Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of cellulose synthases in Arabidopsis secondary cell walls

Secondary cell walls built with speed Plant cell walls provide the cellulose that is integral for wood, cotton fiber, and many biofuels. Cellulose is synthesized outside the cell membrane by cellulose synthase enzymes. Much of the secondary cell wall, responsible for the sturdiness of wood, is formed by xylem cells embedded in the core of the plant. Watanabe et al. leveraged ectopic expression to bring xylem-style cellulose synthase activity to the epidermal surface of the plant (see the Perspective by Schneider and Persson). Combining this improved accessibility with fluorescent tagging showed that secondary cell walls are built faster than primary cell walls, perhaps due to increased velocity and density of cellulose synthase complexes. Science, this issue p. 198, see also p. 156 Cellulose synthesis in secondary plant cell walls is focused in spiral wall thickenings during xylem cell development. [Also see Perspective by Schneider and Perssonn] Cellulose biosynthesis in plant secondary cell walls forms the basis of vascular development in land plants, with xylem tissues constituting the vast majority of terrestrial biomass. We used plant lines that contained an inducible master transcription factor controlling xylem cell fate to quantitatively image fluorescently tagged cellulose synthase enzymes during cellulose deposition in living protoxylem cells. The formation of secondary cell wall thickenings was associated with a redistribution and enrichment of CESA7-containing cellulose synthase complexes (CSCs) into narrow membrane domains. The velocities of secondary cell wall–specific CSCs were faster than those of primary cell wall CSCs during abundant cellulose production. Dynamic intracellular of endomembranes, in combination with increased velocity and high density of CSCs, enables cellulose to be synthesized rapidly in secondary cell walls.
Patients still reacting to a sting challenge while receiving conventional Hymenoptera venom immunotherapy are protected by increased venom doses.

BACKGROUND Up to 20% of patients allergic to Hymenoptera venom are not protected by conventional venom immunotherapy (VIT) with 100 microg of any single venom. OBJECTIVE We sought to evaluate the efficacy of an increased venom dose in patients allergic to Hymenoptera venom still reacting systemically to a sting challenge despite immunotherapy with 100 microg of venom every 4 weeks. METHODS In this retrospective study patients were included who still had reacted systemically to a sting challenge with a living bee or wasp despite VIT with a maintenance dose of 100 microg every 4 weeks. The maintenance dose was increased to 150 or 200 microg every 4 weeks, and a second sting challenge was performed. If a patient reacted again, the dose was further increased. Baseline mast-cell tryptase levels were assessed by using a fluoroenzyme immunoassay in stored patient sera. RESULTS While receiving a maintenance dose of 100 microg of venom every 4 weeks for 7 to 38 months, 18 patients reacted systemically to a bee sting and 22 reacted to a wasp sting. After an increase of the maintenance dose to 150 microg, 2 of 4 patients allergic to bee venom (BV) and 6 of 6 patients allergic to yellow jacket venom (YJV) no longer reacted systemically to the sting challenge. The respective rates of full protection were 13 of 14 and 15 of 16 in patients with an increase of the maintenance dose to 200 microg from the start. Of those 4 individuals not protected by the first dose increase, one patient allergic to BV (prior dose of 150 microg) and one patient allergic to YJV (prior dose of 200 microg) did not react systemically to a further sting challenge while receiving 200 microg of BV or 250 microg of YJV, respectively. One patient allergic to BV who had a systemic reaction to the sting challenge while receiving 150 microg was not protected after a dose increase to 200 microg; she later received a dose of 400 microg of BV, and no further sting challenge was performed. The patient allergic to BV who still reacted systemically after a first dose increase to 200 microg was a female patient with urticaria pigmentosa. She had repeated systemic adverse reactions to further BV immunotherapy, necessitating discontinuation of the treatment; however, she tolerated well VIT with 200 microg of YJV. In all other patients, no unusual adverse reactions to the increased venom doses were observed. Baseline serum tryptase levels were elevated above 13.5 microg/L (95th percentile in normal subjects) in 9 (28.1%) of 32 patients. CONCLUSIONS The majority of patients allergic to Hymenoptera venom who still reacted systemically to a sting challenge despite VIT with a dose of 100 microg every 4 weeks can be fully protected by an increased maintenance dose. This dose increase is well tolerated by most patients. The rather high proportion of patients with elevated baseline serum tryptase levels necessitates further investigation of a possible association between mastocytosis and treatment failure of conventionally dosed VIT.
Cervical cancer screening: Less testing, smarter testing

In its 2009 recommendations for cervical cancer screening, the American College of Obstetricians and Gynecologists (ACOG) calls for less-frequent but smarter screening that integrates testing for human papillomavirus (HPV) infection with the Papanicolaou (Pap) test. We review the recommendations from this and other organizations and how and why they are evolving. The latest guidelines call for less frequent but smarter screening that integrates human papillomavirus testing with the Papanicolaou test.
A Method of Structure Comparison Using Spatial Topological Patterns

The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.
Multiwavelength Switchable Erbium-Doped Fiber Ring Laser using Digital Micromirror Device

We demonstrated a multiwavelength switchable erbium-doped fiber ring laser using digital micromirror device. By controlling the tilt states of micromirrors, we achieved some flexible allocations of wavelength channels and multiwavelength switching operations. We generated up to 8 wavelength channels with 0.8 nm spacing at room temperature.
NESTML: a modeling language for spiking neurons

Biological nervous systems exhibit astonishing complexity . Neuroscientists aim to capture this com- plexity by modeling and simulation of biological processes. Often very comple xm odels are nec- essary to depict the processes, which makes it dif fi cult to create these models. Powerful tools are thus necessary ,which enable neuroscientists to express models in acomprehensi ve and concise way and generate ef fi cient code for digital simulations. Se veral modeling languages for computational neuroscience ha ve been proposed [Gl10, Ra11]. Howe ver, as these languages seek simulator inde- pendence the ytypically only support asubset of the features desired by the modeler . Int his article, we present the modular and extensible domain speci fi cl anguage NESTML, which provides neuro- science domain concepts as fi rst-class language constructs and supports domain experts in creating neuron models for the neural simulation tool NEST . N ESTML and aset of example models are publically available on GitHub.
Norges Teknisk-naturvitenskapelige Universitet Prediction and Retrospective Analysis of Soccer Matches in a League Prediction and Retrospective Analysis of Soccer Matches in a League

A common discussion subject for the male part of the population in particular, is the prediction of next weekend's soccer matches, especially for the local team. Knowledge of offensive and defensive skills is valuable in the decision process before making a bet at a bookmaker. In this article we take an applied statistician's approach to the problem, suggesting a Bayesian dynamic generalised linear model to estimate the time dependent skills of all teams in a league, and to predict next weekend's soccer matches. The problem is more intricate than it may appear at first glance, as we need to estimate the skills of all teams simultaneously as they are dependent. It is now possible to deal with such inference problems using the iterative simulation technique known as Markov Chain Monte Carlo. We will show various applications of the proposed model based on the English Premier League and Division 1 1997-98; Prediction with application to betting, retrospective analysis of the final ranking, detection of surprising matches and how each team's properties vary during the season.
Lycopene Protects against Hypoxia/Reoxygenation-Induced Apoptosis by Preventing Mitochondrial Dysfunction in Primary Neonatal Mouse Cardiomyocytes

Background Hypoxia/reoxygenation(H/R)-induced apoptosis of cardiomyocytes plays an important role in myocardial injury. Lycopene is a potent antioxidant carotenoid that has been shown to have protective properties on cardiovascular system. The aim of the present study is to investigate the potential for lycopene to protect the cardiomyocytes exposed to H/R. Moreover, the effect on mitochondrial function upon lycopene exposure was assessed. Methods and Findings Primary cardiomyocytes were isolated from neonatal mouse and established an in vitro model of H/R which resembles ischemia/reperfusion in vivo. The pretreatment of cardiomyocytes with 5 µM lycopene significantly reduced the extent of apoptosis detected by TUNEL assays. To further study the mechanism underlying the benefits of lycopene, interactions between lycopene and the process of mitochondria-mediated apoptosis were examined. Lycopene pretreatment of cardiomyocytes suppressed the activation of the mitochondrial permeability transition pore (mPTP) by reducing the intracellular reactive oxygen species (ROS) levels and inhibiting the increase of malondialdehyde (MDA) levels caused by H/R. Moreover, the loss of mitochondrial membrane potential, a decline in cellular ATP levels, a reduction in the amount of cytochrome c translocated to the cytoplasm and caspase-3 activation were observed in lycopene-treated cultures. Conclusion The present results suggested that lycopene possesses great pharmacological potential in protecting against H/R-induced apoptosis. Importantly, the protective effects of lycopene may be attributed to its roles in improving mitochondrial function in H/R-treated cardiomyocytes.
Composite model prediction of elastic moduli for flakeboard.

The objective of this research was to develop a model to predict the flexural modulus of elasticity of oriented flakeboards. Variables incorporated into the model included flake geometry, flake orientation, density, resin content, and species. Verification of the model was accomplished by comparing predictions with flexural modulus of elasticity (MOE) values measured parallel and perpendicular to the flake alignment direction of 192 specimens made from two species ( Populus grandidentata , Michx. and Acer rubrum ) at 4 resin levels (3, 5, 7 and 9%) and 3 target densities (35, 42, and 52 pcf). Use of the longitudinal Halpin-Tsai equations in conjunction with measured and estimated wood and resin properties, predicted the moduli of aspen and red maple flakeboard specimens with a standard error of estimate of 93,985 psi, a coefficient of determination of 89.5%, and an average of 25% below experimental values. The statistical correlations were influenced by grouping of data using flake alignment direction and species. Important issues of vertical density gradient, inhomogeneities, and resin compatibility were not accounted for. The approach was easily computed and gave reasonably accurate predictions of elastic moduli of a single oriented flakeboard manufactured over a range of resin levels, density, alignment, flake geometry, and species conditions.
The dressing factor and crossing equations

We utilize the DHM integral representation for the BES dressing factor of the world-sheet S-matrix of the AdS5 × S5 light-cone string theory, and the crossing equations to fix the principal branch of the dressing factor on the rapidity torus. The results obtained are further used, in conjunction with the fusion procedure, to determine the bound state dressing factor of the mirror theory. We convincingly demonstrate that the mirror bound state S-matrix found in this way does not depend on the internal structure of a bound state solution employed in the fusion procedure. This welcome feature is in perfect parallel to string theory, where the corresponding bound state S-matrix has no bearing on bound state constituent particles as well. The mirror bound state S-matrix we found provides the final missing piece in setting up the TBA equations for the AdS5 × S5 mirror theory.
Effective representation using ICA for face recognition robust to local distortion and partial occlusion

The performance of face recognition methods using subspace projection is directly related to the characteristics of their basis images, especially in the cases of local distortion or partial occlusion. In order for a subspace projection method to be robust to local distortion and partial occlusion, the basis images generated by the method should exhibit a part-based local representation. We propose an effective part-based local representation method named locally salient ICA (LS-ICA) method for face recognition that is robust to local distortion and partial occlusion. The LS-ICA method only employs locally salient information from important facial parts in order to maximize the benefit of applying the idea of "recognition by parts". It creates part-based local basis images by imposing additional localization constraint in the process of computing ICA architecture I basis images. We have contrasted the LS-ICA method with other part-based representations such as LNMF (localized nonnegative matrix factorization) and LFA (local feature analysis). Experimental results show that the LS-ICA method performs better than PCA, ICA architecture I, ICA architecture 11, LFA, and LNMF methods, especially in the cases of partial occlusions and local distortions.
Secure Device Pairing: A Survey

In this paper, we discuss secure device pairing mechanisms in detail. We explain man-in-the-middle attack problem in unauthenticated Diffie-Hellman key agreement protocols and show how it can be solved by using out-of-band channels in the authentication procedure. We categorize out-of-band channels into three categories of weak, public, and private channels and demonstrate their properties through some familiar scenarios. A wide range of current device pairing mechanisms are studied and their design circumstances, problems, and security issues are explained. We also study group device pairing mechanisms and discuss their application in constructing authenticated group key agreement protocols. We divide the mechanisms into two categories of protocols with and without the trusted leader and show that protocols with trusted leader are more communication and computation efficient. In our study, we considered both insider and outsider adversaries and present protocols that provide secure group device pairing for uncompromised nodes even in presence of corrupted group members.
Global Distribution and Climate Forcing of Marine Organic Aerosol: 1. Model Improvements and Evaluation

Abstract. Marine organic aerosol emissions have been implemented and evaluated within the National Center of Atmospheric Research (NCAR)'s Community Atmosphere Model (CAM5) with the Pacific Northwest National Laboratory's 7-mode Modal Aerosol Module (MAM-7). Emissions of marine primary organic aerosols (POA), phytoplankton-produced isoprene- and monoterpenes-derived secondary organic aerosols (SOA) and methane sulfonate (MS − ) are shown to affect surface concentrations of organic aerosols in remote marine regions. Global emissions of submicron marine POA is estimated to be 7.9 and 9.4 Tg yr −1 , for the Gantt et al. (2011) and Vignati et al. (2010) emission parameterizations, respectively. Marine sources of SOA and particulate MS − (containing both sulfur and carbon atoms) contribute an additional 0.2 and 5.1 Tg yr −1 , respectively. Widespread areas over productive waters of the Northern Atlantic, Northern Pacific, and the Southern Ocean show marine-source submicron organic aerosol surface concentrations of 100 ng m −3 , with values up to 400 ng m −3 over biologically productive areas. Comparison of long-term surface observations of water insoluble organic matter (WIOM) with POA concentrations from the two emission parameterizations shows that despite revealed discrepancies (often more than a factor of 2), both Gantt et al. (2011) and Vignati et al. (2010) formulations are able to capture the magnitude of marine organic aerosol concentrations, with the Gantt et al. (2011) parameterization attaining better seasonality. Model simulations show that the mixing state of the marine POA can impact the surface number concentration of cloud condensation nuclei (CCN). The largest increases (up to 20%) in CCN (at a supersaturation ( S ) of 0.2%) number concentration are obtained over biologically productive ocean waters when marine organic aerosol is assumed to be externally mixed with sea-salt. Assuming marine organics are internally-mixed with sea-salt provides diverse results with increases and decreases in the concentration of CCN over different parts of the ocean. The sign of the CCN change due to the addition of marine organics to sea-salt aerosol is determined by the relative significance of the increase in mean modal diameter due to addition of mass, and the decrease in particle hygroscopicity due to compositional changes in marine aerosol. Based on emerging evidence for increased CCN concentration over biologically active surface ocean areas/periods, our study suggests that treatment of sea spray in global climate models (GCMs) as an internal mixture of marine organic aerosols and sea-salt will likely lead to an underestimation in CCN number concentration.
Reusable Simulation Models: An MDE-approach to Spatio- temporal Modeling with Cellular Automata

INTRODUCTION Numerous modeling tools, frameworks, and environments support domain experts with the implementation of spatiotemporal simulation models. The implemented models are usually bound to specific frameworks, because specific modeling languages, simulation engines, or processing platforms have to be used. This reduces the degree of model reuse and integration, particularly in a multi-disciplinary context. Our approach addresses two issues: model implementation and model reuse. This approach is conceptually based on the suggestion of Evert et al., (2005) to separate the modeling level, on which simulation models are described by modelers, and the implementation level, on which models are linked and executed. The approach is realized using Model-driven Engineering (MDE) and is presented for modeling cellular automata (CA).
A low-power SRAM using bit-line charge-recycling technique

We propose a new low-power SRAM using bit-line Charge Recycling (CR-SRAM) for the write operation. In the proposed write scheme, differential voltage swing of a bit-line is obtained by recycled charge from its adjacent bit-line capacitance. In order to improve the data retention capability of un-selected cells during write, the power supply lines of memory cells in one column are connected to each other and separated from the power lines of other columns. A test-chip is fabricated in 0. 13μm CMOS and measurement results show 88% reduction in total power compared to the conventional SRAM (CON-SRAM) at VDD=1.5V and f=100MHz.
An XML format for electroencephalogram data presentation (eegML)

With the development of the electronic health record, sharing biomedical and healthcare data among heterogeneous systems has great potential to benefit both clinical healthcare and scientific research. Standardizing the data presentation is the best solution to exchange them among heterogeneous systems. However, electroencephalogram (EEG) data has met problems since existing diverse data formats are unsuitable for this purpose. To address this problem we introduce an XML-based data presentation method named eegML for EEG in this paper. Based on advantages of XML technologies, eegML is a generic system- and application-independent and flexible open solution to the effective presentation of EEG data. Besides, eegML could also be used to aid knowledge management and discovery in biomedical and healthcare informatics. This format, if widely adopted, could better promote EEG data management and mining.
Memory Processes in Perceptual Decision Making

In a decision making task repeated encounters of a visual stimulus attribute to improved performance in identification and classification of that stimulus. This process is termed as repetition priming. Recent studies have proposed that response learning (RL), where previous decision gets associated with that item, accounts for a significant portion of performance gains observed in repetition priming. However, RL is unable to explain intact priming in amnesic patient population and residual priming in healthy population after the decision cue was switched. Furthermore, it is still unclear whether RL is dependent on the well structured knowledge and object representations. In this paper two-fold approach is taken to fully address the aforementioned issues. First, to test the boundaries of RL and its dependence on knowledge structures, a new repetition priming experiment using 2-D novel objects is presented in healthy population. Experimental results indicated that novel objects result in short-term priming, and presenting the object multiple times did not further facilitate reduction in response time. This pattern does not fit prevailing theories of repetition priming, including RL. A new perceptual memory-based association mechanism is thereby required. Second, to formalize and test such a mechanism, a computational model is developed. The model was further extended to formulate priming using known objects, thereby providing explanation for residual priming in case of cue-inversion in healthy population and intact priming in amnesic patient population. Altogether this paper presents the missing link, perceptual memory-based association mechanism, to fully capture all the memory processes involved in decision making.