Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii

As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.
Dynamic Migration of Cloud Services

In the last couple of years, cloud computing records a rapidly increasing popularity due to scalable, elastic infrastructures that are charged according to their usage and do not have to be maintained. However, the offerings of cloud providers sometimes drastically differ and therefore, it gets more and more difficult for users to compare clouds and choose a proper provider for a specific service. Furthermore, the demand of changing the provider and migrating existing services results from the growing market. The main problems and obstacles that follow the migration of services from the technical point of view are: First, cloud providers are using own platforms or APIs so services have to be adapted to them, and second, services cannot be migrated without an interruption. Besides the technical aspects, there are also economical ones. Companies have to spend a lot of time comparing different offerings and adapt their applications. This paper proposes the dynamic Platform as a Service (dynPaaS), a new form of Platform as a Service provider that addresses these issues. The dynPaaS framework abstracts existing clouds, finds the optimal cloud for a service according to its requirements and provides transparency about the underlying clouds. It monitors clouds and hosted services, dynamically migrates services between clouds on the basis of changing parameters, and optimizes the resource usage of integrated clouds. The result is a price reduction for both, the cloud users and the dynPaaS provider.
Multidialectal acoustic modeling: a comparative study

In this paper, multidialectal acoustic modeling based on shar- ing data across dialects is addressed. A comparative study of different methods of combining data based on decision tree clustering algorithms is presented. Approaches evolved differ in the way of evaluating the similarity of sounds between di- alects, and the decision tree structure applied. Proposed systems are tested with Spanish dialects across Spain and Latin Amer- ica. All multidialectal proposed systems improve monodialectal performance using data from another dialect but it is shown that the way to share data is critical. The best combination between similarity measure and tree structure achieves an improvement of 7% over the results obtained with monodialectal systems.
Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy

In spite of the taxonomy of the Aspergillus species of the Nigri Section being regarded as troublesome, a number of methods have been proposed to aid in the classification of this Section. This work aimed to distinguish Aspergillus species of the Nigri Section from foods, grains and caves on the basis in Polyphasic Taxonomy by utilizing morphologic and physiologic characters, and sequencing of ß-tubulin and calmodulin genes. The morphologic identification proved useful for some species, such as A. carbonarius and Aspergillus sp UFLA DCA 01, despite not having been totally effective in elucidating species related to A. niger. The isolation of the species of the Nigri Section on Creatine Sucrose Agar (CREA) enabled to distinguish the Aspergillus sp species, which was characterized by the lack of sporulation and by the production of sclerotia. Scanning Electron microscopy (SEM) allowed distinguishing the species into two distinct groups. The production of Ochratoxin A (OTA) was only found in the A. carbonarius and A. niger species. The sequencing of β-tubulin gene was efficient in differing most of the Aspergillus species from the Nigri Section with the exception of Aspergillus UFLA DCA 01, which could not be distinguished from A. costaricaensis. This species is morphologically similar to A. costaricaencis for its low sporulation capacity and high sclerotia production, but it differs morphologically from A. costaricaensis for its conidial ornamentation and size of vesicles. Equally, based on partial calmodulin gene sequence data Aspergillus UFLA DCA 01 differs from A. costaricaensis.
Procedure-based assessments in trauma and orthopaedic training – The trainees’ perspective

Abstract Introduction: The study aimed to gain an understanding of the attitudes of trauma and orthopaedic (T&O) trainees regarding procedure-based assessments (PBAs) and identify factors that influence any perceived educational benefit. Methods and materials: A questionnaire was emailed to all T&O trainees in the UK via an established e-mail communication tool after an initial pilot exercise. The data were analysed using the online survey software. Results: Of the 616 trainees included 53% found PBAs useful as a learning tool for delivery of feedback. Trainees agreed that there were barriers to the successful use of PBAs (61%). Completing the PBA at the time of the procedure (p < 0.001) and the trainer delivering quality feedback with PBAs (p < 0.001) significantly increased the number of trainees perceiving an improvement in their practice. Completing higher numbers of PBAs did not have this effect (p = 0.26). There was wide geographical variation in the use of PBAs by trainees. Conclusions: This is the first nationwide study offering a deeper insight into factors influencing T&O trainees’ perceptions of the educational benefit gained from using PBAs. This study informs the debate on how to improve the effective use of PBAs in T&O training, and generally, of workplace-based assessments in surgical training.
Dispensation of long-acting β agonists with or without inhaled corticosteroids, and risk of asthma-related hospitalisation: a population-based study

Background The role of long-acting β-agonists (LABA) added to inhaled corticosteroids (ICS) in the management of asthma is extensively debated. We thought to assess the risk of asthma-related hospitalisation in individuals who regularly filled prescriptions for ICS+LABA compared to those who regularly filled prescriptions for ICS alone or LABA alone, and compared to those who did not regularly fill such medications. Methods Using administrative health databases of the province of British Columbia (BC), Canada, from 1997 to 2012, we conducted a nested case-control analysis of a cohort of asthma patients. Cases were defined as those who experienced asthma-related hospitalisation after the first year of their entry into the cohort. For each case, up to 20 controls were matched based on age, sex, date of cohort entry, and several measures of asthma severity. We categorised individuals as regularly exposed, irregularly exposed, or non-exposed to ICS alone, LABA alone, or ICS+LABA based on dispensation records in the past 12 months. The primary outcome measures were the rate ratio (RR) of the asthma-related hospitalisation among categories of regular exposure. Results 3319 cases were matched to 43 023 controls. The RR for regular dispensation of ICS+LABA was 1.14 (95% CI 0.93 to 1.41) compared with regular dispensation of ICS alone and 0.45 (95% CI 0.29 to 0.70) compared with regular dispensation of LABA alone. Those who regularly dispensed LABA had to dispense an ICS for at least three quarters of a year to reduce their risk to that of those who did not dispense LABA. Conclusions Regular dispensation of ICS+LABA was not associated with an increased risk of asthma-related hospitalisation compared with regular dispensation of ICS alone. Adherence to ICS in patients who regularly receive ICS+LABA seems to be an important factor in the prevention of adverse asthma-related outcomes.
A mixture-site model for edge-preserving image restoration

The paper summarizes a new Bayesian method for edge-preserving image restoration from noisy measurements. The line-site method of Geman and Geman (1984) forces region boundaries to lie along pixel boundaries, which is unnatural, particularly for 3D data. The present authors augment the intensity process with a binary "mixture site" process, which has one parameter for each pixel indicating the presence of a boundary at some unknown location within that pixel. The method was motivated by the PET and SPECT transmission images with partial volume effects, and is easily extended to 3D data sets. <<ETX>>
Fighting the Tests: A Practical Guide to Rescuing Our Schools.

Don’t let anyone tell you that standardized tests are not accurate measures. The truth of the matter is they offer a remarkably precise method for gauging the size of the houses near the school where the test was administered. Every empirical investigation of this question has found that socioeconomic status (SES) in all its particulars accounts for an overwhelming proportion of the variance in test scores when different schools, towns, or states are compared. (1) Thus ignorance would be the most charitable explanation for why charts are published that rank schools (or towns or states) by these scores — or why anyone would use those rankings to draw conclusions about classroom quality.
Catechol Tetrahydroisoquinolines Enhance a-Synuclein Aggregation andSpecify the Neurotoxicity to Dopaminergic Neurons

Parkinson disease (PD) is the second most common neurodegenerative disorder after Alzheimer disease with no definitive neuroprotective therapies. Previous studies have demonstrated that Catechol tetra hydroisoquinolines (CTIQs) are toxic to dopaminergic neurons. These toxins can induce mitochondrial dysfunction, which consequently contributes to the pathogenesis of PD. Unlike external neurotoxins, such as agrochemicals and MPTP, CTIQs can be synthesized in the brains of human based on the dopamine and the particular aldehyde. Besides, aggregated α-synuclein (α-syn), one of the hallmarks of PD, has been proved to be a key contributor in the development of PD and can be affected by many neurotoxins. Some studies have presented that CTIQs enhanced the aggregation of α-syn and increased the neurotoxin of α-syn, which might be the pathological mechanism of PD. Therefore, this chapter will reveal the role of CTIQs and α-syn and try to clarify the relationship between them.
Modified Gaussian estimation for correlated binary data

In this paper, we develop a Gaussian estimation (GE) procedure to estimate the parameters of a regression model for correlated (longitudinal) binary response data using a working correlation matrix. A two‐step iterative procedure is proposed for estimating the regression parameters by the GE method and the correlation parameters by the method of moments. Consistency properties of the estimators are discussed. A simulation study was conducted to compare 11 estimators of the regression parameters, namely, four versions of the GE, five versions of the generalized estimating equations (GEEs), and two versions of the weighted GEE. Simulations show that (i) the Gaussian estimates have the smallest mean square error and best coverage probability if the working correlation structure is correctly specified and (ii) when the working correlation structure is correctly specified, the GE and the GEE with exchangeable correlation structure perform best as opposed to when the correlation structure is misspecified.
Redox-Sensitive Signaling by Angiotensin II Involves Oxidative Inactivation and Blunted Phosphorylation of Protein Tyrosine Phosphatase SHP-2 in Vascular Smooth Muscle Cells From SHR

Angiotensin II (Ang II) signaling in vascular smooth muscle cells (VSMCs) involves reactive oxygen species (ROS) through unknown mechanisms. We propose that Ang II induces phosphorylation of growth signaling kinases by redox-sensitive regulation of protein tyrosine phosphatases (PTP) in VSMCs and that augmented Ang II signaling in spontaneously hypertensive rats (SHRs) involves oxidation/inactivation and blunted phosphorylation of the PTP, SHP-2. PTP oxidation was assessed by the in-gel PTP method. SHP-2 expression and activity were evaluated by immunoblotting and by a PTP activity assay, respectively. SHP-2 and Nox1 were downregulated by siRNA. Ang II induced oxidation of multiple PTPs, including SHP-2. Basal SHP-2 content was lower in SHRs versus WKY. Ang II increased SHP-2 phosphorylation and activity with blunted responses in SHRs. Ang II—induced SHP-2 effects were inhibited by valsartan (AT1R blocker), apocynin (NAD(P)H oxidase inhibitor), and Nox1 siRNA. Ang II stimulation increased activation of ERK1/2, p38MAPK, and AKT, with enhanced effects in SHR. SHP-2 knockdown resulted in increased AKT phosphorylation, without effect on ERK1/2 or p38MAPK. Nox1 downregulation attenuated Ang II–mediated AKT activation in SHRs. Hence, Ang II regulates PTP/SHP-2 in VSMCs through AT1R and Nox1-based NAD(P)H oxidase via two mechanisms, oxidation and phosphorylation. In SHR Ang II–stimulated PTP oxidation/inactivation is enhanced, basal SHP-2 expression is reduced, and Ang II–induced PTP/SHP-2 phosphorylation is blunted. These SHP-2 actions are associated with augmented AKT signaling. We identify a novel redox-sensitive SHP-2–dependent pathway for Ang II in VSMCs. SHP-2 dysregulation by increased Nox1-derived ROS in SHR is associated with altered Ang II–AKT signaling.
What Makes Communities Tick? Community Health Analysis Using Role Compositions

Today's Web is social and largely driven by a wide variety of online communities. Many such communities are owned and managed by businesses that draw much value from these communities, in the form of efficient and cheaper customer support, generation of new ideas, fast spreading of information, etc. Understanding how to measure the health of online communities and how to predict its change over time, whether to better or to worse health, is key to developing methods and policies for supporting these communities and managing them more efficiently. In this paper we investigate the prediction of community health based on the social behaviour exhibited by their members. We apply our analysis over 25 SAP online communities, and demonstrate the feasibility of using behaviour analysis to predict change in their health metrics. We show that accuracy of health prediction increases when using community-specific prediction models, rather than using a one-model-fits-all approach.
Vibrational study of some layered structures based on titanium and zirconium phosphates.

A Raman and infrared study was carried out on layered zirconium and titanium acid phosphates of alpha- and gamma-type, alpha-M[O(3)POH](2). H(2)O and gamma-M[PO(4)][O(2)P(OH)(2)]. 2H(2)O, respectively. The spectra were initially approached by means of the classical correlation method in the solid state, which accounts for the complexity of the infrared spectra of both species. However, the number of bands and their relative intensity in the Raman spectra suggest a quite total absence of quadrupolar coupling between the vibrating units. So, if interunit coupling is neglected, a molecular approach considering the vibrations of isolated tetrahedral [PO(4)] and octahedral [MO(6)] building blocks can allow an affordable spectroscopic description of the title compounds. Interesting insights on the relationships between spectral properties and structure can be drawn by comparison with the spectra of alkali phosphates and of MO(6) oxoanions. A significant high-energy shift of the nu(P-O) modes is observed in the layered phosphates with respect to the corresponding salts, which parallels the low-energy shift of the nu(M-O) modes. Surprisingly, an increase of the M-OP interaction can reinforce the P-O bond. A simple theoretical model, based on the interaction between the [PO(4)] unit and four Li(+) in similar geometrical arrangement found in the structures of the layered phosphates, offers a reasonable explanation of this phenomenon.
Nonlinear decentralized control of a multimachine power system

In this paper, the transient stability and voltage regulation of multimachine power systems are simultaneously addressed in a multivariable and nonlinear framework. The design method is based on a new power system model. The main characteristic of this model is that interactions between generators and changes in operating conditions are represented by time-varying parameters. The controller consists of two controllers, known as the terminal voltage controller and speed controller. The methodology adopted is based on backstepping design strategy. The proposed stabilizing feedback laws for the power system are shown to be globally asymptotically stable in the context of Lyapunov theory. The tracking errors are shown to be globally uniformly bounded. Numerical results are presented to demonstrate the effectiveness of the proposed control methodology.
Cuntz Semigroups of Compact-Type Hopf C*-Algebras

The classical Cuntz semigroup has an important role in the study of C*-algebras, being one of the main invariants used to classify recalcitrant C*-algebras up to isomorphism. We consider C*-algebras that have Hopf algebra structure, and find additional structure in their Cuntz semigroups. We show that in many cases, isomorphisms of Cuntz semigroups that respect this additional structure can be lifted to Hopf algebra (bi)isomorphisms, up to a possible flip of the co-product. This shows that the Cuntz semigroup provides an interesting invariant of C*-algebraic quantum groups.
Exploring Traits of Adjectives to Predict Polarity Opinion in Blogs and Semantic Filters in Genomics

: This paper presents the results of our team in the Genomics and Blog tracks in TREC 2007. We used the language model implementation provided by Indri for both tracks. For the BLOG track we explored the use of adjectives with in a post as a way to predict opinion polarity. Our work in the Genomics track explores two approaches to generate queries from the original topics. The first approach performs automatic term expansion using UMLS to generate a structured query that can be submitted using Indri’s query language. The second approach uses a query expansion and re-ranking method based on identification of semantic relatives. This approach tries to capture the semantic of the potential answer, key terms in the topic and detection of gene/protein terms mentioned in the topic.
Médecins avec ou sans frontière: comtradiction et transformation des pratiques professionnelles

Notre etude se penche sur la rationalisation des organisations hospitalieres, plus particulierement celle associee aux certifications qualite-risques. Notre approche envisage les tensions qui peuvent en resulter dans les pratiques professionnelles elles-memes et plus particulierement celles de medecins oeuvrant dans un centre de lutte contre le cancer. Pour ce faire, nous mobilisons la theorie de l'activite, parce qu'elle identifie les contradictions comme dimension intrinseque des situations de travail, et comme participant a leur dynamique d'evolution.
Involvement of a Putative Cyclic AMP Receptor Protein (CRP)-Like Binding Sequence and a CRP-Like Protein in Glucose-Mediated Catabolite Repression of thn Genes in Rhodococcus sp. Strain TFB

ABSTRACT Glucose catabolite repression of tetralin catabolic genes in Rhodococcus sp. strain TFB was shown to be exerted by a protein homologous to transcriptional regulators of the cyclic AMP receptor (CRP)-FNR family. The protein was detected bound to putative CRP-like boxes localized at the promoters of the thnA1 and thnS genes.
Real-time Event Recognition from Video via a " Bag-of-activities "

In this paper we present a new method for high-level event recognition, demonstrated in real-time on video. Human behaviours have underlying activities that can be used as salient features. We do not assume that the exact temporal ordering of such features is necessary, so can represent behaviours using an unordered " bag-of-activities ". A weak temporal ordering is imposed during inference, so fewer training exem-plars are necessary compared to other methods. Our three-tier architecture comprises low-level tracking, event analysis and high-level recognition. High-level inference is performed using a new extension of the Rao-Blackwellised Particle Filter. We validate our approach using the PETS 2006 video surveillance dataset and our own sequences. Further, we simulate temporal disruption and increased levels of sensor noise.
DFTSim: a simulation tool for extended dynamic fault trees

We present DFTSim, a simulation tool for dynamic fault trees (DFT). The simulation is carried out by directly sampling the failure distributions attached to the leaves (called basic events) of the tree and propagating the failure times upwards in the tree. Sampling the distributions of the DFT leaves is however not obvious. To sample from the correct distributions, the analytical expression of the failure distributions of all basic events (BE) must be known. These are indeed known for non-spare BEs; but for spare BEs, they become conditional on the failure of other BEs. Hence, the derivation of the analytical expression of the spares' failure distributions and their sampling is not a trivial task. We evaluate DFTSim by applying it on an extensive benchmark comprised of seven case studies. We compare its results to two other DFT-based reliability tools (namely Galileo and Coral) that, rather than giving simulation-based estimates, compute exact measures. Our simulation-based approach is, in particular for large DFTs, much faster than the existing approaches. In fact, the computation time of the exact solution methods is exponential in the number of DFT leaves, whereas simulation time is linear in the number of leaves. Moreover, DFTSim (and simulation in general) allows to simulate a wide range of distributions and evaluate Markovian as well as non-Markovian models.