Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)1

Premise of the study: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. Methods and Results: A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes. Conclusions: This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.
Toll‐like receptor 4 participates in the myelin disruptions associated with chronic alcohol abuse

Alcohol abuse and alcoholism can cause brain damage, loss of white matter, myelin fiber disruption, and even neuronal injury. The underlying mechanisms of these alterations remain elusive. We have shown that chronic ethanol intake, by activating glial toll‐like receptor 4 (TLR4) receptors, triggers the production of inflammatory mediators and can cause brain damage. Because neuroinflammation may be associated with demyelination and neuronal damage, we evaluate whether the ethanol‐induced TLR4‐dependent proinflammatory environment in the brain could be involved in the myelin disruptions observed in alcoholics. Using brains from wild‐type (WT) and TLR4 knockout (KO, TLR4−/−) mice, we demonstrate that chronic ethanol treatment downregulated proteins involved in myelination [proteolipid protein (PLP), myelin basic protein (MBP), myelin‐oligodendrocyte glycoprotein, 2,3‐cyclic‐nucleotide‐3‐phosphodiesterase, and myelin‐associated glycoprotein], while increased chondroitin sulfate proteoglycan NG2 (NG2)‐proteoglycan in several brain regions of ethanol‐treated WT mice. The immunohistochemistry analysis also revealed that ethanol‐treatment‐altered myelin morphology reduced the number of MBP‐positive fibers and caused oligodendrocyte death, as demonstrated by an increase in caspase‐3‐positive oligodendrocytes. The in vivo imaging system further confirmed that chronic ethanol intake markedly reduced the PLP in WT mice. Most myelin alterations were not observed in brains from ethanol‐treated TLR4−/− mice. Electron microscopy studies revealed that although 41–47% of axons showed myelin sheath disarrangements in the cerebral cortex and corpus callosum of WT ethanol‐treated mice, respectively, small focal fiber disruptions were noticed in these brain areas of ethanol‐treated TLR4−/− mice. In summary, the present results suggest that ethanol‐induced neuroinflammation might be involved in myelin disruptions and white matter loss observed in human alcoholics. © 2012 Wiley Periodicals, Inc.
Determining Future Travel Behavior from Past Travel Experience and Perceptions of Risk and Safety

This study examined the influences of past international travel experience, types of risk associated with international travel, and the overall degree of safety felt during interna tional travel on individuals' likelihood of travel to various geographic regions on their next international vacation trip or avoidance of those regions due to perceived risk. Informa tion integration theory and protection motivation theory served as the theoretical framework for the study. A mail sur vey sent to 500 international travelers achieved a 48% re sponse rate. Nonresponse bias was tested with telephone in terviews. Data were analyzed using cross tabulations and logistic regression. Results revealed that past travel experi ence to specific regions both increases the intention to travel there again and decreases the intention to avoid areas, par ticularly risky areas. Perceived risks and safety were both found to be stronger predictors of avoiding regions than of planning to visit them.
A NEW FUZZY C-MEANS BASED SEGMENTATION STRATEGY. APPLICATIONS TO LIP REGION IDENTIFICATION

The problem of lip contour detection is critical in the lipreading systems based on contour processing. The typical contour detection strategy based on image segmentation in homogeneous regions fails in the case when the mouth images available for lipreading are lowcontrast gray level images. Most of the solutions adopted require manual marking of some contour points. Here we propose a new solution from the image segmentation class suitable to lip contour extraction, using a modified version of the fuzzy c-means image segmentation algorithm. The novelty of the solution proposed consists in the types of features used for segmentation, which include not only luminance information (as in the standard use of fuzzy cmeans), but also spatial information about the pixels in the image. After a simple filtering of the outliers, the contours of the resulting segmented objects are extracted. The experimental results obtained are superior to the ones obtained by standard or other versions of geometrically constrained fuzzy c-means, or by gradient-based edge detection strategies, without the need of manual marking of any contour points. Thus we consider the strategy proposed promising for automatic lip contour extraction applications.
Radial variation of optical and near-infrared colours in luminous early-type galaxies in A2199

We performed K-band surface photometry for luminous early-type galaxies in a nearby rich cluster A2199. Combining it with B- and R-band surface photometry, radial variations of B-R and R-K colours in the galaxies were investigated. It is found that the inner regions of the galaxies are redder in both B-R and R-K colours. Comparing the radial variations of both colours with predictions of simple stellar population models for a range of ages and metallicities, it is suggested that the cluster ellipticals have negative metallicity gradients, but their age gradients are consistent with zero, although our sample is small; the typical metallicity gradient is estimated to be -0.16 ± 0.09 in d log Z/d log r, while the age gradient is estimated to be -0.10 ± 0.14 in d log (age)/d log r. Considering that similar results have also been derived in the other recent studies using samples of ellipticals in the Coma cluster and less dense environments, it seems that there is no strong dependence on galaxy environment in the radial gradient of stellar population in an elliptical galaxy.
AMIGO: accurate mobile image geotagging

With location-based services gaining popularity among mobile users, researchers are exploring the way using the phone-captured image for localization as it contains more context information than the embedded sensory GPS coordinates. We present in this paper a novel mobile image geotagging approach to accurately sense the actual geo-context of a mobile user. The proposed approach, named AMIGO (Accurate Mobile Image GeOtagging), is able to provide a comprehensive set of accurate geo-context based on the current image and its associated scene in the database. The geo-context includes the real locations of a mobile user and the scene, the viewing angle, and the distance between the user and the scene. Specifically, we first perform partial duplicate image retrieval to select crowdsourced images capturing the same scene as the query image. We then employ the structure-from-motion technique to reconstruct a sparse 3D point cloud of the scene. Finally, by projecting the reconstructed scene onto the horizontal plane, we can derive user's location, viewing angle, and distance. The effectiveness of AMIGO has been validated by experimental results.
Implementing a Distributed WSN Based on IPv6 for Ambient Monitoring

Traditionally, Wireless Sensor Networks (WSNs) are used for monitoring an extensive area. In these networks, a centralized server is usually used to collect and store the sensor information. However, new distributed protocols allow connections directly to the WSN nodes without the need of a centralized server. Moreover, these systems are able to establish communications among heterogeneous networks. The new protocols strategy is focused on considering several WSNs as a unique distributed one. This way, a user of the system is able to analyze a process under study as a whole instead of considering it as a set of different subsystems. This is the case in the evaluation of migratory waterbirds' environment. In this case, it is usual to deploy several WSNs in different breeding areas. They are all interconnected and they measure different environmental parameters. However, this improvement in the data access flexibility may result in a loss of network performance and an increase in network power consumption. Focused on this problem, this paper evaluates different communication protocols: distributed and centralized, in order to determine the best trade-off for environmental monitoring in different migratory areas of waterbirds.
Suppression of HIV-1 Infection by APOBEC3 Proteins in Primary Human CD4+ T Cells Is Associated with Inhibition of Processive Reverse Transcription as Well as Excessive Cytidine Deamination

ABSTRACT The Vif protein of human immunodeficiency virus type 1 (HIV-1) promotes viral replication by downregulation of the cell-encoded, antiviral APOBEC3 proteins. These proteins exert their suppressive effects through the inhibition of viral reverse transcription as well as the induction of cytidine deamination within nascent viral cDNA. Importantly, these two effects have not been characterized in detail in human CD4+ T cells, leading to controversies over their possible contributions to viral inhibition in the natural cell targets of HIV-1 replication. Here we use wild-type and Vif-deficient viruses derived from the CD4+ T cells of multiple donors to examine the consequences of APOBEC3 protein function at natural levels of expression. We demonstrate that APOBEC3 proteins impart a profound deficiency to reverse transcription from the initial stages of cDNA synthesis, as well as excessive cytidine deamination (hypermutation) of the DNAs that are synthesized. Experiments using viruses from transfected cells and a novel method for mapping the 3′ termini of cDNAs indicate that the inhibition of reverse transcription is not limited to a few specific sites, arguing that APOBEC3 proteins impede enzymatic processivity. Detailed analyses of mutation spectra in viral cDNA strongly imply that one particular APOBEC3 protein, APOBEC3G, provides the bulk of the antiviral phenotype in CD4+ T cells, with the effects of APOBEC3F and APOBEC3D being less significant. Taken together, we conclude that the dual mechanisms of action of APOBEC3 proteins combine to deliver more effective restriction of HIV-1 than either function would by itself.
3D micro-CT images of ossicles destroyed by middle ear cholesteatoma

Objective To reconstruct the 3D structures of normal ossicles and ossicles destroyed by different cholesteatomas, and to compare the volume fractions of the two types of ossicles. Material and Methods Thirteen pathological ossicles from four kinds of middle ear cholesteatoma obtained during surgery were used. Normal ossicles harvested from cadaveric temporal bone specimens were used as controls. The structures of the ossicles were analyzed using micro-CT by filming 2D cross-sectional images perpendicular to the long axis, from which 3D images were reconstructed. The volume fraction was measured using a CT-Analyzer™ and Ant™. Results The volume fraction, indicating the relative strength of normal ossicles, was lower in the portion close to the articular surface. As the four types of cholesteatoma were found to express their patterns of destruction at various sites in the ossicles, they revealed a different volume fraction in each ossicle. Conclusion Our preliminary data on ossicular structure obtained using micro-CT will be helpful for elucidating the normal and pathological structure of ossicles and for the further development of artificial prostheses.
A promising tool that can predict suicide: the hospital anxiety and depression scale -

Objective: The aim of this study was to compare the anxiety and depressive symptoms between the suicide attempters and non-suicide attempters and to determine the differences in the Hospital Anxiety and Depression Scale (HADS) items inpatient between the two groups. Method: The study participants were age-matched 50 suicide attempters who were admitted to Şisli Etfal Research and Training Hospital, and 50 inpatients who were hospitalized due to their general medical complaints. The sociodemographic form, the HADS and the Mini-International Neuropsychiatric Interview (MINI) were administered. Results: The suicide attempters had significantly higher rate of previous psychiatric history p=0.017, psychiatric hospitalization p=0.041, family history p=0.023, and alcohol/substance use p=0.004. The suicide attempters scored significantly higher on tension, anhedonia, fear, loss of humor, restlessness, and lack of enjoyment. Conclusions: Clinicians should take into account the presence of previous psychiatric history, family history, substance/alcohol use, presence of anhedonia, lack of enjoyment, loss of humor, fear, tension and restlessness. The HADS could be a powerful tool to assess the suicide risk other than psychiatric evaluation.
A novel biophysically-detailed mathematical model of rabbit Purkinje cell electrophysiology

Purkinje fibres play an important role in cardiac conduction and have been implicated in arrhythmia in presence of diseased states, genetic mutations, or adverse side effects of drugs. For these reasons, the Purkinje assay is commonly used in pre-clinical in vitro drug assessment of arrhythmic risk. Several investigators have pointed out that rabbit Purkinje cells, compared to other species, have a better sensitivity in detecting arrhythmic risk.
Lilsys: Sensing Unavailability

As communications systems increasingly gather and propagate information about people's reachability or ``presence'', users need better tools to minimize undesired interruptions while allowing desired ones. We review the salient elements of presence and availability that people use when initiating face-to-face communication. We discuss problems with current strategies for managing one's availability in telecommunication media. We describe a prototype system called Lilsys which passively collects availability cues gathered from users' actions and environment using ambient sensors and provides machine inferencing of unavailability. We discuss observations and design implications from deploying Lilsys.
Grandparents and Grandchildren in Kwahu, Ghana: the Performance of Respect

Abstract This description of relations between grandparents and grandchildren in a rural Ghanaian community argues that the quality of these relations varies according to age and gender. Literature on African kinship has almost entirely focused on very young grandchildren. This article draws attention to changes that occur when those children grow into adolescents and adults. Grandchildren—both young and old—speak respectfully about their grandparents, but older people regret that their grandchildren do not come to them for advice once they have grown up. Older men seem more ‘neglected’ by their grandchildren than older women. The second argument is about performance: respect, affection and relatedness between grandparents and grandchildren are demonstrated in public even when their ‘contents’ have dwindled. The article is based on anthropological fieldwork over a period of almost ten years. Résumé Cette description des relations entre grands-parents et petits-enfants dans une communauté rurale ghanéenne montre que la qualité de ces relations varie selon l'âge et le sexe. La littérature consacrée à la parenté africaine s'est presque exclusivement intéressée aux petits-enfants en bas âge. Cet article attire l'attention sur les changements qui surviennent lorsque ces enfants deviennent adolescents et adultes. Les petits-enfants, jeunes et vieux, parlent respectueusement de leurs grands-parents, mais les personnes âgées regrettent que leurs petits-enfants, une fois adultes, ne viennent plus leur demander conseil. Les hommes âgés semblent plus «négligés» par leurs petits-enfants que les femmes âgées. Le second argument concerne la conduite : respect, affection et parenté entre grands-parents et petits-enfants se manifestent en public même lorsque leur «contenu» s'est réduit. L'article repose sur des études anthropologiques de terrain qui se sont déroulées sur une période de près de dix ans.
Empirical-bias bandwidths for local polynomialnonparametric regression and density estimationDavid

A data-based local bandwidth selector is proposed for nonparametric regression by local tting of polynomials. The estimator, called the empirical-bias bandwidth selector (EBBS), is rather simple and easily allows multivariate predictor variables and estimation of any order derivative of the regression function. EBBS minimizes an estimate of mean square error consisting of a squared bias term plus a variance term. The variance term used is exact, not asymptotic, though it involves the conditonal variance of the response given the predictors that must be estimated. The bias term is estimated empirically, not from an asymptotic expression. Thus, EBBS is similar to the \double smoothing" approach of HH ardle, Hall, and Marron, but is developed here for a far wider class of estimation problems than what those authors consider. EBBS is tested on simulated data and its performance seems quite satisfactory. Local polynomial smoothing of a histogram is a highly eeective technique for density estimation, and several of the examples involve density estimation by EBBS applied to binned data.
Neutrality, Cross-Immunity and Subtype Dominance in Avian Influenza Viruses

Avian influenza viruses (AIVs) are considered a threat for their potential to seed human influenza pandemics. Despite their acknowledged importance, there are significant unknowns regarding AIV transmission dynamics in their natural hosts, wild birds. Of particular interest is the difference in subtype dynamics between human and bird populations–in human populations, typically only two or three subtypes cocirculate, while avian populations are capable of simultaneously hosting a multitude of subtypes. One species in particular–ruddy turnstones (Arenaria interpres)–has been found to harbour a very wide range of AIV subtypes, which could make them a key player in the spread of new subtypes in wild bird populations. Very little is known about the mechanisms that drive subtype dynamics in this species, and here we address this gap in our knowledge. Taking advantage of two independent sources of data collected from ruddy turnstones in Delaware Bay, USA, we examine patterns of subtype diversity and dominance at this site. We compare these patterns to those produced by a stochastic, multi-strain transmission model to investigate possible mechanisms that are parsimonious with the observed subtype dynamics. We find, in agreement with earlier experimental work, that subtype differences are unnecessary to replicate the observed dynamics, and that neutrality alone is sufficient. We also evaluate the role of subtype cross-immunity and find that it is not necessary to generate patterns consistent with observations. This work offers new insights into the mechanisms behind subtype diversity and dominance in a species that has the potential to be a key player in AIV dynamics in wild bird populations.
Covariance-based linear precoding

This paper extends the self-contained theory of linear precoding to the field of covariance based spatio-temporal downlink processing for direct-sequence code-division multiple-access (CDMA) systems and shows the applicability to the release 6 of high-speed downlink packet access (HSDPA). To this end, a unifying theory is developed to formulate the three known linear filters, namely, the transmit matched filter, the transmit zero-forcing filter, and the transmit Wiener filter, as optimization problems even in systems, where only covariance knowledge is available at the transmitter. Second, the solutions of these transmit filters are given for such systems with partial channel state information (CSI). Finally, it is shown how covariance-based linear precoding can be employed in the new generation CDMA system HSDPA, i.e., how channel estimation on the secondary common pilot channel allows for optimum full rank linear precoding employing only partial CSI.
How Design-inclusive UXR Influenced the Integration of Project Activities: Three Design Cases from Industry

In this paper, we discuss how the implementation of design-inclusive User Experience Research (UXR) has influenced the composition of UXR and design activities in the industrial setting of Philips Design. We present three design case studies that were executed in a time span of three years: a baby sleep project; a pregnancy project; and a baby bottle-feeding project. Through a retrospective analysis we conclude that the approach adopted in these cases progressed from complete separation of UXR and design activities to design-inclusive UXR in which design forms an integral part of research. This is reflected by a rearrangement of project activities to identify, envision, enable and evaluate user experiences. Previously the UXR (identify and evaluate) and design (envision and enable) activities were executed sequentially. Now, these four project activities merge in studying design interventions in context over a prolonged time, to iteratively explore and advance UX design qualities.
A 15-step model for writing a research proposal

On occasion midwives may be required to construct a research proposal. In the current climate of evidence-based practice. Such activity is considered an elemental skill for career progression in both education and service. Examples of where writing a research proposal may be required include: writing an assessment for under and post graduate research modules or designing a dissertation, MPhil, Prof Doc or PhD. Within clinical practice there are also audit and evaluation of practice responsibilities. With these factors at the forefront, this article provides a template specifically designed to direct midwives through the procedures of constructing a research proposal. The purpose of a research proposal is to produce a template of common understanding from which tasks are allocated, divided and discussed by researchers, clinical staff and in some cases participants. The finished product is then used to communicate intent to the ethics committees and grant funding bodies before authorization and money are awarded.