Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the impact of surface melt on the hydrology and dynamics of the Greenland Ice Sheet

Increasing surface runoff from the Greenland Ice Sheet due to a warming climate not only accelerates ice mass loss by altering surface mass balance, but may also lead to increased dynamic losses. This is because surface melt draining to the bed can reduce ice-bed coupling, leading to faster ice flow. Understanding the impact of surface melt on ice dynamics is important for constraining the contribution of the Greenland Ice Sheet to sea level rise. The aim of this thesis is to numerically model the influence of surface runoff on ice velocities. Three new models are presented: an updated supraglacial hydrology model incorporating moulin and crevasse drainage, along with lake drainage over the ice surface via channel incision; an ice sheet model implementing a numerically efficient formulation of ice flow; an adjoint code of the ice flow model based on automatic differentiation. Together with a subglacial hydrology model, these represent the key components of the ice sheet system. The supraglacial hydrology model is calibrated in the Paakitsoq region. Model output shows the partitioning of melt between different drainage pathways and the spatial distribution of surface drainage. Melt season intensity is found to be a relevant factor for both. A key challenge for simulations applying a coupled ice-flow/hydrology model is state and parameter initialization. This challenge is addressed by developing a new workflow for incorporating modelled subglacial water pressures into inversions of basal drag. A current subglacial hydrology model is run for a winter season, and the output is incorporated into the workflow to invert for basal drag at the start of summer in the Russell Glacier area. Comparison of the modelled subglacial system to observations suggests that model output is more in line with summer conditions than winter conditions. A multicomponent model integrating the main components of the ice sheet system is developed and applied to the Russell Glacier area. A coupled ice-flow/hydrology model is initialized using the proposed workflow, and driven using output from the supraglacial hydrology model. Three recent melt seasons are modelled. To a first order, predicted ice velocities match measured velocities at multiple GPS sites. This affirms the conceptual model that summer velocity patterns are driven by transitions between distributed and channelized subglacial hydrological systems.
Query Expansion in Information Retrieval Systems using a Bayesian Network-Based Thesaurus

Information Retrieval (IR) is concerned with the identification of documents in a collection that are relevant to a given information need, usually represented as a query containing terms or keywords, which are supposed to be a good description of what the user is looking for. IR systems may improve their effectiveness (i.e., increasing the number of relevant documents retrieved) by using a process of query expansion, which automatically adds new terms to the original query posed by an user. In this paper we develop a method of query expansion based on Bayesian networks. IJsing a learning algorithm, we construct a Bayesian network that represents some of the relationships among the terms appearing in a given document collection; this network is then used as a thesaurus (specific for that collection). We also report the results obtained by our method on three standard test collections.
Mobile Regulatory Cassettes Mediate Modular Shuffling in T4-Type Phage Genomes

Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The ∼275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most of these unique genes encode functions without known homologs. Many of the insertion, deletion, and replacement events that distinguish the two phages are in the hyperplastic regions (HPRs) of their genomes. The HPRs are rich in both nonessential genes and small regulatory cassettes (promoterearly stem-loops [PeSLs]) composed of strong σ70-like promoters and stem-loop structures, which are effective transcription terminators. Modular shuffling mediated by recombination between PeSLs has caused much of the sequence divergence between RB49 and phi1. We show that exchanges between nearby PeSLs can also create small circular DNAs that are apparently encapsidated by the virus. Such PeSL “mini-circles” may be important vectors for horizontal gene transfer.
Effects of Moderate-Volume, High-Load Lower-Body Resistance Training on Strength and Function in Persons with Parkinson's Disease: A Pilot Study

Background. Resistance training research has demonstrated positive effects for persons with Parkinson's disease (PD), but the number of acute training variables that can be manipulated makes it difficult to determine the optimal resistance training program. Objective. The purpose of this investigation was to examine the effects of an 8-week resistance training intervention on strength and function in persons with PD. Methods. Eighteen men and women were randomized to training or standard care for the 8-week intervention. The training group performed 3 sets of 5–8 repetitions of the leg press, leg curl, and calf press twice weekly. Tests included leg press strength relative to body mass, timed up-and-go, six-minute walk, and Activities-specific Balance Confidence questionnaire. Results. There was a significant group-by-time effect for maximum leg press strength relative to body mass, with the training group significantly increasing their maximum relative strength (P < .05). No other significant interactions were noted (P > .05). Conclusions. Moderate volume, high-load weight training is effective for increasing lower-body strength in persons with PD.
The Electronic Properties of O-Doped Pure and Sulfur Vacancy-Defect Monolayer WS2: A First-Principles Study

Based on the density functional theory (DFT), the electronic properties of O-doped pure and sulfur vacancy-defect monolayer WS2 are investigated by using the first-principles method. For the O-doped pure monolayer WS2, four sizes (2 × 2 × 1, 3 × 3 × 1, 4 × 4 × 1 and 5 × 5 × 1) of supercell are discussed to probe the effects of O doping concentration on the electronic structure. For the 2 × 2 × 1 supercell with 12.5% O doping concentration, the band gap of O-doped pure WS2 is reduced by 8.9% displaying an indirect band gap. The band gaps in 3 × 3 × 1 and 4 × 4 × 1 supercells are both opened to some extent, respectively, for 5.55% and 3.13% O doping concentrations, while the band gap in 5 × 5 × 1 supercell with 2.0% O doping concentration is quite close to that of the pure monolayer WS2. Then, two typical point defects, including sulfur single-vacancy (VS) and sulfur divacancy (V2S), are introduced to probe the influences of O doping on the electronic properties of WS2 monolayers. The observations from DFT calculations show that O doping can broaden the band gap of monolayer WS2 with VS defect to a certain degree, but weaken the band gap of monolayer WS2 with V2S defect. Doping O element into either pure or sulfur vacancy-defect monolayer WS2 cannot change their band gaps significantly, however, it still can be regarded as a potential method to slightly tune the electronic properties of monolayer WS2.
Systematic exploration of error sources in pyrosequencing flowgram data

Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several tools available for noise removal, targeting different application fields, data interpretation would benefit from a better understanding of the different error types. Results: By exploring 454 raw data, we quantify to what extent different factors account for sequencing errors. In addition to the well-known homopolymer length inaccuracies, we have identified errors likely to originate from other stages of the sequencing process. We use our findings to extend the flowsim pipeline with functionalities to simulate these errors, and thus enable a more realistic simulation of 454 pyrosequencing data with flowsim. Availability: The flowsim pipeline is freely available under the General Public License from http://biohaskell.org/Applications/FlowSim. Contact: susanne.balzer@imr.no
Secure computation for combinatorial auctions and market exchanges

It was recently shown possible to solve (M+1)^st price single item auctions without revealing absolutely any secret except for the solution. Namely, with vMB-share [2], the seller and the buyer only learn each otherýs identity and learn the selling price for a chosen (M+1)^st pricing scheme. No trusted party is necessary. In this paper we show how vMB-share can be extended for the clearing of combinatorial negotiation problems with several items, buyers and sellers. We first show how the more general problem can be reduced to a virtual form, form that is relatively similar to the single item auctions, by having a virtual bidder for each candidate allocation. Then, some modifications in the cryptographic techniques of vMB-share are made such that it can offer a solution to problems in virtual form. As explained in the paper, it is expected that a secure solution hiding details that can be inferred from the running time will have an exponential computation cost. Our preliminary experimental evaluation shows that some small negotiations can nevertheless be solved with acceptable effort.
Order-Based Disparity Refinement Including Occlusion Handling for Stereo Matching

Accurate stereo matching is still challenging in case of weakly textured areas, discontinuities, and occlusions. Besides, occlusion recovery is often regarded as a subordinate problem and simply handled. To obtain dense high-accuracy depth maps, this letter proposes an efficient multistep disparity refinement framework with occlusion handling. The framework is implemented by classifying the outliers into leftmost occlusions, nonborder occlusions, as well as mismatches, and employing different strategies to recover them. To recover occlusions, a filling order is specially introduced to avoid error propagation and surface decision based on local image content is performed when more than one background surface exists. The evaluations on Middlebury datasets and comparisons with other refinement algorithms show the superiority and robustness of our method.
Lectin Complement Pathway Interactions with Recognition Proteins of the Deciphering Complement Receptor Type 1

Veronique RossiGout, Christine Gaboriaud, Nicole M. Thielens and Mickael Jacquet, Monique Lacroix, Sarah Ancelet, Evelynehttp://www.jimmunol.org/content/190/7/3721doi: 10.4049/jimmunol.1202451March 2013;J Immunol€2013; 190:3721-3731; Prepublished online 4MaterialSupplementary1.DC1. htmlhttp://www.jimmunol.org/content/suppl/2013/03/04/jimmunol.120245Referenceshttp://www.jimmunol.org/content/190/7/3721.full#ref-list-1This article cites 68 articles, 36 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai. org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
A multiplex real-time PCR for differential detection and quantification of Salmonella spp., Salmonella enterica serovar Typhimurium and Enteritidis in meats

Salmonella (S.) Typhimurium and S. Enteritidis are the major causative agents of food-borne illnesses worldwide. Currently, a rapid detection system using multiplex real-time polymerase chain reaction (PCR) has been applied for other food-borne pathogens such as Escherichia coli, Staphylococcus aureus and Streptococcus spp. A multiplex real-time PCR was developed for the simultaneous detection of Salmonella spp. , especially S. Typhimurium and S. Enteritidis, in beef and pork. For the specific and sensitive multiplex real-time PCR, three representative primers and probes were designed based on sequence data from Genbank. Among the three DNA extraction methods (boiling, alkaline lysis, and QIAamp DNA Mini Kit), the QIAamp DNA Mini Kit was the most sensitive in this study. The optimized multiplex real-time PCR was applied to artificially inoculated beef or pork. The detection sensitivity of the multiplex real-time PCR was increased. The specificity of the multiplex real-time PCR assay, using 128 pure-cultured bacteria including 110 Salmonella isolates and 18 non-Salmonella isolates, was 100%, 100% and 99.1% for Salmonella spp. , S. Typhimurium and S. Enteritidis, respectively. The sensitivity was 100%, 100% and 91.7% for Salmonella spp. , S. Typhimurium and S. Enteritidis, respectively. The multiplex real-time PCR assay developed in this study could detect up to 0.54 ± 0.09 and 0.65 ± 0.07 log10 CFU/ml for S. Typhimurium and S. Enteritidis for beef, 1.45 ± 0.21 and 1.65 ± 0.07 log10 CFU/ml for S. Typhimurium and S. Enteritidis for pork, respectively, with all conditions optimized. Our results indicated that the multiplex real-time PCR assay developed in this study could sensitively detect Salmonella spp. and specifically differentiate S. Typhimurium from S. Enteritidis in meats.
Laboratory Investigations Applied to Wood Dust Emmited by Electrical Hand-Held Belt Sander

Abstract Aim of this paper was to investigate the effects of grit size and wood species on mass concentration and size distribution of wood dust produced by hand-held belt sander. Experimental study was designed as 2x2 full factorial experiments. Experimental parameters and their levels were abrasive grain size (P80, P120) and wood species (European beech (Fagus sylvatica L.), Norway spruce (Picea abies)). The mass concentration of emitted wood dust was measured using aerosol monitor (TSI Inc., DustTrak DRX 8533). Sampler head was sited in place representing breathing zone of operator of sander. The results was analysed employing the analysis of variance (ANOVA) with 5% of significance level. Real-time measurements demonstrated that spruce wood generated higher dust concentrations than beech wood due to difference in abrasion durability. Compared to sanding belt with P80 grit size, approximately 16%-32% higher dust concentration was generated when the sanding belt with P120 grit size was used.
Mobile Cloud Computing: Issues from a Security Perspective

: Mobile Cloud Computing (MCC) is exploring prodigious storm in IT due to anywhere anytime data access. Mobile contrivances are enabled with affluent utilizer experience especially, Smartphones. Apple, Google, Facebook and Amazon are the top four horsemen in the mobile world. That is why the mobile cloud computing technology is growing rapidly among the users and at the same time it introduces the incipient security threats withal. In MCC, teemingness of investigations are being carried out to eradicate the issues to make IT more reliable and secure because more precious data are stored in the cloud environment. As the Internet-enabled mobile contrivances including smartphones and tablets perpetuate to grow, web-predicated malignant threats will perpetuate to increment in number to make more involute. Securing data is more critical in the Mobile Cloud Environment. In MCC, Security is the major issue. In this paper, the working concepts of MCC and its assorted security issues and solutions given by researchers are analyzed.
Markerless Hand Gesture Interface Based on LEAP Motion Controller

Hand gesture interfaces provide an intuitive and natural way for interacting with a wide range of applications. Nowadays, the development of these interfaces is supported by an increasing number of sensing devices which are able to track hand and finger movements. Despite this, the physical and technical features of many of these devices make them unsuitable for the implementation of interfaces oriented to the everyday desktop applications. Conversely, the LEAP motion controller has been specifically designed to interact with these applications. Moreover, this latter device has been equipped with a hand skeletal model that provides tracking data with a high level of accuracy. This paper describes a novel approach to define and recognize hand gestures. The proposed method adopts freehand drawing recognition algorithms to interpret the tracking data of the hand and finger movements. Although our approach is applicable to any hand skeletal model, the overall features of that provided by the LEAP motion controller have driven us to use it as a reference model. Extensive preliminary tests have demonstrated the usefulness and the accuracy of the proposed method.
Apoptosis : Mechanisms and Relevance in Liver Diseases

Abbreviations: ATF6 activating transcription factor 6, ATF4 activating transcription factor-4, CHOP C/EBP-homologous protein, ER endoplasmic reticulum, eIF2α eukaryotic translation initiation factor-2α, FADD Fas associated death domain, IRE1 inositol-requiring protein-1, JNK c-jun N-terminal kinase, NK natural killer, NFκB nuclear factor kappa B, PERK protein kinase RNA-like ER kinase, TNF-α tumor necrosis factor alpha, TRAIL tumor necrosis factor-related apoptosis inducing ligand, TNFR1 tumor necrosis factor receptor 1, TNFR2 tumor necrosis factor receptor 2, TRAIL-R1 tumor necrosis factor-related apoptosis inducing ligand receptor 1, TRAIL-R2 tumor necrosis factor-related apoptosis inducing ligand receptor 2, TRAF-2 tumor necrosis factor receptor associated protein, XBP1 X-box binding protein-1,
ELECTRIC IMPEDANCE OF NITELLA DURING ACTIVITY

The changes in the alternating current impedance which occur during activity of cells of the fresh water plant Nitella have been measured with the current flow normal to the cell axis, at eight frequencies from 0.05 to 20 kilocycles per second, and with simultaneous records of the action potential under the impedance electrodes. At each frequency the resting cell was balanced in a Wheatstone bridge with a cathode ray oscillograph, and after electrical stimulation at one end of the cell, the changes in the complex impedance were determined from the bridge unbalance recorded by motion pictures of the oscillograph figure. An extension of the previous technique of interpretation of the transverse impedance shows that the normal membrane capacity of 0.9 µf. /cm.2 decreases about 15 per cent without change of phase angle, while the membrane resistance decreases from 105 ohm cm.2 to about 500 ohm cm.2 during the passage of the excitation wave. This membrane change occurs during the latter part of the rising phase of the action potential, and it is shown that the membrane electromotive force remains unchanged until nearly the same time. The part of the action potential preceding these membrane changes is probably a passive fall of potential ahead of a partial short circuit.
Regional Cerebral Blood Flow in Mild Cognitive Impairment and Alzheimer's Disease Measured with Arterial Spin Labeling Magnetic Resonance Imaging

Alzheimer's disease (AD) depicts dynamic changes in regional brain function from early stages of the disease. Arterial spin labeling- (ASL-) based MRI methods have been applied for detecting regional cerebral blood flow (rCBF) perfusion changes in patients with AD and mild cognitive impairment (MCI). Nevertheless, the results obtained from ASL studies in AD and MCI are still controversial, since rCBF maps may show both hypoperfusion or hyperperfusion areas in brain structures involved in different cognitive functions. The goal of this review is to provide the current state of the art regarding the role of ASL for detecting distinctive perfusion patterns in subjects with MCI and/or AD. The ability to obtain this information using a noninvasive and widely available modality such as ASL should greatly enhance the knowledge into the broad range of hemodynamically related changes taking place during the cognitive decline process in AD.
Ekman and Eddy Exchange of Freshwater and Oxygen across the Labrador Shelf Break

AbstractTransport of freshwater from the Labrador Shelf into the interior Labrador Sea has the potential to impact deep convection via its influence on the salinity of surface waters. To examine this transport, the authors deployed two underwater gliders on a mission to traverse the continental shelf break multiple times between 5 July and 22 August 2014, the period when Arctic meltwater has historically peaked in transport down the Labrador Shelf. The field campaign yielded a unique dataset of temperature, salinity, and oxygen across the shelf break to a depth of 1000 m at unprecedented spatial resolution. Two mechanisms of cross-shelf transport were examined: Ekman transport and transport due to mesoscale eddies. Ekman transport is quantified using satellite wind stress and near-surface hydrographic properties, and eddy-induced transport is scaled using a parameterized eddy diffusivity and thickness gradients of layers of uniform potential density, as well as the tracer gradients along those isopycnals.
Noise constrained transistor sizing and power optimization for dual Vst domino logic

Dynamic logic is susceptible to noise, especially in the ultra-deep submicrometer dual threshold voltage technology. When the dual threshold voltage is applied to the domino logic, noise immunity must be carefully considered since the significant subthreshold current of the low threshold voltage transistor makes the dynamic node much more susceptible to noise. In the first part of this paper, we introduce a new keeper transistor sizing method to determine the optimal keeper transistor size in terms of speed, power, and noise immunity. With the use of data obtained by presimulation, it is unnecessary to simulate all the design corners corresponding to the feasible NMOS evaluation transistor size ranges to find the optimal keeper transistor size. HSPICE simulation results show that the proposed keeper transistor sizing method can be broadly applied to all the domino logic gates. In the second part of this paper, we propose a new dual threshold voltage domino logic synthesis with the keeper transistor sizing to minimize the power consumption while meeting delay and noise constraints. With the optimal keeper transistor size determined by the proposed keeper transistor sizing method, the dual threshold voltage assignment to domino logic can be simplified to the discrete threshold voltage selection. Experimental results for ISCAS85 benchmark circuits show significant savings on leakage power and active power.
Landmark based shape analysis for cerebellar ataxia classification and cerebellar atrophy pattern visualization

Cerebellar dysfunction can lead to a wide range of movement disorders. Studying the cerebellar atrophy pattern associated with different cerebellar disease types can potentially help in diagnosis, prognosis, and treatment planning. In this paper, we present a landmark based shape analysis pipeline to classify healthy control and different ataxia types and to visualize the characteristic cerebellar atrophy patterns associated with different types. A highly informative feature representation of the cerebellar structure is constructed by extracting dense homologous landmarks on the boundary surfaces of cerebellar sub-structures. A diagnosis group classifier based on this representation is built using partial least square dimension reduction and regularized linear discriminant analysis. The characteristic atrophy pattern for an ataxia type is visualized by sampling along the discriminant direction between healthy controls and the ataxia type. Experimental results show that the proposed method can successfully classify healthy controls and different ataxia types. The visualized cerebellar atrophy patterns were consistent with the regional volume decreases observed in previous studies, but the proposed method provides intuitive and detailed understanding about changes of overall size and shape of the cerebellum, as well as that of individual lobules.