Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses

The highly pathogenic avian influenza (HPAI) H5N1 virus lineage has undergone extensive genetic reassortment with viruses from different sources to produce numerous H5N1 genotypes, and also developed into multiple genetically distinct sublineages in China. From there, the virus has spread to over 60 countries. The ecological success of this virus in diverse species of both poultry and wild birds with frequent introduction to humans suggests that it is a likely source of the next human pandemic. Therefore, the evolutionary and ecological characteristics of its emergence from wild birds into poultry are of considerable interest. Here, we apply the latest analytical techniques to infer the early evolutionary dynamics of H5N1 virus in the population from which it emerged (wild birds and domestic poultry). By estimating the time of most recent common ancestors of each gene segment, we show that the H5N1 prototype virus was likely introduced from wild birds into poultry as a non-reassortant low pathogenic avian influenza H5N1 virus and was not generated by reassortment in poultry. In contrast, more recent H5N1 genotypes were generated locally in aquatic poultry after the prototype virus (A/goose/Guangdong/1/96) introduction occurred, i.e., they were not a result of additional emergence from wild birds. We show that the H5N1 virus was introduced into Indonesia and Vietnam 3–6 months prior to detection of the first outbreaks in those countries. Population dynamics analyses revealed a rapid increase in the genetic diversity of A/goose/Guangdong/1/96 lineage viruses from mid-1999 to early 2000. Our results suggest that the transmission of reassortant viruses through the mixed poultry population in farms and markets in China has selected HPAI H5N1 viruses that are well adapted to multiple hosts and reduced the interspecies transmission barrier of those viruses.
Proving liveness properties of concurrent programs using petri-nets

With the increased scale of distributed computations the complexity of liveness proofs have increased. In this paper we endeavor to simplify the process of verifying a concurrent system using well know modeling techniques. The choice of modeling tool as well as the proof is based on future scalability and automation. We translate the formal proof to a petri-net representation and use this to verify basic algorithms. We show that the formal proof of liveness stated by Owiki and Lamport can be adapted to petri-nets. We also show a modification to petri-nets for increased granularity in loop modeling. This is used to clarify the translation of the original proof to our petri-net representation. With these results we discuss the usefulness of our approach and compare it to other methods of ensuring liveness.
Geometric Structure Estimation of Axially Symmetric Pots from Small Fragments

The recovery of geometric structure from noisy data poses difficult non-linear statistical estimation problems. This paper describes a novel, robust, low computational cost approach for finding the geometric structure of an axially symmetric pot from a small fragment of it (an unorganized set of 3D points). This problem is of great archaeological importance to the study of the hundreds and thousands of shards found at excavation sites. Our method is based on the following fact: for each point on the surface, the center of the sphere of principal curvature corresponding to the circles of revolution is on the symmetric axis. By finding the line which minimizes the weighted leastsquares distance to the estimated centers, we can find first the symmetric axis and then the profile curve. Because of the special properties of a surface of revolution, we can do this using only first derivatives, hence this method is robust to noisy data. We then use bootstrap methods to find confidence bounds for the axis and the profile curve. These confidence bounds are essential if the estimations are used for the assembly of the full pot from multiple sherds.
Vestibuloocular reflex dynamics during high-frequency and high-acceleration rotations of the head on body in rhesus monkey.

For frequencies >10 Hz, the vestibuloocular reflex (VOR) has been primarily investigated during passive rotations of the head on the body in humans. These prior studies suggest that eye movements lag head movements, as predicted by a 7-ms delay in the VOR reflex pathways. However, Minor and colleagues recently applied whole-body rotations of frequencies < or =15 Hz in monkeys and found that eye movements were nearly in phase with head motion across all frequencies. The goal of the present study was to determine whether VOR response dynamics actually differ significantly for whole-body versus head-on-body rotations. To address this question, we evaluated the gain and phase of the VOR induced by high-frequency oscillations of the head on the body in monkeys by directly measuring both head and eye movements using the magnetic search coil technique. A torque motor was used to rotate the heads of three Rhesus monkeys over the frequency range 5-25 Hz. Peak head velocity was held constant, first at +/-50 degrees /s and then +/-100 degrees /s. The VOR was found to be essentially compensatory across all frequencies; gains were near unity (1.1 at 5 Hz vs. 1.2 at 25 Hz), and phase lag increased only slightly with frequency (from 2 degrees at 5 Hz to 11 degrees at 25 Hz, a marked contrast to the 63 degrees lag at 25 Hz predicted by a 7-ms VOR latency). Furthermore, VOR response dynamics were comparable in darkness and when viewing a target and did not vary with peak velocity. Although monkeys offered less resistance to the initial cycles of applied head motion, the gain and phase of the VOR did not vary for early versus late cycles, suggesting that an efference copy of the motor command to the neck musculature did not alter VOR response dynamics. In addition, VOR dynamics were also probed by applying transient head perturbations with much greater accelerations (peak acceleration >15,000 degrees /s(2)) than have been previously employed. The VOR latency was between 5 and 6 ms, and mean gain was close to unity for two of the three animals tested. A simple linear model well described the VOR responses elicited by sinusoidal and transient head on body rotations. We conclude that the VOR is compensatory over a wide frequency range in monkeys and has similar response dynamics during passive rotation of the head on body as during passive rotation of the whole body in space.
Active Learning with Spatially Sensitive Labeling Costs

In active learning, it is typically assumed that all instanc es require the same amount of effort to label and that the cost of labeling an inst a ce is independent of other selected instances. In spatially distributed data such as hyperspectral imagery for land-cover classification, the act of labeling a po int (i.e., determining the land-type) may involve physically traveling to a location a nd determining ground truth. In this case, both assumptions about label acquisiti on costs made by traditional active learning are broken, since costs will depend o n physical locations and accessibility of all the visited points. This paper formula tes and analyzes the novel problem of performing active learning on spatial data where lab l acquisition costs are proportional to distance traveled.
Social and economic equality: a human biologist's perspective on the developing world beyond the limits of adaptability

Na medida em que todas as obras da UC Digitalis se encontram protegidas pelo Código do Direito de Autor e Direitos Conexos e demais legislação aplicável, toda a cópia, parcial ou total, deste documento, nos casos em que é legalmente admitida, deverá conter ou fazer-se acompanhar por este aviso. Social and economic equality: a human biologist's perspective on the developing world beyond the limits of adaptability Autor(es): Johnston, Francis E. Publicado por: CIAS Centro de Investigação em Antropologia e Saúde URL persistente: URI:http://hdl.handle. net/10316.2/30238
Frequent Replenishment Sustains the Beneficial Microbiome of Drosophila melanogaster

ABSTRACT We report that establishment and maintenance of the Drosophila melanogaster microbiome depend on ingestion of bacteria. Frequent transfer of flies to sterile food prevented establishment of the microbiome in newly emerged flies and reduced the predominant members, Acetobacter and Lactobacillus spp. , by 10- to 1,000-fold in older flies. Flies with a normal microbiome were less susceptible than germfree flies to infection by Serratia marcescens and Pseudomonas aeruginosa. Augmentation of the normal microbiome with higher populations of Lactobacillus plantarum, a Drosophila commensal and probiotic used in humans, further protected the fly from infection. Replenishment represents an unexplored strategy by which animals can sustain a gut microbial community. Moreover, the population behavior and health benefits of L. plantarum resemble features of certain probiotic bacteria administered to humans. As such, L. plantarum in the fly gut may serve as a simple model for dissecting the population dynamics and mode of action of probiotics in animal hosts. IMPORTANCE Previous studies have defined the composition of the Drosophila melanogaster microbiome in laboratory and wild-caught flies. Our study advances current knowledge in this field by demonstrating that Drosophila must consume bacteria to establish and maintain its microbiome. This finding suggests that the dominant Drosophila symbionts remain associated with their host because of repeated reintroduction rather than internal growth. Furthermore, our study shows that one member of the microbiome, Lactobacillus plantarum, protects the fly from intestinal pathogens. These results suggest that, although not always present, the microbiota can promote salubrious effects for the host. In sum, our work provides a previously unexplored mechanism of microbiome maintenance and an in vivo model system for investigating the mechanisms of action of probiotic bacteria. Previous studies have defined the composition of the Drosophila melanogaster microbiome in laboratory and wild-caught flies. Our study advances current knowledge in this field by demonstrating that Drosophila must consume bacteria to establish and maintain its microbiome. This finding suggests that the dominant Drosophila symbionts remain associated with their host because of repeated reintroduction rather than internal growth. Furthermore, our study shows that one member of the microbiome, Lactobacillus plantarum, protects the fly from intestinal pathogens. These results suggest that, although not always present, the microbiota can promote salubrious effects for the host. In sum, our work provides a previously unexplored mechanism of microbiome maintenance and an in vivo model system for investigating the mechanisms of action of probiotic bacteria.
Algorithm Transformation for FPGA Implementation

High level hardware description languages aim to make hardware design more like programming software. These languages are often used to accelerate legacy software algorithms by porting them to an FPGA based hardware implementation. Porting does not always result in efficient architectures as the original algorithms are usually developed and optimized to run on a serial processor. To obtain an efficient hardware architecture, one that makes use of the available parallelism, the algorithms need to be transformed. Eleven such transformations are identified and explained. While some of these are straightforward, and have been implemented by some compilers, many cannot be automated because they require detailed knowledge of the algorithm.
Android-based mobile payment service protected by 3-factor authentication and virtual private ad hoc networking

This work develops a pair of mobile payment devices, a counter reader and a paying client, on Android-based smartphone platforms for emerging mobile payment or electronic wallet services. These two devices featuring 3-factor authentication and virtual private Ad Hoc networking can make an easier and securer transaction than traditional credit cards or electronic payment cards. 3-factor authentication feature combines PIN code authentication, USIM card authentication, and facial biometric authentication. Especially, this work proposes and implements a simple but practical method, Fast Semi-3D Face Vertical Pose Recovery, to cope with the vertical pose variation issue bothering face recognition systems so far. Experimental results show the proposed method can significantly raise the recognition accuracy and enlarge the operating angle range of face recognition system under various vertical pose conditions. Besides, virtual private Ad Hoc networking feature based on OpenSSL and i-Jetty open-source libraries is also integrated seamlessly.
Employees' perceptions of the effectiveness and fairness of performance management in a South African public sector institution

Orientation: The implementation of performance management systems (PMSs) and performance appraisals (PAs) by public managers remains a challenge and necessitates an investigation into employees’ perceptions of the effectiveness of the PMS and the fairness of PA. Research purpose: This study investigated the association between employee involvement, performance-oriented culture, management commitment and the effectiveness of a PMS. Six factors that determine and influence employees’ perceptions of PA fairness were also investigated. Motivation for the study: Employees’ experiences of the implementation and practice of PMSs and PAs by public managers may differ from what is intended. The motivation for this study was to quantify employee perceptions of the effectiveness of a PMS and the fairness of PA to establish if there is a discrepancy between what is intended and how they are implemented and practiced. Research approach, design and method: This cross-sectional study conducted a census on a total population of 140 employees in a public sector institution. A questionnaire comprising three sections was used to collect data: Section A contained biographical questions, Section B comprised questions on the contextual factors that measure the perceived effectiveness of the PMS while Section C comprised questions related to the perceived fairness of PA. Main findings: The results show that employees perceive their PMS to be ineffective and their PAs to be unfair. The mean perception scores for PA fairness for the Assets and Facilities Department were significantly lower than those of the Human Resources Department. This is indicative of some deficiencies in the appraisal process in the Assets and Facilities Department. Respondents occupying general positions returned significantly lower mean scores for PA fairness compared to those in managerial and professional positions, which indicates serious shortcomings in their appraisal process. Practical/managerial implications: The findings reveal that employees were not involved in the development of the PMS. Also, the results indicated a lack of employee participation in the PA process, that PAs were not conducted for development purposes, performance feedback sessions were not undertaken on a regular basis and employees were not involved in goal setting. A training programme should address these organisational and managerial deficiencies. Contribution: This research study contributes to the body of knowledge by quantifying the perceptions of employees regarding the organisational factors that influence the effectiveness of the PMS and the six factors, namely appraisers’ knowledge, employee participation, clear goal establishment, employee development, goal establishment, appraisal follow-up and goal discussion that influence PA fairness.
Power-Aware System Design of Wireless Sensor Networks: Power Estimation and Power Profiling Strategies

Modern design of wireless devices requires the designers to have a special focus on power consumption to prolong the battery life of the final system. The designer therefore needs power consumption information very early in the process to be able to decide on system parameters, design methods, communication protocols, functionality restrictions. Typically, this is done by running simulations of the system to be developed and performing design space exploration. However, there is a tradeoff between speed and accuracy of simulation, therefore the designer has to be aware of available tools and simulation methods he can choose from to achieve the best possible solution for his case.
Parameters and Predictions for the Long-Period Transiting Planet HD 17156b

We report high-cadence time series photometry of the recently discovered transiting exoplanet system HD 17156, spanning the time of transit on UT 2007 October 1, from three separate observatories. We present a joint analysis of our photometry, previously published radial velocity measurements, and times of transit center for three additional events. Adopting the spectroscopically determined values and uncertainties for the stellar mass and radius, we estimate a planet radius of Rp = 1.01 ± 0.09 RJup and an inclination of i = 86.5+ 1.1−0.7 deg. We find a time of transit center of Tc = 2,454,374.8338 ± 0.0020 HJD and an orbital period of P = 21.21691 ± 0.00071 days and note that the four transits reported to date show no sign of timing variations that would indicate the presence of a third body in the system. Our results do not preclude the existence of a secondary eclipse, but imply that there is only a 9.2% chance for this to be present and an even lower probability (6.9%) that the secondary eclipse would be a nongrazing event. Due to its eccentric orbit and long period, HD 17156b is a fascinating object for the study of the dynamics of exoplanet atmospheres. To aid such future studies, we present theoretical light curves for the variable infrared emission from the visible hemisphere of the planet throughout its orbit.
Mathematical models of HIV pathogenesis and treatment.

We review mathematical models of HIV dynamics, disease progression, and therapy. We start by introducing a basic model of virus infection and demonstrate how it was used to study HIV dynamics and to measure crucial parameters that lead to a new understanding of the disease process. We discuss the diversity threshold model as an example of the general principle that virus evolution can drive disease progression and the destruction of the immune system. Finally, we show how mathematical models can be used to understand correlates of long-term immunological control of HIV, and to design therapy regimes that convert a progressing patient into a state of long-term non-progression.
Involvement of Superoxide in Excitotoxicity and DNA Fragmentation in Striatal Vulnerability in Mice after Treatment with the Mitochondrial Toxin, 3-Nitropropionic Acid

Oxidative stress and excitotoxicity have been implicated in selective striatal vulnerability caused by the mitochondrial toxin, 3-nitropropionic acid (3-NP), which may simulate Huntington's disease in animals and humans. The detailed mechanism of the role of superoxide in striatal vulnerability induced by 3-NP is still unknown. The authors investigated oxidative cellular injury and DNA fragmentation after systemic 3-NP injection in wild-type (Wt) mice and mutant mice with a deficiency in manganese superoxide dismutase (MnSOD; Sod2 −/+). Furthermore, they investigated the effects of decortication after 3-NP treatment in Sod2 −/+ mice, and copper/zinc SOD (CuZnSOD) treatment in recently developed Sod2 −/+ mice that overexpress CuZnSOD (SOD1 +/− / Sod2 −/+ mice). Oxidized hydroethidine, 8-hydroxyguanosine immunoreactivity, and nitrotyrosine immunoreactivity were increased in the Sod2 −/+ mice compared with the Wt mice after 3-NP treatment (P < 0.001). Decortication completely abolished oxidative striatal damage after 3-NP treatment in the Sod2 −/+ mice. Increased CuZnSOD attenuated DNA fragmentation and striatal lesion volume after 3-NP treatment in the Sod2 −/+ mice (P < 0.001). These data suggest that production of superoxide may be a critical step to excitotoxicity and subsequent DNA fragmentation in selective striatal vulnerability after 3-NP treatment.
Concurrent Event Detection for Asynchronous consistency checking of pervasive context

Contexts, the pieces of information that capture the characteristics of computing environments, are often inconsistent in the dynamic and uncertain pervasive computing environments. Various schemes have been proposed to check context consistency for pervasive applications. However, existing schemes implicitly assume that the contexts being checked belong to the same snapshot of time. This limitation makes existing schemes do not work in pervasive computing environments, which are characterized by the asynchronous coordination among computing devices. The main challenge imposed on context consistency checking by asynchronous environments is how to interpret and detect concurrent events. To this end, we propose in this paper the Concurrent Events Detection for Asynchronous consistency checking (CEDA) algorithm. An analytical model, together with corresponding numerical results, is derived to study the performance of CEDA. We also conduct extensive experimental evaluation to investigate whether CEDA is desirable for context-aware applications. Both theoretical analysis and experimental evaluation show that CEDA accurately detects concurrent events in time in asynchronous pervasive computing environments, even with dynamic changes in message delay, duration of events and error rate of context collection.
The Effect of Guided Imagery on Stress and Fatigue in Patients with Thyroid Cancer Undergoing Radioactive Iodine Therapy

This study was conducted to evaluate the effects of guided imagery on stress and fatigue in patients undergoing radioactive iodine therapy after thyroidectomy in Korea. Participants were 84 individuals (44 for experimental group and 40 for control group) with thyroid cancer. The experimental group listened to a guided imagery CD once a day for 4 weeks. Global Assessment of Recent Stress and Revised Piper Fatigue Scale were self-administered, and heart rate variability was measured at three time points; prior to intervention (T1), just before intervention (T2) and 1 week later after intervention (T3). Heart rate variability was consisted of Standard Deviation of all NN interval (SDNN), Total Power (TP), Low Frequency (LF), and High Frequency (HF). There were significant decreases in stress (F = 28.45, P < 0.001) and fatigue (F = 26.17, P < 0.001) over time in the experimental group compared to the control group. Heart rate variability changed over time in the experimental group relative to the control group; SDNN (F = 6.68, P = 0.002), TP (F = 5.29, P = 0.006), LF (F = 4.58, P = 0.012), and HF (F = 3.71, P = 0.026). From the results of this study guided imagery can be recommended as an effective intervention to thyroid cancer patients with stress and fatigue.
Please Sign to Save... : How Online Environmental Petitions Succeed

Social media have become one of the key platforms to support the debate on climate change. In particular, Twitter allows easy information dissemination when running environmental campaigns. Yet, the dynamics of these campaigns on social platforms still remain largely unexplored. In this paper, we study the success factors enabling online petitions to attain their required number of signatures. We present an analysis of e-petitions and identify how their number of users, tweets and retweets correlate with their success. In addition, we show that environmental petitions are actively promoted by popular public campaigns on Twitter. Finally, we present an annotated corpus of petitions posted by environmental campaigns together with their corresponding tweets to enable further exploration.