Complete genomic sequence of the Australian south-west genotype of Sindbis virus: Comparisons with other Sindbis strains and identification of a unique deletion in the 3 '-untranslated region

Our previous studies have shown that two distinct genotypes of Sindbis (SIN) virus occur in Australia. One of these, the Oriental/Australian type, circulates throughout most of the Australian continent, whereas the recently identified south-west (SW) genetic type appears to be restricted to a distinct geographic region located in the temperate south-west of Australia. We have now determined the complete nucleotide and translated amino acid sequences of a SW isolate of SIN virus (SW6562) and performed comparative analyses with other SIN viruses at the genomic level. The genome of SW6562 is 11,569 nucleotides in length, excluding the cap nucleotide and poly (A) tail. Overall this virus differs from the prototype SIN virus (strain AR339) by 23% in nucleotide sequence and 12.5% in amino acid sequence. Partial sequences of four regions of the genome of four SW isolates were determined and compared with the corresponding sequences from a number of SIN isolates from different regions of the World. These regions are the non-structural protein (nsP3), the E2 gene, the capsid gene, and the repeated sequence elements (RSE) of the 3'UTR. These comparisons revealed that the SW SIN viruses were more closely related to South African and European strains than to other Australian isolates of SIN virus. Thus the SW genotype of SIN virus may have been introduced into this region of Australia by viremic humans or migratory birds and subsequently evolved independently in the region. The sequence data also revealed that the SW genotype contains a unique deletion in the RSE of the 3'UTR region of the genome. Previous studies have shown that deletions in this region of the SIN genome can have significant effects on virus replication in mosquito and avian cells, which may explain the restricted distribution of this genotype of SIN virus.

Learning the dynamics of embedded clauses

Recent work by Siegelmann has shown that the computational power of recurrent neural networks matches that of Turing Machines. One important implication is that complex language classes (infinite languages with embedded clauses) can be represented in neural networks. Proofs are based on a fractal encoding of states to simulate the memory and operations of stacks. In the present work, it is shown that similar stack-like dynamics can be learned in recurrent neural networks from simple sequence prediction tasks. Two main types of network solutions are found and described qualitatively as dynamical systems: damped oscillation and entangled spiraling around fixed points. The potential and limitations of each solution type are established in terms of generalization on two different context-free languages. Both solution types constitute novel stack implementations - generally in line with Siegelmann's theoretical work - which supply insights into how embedded structures of languages can be handled in analog hardware.

Impaired postural compensation for respiration in people with recurrent low back pain

This study evaluated the degree to which the disturbance to posture from respiration is compensated for in healthy normals and whether this is different in people with recurrent low back pain (LBP), and to compare the changes when respiratory demand is increased. Angular displacement of the lumbar spine and hips, and motion of the centre of pressure (COP), were recorded with high resolution and respiratory phase was recorded from ribcage motion. With subjects standing in a relaxed posture, recordings were made during quiet breathing, while breathing with increased dead-space to induce hypercapnoea, and while subjects voluntarily increased their respiration to match ribcage expansion that was induced in the hypercapnoea condition. The relationship between respiration and the movement parameters was measured from the coherence between breathing and COP and angular motion at the frequency of respiration, and from averages triggered from the respiratory data. Small angular changes in the lumbopelvic and hip angles were evident at the frequency of respiration in both groups. However, in quiet standing, the LBP subjects had a greater displacement of their COP that was associated with respiration than the control subjects. The LBP group had a trend for less hip motion. There were no changes in the movement parameters when respiratory demand increased involuntarily via hypercapnoea, but when respiration increased voluntarily, the amplitude of motion and the displacement of the COP increased in both groups. The present data suggest that the postural compensation to respiration counteracts at least part of the disturbance to posture caused by respiration and that this compensation may be less effective in people with LBP.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Soleus activity in post-stroke subjects: movement sequence from standing to sitting

O documento em anexo encontra-se na versão post-print (versão corrigida pelo editor).

The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames

We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591.

Risk factors for recurrent wheezing in infants: a case-control study

ABSTRACT OBJECTIVE To evaluate the association between recurrent wheezing and atopy, the Asthma Predictive Index, exposure to risk factors, and total serum IgE levels as potential factors to predict recurrent wheezing. METHODS A case-control study with infants aged 6-24 months treated at a specialized outpatient clinic from November 2011 to March 2013. Evaluations included sensitivity to inhalant and food antigens, positive Asthma Predictive Index, and other risk factors for recurrent wheezing (smoking during pregnancy, presence of indoor smoke, viral infections, and total serum IgE levels). RESULTS We evaluated 113 children: 65 infants with recurrent wheezing (63.0% male) with a mean age of 14.8 (SD = 5.2) months and 48 healthy infants (44.0% male) with a mean age of 15.2 (SD = 5.1) months. In the multiple analysis model, antigen sensitivity (OR = 12.45; 95%CI 1.28–19.11), positive Asthma Predictive Index (OR = 5.57; 95%CI 2.23–7.96), and exposure to environmental smoke (OR = 2.63; 95%CI 1.09–6.30) remained as risk factors for wheezing. Eosinophilia ≥ 4.0% e total IgE ≥ 100 UI/mL were more prevalent in the wheezing group, but failed to remain in the model. Smoking during pregnancy was identified in a small number of mothers, and secondhand smoke at home was higher in the control group. CONCLUSIONS Presence of atopy, positive Asthma Predictive Index and exposure to environmental smoke are associated to recurrent wheezing. Identifying these factors enables the adoption of preventive measures, especially for children susceptible to persistent wheezing and future asthma onset.

Lithostratigraphy, sequence stratigraphy and depositional setting of the Pliensbachian and Toarcian series in the Lusitanian Basin, Portugal

In the Lusitanian Basin (Central Portugal), the Middle-Upper Liassic series are characterized by an expressive marly limestone accumulation, sediments that were deposited on a homoclinal carbonate ramp. These series belong to the Vale das Fontes, Lemede, S. Gião (and the lateral equivalents Prado and Cabo Carvoeiro Formations) and, partially, to the Póvoa da Lomba Formations. These units, in great part controlled by an accurate ammonite biostratigraphic scale, are organized into two secondorder transgressive-regressive sequences. The first one (SP) is dated of early Pliensbachian/lowermost early Toarcian age; the second (ST) is dated of early Toarcian to early Aalenian.

A physical packing sequence algorithm for the container loading problem with static mechanical equilibrium conditions

The container loading problem (CLP) is a combinatorial optimization problem for the spatial arrangement of cargo inside containers so as to maximize the usage of space. The algorithms for this problem are of limited practical applicability if real-world constraints are not considered, one of the most important of which is deemed to be stability. This paper addresses static stability, as opposed to dynamic stability, looking at the stability of the cargo during container loading. This paper proposes two algorithms. The first is a static stability algorithm based on static mechanical equilibrium conditions that can be used as a stability evaluation function embedded in CLP algorithms (e.g. constructive heuristics, metaheuristics). The second proposed algorithm is a physical packing sequence algorithm that, given a container loading arrangement, generates the actual sequence by which each box is placed inside the container, considering static stability and loading operation efficiency constraints.

Multiple sequence alignment correction using constraints

Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics

A teaching-learning sequence of colour informed by history and philosophy of science

In this work, we present a teaching-learning sequence on colour intended to a pre-service elementary teacher programme informed by History and Philosophy of Science. Working in a socio-constructivist framework, we made an excursion on the history of colour. Our excursion through history of colour, as well as the reported misconception on colour helps us to inform the constructions of the teaching-learning sequence. We apply a questionnaire both before and after each of the two cycles of action-research in order to assess students’ knowledge evolution on colour and to evaluate our teaching-learning sequence. Finally, we present a discussion on the persistence of deep-rooted alternative conceptions.

A didactic sequence of elementary geometric optics Informed by history and philosophy of science

The concepts and instruments required for the teaching and learning of geometric optics are introduced in the didactic processwithout a proper didactic transposition. This claim is secured by the ample evidence of both wide- and deep-rooted alternative concepts on the topic. Didactic transposition is a theory that comes from a reflection on the teaching and learning process in mathematics but has been used in other disciplinary fields. It will be used in this work in order to clear up the main obstacles in the teachinglearning process of geometric optics. We proceed to argue that since Newton’s approach to optics, in his Book I of Opticks, is independent of the corpuscular or undulatory nature of light, it is the most suitable for a constructivist learning environment. However, Newton’s theory must be subject to a proper didactic transposition to help overcome the referred alternative concepts. Then is described our didactic transposition in order to create knowledge to be taught using a dialogical process between students’ previous knowledge, history of optics and the desired outcomes on geometrical optics in an elementary pre-service teacher training course. Finally, we use the scheme-facet structure of knowledge both to analyse and discuss our results as well as to illuminate shortcomings that must be addressed in our next stage of the inquiry.

Optochiasmatic tuberculoma as the sole manifestation of late recurrent tuberculosis

Brain tuberculomas account for 10-20% of space occupying brain lesions in developing countries. Most lesions are observed at time of tuberculosis diagnosis or soon after starting treatment. We herein describe a 32 year-old patient with a 14-month history of headache and progressive visual loss. Her past medical history revealed pulmonary tuberculosis treated eight years before. A brain MRI showed a T1- and T2-weighted isointense contrast-enhancing lesion in the optic chiasm. A presumptive diagnosis of optochiasmatic tuberculoma was made and isoniazid, rifampin, pyrazinamide, and ethambutol were started. Despite treatment, the patient evolved to blindness. The prompt recognition of this condition is extremely important since the presence of optochiasmal enhancement is associated with blindness in patients with tuberculosis.

Factor V Leiden and Prothrombin G20210A in Portuguese Women with Recurrent Miscarriage: Is it Worthwhile to Investigate?

OBJECTIVE: To compare the prevalence of factor V Leiden (FVL) and prothrombin (PT) G20210A mutations in Portuguese women with unexplained recurrent miscarriage (RM) and a control group of parous women. MATERIALS AND METHODS: FVL and PT G20210A analysis were carried out in 100 women with three or more consecutive miscarriages and 100 controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal losses). RESULTS: Overall, the prevalence of FVL and PT G20210A was similar in women with RM (5 and 3%) compared with controls (5 and 1%) OR 1.36 (CI 95% 0.45-4.08). In RM embryonic subgroup, PT G20210A was observed in 1.3% of women and FVL prevalence (2.6%) was inclusively lesser than that of controls. Both polymorphisms were more prevalent in women with fetal losses than in controls, although statistical significance was not reached due to the small size of the >10 weeks' subgroup. CONCLUSION: These data indicate that neither FVL nor PT G20210A is associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with embryonic RM and negative personal thromboembolic history.