gebhart/patrepeval huggingface dataset:
Lack of Pathology in a Triple Transgenic Mouse Model of Alzheimer's Disease after Overexpression of the Anti-Apoptotic Protein Bcl-2 (2008)

Alzheimer's disease (AD) is characterized by the accumulation of plaques containing beta-amyloid (Abeta) and neurofibrillary tangles (NFTs) consisting of modified tau. Although Abeta deposition is thought to precede the formation of NFTs in AD, the molecular steps connecting these two pathologies is not known. Previous studies have suggested that caspase activation plays an important role in promoting the pathology associated with AD. To further understand the contribution of caspases in disease progression, a triple transgenic Alzheimer's mouse model overexpressing the anti-apoptotic protein Bcl-2 was generated. Here we show that overexpression of Bcl-2 limited caspase-9 activation and reduced the caspase cleavage of tau. Moreover, overexpression of Bcl-2 attenuated the processing of APP (amyloid precursor protein) and tau and reduced the number of NFTs and extracellular deposits of Abeta associated with these animals. In addition, overexpression of Bcl-2 in 3xTg-AD mice improved place recognition memory. These findings suggest that the activation of apoptotic pathways may be an early event in AD and contributes to the pathological processes that promote the disease mechanisms underlying AD.
Message encryption with image processing (2005)

The paper proposes a new steganographic model for secret data communication. A stack of four modules is used. The "compression module" gives the benefit of entropy coding. The "cryptographic module" provides confidentiality in the communication. To preserve integrity of data, the "hash module" is used with a shared secret key. A technique is proposed in which it is not required that the receiver should know the secret key before reception of the message. For the "steganographic module", an image steganographic method is proposed that is derived from the method of Yeuan-Kuen Lee and Ling-Hwei Chen (see IEEE Proc. Vision, Image and Sig. Process., 2000). As compared to that method, we make little use of the smooth regions of the cover image that provides better image fidelity and perceptual transparency. The proposed method can also hide data in 24 bit true color images. Furthermore, we spread the data on the whole image instead of using part of the image. This steganographic method is used to hide the encrypted communication. Experimental results show the effectiveness and efficiency of the proposed model.
Subcellular Localization and Characterization of Amylases in <i>Arabidopsis</i> Leaf (1988)

Amylolytic enzymes of Arabidopsis leaf tissue were partially purified and characterized. Endoamylase, starch phosphorylase, d-enzyme (transglycosylase), and possibly exoamylase were found in the chloroplasts. Endoamylase, fraction A2, found only in the chloroplast, was resolved from the exoamylases by chromatography on a Mono Q column and migrated with an R(F) of 0.44 on 7% polyacrylamide gel electrophoresis. Exoamylase fraction, A1, has an R(F) of 0.23 on the polyacrylamide gel. Viscometric analysis showed that A1 has a slope of 0.013, which is same as that of A3, the extrachloroplastic amylase. A1, however, can be distinguished from A3 by having much higher amylolytic activity in succinate buffer than acetate buffer, and having much less reactivity with amylose. A1 probably is also localized in the chloroplast, and contributes to the 30 to 40% higher amylolytic activity of the chloroplast preparation in succinate than acetate buffer at pH 6.0. The high activity of d-enzyme compared to the amylolytic activity in the chloroplast suggests that transglycosylation probably has an important role during starch degradation in Arabidopsis leaf. Extrachloroplastic amylase, A3, has an R(F) of 0.55 on 7% electrophoretic gel and constitutes 80% of the total leaf amylolytic activity. The results of substrate specificity studies, action pattern and viscometric analyses indicate that the extrachloroplastic amylases are exolytic.
If Lava Mingled with Ground Ice on Mars (2001)

Clusters of small cones on the lava plains of Mars have caught the attention of planetary geologists for years for a simple and compelling reason: ground ice. These cones look like volcanic rootless cones found on Earth where hot lava flows over wet surfaces such as marshes, shallow lakes or shallow aquifers. Steam explosions fragment the lava into small pieces that fall into cone-shaped debris piles. Peter Lanagan, Alfred McEwen, Laszlo Keszthelyi (University of Arizona), and Thorvaldur Thordarson (University of Hawai`i) recently identified groups of cones in the equatorial region of Mars using new high-resolution Mars Orbiter Camera (MOC) images. They report that the Martian cones have the same appearance, size, and geologic setting as rootless cones found in Iceland. If the Martian and terrestrial cones formed in the same way, then the Martian cones mark places where ground ice or groundwater existed at the time the lavas surged across the surface, estimated to be less than 10 million years ago, and where ground ice may still be today.
An offline browsing system for mobile devices (2009)

With the growing capability of mobile devices, platforms, and wireless communication technologies, Web browsing on mobile devices is made possible and receives more and more attentions. However, environment of mobile device varies; traditionally, Web pages cannot be browsed if mobile user enters an environment where there is no connection to Internet, such as in a basement or countryside. Although Google Gears had been proposed to support offline Web browsing, there are still a lot of Web servers providing their services without support Google Gears. In this paper, we propose a middleware for mobile devices with properties including (1) enabling users to access the predefined Web information without network connection, (2) offline data stored on mobile device should be long-term storage, and (3) even a Web server doesn't support Google Gears, its Web pages still can be browsed offline.
Interaction Parameters of Poly(vinyl methyl ether) in 2-Propanol-Water Mixture as Determined by Small-Angle Neutron Scattering. (1994)

ポリビニルメチルエーテル (PVME) 水溶液は下限臨界共溶温度 (LCST) を示す. 本研究では, PVME水溶液に対するアルコール添加の影響を調べる目的で, PVME- (水+10vol% 2-プロパノール) 系半希薄溶液の中性子小角散乱測定をLCST近傍の温度領域で行い, 高分子セグメント間の2体クラスター積分B1および3体クラスター積分B2を求めた. またPVMEセグメント間相互作用のエントロピーおよびエンタルピーへの寄与をB1とB2の温度依存性から求めた. 我々がすでに測定したPVME-水系およびPVME- (水+メタノール) 系と比較すると, PVME- (水+2-プロパノール) 系のセグメント-セグメント相互作用は, エントロピーをより大きく増大させることがわかった. これは疎水性が強い2-プロパノール分子のPVMEへの選択的溶媒和によるものと考えられる.
Proton transfer reaction ion trap mass spectrometer (2003)

Proton transfer reaction mass spectrometry is a relatively new field that has attracted a great deal of interest in the last few years. This technique uses H(3)O(+) as a chemical ionization (CI) reagent to measure volatile organic compounds (VOCs) in the parts per billion by volume (ppbv) to parts per trillion by volume (pptv) range. Mass spectra acquired with a proton transfer reaction mass spectrometer (PTR-MS) are simple because proton transfer chemical ionization is "soft" and results in little or no fragmentation. Unfortunately, peak identification can still be difficult due to isobaric interferences. A possible solution to this problem is to couple the PTR drift tube to an ion trap mass spectrometer (ITMS). The use of an ITMS is appealing because of its ability to perform MS/MS and possibly distinguish between isomers and other isobars. Additionally, the ITMS duty cycle is much higher than that of a linear quadrupole so faster data acquisition rates are possible that will allow for detection of multiple compounds. Here we present the first results from a proton transfer reaction ion trap mass spectrometer (PTR-ITMS). The aim of this study was to investigate ion injection and storage efficiency of a simple prototype instrument in order to estimate possible detection limits of a second-generation instrument. Using this prototype a detection limit of 100 ppbv was demonstrated. Modifications are suggested that will enable further reduction in detection limits to the low-ppbv to high-pptv range. Furthermore, the applicability of MS/MS in differentiating between isobaric species was determined. MS/MS spectra of the isobaric compounds methyl vinyl ketone (MVK) and methacrolein (MACR) are presented and show fragments of different mass making differentiation possible, even when a mixture of both species is present in the same sample. However, MS/MS spectra of acetone and propanal produce fragments with the same molecular masses but with different intensity ratios. This allows quantitative distinction only if one species is predominant. Fragmentation mechanisms are proposed to explain the results.
Id genes in nervous system development. (2000)

Id genes encode helix-loop-helix proteins that function to mediate processes important for normal development including cellular differentiation, proliferation and apoptosis. Id proteins act as negative regulators of other transcription factors, which are essential for cell determination and differentiation in diverse cell types, and interact with proteins important for cell cycle regulation. Studies of Id gene expression in the nervous system and in neural cells in culture indicate that Id proteins contribute to the regulation of mammalian nervous system development. Also, recognition of a wide variety of proteins with which Id transcription factors are capable of interacting suggests that it will be possible to understand more precisely their specific functions and importantly how these are integrated.
MR Imaging–Guided Vascular Procedures Using CO<sub>2</sub> as a Contrast Agent (2003)

The use of carbon dioxide in combination with a bright blood MR imaging sequence improves vessel conspicuity and provides immediate information about blood flow distal to the catheter. This technique may be used to facilitate MR imaging-guided intravascular procedures.
Loop antenna for mobile and personal communication systems (2002)

This paper presents the results of a loop antenna, which can be used as an antenna element with a portable hand-held cellular telephone, for the first and third generation of mobile and personal communication systems. The antenna is analyzed using the finite-difference time-domain method, and the results are compared with measurements. By grounding and not grounding one end of the loop, the same element can be used to resonate at the appropriate frequencies for the first and third generation of mobile and personal communications systems.
Histidine affinity tags affect MSP1<sub>42</sub> structural stability and immunodominance in mice (2011)

Inclusion of affinity tags has greatly facilitated process development for protein antigens, primarily for their recovery from complex mixtures. Although generally viewed as supportive of product development, affinity tags may have unintended consequences on protein solubility, susceptibility to aggregation, and immunogenicity. Merozoite surface protein 1 (MSP1), an erythrocytic stage protein of Plasmodium falciparum and a candidate malaria vaccine, was used to evaluate the impact of a metal ion affinity-tag on both protein structure and the induction of immunity. To this end, codon harmonized gene sequences from the P. falciparum MSP1(42) of FVO and 3D7 parasites were cloned and purified with and without a histidine (His) tag. We report on the influence of His-affinity tags on protein expression levels, solubility, secondary structure, thermal denaturation, aggregation and the impact on humoral and cellular immune responses in mice. While the overall immunogenicity induced by His-tagged MSP1(42) proteins is greater, the fine specificity of the humoral and cellular immune responses is altered relative to anti-parasitic antibody activity and the breadth of T-cell responses. Thus, the usefulness of protein tags may be outweighed by their potential impact on structure and function, stressing the need for caution in their use. See accompanying commentary by Randolph DOI: 10.1002/biot.201100459.
Dynamic Filter Networks (2016)

In a traditional convolutional layer, the learned filters stay fixed after training. In contrast, we introduce a new framework, the Dynamic Filter Network, where filters are generated dynamically conditioned on an input. We show that this architecture is a powerful one, with increased flexibility thanks to its adaptive nature, yet without an excessive increase in the number of model parameters. A wide variety of filtering operation can be learned this way, including local spatial transformations, but also others like selective (de)blurring or adaptive feature extraction. Moreover, multiple such layers can be combined, e.g. in a recurrent architecture. We demonstrate the effectiveness of the dynamic filter network on the tasks of video and stereo prediction, and reach state-of-the-art performance on the moving MNIST dataset with a much smaller model. By visualizing the learned filters, we illustrate that the network has picked up flow information by only looking at unlabelled training data. This suggests that the network can be used to pretrain networks for various supervised tasks in an unsupervised way, like optical flow and depth estimation.
The Effect of Recommendations on Network Structure (2016)

Online social networks regularly offer users personalized, algorithmic suggestions of whom to connect to. Here we examine the aggregate effects of such recommendations on network structure, focusing on whether these recommendations increase the popularity of niche users or, conversely, those who are already popular. We investigate this issue by empirically and theoretically analyzing abrupt changes in Twitter's network structure around the mid-2010 introduction of its "Who to Follow" feature. We find that users across the popularity spectrum benefitted from the recommendations; however, the most popular users profited substantially more than average. We trace this "rich get richer" phenomenon to three intertwined factors. First, as is typical of network recommenders, the system relies on a "friend-of-friend"-style algorithm, which we show generally results in users being recommended proportional to their degree. Second, we find that the baseline growth rate of users is sublinear in degree. This mismatch between the recommender and the natural network dynamics thus alters the structural evolution of the network. Finally, we find that people are much more likely to respond positively to recommendations for popular users---perhaps because of their greater name recognition---further amplifying the cumulative advantage of well-known individuals.
Cost-distance: two metric network design (2002)

Presents the cost-distance problem, which consists of finding a Steiner tree which optimizes the sum of edge costs along one metric and the sum of source-sink distances along an unrelated second metric. We give the first known O(log k) randomized approximation scheme for the cost-distance problem, where k is the number of sources. We reduce several common network design problems to cost-distance problems, obtaining (in some cases) the first known logarithmic approximation for them. These problems include a single-sink buy-at-bulk problem with variable pipe types between different sets of nodes, facility location with buy-at-bulk-type costs on edges, constructing single-source multicast trees with good cost and delay properties, and multi-level facility location. Our algorithm is also easier to implement and significantly faster than previously known algorithms for buy-at-bulk design problems.
Parallel spatial processing: A cure for signal cancellation in adaptive arrays (1986)

A spatial processing algorithm with parallel structure is presented for the prevention of signal caneellation phenomena in conventional adaptive arrays. This algorithm basically uses a parallel structure with a spatial averaging effect to combat coherent jamming. It results in a spatially smoothed maximum-likelihood estimate of the desired signal when the adaptive beamformer converges. Simulations have been conducted which verify the effectiveness of the proposed structure.
High-power single spatial mode AlGaAs channeled-substrate-planar semiconductor diode lasers for spaceborne communications (1989)

A high power single spatial mode channeled substrate planar AlGaAs semiconductor diode laser was developed. The emission wavelength was optimized at 860 to 880 nm. The operating characteristics (power current, single spatial mode behavior, far field radiation patterns, and spectral behavior) and results of computer modeling studies on the performance of the laser are discussed. Reliability assessment at high output levels is included. Performance results on a new type of channeled substrate planar diode laser incorporating current blocking layers, grown by metalorganic chemical vapor deposition, to more effectively focus the operational current to the lasing region was demonstrated. The optoelectronic behavior and fabrication procedures for this new diode laser are discussed. The highlights include single spatial mode devices with up to 160 mW output at 8600 A, and quantum efficiencies of 70 percent (1 W/amp) with demonstrated operating lifetimes of 10,000 h at 50 mW.
The use of graft materials in vaginal pelvic floor surgery (2006)

Due to a lack of well-designed prospective randomized trials, recommendations for using graft materials in vaginal reconstructive surgery cannot be made. At this time, grafts should have limited use in a carefully selected patient population.
Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography (2009)

We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen.The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401.
Burn resuscitation: is it straightforward or a challenge? (2011)

Burn shock resuscitation has been extensively studied over the past four decades. Many formulas exist and many parameters have been suggested to assess the adequacy of resuscitation. The most commonly used formula is the Parkland formula, the most commonly used fluids are crystalloids, and the most commonly used parameter is urine output. However, until now, no conclusive evidence has suggested that one formula is superior to another or that one parameter is a better predictor than another. In this article we will review the updated information about the subject and we will look into new advancements in this field. We will pose some questions at the end that will help researchers concentrate their future efforts to solve this important challenge in burn care.
Experimental Verification of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>n</mml:mi><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:math>Structures for Visible Light (2013)

We fabricate and characterize a metal-dielectric nanostructure with an effective refractive index n = 0 in the visible spectral range. Light is excited in the material at deep subwavelength resolution by a 30-keV electron beam. From the measured spatially and angle-resolved emission patterns, a vanishing phase advance, corresponding to an effective [Symbol: see text] = 0 and n = 0, is directly observed at the cutoff frequency. The wavelength at which this condition is observed can be tuned over the entire visible or near-infrared spectral range by varying the waveguide width. This n = 0 plasmonic nanostructure may serve as a new building block in nanoscale optical integrated circuits and to control spontaneous emission as experimentally demonstrated by the strongly enhanced radiative optical density of states over the entire n = 0 structure.
HmsP, a putative phosphodiesterase, and HmsT, a putative diguanylate cyclase, control Hms‐dependent biofilm formation in <i>Yersinia pestis</i> (2004)

The Hms(+) phenotype of Yersinia pestis promotes the binding of haemin or Congo red (CR) to the cell surface at temperatures below 34 degrees C. We previously demonstrated that temperature regulation of the Hms(+) phenotype is not controlled at the level of transcription. Instead, HmsH, HmsR and HmsT are degraded upon a temperature shift from 26 degrees C to 37 degrees C. We used random transposon mutagenesis to identify new genes involved in the temperature-regulated expression of the Hms phenotype. One of these genes, which we designated hmsP, encodes a putative phosphodiesterase with a conserved EAL motif. Mutations in hmsP caused formation of red colonies on CR plates at 26 degrees C and 37 degrees C. Strains complemented with hmsP(+) on a plasmid form white colonies at both temperatures. We used a crystal violet assay and confocal laser scanning microscopy to demonstrate Hms-dependent biofilm formation by Y. pestis cells. Y. pestis Hms(+) strains grown at 26 degrees C but not at 37 degrees C form a biofilm on borosilicate glass surfaces. Strains that either overexpress HmsT (a GGDEF domain protein) or have a mutation in hmsP produced an extremely thick biofilm. Alanine substitutions for each of the GGEE residues (amino acids 296-299) of HmsT as well as the E506 and L508 residues of HmsP caused a loss of function. We propose that HmsT and HmsP together control the amount of biofilm produced in Y. pestis. Degradation of HmsT at 37 degrees C may be a critical factor in controlling the temperature-dependent expression of the Hms biofilm.
Assessment of pipeline stability in the Gulf of Mexico during hurricanes using dynamic analysis (2015)

Pipelines are the critical link between major offshore oil and gas developments and the mainland. Any inadequate on-bottom stability design could result in disruption and failure, having a devastating impact on the economy and environment. Predicting the stability behavior of offshore pipelines in hurricanes is therefore vital to the assessment of both new design and existing assets. The Gulf of Mexico has a very dense network of pipeline systems constructed on the seabed. During the last two decades, the Gulf of Mexico has experienced a series of strong hurricanes, which have destroyed, disrupted and destabilized many pipelines. This paper first reviews some of these engineering cases. Following that, three case studies are retrospectively simulated using an in-house developed program. The study utilizes the offshore pipeline and hurricane details to conduct a Dynamic Lateral Stability analysis, with the results providing evidence as to the accuracy of the modeling techniques developed.
Synthesis and Structure/Antioxidant Activity Relationship of Novel Catecholic Antioxidant Structural Analogues to Hydroxytyrosol and Its Lipophilic Esters (2012)

A large panel of novel catecholic antioxidants and their fatty acid or methyl carbonate esters has been synthesized in satisfactory to good yields through a 2-iodoxybenzoic acid (IBX)-mediated aromatic hydroxylation as the key step. The new catechols are structural analogues of naturally occurring hydroxytyrosol (3,4-DHE). To evaluate structure/activity relationships, the antioxidant properties of all catecholic compounds were evaluated in vitro by ABTS assay and on whole cells by DCF fluorometric assay and compared with that of the corresponding already known hydroxytyrosyl derivatives. Results outline that all of the new catechols show antioxidant capacity in vitro higher than that of the corresponding hydroxytyrosyl derivatives. Less evident positive effects have been detected in whole cells experiments. Cytotoxicity experiments, using MTT assay, on a representative set of compounds evidenced no influence in cell survival.