Miracle-dz/UniFAR-FTUs huggingface dataset:
APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host

Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary “arms-race” between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary “arms-race” hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations.
Real-time urban traffic sensing with GPS equipped Probe Vehicles

GPS-based Vehicle Probe (GVP) has become an important floating car source in Intelligent Transportation System (ITS) for its efficiency and accuracy. We develop a real time GVP traffic estimation system in Taiwan by collecting the GPS data of commercial fleet and taxi. After filtering out some improper data, the retained GPS data are processed by an incremental map matching method which maps the GPS trajectories to real road map concerning of latency and accuracy. Then, road speed information can be produced by Speed Estimation module. To supply traffic information for public, road speed information are summarized and broadcast through a traffic information website. The experiments show that our system can reach good map matching accuracy and traffic information accuracy. Therefore, reasonable traffic information of freeways and urban areas can be sensed efficiently.
Validation of a computer-aided EMG decomposition method

This paper presents an objective assessment of the accuracy of EMGLAB, a computer-aided EMG decomposition program that we developed. EMG signals were recorded simultaneously using monopolar needle and fine-wire electrodes from nearby sites in the tibialis anterior muscle during moderate isometric contractions. The signals were decomposed independently by an experienced operator, yielding 3-12 (mean 8.7) motor-unit action potential (MUAP) trains per signal. Decomposition accuracy was estimated by crosschecking 83 pairs of trains from different signals that corresponded to the same motor units. The results show that EMGLAB was able to decompose large MUAPs (peak amplitudes greater than 2.5 times rms signal amplitude) with 98-100% accuracy, and smaller MUAPs with 80-100% accuracy. Many of the errors involved misalignment of small MUAPs within superimpositions and amounted to less than 5 ms. These results validate the accuracy of EMGLAB for decomposing EMG signals of moderate complexity.
VISTA: VPO interactive system for tuning applications

Software designers face many challenges when developing applications for embedded systems. One major challenge is meeting the conflicting constraints of speed, code size, and power consumption. Embedded application developers often resort to hand-coded assembly language to meet these constraints since traditional optimizing compiler technology is usually of little help in addressing this challenge. The results are software systems that are not portable, less robust, and more costly to develop and maintain. Another limitation is that compilers traditionally apply the optimizations to a program in a fixed order. However, it has long been known that a single ordering of optimization phases will not produce the best code for every application. In fact, the smallest unit of compilation in most compilers is typically a function and the programmer has no control over the code improvement process other than setting flags to enable or disable certain optimization phases. This paper describes a new code improvement paradigm implemented in a system called VISTA that can help achieve the cost/performance trade-offs that embedded applications demand. The VISTA system opens the code improvement process and gives the application programmer, when necessary, the ability to finely control it. VISTA also provides support for finding effective sequences of optimization phases. This support includes the ability to interactively get static and dynamic performance information, which can be used by the developer to steer the code improvement process. This performance information is also internally used by VISTA for automatically selecting the best optimization sequence from several attempted. One such feature is the use of a genetic algorithm to search for the most efficient sequence based on specified fitness criteria. We include a number of experimental results that evaluate the effectiveness of using a genetic algorithm in VISTA to find effective optimization phase sequences.
Human pharmacology of a low‐molecular‐weight heparin (ALFA‐LMWH): An update

During the last 15 years a renewed interest has occurred in the study of the biological action of he~a r in . l -~ An outstanding outcome of these studies has been the discovery that the biological activities of heparin are not necessarily related to the whole series of components of the drug. Instead, heparin fractions and fragments still retain certain heparin activities (e.g., the anti-Xa activity) but not others (e.g., the effects on the activated partial thromboplastin time), suggesting the possibility that heparin derivatives might have therapeutic advantages over the parent c ~ m p o u n d . ~ ~ The heparin fragments and derivatives are generally indicated as lowmolecular-weight heparins (LMWH). They are heterogeneous in their chemical composition and molecular weight, are produced today by several manufacturers using different depolymerization methods, and are currently being evaluated clinically. The pharmacological properties of one of these* will be examined in this review.
One-Shot Classical Data Compression With Quantum Side Information and the Distillation of Common Randomness or Secret Keys

The task of compressing classical information in the one-shot scenario is studied in the setting where the decompressor additionally has access to some given quantum side information. In this hybrid classical-quantum version of the famous Slepian-Wolf problem, the smooth max entropy is found to govern the number of bits into which classical information can be compressed so that it can be reliably recovered from the compressed version and quantum side information. Combining this result with known results on privacy amplification then yields tight bounds on the amount of common randomness and secret key that can be recovered in one shot from hybrid classical-quantum systems using one-way classical communication.
Analysing Performance of Lift Systems in PEPA

We use the stochastic process algebra PEPA 8] to specify lift systems and analyse their performance. We focus on the mean passenger waiting time versus the speed of the lift (given by the slowest rate such as the closing of the doors) and the rate of passengers arrivals. The results are obtained by compiling the speciication in the PEPA workbench, and then solving the resulting equilibrium state equation in Matlab. The outcome of the PEPA analysis is compared with traditional engineering methods for lift traac analysis known from the literature 2]. We nd that PEPA has potential for ner grain analysis than existing methods. Finally, we brieey discuss our experience with the PEPA workbench.
A test of the nutrient-productivity model in the Gulf of Maine using the intertidal mussel Mytilus edulis

Historical concepts of top-down control (predator-prey interactions) on rocky intertidal community structure have transitioned to studies on bottom-up effects (nutrient supply and larval transport) as significant factors affecting rocky intertidal community structure. Studies performed on rocky intertidal locations along the Gulf of Maine (GOM) at multiple sites and seasons in 2004 and 2006 examined the ecology of Mytilus edulis populations by measuring size frequency distributions, diet quality (stable isotope composition) and physiological performance of individuals using condition indices and RNA/DNA ratios. Data were correlated to satellite imagery for sea surface temperature and chlorophyll a concentration and individuals were genetically tested to look for lineage sorting. Populations of M. edulis in the GOM were found to be genetically homogenous, consuming a mixed diet of phytoplankton and detritus, with shell size and physiological performance tied to chlorophyll a concentration and temperature, providing strong evidence for community structure being linked to environmental variability.
Modeling the Hydrological Cycle in the Atmosphere of Mars: Influence of a Bimodal Size Distribution of Aerosol Nucleation Particles

We present a new implementation of the hydrological cycle scheme into a general circulation model of the Martian atmosphere. The model includes a semi‐Lagrangian transport scheme for water vapor and ice and accounts for microphysics of phase transitions between them. The hydrological scheme includes processes of saturation, nucleation, particle growth, sublimation, and sedimentation under the assumption of a variable size distribution. The scheme has been implemented into the Max Planck Institute Martian general circulation model and tested assuming monomodal and bimodal lognormal distributions of ice condensation nuclei. We present a comparison of the simulated annual variations, horizontal and vertical distributions of water vapor, and ice clouds with the available observations from instruments on board Mars orbiters. The accounting for bimodality of aerosol particle distribution improves the simulations of the annual hydrological cycle, including predicted ice clouds mass, opacity, number density, and particle radii. The increased number density and lower nucleation rates bring the simulated cloud opacities closer to observations. Simulations show a weak effect of the excess of small aerosol particles on the simulated water vapor distributions.
Climate change and the risks associated with delayed breeding in a tropical wild bird population

There is growing evidence of changes in the timing of important ecological events, such as flowering in plants and reproduction in animals, in response to climate change, with implications for population decline and biodiversity loss. Recent work has shown that the timing of breeding in wild birds is changing in response to climate change partly because individuals are remarkably flexible in their timing of breeding. Despite this work, our understanding of these processes in wild populations remains very limited and biased towards species from temperate regions. Here, we report the response to changing climate in a tropical wild bird population using a long-term dataset on a formerly critically endangered island endemic, the Mauritius kestrel. We show that the frequency of spring rainfall affects the timing of breeding, with birds breeding later in wetter springs. Delays in breeding have consequences in terms of reduced reproductive success as birds get exposed to risks associated with adverse climatic conditions later on in the breeding season, which reduce nesting success. These results, combined with the fact that frequency of spring rainfall has increased by about 60 per cent in our study area since 1962, imply that climate change is exposing birds to the stochastic risks of late reproduction by causing them to start breeding relatively late in the season.
When and Why Ruppert's Algorithm Works

An “adaptive” variant of Ruppert’s Algorithm for producing quality triangular planar meshes is introduced. The algorithm terminates for arbitrary Planar Straight Line Graph (PSLG) input. The algorithm outputs a Delaunay mesh where no triangle has minimum angle smaller than 26.45◦ except “across” from small angles of the input. No angle of the output mesh is smaller than arctan [(sin θ∗)/(2 − cos θ∗)] where θ∗ is the minimum input angle. Moreover no angle of the mesh is larger than 137.1◦. The adaptive variant is unnecessary when θ∗ is larger than 36.53◦, and thus Ruppert’s Algorithm (with concentric shell splitting) can accept input with minimum angle as small as 36.53◦. An argument is made for why Ruppert’s Algorithm can terminate when the minimum output angle is as large as 30◦.
NectaRSS, an RSS feed ranking system that implicitly learns user preferences

In this paper a new RSS feed ranking method called NectaRSS is introduced. The system recommends information to a user based on his/her past choices. User preferences are automatically acquired, avoiding explicit feedback, and ranking is based on those preferences distilled to a user profile. NectaRSS uses the well-known vector space model for user profiles and new documents, and compares them using information-retrieval techniques, but introduces a novel method for user profile creation and adaptation from users' past choices. The efficiency of the proposed method has been tested by embedding it into an intelligent aggregator (RSS feed reader), which has been used by different and heterogeneous users. Besides, this paper proves that the ranking of newsitems yielded by NectaRSS improves its quality with user's choices, and its superiority over other algorithms that use a different information representation method.
Molecular documentation of polyembryony and the micro-spatial dispersion of clonal sibships in the nine-banded armadillo, Dasypus novemcinctus

A battery of allelic markers at highly polymorphic microsatellite loci was developed and employed to confirm, genetically, the clonal nature of sibships in nine-banded armadillos. This phenomenon of consistent polyembryony, otherwise nearly unknown among the vertebrates, was capitalized upon to describe the micro-spatial distributions of numerous clonal sibships in a natural population of armadillos. Adult clone mates were significantly more dispersed than were juvenile sibs, suggesting limited opportunities for altruistic behavioural interactions among mature individuals. These results, and considerations of armadillo natural history, suggest that evolutionary explanations for polyembryony in this species may not reside in the kinds of ecological and kin selection theories relevant to some of the polyembryonic invertebrates. Rather, polyembryony in armadillos may be associated evolutionarily with other reproductive peculiarities of the species, including delayed uterine implantation of a single egg.
Geographic Patterns of Fire Severity Following an Extreme Eucalyptus Forest Fire in Southern Australia: 2013 Forcett-Dunalley Fire

Fire severity is an important characteristic of fire regimes; however, global assessments of fire regimes typically focus more on fire frequency and burnt area. Our objective in this case study is to use multiple lines of evidence to understand fire severity and intensity patterns and their environmental correlates in the extreme 2013 Forcett-Dunalley fire in southeast Tasmania, Australia. We use maximum likelihood classification of aerial photography, and fire behavior equations, to report on fire severity and intensity patterns, and compare the performance of multiple thresholds of the normalised burn ratio (dNBR) and normalized difference vegetation index (dNDVI) (from pre- and post-fire Landsat 7 images) against classified aerial photography. We investigate how vegetation, topography, and fire weather, and therefore intensity, influenced fire severity patterns. According to the aerial photographic classification, the fire burnt 25,950 ha of which 5% burnt at low severities, 17% at medium severity, 32% at high severity, 23% at very high severities, while 22% contained unburnt patches. Generalized linear modelling revealed that fire severity was strongly influenced by slope angle, aspect, and interactions between vegetation type and fire weather (FFDI) ranging from moderate (12) to catastrophic (>90). Extreme fire weather, which occurred in 2% of the total fire duration of the fire (16 days), caused the fire to burn nearly half (46%) of the total area of the fireground and resulted in modelled extreme fireline intensities among all vegetation types, including an inferred peak of 68,000 kW·m−1 in dry forest. The best satellite-based severity map was the site-specific dNBR (45% congruence with aerial photography) showing dNBR potential in Eucalyptus forests, but the reliability of this approach must be assessed using aerial photography, and/or ground assessment.
VSLP: Voronoi-socialspot-aided packet forwarding protocol with receiver Location Privacy in MSNs

With the pervasive use of smart phones in the daily life, location privacy has become one of cruxes for the success of mobile social networks (MSNs). In this paper, we propose a Voronoi-social-spot-aided Location Privacy-preserving (VSLP) packet forwarding protocol to improve the packet forwarding efficiency and at the same time protect receiver's location privacy. In VSLP, we first identify the social spot locations according to the user mobility information, and then build a Voronoi diagram based on the defined social spots. On the edge of Delaunay triangulation over the Voronoi diagram, we deploy multiple storage devices to help receivers to temporarily store the packets. With the security analysis, we show that the location privacy can be achieved. Using extensive simulations, we show that VSLP can enhance the packet forwarding efficiency with improved packet delivery ratio and reduced average packet delay.
Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2) defects predicts differential effects on aminoacylation

The accuracy of mitochondrial protein synthesis is dependent on the coordinated action of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mtARSs) and the mitochondrial DNA-encoded tRNAs. The recent advances in whole-exome sequencing have revealed the importance of the mtARS proteins for mitochondrial pathophysiology since nearly every nuclear gene for mtARS (out of 19) is now recognized as a disease gene for mitochondrial disease. Typically, defects in each mtARS have been identified in one tissue-specific disease, most commonly affecting the brain, or in one syndrome. However, mutations in the AARS2 gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS) have been reported both in patients with infantile-onset cardiomyopathy and in patients with childhood to adulthood-onset leukoencephalopathy. We present here an investigation of the effects of the described mutations on the structure of the synthetase, in an effort to understand the tissue-specific outcomes of the different mutations. The mtAlaRS differs from the other mtARSs because in addition to the aminoacylation domain, it has a conserved editing domain for deacylating tRNAs that have been mischarged with incorrect amino acids. We show that the cardiomyopathy phenotype results from a single allele, causing an amino acid change R592W in the editing domain of AARS2, whereas the leukodystrophy mutations are located in other domains of the synthetase. Nevertheless, our structural analysis predicts that all mutations reduce the aminoacylation activity of the synthetase, because all mtAlaRS domains contribute to tRNA binding for aminoacylation. According to our model, the cardiomyopathy mutations severely compromise aminoacylation whereas partial activity is retained by the mutation combinations found in the leukodystrophy patients. These predictions provide a hypothesis for the molecular basis of the distinct tissue-specific phenotypic outcomes.
Navigation and control of a mobile robot among moving obstacles

The issues related to navigation and control of a mobile robot which enable it to deal with unexpected moving obstacles by sensor-based control are addressed. A probabilistic approach to deal with collision avoidance under uncertainty is proposed. It is assumed that the uncertainties both in the position of a moving obstacle and the error of the measurements are normally distributed. The mean and variance of the distribution are determined by a recursive Kalman filter both from a priori information and the available sensor data. The authors define a safe circle for the robot and bound a high-confidence position error ellipse of the moving obstacles. Collisions can be avoided by controlling the speed and steering of the mobile robot along the preplanned path to keep the safe circle from intersecting the ellipse. A local robot frame was chosen for collision judgement and avoidance control. <<ETX>>
Digisketch: taming anoto technology on LCDs

The Anoto technology uses a non-repetitive pattern printed on paper to enable a camera-equipped pen to locate its absolute position on that pattern. This technology is also used on projection screens to create large-sized interactive areas, but suffers from the drawbacks such as shadow casting or space requirements. Up to now, no implementation exists that enables a tracking on LC-displays using the Anoto technology. Thus, we introduce Digisketch, which uses special films that can be applied to LC-displays, to back and front projections, or to glass, allowing pattern recognition for the pen's camera. After describing the technical development of a prototype, we compare this new possibility of using Anoto compatible surfaces with other traditional tracking systems for LC-screens.
Probing TCP Implementations

In this paper, we demonstrate a technique called active probing used to study TCP implementations. Active probing treats a TCP implementation as a black box, and uses a set of procedures to probe the black box. By studying the way TCP responds to the probes, one can deduce several characteristics of the implementation. The technique is particularly useful if TCP source code is unavailable. To demonstrate the technique, the paper shows example probe procedures that examine three aspects of TCP. The results are informative: they reveal implementation flaws, protocol violations, and the details of design decisions in five vendor-supported TCP implementations. The results of our experiment suggest that active probing can be used to test TCP implementations.