Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptively sampled particle fluids

We present novel adaptive sampling algorithms for particle-based fluid simulation. We introduce a sampling condition based on geometric local feature size that allows focusing computational resources in geometrically complex regions, while reducing the number of particles deep inside the fluid or near thick flat surfaces. Further performance gains are achieved by varying the sampling density according to visual importance. In addition, we propose a novel fluid surface definition based on approximate particle-to-surface distances that are carried along with the particles and updated appropriately. The resulting surface reconstruction method has several advantages over existing methods, including stability under particle resampling and suitability for representing smooth flat surfaces. We demonstrate how our adaptive sampling and distance-based surface reconstruction algorithms lead to significant improvements in time and memory as compared to single resolution particle simulations, without significantly affecting the fluid flow behavior.
Evolutionary history of the sequestrate genus Rossbeevera (Boletaceae) reveals a new genus Turmalinea and highlights the utility of ITS minisatellite-like insertions for molecular identification

The sequestrate (truffle-like) basidiomycete genera Rossbeevera, Chamonixia, and Octaviania are closely related to the epigeous mushroom genera Leccinum and Leccinellum. In order to elucidate the properties and placement of several undescribed sequestrate taxa in the group and to reveal the evolutionary history of Rossbeevera and its allies, we conducted phylogenetic analyses based on three nuclear (ITS, nLSU, EF-1α) and two mitochondrial DNA loci (ATP6 and mtSSU) as well as precise morphological observations. Phylogenetic analyses of three nuclear loci suggest a complex evolutionary history with sequestrate fruiting bodies present in several clades, including a previously unrecognized sister clade to Rossbeevera. Here we propose a new sequestrate genus, Turmalinea, with four new species and one new subspecies as well as two new species of Rossbeevera. The three-locus nuclear phylogeny resolves species-level divergence within the Rossbeevera-Turmalinea lineage, whereas a separate phylogeny based on two mitochondrial genes corresponds to geographic distance within each species-level lineage and suggests incomplete lineage sorting (ILS) and gene introgression within several intraspecific lineages of Rossbeevera. Furthermore, topological incongruence among the three nuclear single-locus phylogenies suggests that ancient speciation within Rossbeevera probably involved considerable ILS. We also found an unusually long, minisatellite-like insertion within the ITS2 in all Rossbeevera and Turmalinea species. A barcode gap analysis demonstrates that the insertion is more informative for discrimination at various taxonomic levels than the rest of the ITS region and could therefore serve as a unique molecular barcode for these genera.
Design of Dynamic Asynchronous Flip-Flops and Counters based on Dynamic STG Prof

Abstract. This paper presents a synthesis method for generating true single-clock dynamic CMOS flip-flops. Such dynamic circuits are used today for very high performance microprocessors and ASICs, however with some supplementary keeper transistors. Many references [1, 11, 12, 13, 16, 17, 20, 22] have presented dynamic single-phase clock latches and flip-flops, however without a corresponding synthesis method. The goal of this paper is to present “asynchronous” synthesis methods based on STG that are commonly used for asynchronous static circuits [2, 3, 4, 5, 6], while modifying these known methods for the generation of dynamic circuits. In this way, dynamic single-phase clock design and asynchronous STG-based methods are unified. The second goal of this paper is to be able to analyze and to synthesize hazard-free dynamic circuits. It is known that some versions of latches and flip-flops presented in literature may present some hazards, races or glitches. The presented design method, based on the properties of negative gates, can produce dynamic circuits that are hazard-free. Furthermore, it helps to analyze existing circuits to detect hazards and glitches, while providing other structures that can be more convenient to specific applications. The presented method is not limited to flip-flops, but can be used for latches and any dynamic sequential circuit described by a STG or a flow table.
Framework for Key Management Scheme in Heterogeneous Wireless Sensor Networks

Ubiquitous computing environments find their practical implementations through wireless sensor networks, which sense a relationship among themselves and the environment. Presently devised key management schemes are classified namely for homogeneous environments, or heterogeneous environments. In this paper, we propose a deployment conscious security framework supporting, a shift of complex operations to more capable nodes of heterogeneous environment and relieving resource constrained generic sensor nodes of major activities. We introduced a concept of deployment knowledge independent group key generation using a special kind of heterogeneity-multilevel transmission. Performance of proposed key management schemes is evaluated across relevant matrices and concluded to be satisfactory. Findings show that asymmetric key cryptography is comparatively more demanding in resources than symmetric version but ensures maximum security. Through our work we able to conclude that a hybrid of asymmetric and symmetric key cryptography best suits heterogeneous environments.
Fgf10-Expressing Tanycytes Add New Neurons to the Appetite/Energy-Balance Regulating Centers of the Postnatal and Adult Hypothalamus

Increasing evidence suggests that neurogenesis occurs in the postnatal and adult mammalian hypothalamus. However, the identity and location of the putative progenitor cells is under much debate, and little is known about the dynamics of neurogenesis in unchallenged brain. Previously, we postulated that Fibroblast growth factor 10-expressing (Fgf10+) tanycytes constitute a population of progenitor cells in the mouse hypothalamus. Here, we show that Fgf10+ tanycytes express markers of neural stem/progenitor cells, divide late into postnatal life, and can generate both neurons and astrocytes in vivo. Stage-specific lineage-tracing of Fgf10+ tanycytes using Fgf10-creERT2 mice, reveals robust neurogenesis at postnatal day 28 (P28), lasting as late as P60. Furthermore, we present evidence for amplification of Fgf10-lineage traced neural cells within the hypothalamic parenchyma itself. The neuronal descendants of Fgf10+ tanycytes predominantly populate the arcuate nucleus, a subset of which express the orexigenic neuronal marker, Neuropeptide-Y, and respond to fasting and leptin-induced signaling. These studies provide direct evidence in support of hypothalamic neurogenesis during late postnatal and adult life, and identify Fgf10+ tanycytes as a source of parenchymal neurons with putative roles in appetite and energy balance.
Simplification of Reconstructed Meshes in Real Time

Immersing a scanned replication of a person into a virtual reality environment is a multifaceted challenge. One key issue of this task is to improve the result and performance of the reconstruction algorithm that is used to create the 3D model out of pictures taken from the person. In this paper, we present a method to reduce the effort of a 3D model reconstruction process by polygonal simplification in real time (in less than 0.06 seconds). Besides being a relative fast algorithm, in every step the method holds a consistent mesh, so it can be aborted if calculation time runs short. Furthermore, we describe a data structure called AI-Tree (Adjustable Index Tree), that allows to speeding up the process of rebuilding a mesh data structure out of lists of vertices, edges and polygons that appear in file formats of 3D models and network communication. AI-Trees offer a fast way to find indices out of linked lists, and a scaleable trade-off between performance and memory consumption.
Topological Interference Management with Alternating Connectivity: The Wyner-Type Three User Interference Channel

Interference management in a three-user interference channel with alternating connectivity with only topological knowledge at the transmitters is considered. The network has a Wyner-type channel flavor, i.e., for each connectivity state the receivers observe at most one interference signal in addition to their desired signal. Degrees of freedom (DoF) upper bounds and lower bounds are derived. The lower bounds are obtained from a scheme based on joint encoding across the alternating states. Given a uniform distribution among the connectivity states, it is shown that the channel has 2+ 1/9 DoF. This provides an increase in the DoF as compared to encoding over each state separately, which achieves 2 DoF only.
Consequences of habitat change and resource selection specialization for population limitation in cavity‐nesting birds

Summary Resource selection specialization may increase vulnerability of populations to environmental change. One environmental change that may negatively impact some populations is the broad decline of quaking aspen Populus tremuloides, a preferred nest tree of cavity-nesting organisms who are commonly limited by nest-site availability. However, the long-term consequences of this habitat change for cavity-nesting bird populations are poorly studied. I counted densities of woody plants and eight cavity-nesting bird species over 29 years in 15 high-elevation riparian drainages in Arizona, USA. I also studied nest-tree use and specialization over time based on 4946 nests across species. Aspen suffered a severe decline in availability over time, while understorey woody plants and canopy deciduous trees also declined. The decline of plants resulted from increased elk Cervus canadensis browsing linked to declining snowfall. Woodpeckers exhibited very high specialization (>95% of nests) on aspen for nesting, and densities of all six species declined with aspen over time. Mountain chickadees Poecile gambeli and house wrens Troglodytes aedon exhibited increasingly less specialization on aspen. Chickadees strongly increased in density over time, despite a relatively high specialization on aspen. House wren densities declined moderately over time, but nest-box addition experiments demonstrated that nest-site availability was not limiting their population. House wren densities increased with understorey vegetation recovery in elk exclosures via increased generality of nest-site use, demonstrating that the decline in understorey vegetation on the broader landscape was the cause of their population decline. Synthesis and applications. Management should target species that specialize in resource selection on a declining resource. Species with greater resource selection generalization can reduce population impacts of environmental change. Resource generalization can allow a species like the wren to take advantage of habitat refuges, such as those provided by the elk exclosures. Yet, resource generalization cannot offset the negative impacts of broad-scale declines in habitat quality on the landscape, as demonstrated by the general decline of wrens. Ultimately, aspen is an important habitat for biodiversity, and land management programmes that protect and aid recovery of aspen habitats may be critical.
Security Evaluation of the Signature Scheme and Primitive

Executive summary. This report is a security evaluation of the standard signature algorithm DSA. The main conclusion is that the implementers need to be very careful and trusted. The length of the main parameter (1024 bits) needs to be evaluated correctly: it means that very soon the value of about 1500 bits will be a useful addition and the relevant 160 bit parameters must be ajusted to 256 bits for taking into account a level of security valid for the next 20 years.
A sparse regression based approach for cuff-less blood pressure measurement

This paper proposes a sparse regression based approach for accurate continuous Blood Pressure (BP) monitoring. ECG and Finger PPG signals serve as the input; from which 32 parameters are extracted. Not all parameters are indicative of BP; to automatically trim the redundant parameters a sparse regression based approach is proposed. To build the BP predicting model the necessary parameters and their corresponding weights are learned using data from 99 subjects. The learned model is applied on 10 test subjects. The ground truth BP is measured using a clinically proven, professional automatic digital BP monitor OMRON HBP1300. , The BP prediction results show that the SBP/DBP mean absolute error and error standard deviation, with OMRON monitor as a reference, is 4.43/2.46 and 4.90/3.31 mmHg respectively, which falls under the standard allowable error mentioned by Association for the Advancement of Medical Instrumentation for estimation of BP. We have compared our work with other BP prediction techniques (Linear Regression and Feed Forward Neural Network) and have seen that our proposed method yields considerably better results, especially for diastolic BP.
Lifelong Obesity in a Polygenic Mouse Model Prevents Age- and Diet-Induced Glucose Intolerance– Obesity Is No Road to Late-Onset Diabetes in Mice

Aims/Hypothesis Visceral obesity holds a central position in the concept of the metabolic syndrome characterized by glucose intolerance in humans. However, until now it is unclear if obesity by itself is responsible for the development of glucose intolerance. Methods We have used a novel polygenic mouse model characterized by genetically fixed obesity (DU6) and addressed age- and high fat diet-dependent glucose tolerance. Results Phenotype selection over 146 generations increased body weight by about 2.7-fold in male 12-week DU6 mice (P<0.0001) if compared to unselected controls (Fzt:DU). Absolute epididymal fat mass was particularly responsive to weight selection and increased by more than 5-fold (P<0.0001) in male DU6 mice. At an age of 6 weeks DU6 mice consumed about twice as much food if compared to unselected controls (P<0.001). Absolute food consumption was higher at all time points measured in DU6 mice than in Fzt:DU mice. Between 6 and 12 weeks of age, absolute food intake was reduced by 15% in DU6 mice (P<0.001) but not in Fzt:DU mice. In both mouse lines feeding of the high fat diet elevated body mass if compared to the control diet (P<0.05). In contrast to controls, DU6 mice did not display high fat diet-induced increases of epididymal and renal fat. Control mice progressively developed glucose intolerance with advancing age and even more in response to the high fat diet. In contrast, obese DU6 mice did neither develop a glucose intolerant phenotype with progressive age nor when challenged with a high fat diet. Conclusions/Interpretation Our results from a polygenic mouse model demonstrate that genetically pre-determined and life-long obesity is no precondition of glucose intolerance later in life.
Additive Genetic Variability and the Bayesian Alphabet

The use of all available molecular markers in statistical models for prediction of quantitative traits has led to what could be termed a genomic-assisted selection paradigm in animal and plant breeding. This article provides a critical review of some theoretical and statistical concepts in the context of genomic-assisted genetic evaluation of animals and crops. First, relationships between the (Bayesian) variance of marker effects in some regression models and additive genetic variance are examined under standard assumptions. Second, the connection between marker genotypes and resemblance between relatives is explored, and linkages between a marker-based model and the infinitesimal model are reviewed. Third, issues associated with the use of Bayesian models for marker-assisted selection, with a focus on the role of the priors, are examined from a theoretical angle. The sensitivity of a Bayesian specification that has been proposed (called “Bayes A”) with respect to priors is illustrated with a simulation. Methods that can solve potential shortcomings of some of these Bayesian regression procedures are discussed briefly.
Unsupervised Speaker Clustering in a Linear Discriminant Subspace

We present an approach for grouping single-speaker speech segments into speaker-specific clusters. Our approach is based on applying the K-means clustering algorithm to a suitable discriminant subspace, where the euclidean distance reflect speaker differences. A core feature of our approach is approximating speaker-conditional statistics, that are not available, with single-speaker segments statistics, which can be evaluated, thus making possible to apply the LDA algorithm for finding the optimal discriminative subspace, using unlabeled data. To illustrate our method, we present examples of clusters generated by our approach when applied to the ICMLA 2010 Speaker Clustering Challenge datasets.
An Effective super-resolution image reconstruction of blurry images using sparse representation method

Super-Resolution (SR) imagery plays an important role in many diverse areas of application, such as medical imaging, remote sensing and video surveillance. The superresolution (SR) is to increase the resolution of an image or a sequence of images beyond the resolving power of the imaging system. Superresolution is the process of obtaining either a higher resolution still image or a sequence of higher resolution images from a corresponding sequence of low resolution images of a particular scene. In this paper, we deploy the high resolution image from the low resolution image using a powerful statistical image modeling technique. The sparse representation has been successfully used in various image restoration areas as stated above. The sparse representation success is depending on the development of l1-norm optimization techniques and also the natural images are intrinsically sparse in some domain. The resulted high-resolution generated images quality largely depends on whether the employed sparse domain can represent well the underlying image. Extensive experiments on image super-resolution validate that by using adaptive sparse domain selection, the proposed method achieves better results than many state-of-the-art algorithms in terms of both PSNR and structure similarity(SSIM).
Structural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system

The Tat system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of plant chloroplasts. In Escherichia coli substrate proteins initially bind to the integral membrane TatBC complex which then recruits the protein TatA to effect translocation. Overproduction of TatBC and the substrate protein SufI in the absence of TatA led to the accumulation of TatBC-SufI complexes that could be purified using an affinity tag on the substrate. Three-dimensional structures of the TatBC-SufI complexes and unliganded TatBC were obtained by single-particle electron microscopy and random conical tilt reconstruction. Comparison of the structures shows that substrate molecules bind on the periphery of the TatBC complex and that substrate binding causes a significant reduction in diameter of the TatBC part of the complex. Although the TatBC complex contains multiple copies of the signal peptide-binding TatC protomer, purified TatBC-SufI complexes contain only 1 or 2 SufI molecules. Where 2 substrates are present in the TatBC-SufI complex, they are bound at adjacent sites. These observations imply that only certain TatC protomers within the complex interact with substrate or that there is a negative cooperativity of substrate binding. Similar TatBC-substrate complexes can be generated by an alternative in vitro reconstitution method and using a different substrate protein.
Increased accuracy through noise injection in abstract RTOS simulation

Today, mobile and embedded real-time systems have to cope with the migration and allocation of multiple software tasks running on top of a real-time operating system (RTOS) residing on one or multiple system processors. Abstract RTOS simulations and timing analysis applies for fast and early estimation to configure it towards the individual needs of the application and environment. In this context, a high accuracy of the simulation compared to an instruction set simulation (ISS) is of key importance. In this paper, we investigate the accuracy of abstract RTOS simulation and compare it to ISS and the behavior of the physical system. We show that we can reach an increased accuracy of the simulation when we inject noise into the time model. Our results indicate that it is sufficient to inject uniformly distributed random time values to the RTOS real-time clock.
Modelling of human Wiskott–Aldrich syndrome protein mutants in zebrafish larvae using in vivo live imaging

Summary Wiskott–Aldrich syndrome (WAS) and X-linked neutropenia (XLN) are immunodeficiencies in which the function of several haematopoietic cell lineages is perturbed as a result of mutations in the actin regulator WASp. From in vitro cell biology experiments, and biochemical and structural approaches, we know much about the functional domains of WASp and how WASp might regulate the dynamic actin cytoskeleton downstream of activators such as Cdc42, but in vivo experiments are much more challenging. In patients, there is a correlation between clinical disease and genotype, with severe reductions in WASp expression or function associating with complex multilineage immunodeficiency, whereas specific mutations that cause constitutive activation of WASp result in congenital neutropenia. Here, we take advantage of the genetic tractability and translucency of zebrafish larvae to first characterise how a null mutant in zfWASp influences the behaviour of neutrophils and macrophages in response to tissue damage and to clearance of infections. We then use this mutant background to study how leukocyte lineage-specific transgenic replacement with human WASp variants (including normal wild type and point mutations that either fail to bind Cdc42 or cannot be phosphorylated, and a constitutively active mutant equivalent to that seen in XLN patients) alter the capacity for generation of neutrophils, their chemotactic response to wounds and the phagocytic clearance capacity of macrophages. This model provides a unique insight into WASp-related immunodeficiency at both a cellular and whole organism level.
The ecology and evolution of non-domesticated Saccharomyces species

Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae, the seven species in the genus Saccharomyces. The best‐studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the genus Saccharomyces have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography and ecology are only beginning. Much remains to be understood about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context and to develop the genus Saccharomyces as a model clade for ecology and evolution. © 2014 The Authors. Yeast published by John Wiley & Sons Ltd.