kDa p21ras GTPase-activating protein. Furthermore, LPA, like epidermal growth factor, causes tyrosine phosphorylation and activation of the p42/p44 mitogen-activated protein (MAP) kinases, paralleling p21ras activation. In contrast, endothelin fails to phosphorylate MAP kinase. Treatment of the cells with pertussis toxin blocks LPA-induced MAP kinase phosphorylation without affecting the other tyrosine phosphorylations. The kinase inhibitor staurosporine (1 microM) blocks LPA-induced, but not epidermal growth factor-induced, activation of p21ras and MAP kinase, consistent with an intermediate protein kinase linking the LPA receptor to p21ras activation. The results support a model in which LPA-induced phosphorylation of MAP kinase is mediated by p21ras, and tyrosine phosphorylation of the other substrates, including p125FAK, is associated with phospholipase C activation.
The fate of pro-TNF-alpha following inhibition of metalloprotease-dependent processing to soluble TNF-alpha in human monocytes (1997)

Human monocytes rapidly produce TNF-alpha following activation by bacterial LPS. The message for TNF-alpha encodes a 26-kDa protein that is proteolytically processed to the secreted 17-kDa form. Sequencing of the N terminus of the protein secreted by monocytes shows processing of the 26-kDa pro-TNF-alpha to a mature form at the projected metalloprotease cleavage site to generate 17-kDa TNF-alpha with the N terminus VRSSSR-. The addition of hydroxamic acid-based metalloprotease inhibitors to the cell culture is capable of blocking >95% of the production of soluble TNF-alpha and leads to a transient, but reproducible, increase in cell surface TNF-alpha as measured by FACS analysis. The cell surface TNF-alpha was demonstrated to increase the cell's ability to kill L929 tumor targets and induce PG production from human gingival fibroblasts. The buildup of cell surface TNF-alpha is unable to account for the TNF-alpha that is not secreted when inhibitor is present. Pulse-chase analysis of the cells demonstrates rapid degradation of the pro-TNF-alpha that remains unprocessed in the monocytes. Through inhibition of processing and secretion by brefeldin A, processing was shown to occur at a postendoplasmic reticulum site and is closely associated with movement to the cell surface.
Image Super-Resolution Via Iterative Refinement (2022)

We present SR3, an approach to image Super-Resolution via Repeated Refinement. SR3 adapts denoising diffusion probabilistic models (Ho et al. 2020), (Sohl-Dickstein et al. 2015) to image-to-image translation, and performs super-resolution through a stochastic iterative denoising process. Output images are initialized with pure Gaussian noise and iteratively refined using a U-Net architecture that is trained on denoising at various noise levels, conditioned on a low-resolution input image. SR3 exhibits strong performance on super-resolution tasks at different magnification factors, on faces and natural images. We conduct human evaluation on a standard 8× face super-resolution task on CelebA-HQ for which SR3 achieves a fool rate close to 50%, suggesting photo-realistic outputs, while GAN baselines do not exceed a fool rate of 34%. We evaluate SR3 on a 4× super-resolution task on ImageNet, where SR3 outperforms baselines in human evaluation and classification accuracy of a ResNet-50 classifier trained on high-resolution images. We further show the effectiveness of SR3 in cascaded image generation, where a generative model is chained with super-resolution models to synthesize high-resolution images with competitive FID scores on the class-conditional 256×256 ImageNet generation challenge.