Miracle-dz/UniFAR-FTUs huggingface dataset:
A COMPARISON OF PHENOTYPIC VARIATION AND COVARIATION PATTERNS AND THE ROLE OF PHYLOGENY, ECOLOGY, AND ONTOGENY DURING CRANIAL EVOLUTION OF NEW WORLD MONKEYS

Abstract Similarity of genetic and phenotypic variation patterns among populations is important for making quantitative inferences about past evolutionary forces acting to differentiate populations and for evaluating the evolution of relationships among traits in response to new functional and developmental relationships. Here, phenotypic covariance and correlation structure is compared among Platyrrhine Neotropical primates. Comparisons range from among species within a genus to the superfamily level. Matrix correlation followed by Mantel's test and vector correlation among responses to random natural selection vectors (random skewers) were used to compare correlation and variance/covariance matrices of 39 skull traits. Sampling errors involved in matrix estimates were taken into account in comparisons using matrix repeatability to set upper limits for each pairwise comparison. Results indicate that covariance structure is not strictly constant but that the amount of variance pattern divergence observed among taxa is generally low and not associated with taxonomic distance. Specific instances of divergence are identified. There is no correlation between the amount of divergence in covariance patterns among the 16 genera and their phylogenetic distance derived from a conjoint analysis of four already published nuclear gene datasets. In contrast, there is a significant correlation between phylogenetic distance and morphological distance (Mahalanobis distance among genus centroids). This result indicates that while the phenotypic means were evolving during the last 30 millions years of New World monkey evolution, phenotypic covariance structures of Neotropical primate skulls have remained relatively consistent. Neotropical primates can be divided into four major groups based on their feeding habits (fruit-leaves, seed-fruits, insect-fruits, and gum-insect-fruits). Differences in phenotypic covariance structure are correlated with differences in feeding habits, indicating that to some extent changes in interrelationships among skull traits are associated with changes in feeding habits. Finally, common patterns and levels of morphological integration are found among Platyrrhine primates, suggesting that functional/developmental integration could be one major factor keeping covariance structure relatively stable during evolutionary diversification of South American monkeys. Corresponding Editor: T. Mousseau
Climate, fishing, and fluctuations of sardine and anchovy in the California Current

Since the days of Elton, population cycles have challenged ecologists and resource managers. Although the underlying mechanisms remain debated, theory holds that both density-dependent and density-independent processes shape the dynamics. One striking example is the large-scale fluctuations of sardine and anchovy observed across the major upwelling areas of the world. Despite a long history of research, the causes of these fluctuations remain unresolved and heavily debated, with significant implications for fisheries management. We here model the underlying causes of these fluctuations, using the California Current Ecosystem as a case study, and show that the dynamics, accurately reproduced since A.D. 1661 onward, are explained by interacting density-dependent processes (i.e., through species-specific life-history traits) and climate forcing. Furthermore, we demonstrate how fishing modifies the dynamics and show that the sardine collapse of the 1950s was largely unavoidable given poor recruitment conditions. Our approach provides unique insight into the origin of sardine–anchovy fluctuations and a knowledge base for sustainable fisheries management in the California Current Ecosystem and beyond.
Adaptive Spatio-temporal Filtering of 4 D CT-Heart

The aim of this project is to keep the x-ray exposure of the patient as low as reasonably achievable while improving the diagnostic image quality for the radiologist. The means to achieve these goals is to develop and evaluate an efficient adaptive filtering (denoising/image enhancement) method that fully explores true 4D image acquisition modes. The proposed prototype system uses a novel filter set having directional filter responses being monomials. The monomial filter concept is used both for estimation of local structure and for the anisotropic adaptive filtering. Initial tests on clinical 4D CT-heart data with ECG-gated exposure has resulted in a significant reduction of the noise level and an increased detail compared to 2D and 3D methods. Another promising feature is that the reconstruction induced streak artifacts which generally occur in low dose CT are remarkably reduced in 4D.
Romanian Roma migration: the interplay between structures and agency

Prior studies on Roma migration put much emphasis on either structural factors or networks that become key elements for explaining the growing migration flows of a population lacking economic resources and characterized by poor education. Although very relevant for explaining the perpetuation of migration, these studies posit the limit of downplaying migrants' agency and the role of identity markers mediating the influence of structural conditions in both destination and origin countries. Drawing on quantitative data from the Roma Inclusion Barometer (2006) as well as on in-depth interviews with Roma migrants from Eastern Romania, the paper provides a more comprehensive account of contemporary Romanian Roma migration towards Western European countries. The paper challenges the portrayal of the Roma migrant population, as conveyed by many scholars, as a rather passive one and argues that gender, religion and subgroup identities constitute key elements in explaining Roma migrants' agency.
“So What's Up?”: Using the Discourse Marker So to Launch Conversational Business

In this article, I use conversation analytic methods to analyze interactional junctures in which transitions to the first conversational topic are accomplished. I examine several ways in which parties in ordinary (and especially telephone) conversations coordinate the launching of first “talkables,” focusing specifically on environments in which such moves are delayed. I observed that many such moves are prefaced with the discourse marker so suggesting that it plays an important role at this interactional juncture. In the article, I demonstrate that the underlying meaning of so as a marker of “emergence from incipiency” serves to characterize the upcoming action as introducing the conversation's first intended topic—something that was projected by the very act of initiating the contact and oriented to by participants as having been pending or incipient. In addition to mundane telephone conversations, I briefly examine several institutional encounters to explore how so gets deployed for introducing institutional agendas.
Bioactive coating of decellularized vascular grafts with a temperature‐sensitive VEGF‐conjugated hydrogel accelerates autologous endothelialization in vivo

No ideal small‐diameter vascular graft for widespread clinical application has yet been developed and current approaches still suffer from graft failure because of thrombosis or degeneration. Decellularized vascular grafts are a promising strategy as they preserve native vessel architecture while eliminating cell‐based antigens and allow for autologous recellularization. In the present study, a functional in vivo rodent aortic transplantation model was used in order to evaluate the benefit of bioactive coating of decellularized vascular grafts with vascular endothelial growth factor (VEGF) conjugated to a temperature‐sensitive aliphatic polyester hydrogel (HG). Luminal HG‐VEGF coating persistence up to 4 weeks was confirmed in vivo by rhodamine‐labelling. Doppler‐sonography showed that the grafts were functional for up to 8 weeks in vivo. Histological and immunohistochemical analysis of the explanted grafts after 4 weeks and 8 weeks in vivo demonstrated significantly increased endothelium formation in the HG‐VEGF group compared with the control group (luminal surface covered with single‐layered endothelium, 4 weeks: 64.8 ± 7.6% vs. 40.4 ± 8.3%, p = 0.025) as well as enhanced media recellularization (absolute cell count, 8 weeks: 22.1 ± 13.0 vs. 3.2 ± 3.6, p = 0.0039). However, HG‐VEGF coating also led to increased neo‐intimal hyperplasia, resulting in a significantly increased intima‐to‐media ratio in the perianastomotic regions (intima‐to‐media ratio, 8 weeks: 1.61 ± 0.17 vs. 0.93 ± 0.09, p = 0.008; HG‐VEGF vs. control). The findings indicate that HG‐VEGF coating has potential for the development of engineered small‐diameter artificial grafts, although further research is needed to prevent neo‐intimal hyperplasia. Copyright © 2016 John Wiley & Sons, Ltd.
Discovering action idioms bridging the gap between system-level events and human-level actions

As computing devices become more pervasive in our daily lives, effective communication between the user and the system becomes increasingly important. The ability to describe actions at a human level of abstraction is key. However, the level at which computer system events is most easily captured is often well below the level at which humans conceptualize actions. We present a sequential pattern mining approach to discovering human-level actions-action idioms - from instrumentation logs of lower-level events. To support validation by a human expert, idiom discovery is designed to maximize recall, with filtering heuristics applied to help eliminate false positives. Empirical evaluation on data from a fielded application shows the promise of the approach for the automatic discovery of action idioms.
EHU-ALM: Similarity-Feature Based Approach for Student Response Analysis

We present a 5-way supervised system based on syntactic-semantic similarity features. The model deploys: Text overlap measures, WordNet-based lexical similarities, graphbased similarities, corpus-based similarities, syntactic structure overlap and predicateargument overlap measures. These measures are applied to question, reference answer and student answer triplets. We take into account the negation in the syntactic and predicateargument overlap measures. Our system uses the domain-specific data as one dataset to build a robust system. The results show that our system is above the median and mean on all the evaluation scenarios of the SemEval2013 task #7.
Estimation of Temperature Rise in Stator Winding and Rotor Magnet of PMSM Based on EKF

Abstract—This paper proposed an estimation approach of temperature rise in stator winding and rotor magnet of a surfaced-mounted permanent magnet (PM) AC motor. By using the 3rd-order extended Kalman filter (EKF) algorithm in rotating reference frame, stator winding resistance and rotor PM flux-linkage can be estimated independently. After comparing the estimation results of resistance and flux-linkage to the rated values measured at 20 respectively, the corresponding temperature rise in stator winding and rotor magnet °C can be calculated according to some certain rules. The proposed method was confirmed to be correct and effective by the simulation results from MATLAB/SIMULINK.
Low rank recovery based image interpolation using local and nonlocal modeling

Linear representation models are effective to represent the correlation in image interpolation. However, linear models usually lack constraints of the representation coefficient. In this paper, we propose a low rank matrix recovery based image interpolation to reinforce the sparsity of representation coefficient implicitly. Since both the local and nonlocal correlation is pervasive in natural images, we exploit such correlations by incorporating the local and nonlocal modeling, which fully utilizes the redundancy in images and improves the representation ability of our model. By minimizing the sum of the rank of data matrices which reflect the linear relationship among local patch pixels and nonlocal similar patch pixels, a precise low rank approximation of the missing pixels is obtained according to the low rank matrix recovery theory. A Split Bregman based minimization algorithm is developed to efficiently solve the low rank recovery problem. Extensive experimental results indicate the proposed method outperforms the traditional methods in both the objective and subjective visual quality.
Performance of broadcast authentication for secure V2V safety applications: A holistic view

Efficient broadcast authentication has seen a lot of work in the recent past. Most broadcast authentication protocols rely on an underlying Public Key Infrastructure (PKI) to provide a point of trust from which credentials for more efficient cryptographic mechanisms for broadcast authentication can be derived. Thus, there is a logical dependence of some cryptographic credentials (e.g., verifiers for one-time signatures) on others (e.g., certificates from the PKI). However, since V2V messages are transmitted using a random access broadcast, messages containing these credentials could be lost, thereby preventing the verification of credentials depending on the lost ones. Further, since the wireless bandwidth is precious, there have been proposals to optimize the transmission of certificates and other credentials over the air. The more infrequently these are transmitted, the more is the temporal dependence on the verification times of V2V messages. On the flip side, the more frequently these are transmitted, the more is the bandwidth overhead (i.e., greater packet size) and the more the chances of packet collisions over the air. We illustrate this dilemma by means of a case-study, and advocate a holistic approach to broadcast authentication.
Albidoferax, a new genus of Comamonadaceae and reclassification of Rhodoferax ferrireducens (Finneran et al., 2003) as Albidoferax ferrireducens comb. nov.

We propose the reclassifi cation of Rhodoferax ferrireducens (Finneran et al., 2003) into a new genus, as the strain does not have the property of anoxygenic photosynthesis, which is a genus-specifi c property of the phototrophic Proteobacteria. The genus-specifi c character of the phototrophic Proteobacteria is that they all perform anoxygenic photosynthesis with the help of bacteriochlorophylls and carotenoids, which delineates them from the chemotrophs that are interspersed among them. Thus, though Haematobacter massiliensis initially was placed in the phototrophic genus Rhodobacter (as Rhodobacter massiliensis; Greub and Raoult, 2003) based on 16S rRNA gene sequence analysis, lack of phototrophy coupled with other differences necessitated identifi cation of a new genus and reclassifi cation (Leta et al., 2007). Rhodoferax ferrireducens is another example of a chemotroph which is placed in the photosynthetic genus for which we propose identifi cation of a new genus and reclassifi cation. 16S rRNA gene sequences of two uncultured bacterial clones (showing 98‒99% sequence similarity) along with Rhodoferax ferrireducens and other related type strains of the family Comamonadaceae were used for the phylogenetic analysis. 16S rRNA gene sequences were aligned using the CLUSTAL X Program (Thompson et al., 1997) and the alignment was corrected manually. The alignment fi le was saved with the “. phy” extenstion. The dendrogram was constructed using the PhyML (Guindon and Gascuel, 2003) program using 100 replicates of non parametric bootstrap analysis, the GTR model of nucleotide substitution and 4 substitution rate categories. Phylogenetically based on 16S rRNA gene sequence similarity, Rhodoferax ferrireducens has 98.3% and 97.25% sequence similarity with Rhodoferax antarcticus and Rhodoferax fermentans, respectively, though clustered separately from the two species (Fig. 1). Lack of phototrophic growth and photosynthetic pigments (Table 1) necessitated the reclassifi cation of this organism into a new genus. This observation is strongly supported by the whole genome data (http://www. genome.jp/dbget-bin/www_bget? refseq+NC_ 007908) which clearly provided evidence for the lack J. Gen. Appl. Microbiol. , 55, 301‒304 (2009)
A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A

Histone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain to gain insight into how JMJD2A discriminates between the methylation states of H3K9. The methyl groups are located at specific distances and orientations with respect to Fe(II) in methylammonium binding pocket. For the trimethyllysine the mechanism which provides the effectual orientation of methyl groups is the symmetry, whereas for the dimethyllysine case the determining factors are the interactions between methyllysine head and its environment and subsequently the restriction on angular motion. The occurrence frequency of methyl groups in a certain proximity of Fe(II) comes out as the explanation of the enzyme activity difference on di- and tri-methylated peptides. Energy analysis suggests that recognition is mostly driven by van der Waals and followed by Coulombic interactions in the enzyme-substrate interface. The number (mono, di or tri) and orientations of methyl groups and water molecules significantly affect the extent of van der Waals interaction strengths. Hydrogen bonding analysis suggests that the interaction between JMJD2A and its substrates mainly comes from main chain-side chain interactions. Binding free energy analysis points out Arg8 as an important residue forming an intra-substrate hydrogen bond with tri and dimethylated Lys9 of the H3 chain. Our study provides new insights into how JMJD2A discriminates between its substrates from both a structural and dynamical point of view.
Tomographic Imaging and Monitoring of Buildings With Very High Resolution SAR Data

Layover is frequent in imaging and monitoring with synthetic aperture radar (SAR) areas characterized by a high density of scatterers with steep topography, e.g., in urban environment. Using medium-resolution SAR data tomographic techniques has been proven to be capable of separating multiple scatterers interfering (in layover) in the same pixel. With the advent of the new generation of high-resolution sensors, the layover effect on buildings becomes more evident. In this letter, we exploit the potential of the 4-D imaging applied to a set of TerraSAR-X spotlight acquisitions. Results show that the combination of high-resolution data and advanced coherent processing techniques can lead to impressive reconstruction and monitoring capabilities of the whole 3-D structure of buildings.
Adherence to Hormone Replacement Therapy: A Longitudinal Study Using the Theory of Planned Behaviour

The aim of this longitudinal study was to assess the stability and determinants of the intention to adopt HRT over a one-year period using the Theory of Planned Behaviour. At baseline, a total of 644 middle-aged premenopausal women who had never used HRT, were recruited. At follow-up, 417 women completed an interview to assess any change in their reproductive status and in their behavioural intention. Among women who stayed premenopausal (n = 172) and among those who became perimenopausal (n = 209), the intention to adopt HRT was quite stable over the one-year period. However, being perimenopausal had a significant effect on the intention to adopt HRT at follow-up, as did subjective norm, perceived behavioural control and moral norm measured at baseline. Attitude towards HRT did not have a significant effect on the intention to adopt HRT one year later. Therefore, interventions to support women's decision-making about HRT should be tailored to their menopausal status and take into account their perception of social pressure to perform, control over this behaviour and moral obligation.
Ensino, pesquisa e gestão acadêmica na universidade: Teaching, research and higher education academic management

This article discusses the relations between the teacher's teaching activities and research work, trying to clarify in which aspects both are different and in which aspects they are closely inter-related. It emphasizes the processes which act as a strong incentive to research and to the publication of its results, whereas the same incentive is absent from the teaching activities and pedagogical innovation. It also discusses the problems of academic management, pointing to some aspects which indicate the fragility of the conditions under which management is taking place, conditions which do not lead to spaces of reflection on the processes of construction and dissemination of knowledge which point towards innovative pedagogical practices which might explicit or strengthen the necessary interaction of teaching and research.
Imitation as a dual-route process featuring prediction and learning components: A biologically plaus

We do not exist alone. Humans and most other animal species live in societies where the behaviour of an individual influences and is influenced by other members of the society. Within societies, an individual learns not only on its own, through classical conditioning and reinforcement, but to a large extent through its conspecifics, by observation and imitation. Species from rats to birds to humans have been observed to turn to their conspecifics for efficient learning of useful knowledge. One of the most important mechanisms for the transmission of this knowledge is imitation.
Bilingual children's production of regular and irregular past

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Association Between Platelet Count as a Noninvasive Marker and Ultrasonographic Grading in Patients With Nonalcoholic Fatty Liver Disease

Background: Nonalcoholic fatty liver disease has become a worldwide challenge. Liver biopsy remains the single most reliable approach to determine the severity of this disease. As patients with nonalcoholic fatty liver disease require close follow-up, performing this invasive method repeatedly seems impractical; therefore, designing a noninvasive system to follow up patients has become a common interest. Objectives: We intended to investigate the association between platelet counts of patients with nonalcoholic fatty liver disease and the severity of their disease based on serum levels of liver enzymes and grade of fatty liver on ultrasonography. Patients and Methods: One thousand, three hundred and five patients with nonalcoholic fatty liver disease were included in this descriptive study. Serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP) and platelet counts of patients were measured. The grade of fatty liver was determined by abdominal ultrasonography. Results: Of our study population, 54.3% (n = 708) were women. Patients with mild fatty liver on ultrasonography had lower platelet counts than those with moderate and severe fatty liver. However, no cutoff value of platelet count could reliably distinguish different grades of fatty liver. We found no significant association between platelet counts and serum levels of AST, ALT or ALP. However, we showed that male patients with abnormal levels of ALT had higher platelet counts. Conclusions: Platelet count in nonalcoholic fatty liver disease can serve as a clue to the severity of disease, but it cannot be considered as a sole test to follow up patients.