Automatic assignment of absolute configuration from 1D NMR data

Opposite enantiomers exhibit different NMR properties in the presence of an external common chiral element, and a chiral molecule exhibits different NMR properties in the presence of external enantiomeric chiral elements. Automatic prediction of such differences, and comparison with experimental values, leads to the assignment of the absolute configuration. Here two cases are reported, one using a dataset of 80 chiral secondary alcohols esterified with (R)-MTPA and the corresponding 1H NMR chemical shifts and the other with 94 13C NMR chemical shifts of chiral secondary alcohols in two enantiomeric chiral solvents. For the first application, counterpropagation neural networks were trained to predict the sign of the difference between chemical shifts of opposite stereoisomers. The neural networks were trained to process the chirality code of the alcohol as the input, and to give the NMR property as the output. In the second application, similar neural networks were employed, but the property to predict was the difference of chemical shifts in the two enantiomeric solvents. For independent test sets of 20 objects, 100% correct predictions were obtained in both applications concerning the sign of the chemical shifts differences. Additionally, with the second dataset, the difference of chemical shifts in the two enantiomeric solvents was quantitatively predicted, yielding r2 0.936 for the test set between the predicted and experimental values.

Learning techniques for automatic email message tagging

A organização automática de mensagens de correio electrónico é um desafio actual na área da aprendizagem automática. O número excessivo de mensagens afecta cada vez mais utilizadores, especialmente os que usam o correio electrónico como ferramenta de comunicação e trabalho. Esta tese aborda o problema da organização automática de mensagens de correio electrónico propondo uma solução que tem como objectivo a etiquetagem automática de mensagens. A etiquetagem automática é feita com recurso às pastas de correio electrónico anteriormente criadas pelos utilizadores, tratando-as como etiquetas, e à sugestão de múltiplas etiquetas para cada mensagem (top-N). São estudadas várias técnicas de aprendizagem e os vários campos que compõe uma mensagem de correio electrónico são analisados de forma a determinar a sua adequação como elementos de classificação. O foco deste trabalho recai sobre os campos textuais (o assunto e o corpo das mensagens), estudando-se diferentes formas de representação, selecção de características e algoritmos de classificação. É ainda efectuada a avaliação dos campos de participantes através de algoritmos de classificação que os representam usando o modelo vectorial ou como um grafo. Os vários campos são combinados para classificação utilizando a técnica de combinação de classificadores Votação por Maioria. Os testes são efectuados com um subconjunto de mensagens de correio electrónico da Enron e um conjunto de dados privados disponibilizados pelo Institute for Systems and Technologies of Information, Control and Communication (INSTICC). Estes conjuntos são analisados de forma a perceber as características dos dados. A avaliação do sistema é realizada através da percentagem de acerto dos classificadores. Os resultados obtidos apresentam melhorias significativas em comparação com os trabalhos relacionados.

Methods for automatic and assisted image annotation

Personal memories composed of digital pictures are very popular at the moment. To retrieve these media items annotation is required. During the last years, several approaches have been proposed in order to overcome the image annotation problem. This paper presents our proposals to address this problem. Automatic and semi-automatic learning methods for semantic concepts are presented. The automatic method is based on semantic concepts estimated using visual content, context metadata and audio information. The semi-automatic method is based on results provided by a computer game. The paper describes our proposals and presents their evaluations.

Binocular vision and reading ability in a Portuguese population of school age children

Preventable visual loss caused by amblyopia (2 to 4%) and its risk factors such as strabismus (3%) and uncorrected refractive errors (5 to 7%) represent an important public health problem. Children with binocular vision anomalies could be at disadvantage in reading and writing. Objectives: (1) Describe binocular vision measures in children of school age; and (2) Describe the impact of abnormal binocular vision on reading ability (reading errors and reading speed).

Exposure to particles and fungi in Portuguese swine production

Versão preprint.

Automatic vehicle detection and classification

This paper presents a proposal for an automatic vehicle detection and classification (AVDC) system. The proposed AVDC should classify vehicles accordingly to the Portuguese legislation (vehicle height over the first axel and number of axels), and should also support profile based classification. The AVDC should also fulfill the needs of the Portuguese motorway operator, Brisa. For the classification based on the profile we propose:he use of Eigenprofiles, a technique based on Principal Components Analysis. The system should also support multi-lane free flow for future integration in this kind of environments.

Disruption and phenotypic analysis of six open reading frames from chromosome VII of Saccharomyces cerevisiae reveals one essential gene

Six open reading frames (ORFs) located on chromosome VII of Saccharomyces cerevisiae (YGR205w, YGR210c, YGR211w, YGR241c, YGR243w and YGR244c) were disrupted in two different genetic backgrounds using short-flanking homology (SFH) gene replacement. Sporulation and tetrad analysis showed that YGR211w, recently identified as the yeast ZPR1 gene, is an essential gene. The other five genes are non-essential, and no phenotypes could be associated to their inactivation. Two of these genes have recently been further characterized: YGR241c (YAP1802) encodes a yeast adaptor protein and YGR244c (LSC2) encodes the b-subunit of the succinyl-CoA ligase. For each ORF, a replacement cassette with long flanking regions homologous to the target locus was cloned in pUG7, and the cognate wild-type gene was cloned in pRS416.

Analysis of a 17.9 kb region from Saccharomyces cerevisiae chromosome VII reveals the presence of eight open reading frames, including BRF1 (TFIIIB70) and GCN5 genes

We report the nucleotide sequence of a 17,893 bp DNA segment from the right arm of Saccharomyces cerevisiae chromosome VII. This fragment begins at 482 kb from the centromere. The sequence includes the BRF1 gene, encoding TFIIIB70, the 5' portion of the GCN5 gene, an open reading frame (ORF) previously identified as ORF MGA1, whose translation product shows similarity to heat-shock transcription factors and five new ORFs. Among these, YGR250 encodes a polypeptide that harbours a domain present in several polyA binding proteins. YGR245 is similar to a putative Schizosaccharomyces pombe gene, YGR248 shows significant similarity with three ORFs of S. cerevisiae situated on different chromosomes, while the remaining two ORFs, YGR247 and YGR251, do not show significant similarity to sequences present in databases.

Sequencing of a 9.9 kb segment on the right arm of yeast chromosome VII reveals four open reading frames, including PFK1, the gene coding for succinyl-CoA synthetase (beta-chain) and two ORFs sharing homology with ORFs of the yeast chromosome VIII

A 9.9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the beta-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII.

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.

Do close reading à encenação: Frei Luís de Sousa

O presente artigo teve origem num texto escrito para o programa do espectáculo Frei Luís de Sousa, com encenação de Carlos Avilez, no Teatro Nacional D. Maria II, na abertura das Comemorações do Bicentenário do nascimento de Almeida Garrett.

Automatic synthesis of VHDL Hardware Components from IOPT Petri Net models

Conferência: 39th Annual Conference of the IEEE Industrial-Electronics-Society (IECON), Vienna, Austria, Nov 10-14, 2013

Reading performance in children with visual function anomalies

Aims - To compare reading performance in children with and without visual function anomalies and identify the influence of abnormal visual function and other variables in reading ability. Methods - A cross-sectional study was carried in 110 children of school age (6-11 years) with Abnormal Visual Function (AVF) and 562 children with Normal Visual Function (NVF). An orthoptic assessment (visual acuity, ocular alignment, near point of convergence and accommodation, stereopsis and vergences) and autorefraction was carried out. Oral reading was analyzed (list of 34 words). Number of errors, accuracy (percentage of success) and reading speed (words per minute - wpm) were used as reading indicators. Sociodemographic information from parents (n=670) and teachers (n=34) was obtained. Results - Children with AVF had a higher number of errors (AVF=3.00 errors; NVF=1.00 errors; p<0.001), a lower accuracy (AVF=91.18%; NVF=97.06%; p<0.001) and reading speed (AVF=24.71 wpm; NVF=27.39 wpm; p=0.007). Reading speed in the 3rd school grade was not statistically different between the two groups (AVF=31.41 wpm; NVF=32.54 wpm; p=0.113). Children with uncorrected hyperopia (p=0.003) and astigmatism (p=0.019) had worst reading performance. Children in 2nd, 3rd, or 4th grades presented a lower risk of having reading impairment when compared with the 1st grade. Conclusion - Children with AVF had reading impairment in the first school grade. It seems that reading abilities have a wide variation and this disparity lessens in older children. The slow reading characteristics of the children with AVF are similar to dyslexic children, which suggest the need for an eye evaluation before classifying the children as dyslexic.

Automatic diagnosis of liver steatosis by ultrasound using autoregressive tissue characterization

Liver steatosis is mainly a textural abnormality of the hepatic parenchyma due to fat accumulation on the hepatic vesicles. Today, the assessment is subjectively performed by visual inspection. Here a classifier based on features extracted from ultrasound (US) images is described for the automatic diagnostic of this phatology. The proposed algorithm estimates the original ultrasound radio-frequency (RF) envelope signal from which the noiseless anatomic information and the textural information encoded in the speckle noise is extracted. The features characterizing the textural information are the coefficients of the first order autoregressive model that describes the speckle field. A binary Bayesian classifier was implemented and the Bayes factor was calculated. The classification has revealed an overall accuracy of 100%. The Bayes factor could be helpful in the graphical display of the quantitative results for diagnosis purposes.

Alice's anima or the obligation of a reading transliteracy

This paper suggests an analysis of "Inanimate Alice" by Kate Pullinger, Chris Joseph and Ian Harper as an example of a transmedia narrative that triggers a new reading experience whilst proposing a literary alterity between reading and performance. Narrative experiences that elect the visual plasticity, interchanging games and tactility as drivers of the creative process are not new. Yet, narrative experiences, which have been created in the gap between reality and fiction, have found on the digital realm the perfect environment to multiple hybrid experiences. Bearing in mind Walter Benjamin’s concept of Erlebnis and Erfahrung, a critical analysis of this digital fiction tries to illustrate how literary art finds its space and time in a metamorphosed continuum only activated by the “patient reader”. All the multimedia hybrids, which this digital literary work may have, challenge readers to interpret different signals and poetic structures that most of readers might not be accustomed to; however even among a cognitive dissonance, meaning is found and reading happens only if time, space and attention are available. All possible transmedia literacies can only respond to this experience of online reading, if they are able to focus and draw attention not to a simple new behaviour or a single new practice, but to a demanding state of affairs that assemble different objective and subjective value forms.