Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with ambiguous data to produce misleading estimates of topology and branch lengths. Furthermore, within a Bayesian framework, priors on branch lengths and rate heterogeneity parameters can exacerbate the effects of ambiguous data, resulting in strongly misleading bipartition posterior probabilities. The magnitude and direction of the ambiguous data bias are a function of the number and taxonomic distribution of ambiguous characters, the strength of topological support, and whether or not the model is correctly specified. The results of this study have major implications for all analyses that rely on accurate estimates of topology or branch lengths, including divergence time estimation, ancestral state reconstruction, tree-dependent comparative methods, rate variation analysis, phylogenetic hypothesis testing, and phylogeographic analysis.
Intrahospital transport of patients on invasive ventilation: cardiorespiratory repercussions and adverse events.

OBJECTIVE To determine the occurrence of cardiorespiratory alterations and to identify adverse events during the intrahospital transport of patients on invasive ventilation. METHODS A prospective observational non-randomized study was conducted at two tertiary hospitals between April of 2005 and December of 2006. We included patients on invasive ventilation who required intrahospital transport during the study period. Exclusion criteria were as follows: being under suspicion of brain death; being submitted to alternate periods of mechanical ventilation/nebulization via a T-piece; and being transported to the operating room. Prior to and after transport, we evaluated blood gas analysis results, vital signs, use of medications by means of a continuous infusion pump, parameters regarding the mechanical ventilator, duration of transport, transport distance and number of professionals involved. RESULTS We included 48 patients in a total of 58 intrahospital transports. Relevant cardiorespiratory alterations were identified in 39 transports, totaling 86 episodes, as well as 16 adverse events related to equipment or personnel failure, such as problems related to batteries and to miscommunication. CONCLUSIONS During the intrahospital transport of patients on invasive ventilation, cardiorespiratory alterations were common (67.2%), and adverse events occurred in 75.7% of the transports.
Envelope Exchange for the Generation of Live-Attenuated Arenavirus Vaccines

Arenaviruses such as Lassa fever virus cause significant mortality in endemic areas and represent potential bioterrorist weapons. The occurrence of arenaviral hemorrhagic fevers is largely confined to Third World countries with a limited medical infrastructure, and therefore live-attenuated vaccines have long been sought as a method of choice for prevention. Yet their rational design and engineering have been thwarted by technical limitations. In addition, viral genes had not been identified that are needed to cause disease but can be deleted or substituted to generate live-attenuated vaccine strains. Lymphocytic choriomeningitis virus, the prototype arenavirus, induces cell-mediated immunity against Lassa fever virus, but its safety for humans is unclear and untested. Using this virus model, we have developed the necessary methodology to efficiently modify arenavirus genomes and have exploited these techniques to identify an arenaviral Achilles' heel suitable for targeting in vaccine design. Reverse genetic exchange of the viral glycoprotein for foreign glycoproteins created attenuated vaccine strains that remained viable although unable to cause disease in infected mice. This phenotype remained stable even after extensive propagation in immunodeficient hosts. Nevertheless, the engineered viruses induced T cell–mediated immunity protecting against overwhelming systemic infection and severe liver disease upon wild-type virus challenge. Protection was established within 3 to 7 d after immunization and lasted for approximately 300 d. The identification of an arenaviral Achilles' heel demonstrates that the reverse genetic engineering of live-attenuated arenavirus vaccines is feasible. Moreover, our findings offer lymphocytic choriomeningitis virus or other arenaviruses expressing foreign glycoproteins as promising live-attenuated arenavirus vaccine candidates.
Testing of "Venetian-Blind" silicon microstructures with optical methods

In this paper, we illustrate the design and testing of new silicon microstructures, fabricated by means of a conventional planar process. These "Venetian-blind" structures consist of arrays of narrow, rectangular suspended masses (width =31 /spl mu/m, length =400 /spl mu/m, thickness =15 /spl mu/m), which can be tilted using electrostatic actuation. Characterization of their static and dynamic behavior was performed with optical methods. The diffraction patterns in monochromatic light were analyzed and vibration measurements were performed by means of semiconductor laser feedback interferometry: experimental data on the tilt angle as a function of the applied voltage and on the resonance frequencies are reported. A maximum tilt angle of approximately 1.9/spl deg/ was obtained with a driving voltage in the range of 70-95 V. All the tested devices showed resonance frequencies higher than 80 kHz, which is fast enough (i.e., switching time in the millisecond range) for future use in optical interconnections. Numerical analyses were performed to evaluate the coupled electromechanical behavior of the microstructures, confirming the observed experimental behavior.
NeuroAIDS: Contributions of the human immunodeficiency virus‐1 proteins tat and gp120 as well as CD40 to microglial activation

Microglia are the resident phagocytes of the brain and are an important source of proinflammatory mediators. Human immunodeficiency virus (HIV)‐1 infects the central nervous system early in the course of disease, and it is believed that this occurs, in part, through the transmigration of HIV‐1‐infected cells across the blood–brain barrier. Infected cells release viral proteins, such as Tat and gp120. After microglia interact with these proteins, they become activated and secrete chemokines; up‐regulate key surface receptors, such as CD40, and also activate resident cells. This review focuses on the consequences of microglial activation in NeuroAIDS, with an emphasis on chemokine production and CD40 up‐regulation after interaction with tat or gp120. The importance of microglial CD40 in two other neurological diseases, Alzheimer's disease and multiple sclerosis, is also discussed. © 2005 Wiley‐Liss, Inc.
Biological responses to electromagnetic fields 1

Electrification in developed countries has progressively increased the mean level of extremely low‐frequency electromagnetic fields (ELF‐EMFs) to which populations are exposed; these humanmade fields are substantially above the naturally occurring ambient electric and magnetic fields of ~10‐3 Vm‐1 and ~10‐13 T, respectively. Several epidemiological studies have concluded that ELF‐EMFs may be linked to an increased risk of cancer, particularly childhood leukemia. These observations have been reinforced by cellular studies reporting EMF‐induced effects on biological systems, most notably on the activity of components of the pathways that regulate cell proliferation. However, the limited number of attempts to directly replicate these experimental findings have been almost uniformly unsuccessful, and no EMF‐induced biological response has yet been replicated in independent laboratories. Many of the most well‐defined effects have come from gene expression studies; several attempts have been made recently to repeat these key findings. This review analyses these studies and summarizes other reports of major cellular responses to EMFs and the published attempts at replication. The opening sections discuss quantitative aspects of exposure to EMFs and the incidence of cancers that have been correlated with such fields. The concluding section considers the problems that confront research in this area and suggests feasible strategies. —Lacy‐hulbert, A. , Metcalfe, J. C. , Hesketh, R. Biological responses to electromagnetic fields. FASEB J. 12, 395–420 (1998)
Iridium interdigital transducers for ultra-high-temperature SAW devices

Iridium is investigated as a potential metal for interdigital transducers (IDTs) in surface acoustic wave (SAW) devices operating at high temperatures. SAW delay lines based on such IDTs and langasite (LGS) substrate are fabricated and electrically characterized. The results show reliable frequency responses up to 1000°C. The strong increase of insertion losses beyond this temperature, leading to the vanishing of the signal between 1140 and 1200°C, is attributed to surface transformation of LGS crystal, consisting in relevant gallium and oxygen losses, as evidenced by scanning electron microscopy, energy-dispersive X-ray spectroscopy and secondary ion mass spectroscopy.
Comparing the effects of an NLCD-derived dasymetric refinement on estimation accuracies for multiple areal interpolation methods

Comparability among population data enumerated within different time periods may be complicated by changing enumeration boundaries over time. Areal interpolation methods are commonly used to solve such zoning incompatibilities, but are frequently based on the questionable assumption of homogeneous population density within the different zones. To achieve more accurate estimates, land cover or other ancillary data may be used to better characterize the underlying source zone population density surface prior to areal interpolation. Although dasymetric techniques such as these are well documented, their effectiveness across different areal interpolation methods are not well established. This research compares the accuracy of a number of areal interpolation methods used to support temporal analysis of population data, and evaluates the effect of dasymetric mapping on interpolation accuracy. Our findings demonstrate that dasymetric refinement noticeably improves interpolation accuracy for the areal weighting, pycnophylactic, and target density weighting (TDW) methods of areal interpolation. A fourth method in which land cover densities are inherently incorporated, the expectation–maximization algorithm (EM), performs equally well. Our results show that the dasymetrically refined TDW method outperforms other areal interpolation methods in most instances, but suggest that the EM algorithm may be preferred as the interval between enumeration periods grows large.
A Robust Deep-Learning-Based Detector for Real-Time Tomato Plant Diseases and Pests Recognition

Plant Diseases and Pests are a major challenge in the agriculture sector. An accurate and a faster detection of diseases and pests in plants could help to develop an early treatment technique while substantially reducing economic losses. Recent developments in Deep Neural Networks have allowed researchers to drastically improve the accuracy of object detection and recognition systems. In this paper, we present a deep-learning-based approach to detect diseases and pests in tomato plants using images captured in-place by camera devices with various resolutions. Our goal is to find the more suitable deep-learning architecture for our task. Therefore, we consider three main families of detectors: Faster Region-based Convolutional Neural Network (Faster R-CNN), Region-based Fully Convolutional Network (R-FCN), and Single Shot Multibox Detector (SSD), which for the purpose of this work are called “deep learning meta-architectures”. We combine each of these meta-architectures with “deep feature extractors” such as VGG net and Residual Network (ResNet). We demonstrate the performance of deep meta-architectures and feature extractors, and additionally propose a method for local and global class annotation and data augmentation to increase the accuracy and reduce the number of false positives during training. We train and test our systems end-to-end on our large Tomato Diseases and Pests Dataset, which contains challenging images with diseases and pests, including several inter- and extra-class variations, such as infection status and location in the plant. Experimental results show that our proposed system can effectively recognize nine different types of diseases and pests, with the ability to deal with complex scenarios from a plant’s surrounding area.
Standardizing the gamma-ray bursts with the Amati Ep,i–Eiso relation: the updated Hubble diagram and implications for cosmography

The correlation between the peak photon energy of the internal spectrum Ep,i and isotropic equivalent radiated energy Eiso (the Amati relation) is explored in a scalar field model of dark energy. Using an updated data set of 109 high-redshift gamma-ray bursts (GRBs), we show that the correlation parameters only weakly depend on the cosmological model. Once the parameters of the Amati relation have been determined, we use this relation to construct a fiducial GRB Hubble diagram (HD) that extends up to redshifts ∼8. Moreover, we apply a local regression technique to estimate, in a model-independent way, the distance modulus from the recently updated Union Type Ia supernova (SNIa) sample, containing 557 SNIa spanning the redshift range of 0.015 ≤ z ≤ 1.55. The derived calibration parameters are used to construct an updated GRB HD, which we call the calibrated GRB HD. We also compare the fiducial and calibrated GRB HDs, which turned out to be fully statistically consistent, thus indicating that they are not affected by any systematic bias induced by the different calibration procedures. This means that the high-redshift GRBs can be used to test different models of dark energy settling the circularity problem. Furthermore, we investigate possible evolutionary effects that might have important influence on our results. Our analysis indicates that the presently available GRB data sets do not show statistically unambiguous evolutionary effect with the cosmological redshift. Finally, we propose another approach to calibrate the GRB relations, by using an approximate luminosity–distance relation, which holds in any cosmological model. We use this calibration of the Amati relation to construct an empirical approximate HD, which we compare with the calibrated GRB HD. We finally investigate the implications of this approach for the high-redshift cosmography.
Relationships Among Dispositional Mindfulness, Distress Tolerance, and Women’s Dating Violence Perpetration: A Path Analysis

Scant research examined mechanisms underlying the relationship between dispositional mindfulness and dating violence (DV) perpetration. Using a cross-sectional design with 203 college women, we examined whether distress tolerance mediated the relationship between dispositional mindfulness and DV perpetration (i.e., psychological aggression and physical assault). Path analyses results revealed indirect effects of mindfulness facets nonjudging of inner experiences and nonreactivity to inner experiences on both psychological aggression and physical assault through distress tolerance. Mindfulness facets observing, describing, and acting with awareness were not linked to DV perpetration through distress tolerance. Results suggest that women who allow internal experiences to come and go without assigning criticism or avoidance are better able to tolerate transient distress and less likely to abuse a dating partner. Future research may examine distress tolerance and dispositional mindfulness facets as potential intervention targets for women who abuse dating partners.
Work-Function Variation Effects of Tunneling Field-Effect Transistors (TFETs)

The work-function variation (WFV) effects of tunneling field-effect transistors (TFETs) are discussed for the first time. According to the 3-D device simulation results, TFETs are less immune to the WFV than metal-oxide-semiconductor FETs (MOSFETs) in terms of subthreshold swing (S) and threshold voltage (Vth). TFETs show ~ 1.4× larger Vth standard deviation (σVth) and ~ 4.6× larger S standard deviation (σS) than MOSFETs at high drain voltage (VD). It is because TFET characteristics are mainly determined by WF values of metal grains near to the source region where band-to-band tunneling occurs.
Loss Characterization and Calculation of Nanocrystalline Cores for High-Frequency Magnetics Applications

The loss density of the nanocrystalline magnetic material is experimentally characterized up to 500 kHz and above 1 Tesla in this paper. B-H hysteresis magnetization curves and loss density of the material under various operating temperatures up to 150degC are measured and presented. The core preparing effect on magnetic loss density is also identified by experiments, which provides information necessary to practical magnetic designs. A new empirical core loss calculation method, flux-wave-form-coefficient Steinmetz equation, is proposed and verified for the nanocrystalline material under resonant operations, which are often employed in high-frequency power converter applications. The proposed approach is either more accurate or easier to use than the previous methods.
Wombling Analysis of Childhood Tumor Rates in Florida

The Florida Association of Pediatric Tumor Program (FAPTP) is a statewide network charged with the responsibility to monitor and evaluate children’s cancer care in Florida. As part of this responsibility, the FAPTP collects data about the race, gender, age, ZIP code tabulation area of residence, and year of diagnosis for cancer cases across Florida. In accord with the goals of the FAPTP, this article seeks to identify spatial, temporal, and covariate regions of rapid change in the rate of cancer occurrence with the goal of understanding important spatial and demographic factors that determine the occurrence of childhood cancer. Herein, the FAPTP data are modeled as a marked point pattern (process) with an unknown intensity function. By estimating the intensity function from data, regions of high cancer occurrences and boundaries denoting rapid increases (or decreases) in the corresponding cancer rates can be identified. Results indicate that regions of high cancer risk vary with race. Furthermore, younger populations are found to have the highest risk.
Clay mineral assemblages as indicators of hydrothermalism in the basal part of the CRP-3 core (Victoria Land Basin, Antarctica)

Abstract The CRP-3 drilling project collected sediments from 3 to 939 mbsf (metres below sea floor) in the Victoria Land Basin in Antarctica.The upper sequence (down to ~790 m bsf) is of Cenozoic age and made up of detrital glaciogenic sediments; the characteristics of clay minerals in this part have been reported elsewhere.Here, the compositional features of clay minerals in the lower sequence such as conglomerates, Devonian sandstones and dolerites are described and genetic processes clarified.Clay minerals in the deepest part of the sequence derive from the alteration of different lithologies that mostly make up the sedimentary basin. Two clay mineral assemblages were characterized through analysis by X-ray diffraction (XRD), transmission electron microscopy (TEM) and scanning electron microscopy (SEM). From 790 to 823 mbsf, samples consist of authigenic smectite of variable chemical composition forming imbricated texture of plates or flakes.The smectites probably result from hydrothermal/diagenetic transformation of earlier minerals.The primary smectite cement underwent reorganization during shearing and cataclasis.The lowest part of the sequence (below 823 mbsf) is characterized by an assemblage of kaolinite, mixed-layer illite-smectite, Fe oxyhydroxide, sporadic smectite and poorly crystallized illite.It reflects a stronger alteration process than that recorded in the upper units of core CRP-3, related to hydrothermalism connected with the intrusion of an igneous body.Both assemblages show clear differences in particle morphology, texture and smectite composition to the clay assemblages found in the Cenozoic glaciomarine sediments in the upper sequence.The different phases of alteration appear related to the processes of rifting, exhumation and faulting that characterized this region since the Mesozoic.
Web-Based STAR E-Learning Course Increases Empathy and Understanding in Dementia Caregivers: Results from a Randomized Controlled Trial in the Netherlands and the United Kingdom

Background The doubling of the number of people with dementia in the coming decades coupled with the rapid decline in the working population in our graying society is expected to result in a large decrease in the number of professionals available to provide care to people with dementia. As a result, care will be supplied increasingly by untrained informal caregivers and volunteers. To promote effective care and avoid overburdening of untrained and trained caregivers, they must become properly skilled. To this end, the European Skills Training and Reskilling (STAR) project, which comprised experts from the domains of education, technology, and dementia care from 6 countries (the Netherlands, Sweden, Italy, Malta, Romania, and the United Kingdom), worked together to create and evaluate a multilingual e-learning tool. The STAR training portal provides dementia care training both for informal and formal caregivers. Objective The objective of the current study was to evaluate the user friendliness, usefulness, and impact of STAR with informal caregivers, volunteers, and professional caregivers. Methods For 2 to 4 months, the experimental group had access to the STAR training portal, a Web-based portal consisting of 8 modules, 2 of which had a basic level and 6 additional modules at intermediate and advanced levels. The experimental group also had access to online peer and expert communities for support and information exchange. The control group received free access to STAR after the research had ended. The STAR training portal was evaluated in a randomized controlled trial among informal caregivers and volunteers in addition to professional caregivers (N=142) in the Netherlands and the United Kingdom. Assessments were performed with self-assessed, online, standardized questionnaires at baseline and after 2 to 4 months. Primary outcome measures were user friendliness, usefulness, and impact of STAR on knowledge, attitudes, and approaches of caregivers regarding dementia. Secondary outcome measures were empathy, quality of life, burden, and caregivers’ sense of competence. Results STAR was rated positively by all user groups on both usefulness and user friendliness. Significant effects were found on a person-centered care approach and on the total score on positive attitudes to dementia; both the experimental and the control group increased in score. Regarding empathy, significant improvements were found in the STAR training group on distress, empathic concern, and taking the perspective of the person with dementia. In the experimental group, however, there was a significant reduction in self-reported sense of competence. Conclusions The STAR training portal is a useful and user-friendly e-learning method, which has demonstrated its ability to provide significant positive effects on caregiver attitudes and empathy.