Miracle-dz/UniFAR-FTUs huggingface dataset:
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.
Mutual Information and Energy Tradeoff in Correlated Wireless Sensor Networks

We consider comparison of Mutual Information (MI)-Energy tradeoff in correlated wireless sensor network (WSN) for cooperative multiple input and multiple output (MIMO) and non-cooperative (referred to as single input and single output (SISO)) transmission schemes. Our numerical results indicate that for short distances SISO schemes achieve better Mi-Energy tradeoff than the cooperative MIMO schemes, while for long distances the cooperative MIMO schemes achieve better Mi-Energy tradeoff. We next consider the issue of sensor placement in a correlated WSN. Specifically, we prove that the spacing between nodes to maximize MI is in general an increasing function of observation SNR. From this structural result, we conclude that at high SNR, the various stages of the WSN can be separated by relatively large distances than at low SNR.
Testing Gricean Constraints on a WordNet-based Coherence Evaluation System

This paper presents a computational method for analyzing Gricean constraints for the purpose of evaluating text coherence. Our system consists of a knowledge base constructed on top of WordNet, an inference engine that establishes discourse semantic paths between the input concepts and a mechanism of relating them to the context. Grice's maxims provide conditions to test coherence, while the semantic paths provide the space on which these conditions are tested. The computational method is based on a marker-propagation technique that is independent of the size of the knowledge base. The paper describes the method and provides results obtained with the system. The key idea of this paper is to link Grice's maxims for conversational logic with high level inferences drawn from a linguistic knowledge base. We discuss how the Gricean maxims may be tested in a real natural language processing system and how the information extracted plays a role in the analysis of context, dialogue coherence, and intentions. A text is considered to be coherent when it is logically connected and intelligible. The logical connections are semantic relationships between concepts. We are experimenting with a text understanding system that operates on a large linguistic knowledge base with concepts and relations between concepts. Inference rules are constructed by chaining semantic relations in the knowledge base. A few of these rules lead to deductions , but many provide only plausible inferences. Semantic paths between concepts may be established as patterns of inference rules. The information along such paths provides an explanation for the relationship between two concepts. In this paper, we link these semantic paths to Gricean constraints. The concepts and the relations that form the semantic paths provide context and information about text coherence. The Gricean constraints are rst tested by analyzing the paths; and this provides information to validate or lter out irrelevant inferences. The path nding algorithm designed by us uses a marker propagation paradigm that is highly parallel and asynchronous. Unlike other attempts that use marker-passing (Charniak 1986), (Norvig 1987), we use propagation rules that guide the movement of markers along some selected relations. Any marker present on a node may further propagate along semantic relations that (a) generalize, (b) deene the features or (c) entail or are entailed by the properties of the concept represented by that node. Whenever two markers originated from diierent nodes of the knowledge base reach the same node, a collision of the …
Ideología y voto: dimensiones de competencia política en México en los noventa

There is a strong relationship between individual ideological orientations and partisan preferences in Mexico. During the nineties, attitudes towards democracy have defines the most central meaning of the left-right axis of competition, leaving the classic socio- conomic concerns as secondary. However, Mexicans'preferences seem to be evolving from the gradual abandonment of the issue of democracy toward the incorporation of other social and cultural issues, This article analyzes the ideological distribution in Mexico, the average positions that partisan electorates take on that distribution, and the implications that both aspects have for party strategies. It also analyzes the social bases of ideological orientations and the role of ideology in the development of partisan identifications.
Intelligentsia: A Front-End Tool for Collecting Internet Anxiety Data

This paper presents a front-end interface named ‘Intelligentsia’ for collecting Internet anxiety types. Four diverse age groups of users (e.g. child, old men/women, and a young adult) were recruited to perform a task of randomly browsing contents on the Internet to gather data of Internet anxiety. The results include behavioural observations and symptoms of Internet anxiety types. Among seven types of Internet anxiety tested using Intelligentsia: Internet time delay anxiety, Net search anxiety, and Experience anxieties are most significant types of Internet anxiety. Keywords: Front-end, Measurement, Internet anxiety, Tool, Human anxiety;
A 3D Reconstruction with High Density and Accuracy Using Laser Profiler and Camera Fusion System on a Rover

3D Sensing systems mounted on mobile platform are emerging and have been developed for various applications. In this paper, we propose a profiler scanning system mounted on a rover to scan and reconstruct a bas-relief with high density and accuracy. Our hardware system consists of an omnidirectional camera and a 3D laser scanner. Our method selects good projection points for tracking to estimate motion stably and reject mismatches caused by difference between the positions of laser scanner and camera using an error metric based on the distance from omnidirectional camera to scanned point. We demonstrate that our results has better accuracy than comparable approach. In addition to local motion estimation method, we propose global poses refinement method using multi modal 2D-3D registration and our result shows good consistency between reflectance image and 2D RGB image.
The Tactile Modality: A Review of Tactile Sensitivity and Human Tactile Interfaces

Abstract : Even though vision is only one modality humans use to interact with their environment, most people consider it to be the most important. Hearing also is viewed as necessary for interpreting environmental stimuli. In contrast, touch, smell, and taste are largely ignored as being essential to humans' interaction with the environment. The brain seldom processes environmental information sequentially using successive sensory modalities; rather, it simultaneously processes stimuli from several or all of the sensory modalities. Because humans have a limited capacity to receive, hold in working memory, and cognitively process information taken from the environment, the use of one sensory modality to convey information within a system can overload that modality. Multimodal systems can help to alleviate overload for any one modality, and such systems have been favorable in showing that the touch or tactile modality can be used as an independent input modality to convey information to the user, or as a redundant modality to increase information prominence of the visual and auditory modalities. The purpose of this review, which reflects work that occurred before mid-2006, is to discuss the tactile modality, specifically measures of tactile sensitivity for the human body, capabilities and limitations of the tactile modality, and applications of human tactile interfaces. Compared to other areas of the body, tactile research for the head and interfaces for the head is sparse. Therefore, a secondary concern of this review is to highlight this gap in the tactile literature.
A Riboswitch Regulates RNA Dimerization and Packaging in Human Immunodeficiency Virus Type 1 Virions

ABSTRACT The genome of retroviruses, including human immunodeficiency virus type 1 (HIV-1), consists of two identical RNA strands that are packaged as noncovalently linked dimers. The core packaging and dimerization signals are located in the downstream part of the untranslated leader of HIV-1 RNA—the Ψ and the dimerization initiation site (DIS) hairpins. The HIV-1 leader can adopt two alternative conformations that differ in the presentation of the DIS hairpin and consequently in their ability to dimerize in vitro. The branched multiple-hairpin (BMH) structure folds the poly(A) and DIS hairpins, but these domains are base paired in a long distance interaction (LDI) in the most stable LDI conformation. This LDI-BMH riboswitch regulates RNA dimerization in vitro. It was recently shown that the Ψ hairpin structure is also presented differently in the LDI and BMH structures. Several detailed in vivo studies have indicated that sequences throughout the leader RNA contribute to RNA packaging, but how these diverse mutations affect the packaging mechanism is not known. We reasoned that these effects may be due to a change in the LDI-BMH equilibrium, and we therefore reanalyzed the structural effects of a large set of leader RNA mutations that were presented in three previous studies (J. L. Clever, D. Mirandar, Jr., and T. G. Parslow, J. Virol. 76:12381-12387, 2002; C. Helga-Maria, M. L. Hammarskjold, and D. Rekosh, J. Virol. 73:4127-4135, 1999; R. S. Russell, J. Hu, V. Beriault, A. J. Mouland, M. Laughrea, L. Kleiman, M. A. Wainberg, and C. Liang, J. Virol. 77:84-96, 2003). This analysis revealed a strict correlation between the status of the LDI-BMH equilibrium and RNA packaging. Furthermore, a correlation is apparent between RNA dimerization and RNA packaging, and these processes may be coordinated by the same LDI-BMH riboswitch mechanism.
How Children Succeed: Grit, Curiosity, and the Hidden Power of Character

10.56 MB Free download How Children Succeed: Grit, Curiosity and the Hidden Power of Character book PDF, FB2, EPUB and MOBI. Read online How Children Succeed: Grit, Curiosity and the Hidden Power of Character which classified as Other that has 256 pages that contain constructive material with lovely reading experience. Reading online How Children Succeed: Grit, Curiosity and the Hidden Power of Character book will be provide using wonderful book reader and it's might gives you some access to identifying the book content before you download the book.
Nodal domain distributions for quantum maps

The statistics of the nodal lines and nodal domains of the eigenfunctions of quantum billiards have recently been observed to be fingerprints of the chaoticity of the underlying classical motion by Blum et al (2002 Phys. Rev. Lett. 88 114101) and by Bogomolny and Schmit (2002 Phys. Rev. Lett. 88 114102). These statistics were shown to be computable from the random wave model of the eigenfunctions. We here study the analogous problem for chaotic maps whose phase space is the two-torus. We show that the distributions of the numbers of nodal points and nodal domains of the eigenvectors of the corresponding quantum maps can be computed straightforwardly and exactly using random matrix theory. We compare the predictions with the results of numerical computations involving quantum perturbed cat maps.
Minimum inhibitory (MIC) and minimum microbicidal concentration (MMC) of polihexanide and triclosan against antibiotic sensitive and resistant Staphylococcus aureus and Escherichia coli strains

Background: An in-vitro study was conducted investigating the antimicrobial efficacy of polihexanide and triclosan against clinical isolates and reference laboratory strains of Staphylococcus aureus and Escherichia coli. Methods: The minimal inhibitory concentration (MIC) and the minimal microbicidal concentration (MMC) were determined following DIN 58940-81 using a micro-dilution assay and a quantitative suspension test following EN 1040. Polihexanide was tested in polyethylene glycol 4000, triclosan in aqueous solutions. Results: Against all tested strains the MIC of polihexanide ranged between 1–2 µg/mL. For triclosan the MICs varied depending on strains ranging between 0.5 µg/mL for the reference strains and 64 µg/mL for two clinical isolates. A logRF >5 without and logRF >3 with 0.2% albumin burden was achieved at 0.6 µg/mL triclosan. One exception was S. aureus strain H-5-24, where a triclosan concentration of 0.6 µg/mL required 1 minute without and 10 minutes with albumin burden to achieve the same logRFs. Polihexanide achieved a logRF >5 without and logRF >3 with albumin burden at a concentration of 0.6 µg/mL within 30 sec. The exception was the North-German epidemic MRSA strain, were an application time of 5 minutes was required. Conclusion: The clinical isolates of E. coli generally showed higher MICs against triclosan, both in the micro-dilution assay as well in the quantitative suspension test than comparable reference laboratory strains. For polihexanide and triclosan strain dependant susceptibility was shown. However, both antimicrobial compounds are effective when used in concentrations common in practice.
More on N = 1 matrix model curve for arbitrary N

Using both the matrix model prescription and the strong-coupling approach, we describe the intersections of n = 0 and n = 1 non-degenerated branches for quartic (polynomial of adjoint matter) tree-level superpotential in N = 1 supersymmetric SO(N)/USp(2N) gauge theories with massless flavors. We also apply the method to the degenerated branch. The general matrix model curve on the two cases we obtain is valid for arbitrary N and extends the previous work from strong-coupling approach. For SO(N) gauge theory with equal massive flavors, we also obtain the matrix model curve on the degenerated branch for arbitrary N. Finally we discuss on the intersections of n = 0 and n = 1 non-degenerated branches for equal massive flavors.
Calpain-Mediated N-Cadherin Proteolytic Processing in Brain Injury

Neural-cadherin (N-cadherin), a member of the classical cadherin family of transmembrane glycoproteins, mediates cellular recognition and cell–cell adhesion through calcium-dependent homophilic interactions and plays important roles in the development and maintenance of the nervous system. Metalloproteinase is known to cleave N-cadherin, which is further cleaved by γ-secretase. The intracellular domain of N-cadherin interacts with β-catenin, and β-catenin stability is critical for cell–cell adhesion and cell survival. In the present study, we showed that N-cadherin is cleaved specifically by calpain, resulting in the generation of a novel 110 kDa fragment. The cleavage occurred in ischemic brain lesions and in vitro neural cells in the presence of NMDA and ionomycin, and was restored by calpain inhibitors but not matrix metalloproteinase or γ-secretase inhibitors. Calpain directly cleaved N-cadherin in in vitro calpain assays, and calpain inhibitors prevented its cleavage in a dose-dependent manner. Using N-cadherin deletion mutants, we found that calpain cleavage sites exist in at least four regions of the cytoplasmic domain. Treatment with NMDA induced neuronal death, and it suppressed the expression of surface N-cadherin and the N-cadherin/β-catenin interaction, effects that were prevented by calpain inhibitor. Furthermore, calpain-mediated N-cadherin cleavage significantly affected cell–cell adhesion, AKT signaling, the N-cadherin/β-catenin interaction and the Wnt target gene expressions through the accumulation of nuclear β-catenin.
Inference System of Body Sensors for Health and Internet of Things Networks

Wearable devices have become popular and innovative and are converging with technologies such as big data, Cloud and Internet of Things (IoT). Traditional physiological sensors in fitness tracking and mHealth provide health data periodically or are captured manually when required. In future, physicians as well as IoT devices will benefit from this data to provide their services. These situations can cause rapid battery consumption, consume significant bandwidth, and raise privacy issues. There have been many attempts to extend battery life and improve communication methodologies; however, they have not been able to solve the resource constraints arising from physical hardware limits, such as the size of sensors. As an alternative, this paper presents a novel approach and solution to controlling body sensors to reduce both unnecessary data transmission and battery consumption. This can be done by implementing an inference system on sensors using sensed data to transfer it efficiently to other networks without burdening the workload from IoT onto sensor devices. In this paper, we experimented with reducing the bandwidth requirements for heart-rate sensors. Our results show savings in resource usage of between 66% and 99%. Such savings have the potential of making always-on mHealth devices a practical reality.
Understanding Retinal Color Coding from First Principles

A previously proposed theory of visual processing, based on redundancy reduction, is used to derive the retinal transfer function including color. The predicted kernels show the nontrivial mixing of space-time with color coding observed in experiments. The differences in color-coding between species are found to be due to differences among the chromatic autocorrelators for natural scenes in different environments.
Internal Carotid Artery Redundancy Is Significantly Associated With Dissection

Background and Purpose Redundant internal carotid arteries have been considered a risk factor in tonsillectomy, adenoidectomy, and surgical treatment of peritonsillar abscess and also a potentially treatable cause of stroke. However, an association between internal carotid artery redundancy and spontaneous dissection has not yet been clearly demonstrated. Methods We reviewed, for spontaneous carotid artery dissection, records of all patients admitted to our institution during the period from 1986 through 1992 with the diagnosis of stroke or transient ischemic attack. We also reviewed 108 percutaneous cerebral arteriograms performed between September 1992 and December 1992 for presence of carotid artery redundancies. Results Thirteen patients exhibited spontaneous dissection. Of these, 8 of 13 (62%) patients and 13 of 20 (65%) internal carotid arteries, viewed to the siphon, had significant redundancies, kinks, coils, or loops. Of 108 consecutive arteriograms of patients without dissection, in which 187 internal carotid arteries were viewed to the siphon, there were 20 (19%) patients and 22 (12%) of 187 vessels with significant redundancy. Five patients in the dissection group and 2 in the nondissection group had bilateral internal carotid artery redundancy (P=.0019 and P=.0001, respectively). Conclusions We found a significant correlation between internal carotid artery redundancy and dissection, particularly if redundancy is present bilaterally.
Supremacy distribution in evolving networks.

We study a supremacy distribution in evolving Barabasi-Albert networks. The supremacy s(i) of a node i is defined as the total number of all nodes that are not older than i and can be linked to it by a directed path (including the node i ). The nodes form a basin connected to the node i as its in-component. For a network with a characteristic parameter m=1,2,3,. , the supremacy of an individual node increases with the network age as t((1+m)/2) in an appropriate scaling region. It follows that there is a relation s(k) approximately k(m+1) between a node degree k and its supremacy s , and the supremacy distribution P(s) scales as s(-1-2/(1+m)) . Analytic calculations basing on a continuum theory of supremacy evolution and on a corresponding rate equation have been confirmed by numerical simulations.
A strongly degenerate parabolic aggregation equation

This paper is concerned with a strongly degenerate convection-diffusion equation in one space dimension whose convective flux involves a non-linear function of the total mass to one side of the given position. This equation can be understood as a model of aggregation of the individuals of a population with the solution representing their local density. The aggregation mechanism is balanced by a degenerate diffusion term accounting for dispersal. In the strongly degenerate case, solutions of the non-local problem are usually discontinuous and need to be defined as weak solutions satisfying an entropy condition. A finite difference scheme for the non-local problem is formulated and its convergence to the unique entropy solution is proved. The scheme emerges from taking divided differences of a monotone scheme for the local PDE for the primitive. Numerical examples illustrate the behaviour of entropy solutions of the non-local problem, in particular the aggregation phenomenon.
The Roots of Bilingualism in Newborns

The first steps toward bilingual language acquisition have already begun at birth. When tested on their preference for English versus Tagalog, newborns whose mothers spoke only English during pregnancy showed a robust preference for English. In contrast, newborns whose mothers spoke both English and Tagalog regularly during pregnancy showed equal preference for both languages. A group of newborns whose mothers had spoken both Chinese and English showed an intermediate pattern of preference for Tagalog over English. Preference for two languages does not suggest confusion between them, however. Study 2 showed that both English monolingual newborns and Tagalog-English bilingual newborns could discriminate English from Tagalog. The same perceptual and learning mechanisms that support acquisition in a monolingual environment thus also naturally support bilingual acquisition.
Thermal Processing of Silicate Dust in the Solar Nebula: Clues from Primitive Chondrite Matrices

The most abundant matrix minerals in chondritic meteorites—hydrated phyllosilicates and ferrous olivine crystals—formed predominantly in asteroids during fluid-assisted metamorphism. We infer that they formed from minerals present in three less altered carbonaceous chondrites that have silicate matrices composed largely of micrometer- and nanometer-sized grains of crystalline forsterite Mg2SiO4 and enstatite MgSiO3 and amorphous, ferromagnesian silicate. Compositional and structural features of enstatite and forsterite suggest that they formed as condensates that cooled below 1300 K at ~1000 K hr-1. Most amorphous silicates are likely to be solar nebula condensates also, as matrix, which is approximately solar in composition, is unlikely to be a mixture of genetically unrelated materials with different compositions. Since chondrules cooled at 10-1000 K hr-1 and matrix and chondrules are chemically complementary, most matrix silicates probably formed close to chondrules in transient heating events. Shock heating is favored, as nebular shocks capable of melting millimeter-sized aggregates vaporize dust. The crystalline and amorphous silicates in the primitive chondrite matrices share many characteristic features with silicates in chondritic interplanetary dust particles, suggesting that most of the crystalline silicates and possibly some amorphous silicates in the interplanetary dust particles are also nebular condensates. Except for small amounts of refractory oxides from the innermost region where refractory inclusions formed and presolar dust, most of the crystalline silicate dust that accreted into chondritic asteroids and long-period comets appears to have formed from shock heating at ~2-10 AU. Forsterite crystals around young stars may have a similar origin.