Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Lack of resolution in a phylogenetic tree is usually represented as a polytomy, and often adding more data (loci and taxa) resolves the species tree. These are the ‘soft’ polytomies, but in other cases additional data fail to resolve relationships; these are the ‘hard’ polytomies. This latter case is often interpreted as a simultaneous radiation of lineages in the history of a clade. Although hard polytomies are difficult to address, model-based approaches provide new tools to test these hypotheses. Here, we used a clade of 144 species of the South American lizard clade Eulaemus to estimate phylogenies using a traditional concatenated matrix and three species tree methods: *BEAST, BEST, and minimizing deep coalescences (MDC). The different species tree methods recovered largely discordant results, but all resolved the same polytomy (e.g. very short internodes amongst lineages and low nodal support in Bayesian methods). We simulated data sets under eight explicit evolutionary models (including hard polytomies), tested these against empirical data (a total of 14 loci), and found support for two polytomies as the most plausible hypothesis for diversification of this clade. We discuss the performance of these methods and their limitations under the challenging scenario of hard polytomies. © 2015 The Linnean Society of London
Interpretation and Use of Statistics in Nursing Research

A working understanding of the major fundamentals of statistical analysis is required to incorporate the findings of empirical research into nursing practice. The primary focus of this article is to describe common statistical terms, present some common statistical tests, and explain the interpretation of results from inferential statistics in nursing research. An overview of major concepts in statistics, including the distinction between parametric and nonparametric statistics, different types of data, and the interpretation of statistical significance, is reviewed. Examples of some of the most common statistical techniques used in nursing research, such as the Student independent t test, analysis of variance, and regression, are also discussed. Nursing knowledge based on empirical research plays a fundamental role in the development of evidence-based nursing practice. The ability to interpret and use quantitative findings from nursing research is an essential skill for advanced practice nurses to ensure provision of the best care possible for our patients.
Clinical profile, management and outcomes of patients with pulmonary embolism: a retrospective tertiary centre study in Angola

Summary Objective: Pulmonary embolism (PE) is a potentially fatal disease. In Angola, few data are available on its occurrence. The aim of the study was to characterise the clinical profile, management and outcomes of patients with PE. Methods: A retrospective observational study was conducted at the Girassol Clinic in Luanda, Angola. The medical records of patients admitted to the intensive care unit were analysed from 2011 to 2015. Results: Fifty patients were included and the median age was 50.5 ± 17.8 years. Dyspnoea and immobilisation for more than 72 hours were the most frequently seen risk factors at admission; 28% of the patients had massive PE, 36% sub-massive PE, 28% were haemodynamically unstable at admission and 30% had a very high risk of mortality. The in-hospital mortality rate was 20%. Conclusions: The clinical characteristics of our patients were similar to those described in the literature. The high prevalence of patients with very high risk at admisson highlights the need to investigate the cause of worst cardiovascular disease outcomes in Africans.
Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering

Chromatin modifications, such as post-translational modification of histone proteins and incorporation of histone variants, play an important role in regulating gene expression. Joint analyses of multiple histone modification maps are starting to reveal combinatorial patterns of modifications that are associated with functional DNA elements, providing support to the ‘histone code’ hypothesis. However, due to the lack of analytical methods, only a small number of chromatin modification patterns have been discovered so far. Here, we introduce a scalable subspace clustering algorithm, coherent and shifted bicluster identification (CoSBI), to exhaustively identify the set of combinatorial modification patterns across a given epigenome. Performance comparisons demonstrate that CoSBI can generate biclusters with higher intra-cluster coherency and biological relevance. We apply our algorithm to a compendium of 39 genome-wide chromatin modification maps in human CD4+ T cells. We identify 843 combinatorial patterns that recur at >0.1% of the genome. A total of 19 chromatin modifications are observed in the combinatorial patterns, 10 of which occur in more than half of the patterns. We also identify combinatorial modification signatures for eight classes of functional DNA elements. Application of CoSBI to epigenome maps of different cells and developmental stages will aid in understanding how chromatin structure helps regulate gene expression.
Functional analysis of the venom of mealybug parasitoid Aenasius bambawalei (Hymenoptera: Encyrtidae)

Aenasius bambawalei (Hymenoptera: Encyrtidae) is a koinobiont nymphal endoparasitoid of cotton mealybug, Phenacoccus solenopsis (Hemiptera: Pseudocccidae). Functional analysis of the venom of the wasp was performed by artificial microinjections of both crude and treated venom (heat and proteinase) of the wasp containing 0.3 and 0.5 μl in non-parasitized and synchronized adult hosts (mealybugs) and the mortality data were recorded 24, 48, 72 and 96 hours post injecton while mealybugs receiving saline injections were acted as control. The main effects for artificially envenomated mealybugs were observed on their mortality and survival. The biological activity of crude venom was also evaluated by heat and protease treatment. Here, we demonstrate that maximum mortality (82 ± 2.0%) was achieved by microinjections containing higher volume (0.5 μl) of crude venom while lower mortality (68 ± 4.0%) was achieved with lower volume of venom (0.3 μl). On the other hand, heat and proteinase K treated venom did not show any significant effect on mortality of the host insect. Our findings suggest that bioactive components of the crude venom are proteins which lost their activity upon heat and protease treatment. This basic information regarding the functional role of the venom of A. bambawalei serves as a starting point for comprehensive analysis of the role of the venom of the parasitoid on the regulation processes in its host.
Regulation of staphylococcal enterotoxin B-elicited nitric oxide production by endothelial cells

The effect of staphylococcal enterotoxin B (SEB)-elicited inducible nitric oxide synthase (iNOS) in mouse endothelial cells was investigated. Results showed that SEB stimulated the same level of NO production in gamma interferon (IFN-gamma)-primed cells as did trichloroacetic acid-extracted lipopolysaccharide. The kinetics of induced NO production and expression of mRNA for iNOS differed markedly in endothelial and macrophage cells. Induced endothelial nitrite production was transient and was 15 to 20% of that generated by macrophage cells; mRNA levels peaked by 2 h and then steadily declined, whereas macrophage message levels continually increased. The ability of endothelial cells to produce SEB-induced NO depended on priming with IFN-gamma, although detectable mRNA could be elicited by SEB alone. Induction of endothelial iNOS mRNA was inhibited by cycloheximide, which indicated a requirement for de novo protein synthesis. Niacinamide and interleukin-10 significantly reduced SEB-induced endothelial NO production. Both are reported to affect IFN-gamma-induced class II major histocompatibility complex (MHC) expression on antigen-presenting cells. Niacinamide reduced iNOS mRNA levels and markedly reduced IFN-gamma induction of endothelial class II MHC surface antigen. Interleukin-10 did not consistently reduce iNOS mRNA expression and had no effect on IFN-gamma induction of endothelial class II MHC surface antigen. These results suggest that SEB interacts with IFN-gamma-primed endothelial cells to elicit induced NO and that this induction can be effectively modulated at the receptor or transcriptional level.
The Impact of the Latest Danian Event on Planktic Foraminiferal Faunas at ODP Site 1210 (Shatsky Rise, Pacific Ocean)

The marine ecosystem has been severely disturbed by several transient paleoenvironmental events (<200 kyr duration) during the early Paleogene, of which the Paleocene-Eocene Thermal Maximum (PETM, ~56 Ma) was the most prominent. Over the last decade a number of similar events of Paleocene and Eocene age have been discovered. However, relatively little attention has been paid to pre-PETM events, such as the “Latest Danian Event” ("LDE", ~62.18 Ma), specifically from an open ocean perspective. Here we present new foraminiferal isotope (δ13C, δ18O) and faunal data from Ocean Drilling Program (ODP) Site 1210 at Shatsky Rise (Pacific Ocean) in order to reconstruct the prevailing paleoceanographic conditions. The studied five-meter-thick succession covers ~900 kyr and includes the 200-kyr-lasting LDE. All groups surface dwelling, subsurface dwelling and benthic foraminifera show a negative δ13C excursion of >0.6‰, similar in magnitude to the one previously reported from neighboring Site 1209 for benthic foraminifera. δ18O-inferred warming by 1.6 to 2.8°C (0.4–0.7‰ δ18O measured on benthic and planktic foraminiferal tests) of the entire water column accompanies the negative δ13C excursion. A well stratified upper ocean directly before and during the LDE is proposed based on the stable isotope gradients between surface and subsurface dwellers. The gradient is less well developed, but still enhanced after the event. Isotope data are supplemented by comprehensive planktic foraminiferal faunal analyses revealing a dominance of Morozovella species together with Parasubbotina species. Subsurface-dwelling Parasubbotina shows high abundances during the LDE tracing changes in the strength of the isotope gradients and, thus, may indicate optimal living conditions within a well stratified surface ocean for this taxon. In addition, distinct faunal changes are reported like the disappearance of Praemurica species right at the base of the LDE and the continuous replacement of M. praeangulata with M. angulata across the LDE.
Real-time high-quality View-Dependent Texture Mapping using per-pixel visibility

We present an extension of View-Dependent Texture Mapping (VDTM) allowing rendering of complex geometric meshes at high frame rates without usual blurring or skinning artifacts. We combine a hybrid geometric and image-based representation of a given 3D object to speed-up rendering at the cost of a little loss of visual accuracy.During a precomputation step, we store an image-based version of the original mesh by simply and quickly computing textures from viewpoints positionned around it by the user. During the rendering step, we use these textures in order to map on the fly colors and geometric details onto the surface of a low-polygon-count version of the mesh.Real-time rendering is achieved while combining up to three viewpoints at a time, using pixel shaders. No parameterization of the mesh is needed and occlusion effects are taken into account while computing on the fly the best viewpoints for a given pixel. Moreover, the integration of this method in common real-time rendering systems is straightforward and allows applying self-shadowing as well as other z-buffer effects.
Myosin-X Induces Filopodia by Multiple Elongation Mechanism*

Filopodia are actin-rich finger-like cytoplasmic projections extending from the leading edge of cells. Unconventional myosin-X is involved in the protrusion of filopodia. However, the underlying mechanism of myosin-X-induced filopodia formation is obscure. Here, we studied the movements of myosin-X during filopodia protrusion using a total internal reflection microscope to clarify the mechanism of myosin-X-induced filopodia formation. Myosin-X was recruited to the discrete site at the leading edge where it assembles with exponential kinetics before the filopodia extension. The myosin-X-induced filopodia showed repeated extension-retraction cycles with each extension of 2.4 μm, which was critical to produce long filopodia. Myosin-X, lacking the FERM domain, could move to the tip as does the wild type. However, it was transported toward the cell body during filopodia retraction, did not undergo multiple extension-retraction cycles, and failed to produce long filopodia. During the filopodia protrusion, the single molecules of full-length myosin-X moved within filopodia. The majority of the fluorescence spots showed two-step photobleaching, suggesting that the moving myosin-X is a dimer. Deletion of the FERM domain did not change the movement at the single molecule level with the same velocity of ∼600 nm/s as wild-type, suggesting that the myosin-X in filopodia moves without interaction with the attached membrane via the FERM domain. Based upon these results, we have proposed a model of myosin-X-induced filopodia protrusion.
Windsurf: a Region-Based Image Retrieval System

Content-based image retrieval systems characterize images by means of relevant features, such as color distribution and texture information, and then use such feature values to determine those images which are most similar to a query image. However, this approach is not adequate when images have a complex, not homogeneous, structure, in which case using global features leads to inaccurate content descriptions. In this paper we present Windsurf, an image retrieval system that implements a new approach to content-based image search. Windsurf applies the wavelet transform to extract color and texture features from an image, and then partitions the image into a set of “homogeneous” regions, each described by a set of local features. Similarity between images is then assessed by first computing similarity scores between regions and then combining the results at the image level. Remarkably, Windsurf image similarity model only requires that the overall similarity score between two images is a monotonic function of the similarity scores of matching regions. From the query processing point of view, we introduce a novel index-based algorithm that can make use of any distance-based access method to retrieve the k best-matching images for a given query. It turns out that this is the first correct algorithm for region-based image similarity queries. Experimental results on a medium-size image data-set demonstrate the effectiveness and the efficiency of our approach.
The evaluation of nitric oxide scavenging activity of certain herbal formulations in vitro: a preliminary study

The nitric oxide (NO) scavenging activities of traditional polyherbal drugs like abana, chyavanaprasha, geriforte, septilin, mentat and triphala were examined using sodium nitroprusside as a NO donor in vitro. All the drugs tested demonstrated direct scavenging of NO and were superior to Gingko biloba, which was used as a positive control. The extracts of various polyherbal drugs exhibited dose‐dependent NO scavenging activities and the potency was in the following order: abana > chyavanaprasha > triphala > geriforte > septilin > mentat > Gingko biloba. The present results suggest that the traditional Indian polyherbal crude drugs may be potent and novel therapeutic agents for scavenging of NO, and thereby inhibit the pathological conditions caused by excessive generation of NO and its oxidation product, peroxynitrite. These ﬁndings may also help to explain, at least in part, the pharmacological activities like rejuvenating, adaptogenic, anti‐infection, anti‐inﬂammatory, cardioprotective and neuroprotective activities of these traditional, clinically used non toxic drugs. Copyright © 2004 John Wiley & Sons, Ltd.
Cito: An Actuated Smartwatch for Extended Interactions

We propose and explore actuating a smartwatch face to enable extended interactions. Five face movements are defined: rotation, hinging, translation, rising, and orbiting. These movements are incorporated into interaction techniques to address limitations of a fixed watch face. A 20-person study uses concept videos of a passive low fidelity prototype to confirm the usefulness of the actuated interaction techniques. A second 20-person study uses 3D rendered animations to access social acceptability and perceived comfort for different actuation dynamics and usage contexts. Finally, we present Cito, a high-fidelity proof-of-concept hardware prototype that investigates technical challenges.
Regulation of Socs Gene Expression by the Proto-oncoprotein GFI-1B

SOCS proteins take part in a classical negative feedback loop to attenuate cytokine signaling. Although STAT family members positively modulate Socs gene expression, little else is known about Socs gene regulation. Here, we identify functional binding sites for GFI-1B, a proto-oncogenic transcriptional repressor, in the promoters of murine Socs1and Socs3. Thus, mutating these sites relieved transcriptional repression, as determined by luciferase reporter assays of transiently transfected erythropoietin-responsive 32D-EpoR and HCD57 cells. Furthermore, cotransfection of Gfi-1Bexpression plasmid repressed reporter activity of wild-type (but not mutagenized) Socs1 and Socs3 promoters, strongly suggestive of direct GFI-1B binding to these promoters. In addition, overexpression of Gfi-1B resulted in reduced transcript levels of Socs1 and Socs3, but notSocs2 or Cis. Upon stimulation with erythropoietin, Socs transcripts were rapidly induced, whereas Gfi-1B mRNA was down-regulated. Interestingly, the latter effect appears to rely on STAT5 activity, but not on phosphoinositide 3-kinase or MAPK pathways. Thus, cytokine-mediated STAT5 activation allows relief of direct repression by GFI-1B of theSocs1 and Socs3 promoters, but apparently not of the Socs2 and Cis promoters. This constitutes a previously undescribed mode of controlling cytokine responsiveness, through the direct repression of a tumor suppressor (SOCS1) by a proto-oncoprotein (GFI-1B).
Stably integrated mouse mammary tumor virus long terminal repeat DNA requires the octamer motifs for basal promoter activity

In the mouse mammary tumor virus promoter, a tandem of octamer motifs, recognized by ubiquitous and tissue-restricted Oct transcription factors, is located upstream of the TATA box and next to a binding site for the transcription factor nuclear factor I (NF-I). Their function was investigated with mutant long terminal repeats under different transfection conditions in mouse Ltk- cells and quantitative S1 nuclease mapping of the transcripts. In stable transfectants, which are most representative of the state of proviral DNA with respect to both number of integrated DNA templates and chromatin organization, a long terminal repeat mutant of both octamer sites showed an average 50-fold reduction of the basal transcription level, while the dexamethasone-stimulated level was unaffected. DNase I in vitro footprinting assays with L-cell nuclear protein extracts showed that the mutant DNA was unable to bind octamer factors but had a normal footprint in the NF-I site. I conclude that mouse mammary tumor virus employs the tandem octamer motifs of the viral promoter, recognized by the ubiquitous transcription factor Oct-1, for its basal transcriptional activity and the NF-I binding site, as previously shown, for glucocorticoid-stimulated transcription. A deletion mutant with only one octamer site showed a marked base-level reduction at high copy number but little reduction at low copies of integrated plasmids. The observed transcription levels may depend both on the relative ratio of transcription factors to DNA templates and on the relative affinity of binding sites, as determined by oligonucleotide competition footprinting.
Improvement of PHBV Scaffolds with Bioglass for Cartilage Tissue Engineering

Polymer scaffold systems consisting of poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) have proven to be possible matrices for the three-dimensional growth of chondrocyte cultures. However, the engineered cartilage grown on these PHBV scaffolds is currently unsatisfactory for clinical applications due to PHBV’s poor hydrophilicity, resulting in inadequate thickness and poor biomechanical properties of the engineered cartilage. It has been reported that the incorporation of Bioglass (BG) into PHBV can improve the hydrophilicity of the composites. In this study, we compared the effects of PHBV scaffolds and PHBV/BG composite scaffolds on the properties of engineered cartilage in vivo. Rabbit articular chondrocytes were seeded into PHBV scaffolds and PHBV/BG scaffolds. Short-term in vitro culture followed by long-term in vivo transplantation was performed to evaluate the difference in cartilage regeneration between the cartilage layers grown on PHBV and PHBV/BG scaffolds. The results show that the incorporation of BG into PHBV efficiently improved both the hydrophilicity of the composites and the percentage of adhered cells and promoted cell migration into the inner part the constructs. With prolonged incubation time in vivo, the chondrocyte-scaffold constructs in the PHBV/BG group formed thicker cartilage-like tissue with better biomechanical properties and a higher cartilage matrix content than the constructs in the PHBV/BG group. These results indicate that PHBV/BG scaffolds can be used to prepare better engineered cartilage than pure PHBV.
Differential esterase activity in leaves and roots of Centaurea ragusina L. as a consequence of salinity

Background and Purpose: Centaurea ragusina L. is an endemic Croatian plant species adapted to life in arid and salt-affected environments. Esterase activity (EST) and isoesterase patterns of C. ragusina plants cultured in vitro under saline and osmotic conditions were determined with an aim to evaluate the potential value of esterase activity as a biomarker of salt/osmotic stress as well as physiological significance of EST variations. Material and Methods: Rooted plantlets grown on MS 1⁄2 nutrient media supplemented with 150, 300, 450 or 600 mM NaCl or 300 mM mannitol were investigated after 5, 10 and 15 days. Esterase activity was determined using either 1or 2-naphthylacetate as substrates. Results and Conclusion: Esterase activities in shoots increased under low saline and mannitol treatments and decreased in response to increased saline treatments. The highest salt and concentration and mannitol stimulated EST activity in roots. In total, twelve and fourteen esterase isoenzymes were resolved in C. ragusina leaves and roots, respectively. Both salt and mannitol induced new esterase isoenzyme (EST11) while mannitol specifically induced two more (EST4-5); otherwise some bands were weakly expressed or even disappeared as a result of salinity in C. ragusina leaves. Two new isosterases (EST10-11) were resolved in mannitoland salt-treated roots and four (EST2, EST12-14) only in salt-treated roots. Presented results demonstrate that esterase activities and their isoenzymic patterns could serve as useful bioindicators of salinity.