An algebraic generalization of Kripke structures

The Kripke semantics of classical propositional normal modal logic is made algebraic via an embedding of Kripke structures into the larger class of pointed stably supported quantales. This algebraic semantics subsumes the traditional algebraic semantics based on lattices with unary operators, and it suggests natural interpretations of modal logic, of possible interest in the applications, in structures that arise in geometry and analysis, such as foliated manifolds and operator algebras, via topological groupoids and inverse semigroups. We study completeness properties of the quantale based semantics for the systems K, T, K4, S4, and S5, in particular obtaining an axiomatization for S5 which does not use negation or the modal necessity operator. As additional examples we describe intuitionistic propositional modal logic, the logic of programs PDL, and the ramified temporal logic CTL.Comment: 39 page

Adding an Implication to Logics of Perfect Paradefinite Algebras

Perfect paradefinite algebras are De Morgan algebras expanded with a perfection (or classicality) operation. They form a variety that is term-equivalent to the variety of involutive Stone algebras. Their associated multiple-conclusion (Set-Set) and single-conclusion (Set-Fmla) order-preserving logics are non-algebraizable self-extensional logics of formal inconsistency and undeterminedness determined by a six-valued matrix, studied in depth by Gomes et al. (2022) from both the algebraic and the proof-theoretical perspectives. We continue hereby that study by investigating directions for conservatively expanding these logics with an implication connective (essentially, one that admits the deduction-detachment theorem). We first consider logics given by very simple and manageable non-deterministic semantics whose implication (in isolation) is classical. These, nevertheless, fail to be self-extensional. We then consider the implication realized by the relative pseudo-complement over the six-valued perfect paradefinite algebra. Our strategy is to expand such algebra with this connective and study the (self-extensional) Set-Set and Set-Fmla order-preserving logics, as well as the T-assertional logics of the variety induced by the new algebra. We provide axiomatizations for such new variety and for such logics, drawing parallels with the class of symmetric Heyting algebras and with Moisil's `symmetric modal logic'. For the Set-Set logic, in particular, the axiomatization we obtain is analytic. We close by studying interpolation properties for these logics and concluding that the new variety has the Maehara amalgamation property

Avaliação do efeito do Azevém (Lolium perenne) resistente ao glifosato na produção e qualidade das uvas em vinha não irrigada

O glifosato é o herbicida mais utilizado a nível nacional, principalmente para controlar infestantes em culturas perenes e em áreas não cultivadas. O ensaio teve como o objetivo inicial encontrar uma alternativa ao glifosato nos vinhos do Douro onde o azevém (Lolium perenne L.) foi registado como sendo resistente a este herbicida. Atendendo a que a eficácia dos herbicidas não é igual, pôde- se estabelecer intervalos de eficácia, complementando-se o estudo inicial com a avaliação de diferentes níveis de eficácia dos herbicidas, e com isso diferentes níveis de azevém, utilizados para a avaliar a influência deste na quantidade e qualidade da uva para vinificação. O ensaio teve lugar numa Quinta localizada no Douro, concelho de Santa Marta de Penaguião. Foram utilizadas 5 modalidades, com 3 repetições cada. Os intervalos de eficácia foram os seguintes: 0-10; 20-30; 40-50; 60-70; 90-100. Com o objetivo de avaliar se existem alteração na quantidade e qualidade de produção em função das infestantes presentes no solo, no que se refere à quantidade foram pesados e medidos 5 cachos por cepa, num total de 5 cepas em cada modalidade. Relativamente à qualidade, recolheram-se 2 amostras aleatórias de 100 bagos cada, representativas de cada repetição em cada uma das 5 modalidades. Em laboratório determinaram-se os seguintes parâmetros: pH, acidez total, percentagem de bagaço (%), antocianinas, índice de polifenóis totais e intensidade corante. Aos dados aplicou-se a ANOVA e o teste de Tuckey, tendo-se verificado a existência de diferenças nos parâmetros: comprimento dos cachos e peso dos cachos. As perdas de produção podem atingir os 20% quando a eficácia dos herbicidas é nula

Governo Electrónico nas Juntas de Freguesia: situação na região do Minho

Neste artigo apresentamos um estudo realizado com o objectivo de analisar a adopção do Governo Electrónico pelas Juntas de Freguesia do Minho, incluindo a análise da evolução ocorrida entre 2003 e 2005. Apesar de ter crescido significativamente, o Governo Electrónico ainda é uma miragem para a esmagadora maioria das Juntas de Freguesia do Minho, particularmente no que respeita à disponibilização de informações e serviços por meio de websites

Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data

Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now use RNA sequencing (RNA-seq) data to identify which isoforms of each gene are being expressed in a specific condition, by quantifying the expression level of each isoform of a gene, even though quantification of isoforms remains a difficult task. In this way, we can better understand how prevalent this process is and how often a gene expresses different isoforms. It can also be evaluated if all isoforms of a gene are about equally expressed or if there is one dominant isoform that is significantly more expressed than the others. Moreover, by applying this analysis to different tissues, it can be assessed if there are changes in splicing between different conditions and if such a change has a biological role. A dataset of 32 normal human tissues was used in this study. The results show that, although alternative splicing can lead to the expression of different transcripts of a gene, many genes have an n-fold dominant transcript – a transcript that is expressed at n times higher level than the second most expressed one. On average, 68% of protein-coding genes expressed in a given tissue have a 2-fold dominant transcript and 47% have a 5-fold dominant transcript. It was observed that the dominant transcript of a gene tends to be the same across tissues, but there are cases where the dominant isoform switches between tissues, these cases are designated switch events. For a given pair of tissues, there are on average around thirty 2-fold switch events and just below four 5-fold switch events. The switching exons often significantly overlap and the most common types of alternative splicing are alternative 3’ selection (24% of the cases) and alternative 5’ selection (21%). To evaluate the conservation of the transcripts, the dominant transcripts were compared to APPRIS principal isoforms. These isoforms are annotated based on their function, protein structure, and cross-species conservation. 69.2% of the 2-fold dominant transcripts and 81.1% of the 5-fold dominant transcripts are APPRIS principal isoforms. It was also observed that in 80% of the switches there are no protein domain changes. Similar results were obtained when the same analysis was done using the GTEx dataset, which has a much higher number of samples, containing data from 54 conditions. In this case, on average 59% of expressed genes in a given condition had a 2-fold dominant transcript and 31% had a 5-fold dominant transcript. The number of switch events was again low, given the number of dominant transcripts, indicating that dominant transcripts tend to be conserved across normal tissues. A comparative analysis of matching tissues common to the two mentioned datasets was also performed and, although the datasets are different, there were switch events in common between both of them. 5 examples of 5-fold switches involving domain swaps were analysed in detail and it was revealed that the type of genes affected by switches can be quite distinct and the protein domains that change between isoforms can vary both in number and function. The tissues found to be particularly more represented on these switch events were skeletal muscle, testis and cerebral cortex. These results show that in most cases, changes in alternative splicing do not change transcripts significantly, and respectively, the changes at the protein level are minor. This and similar observations indicate that alternative splicing may not be the main process responsible for generating protein diversity. In the last study presented in this thesis, it is analysed how RNA-seq data can be integrated with a data-independent acquisition (DIA) mass spectrometry method, SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry), to study the impact of depleting PRPF8, a core spliceosomal component, on the proteome. The results show that intron retention events lead to decreased protein abundance. It is also shown that differential transcript usage and gene expression have effects on protein abundance, altering it proportionally to transcript levels. Overall, some links between transcript and protein level are revealed and it is demonstrated how perturbed systems can be used in the study of alternative splicing

Estudo computacional das interacções proteína-proteína

Tese de mestrado. Biologia (Bioinformática e Biologia Computacional - Bioinformática). Universidade de Lisboa, Faculdade de Ciências, 2010O reconhecimento molecular é um processo chave em sistemas biológicos. A replicação e transcrição do ADN, a adesão celular, as cascatas de sinalização e ciclos metabólicos são alguns dos processos que têm por base o reconhecimento molecular. A compreensão destes processos exige que se conheçam as interacções de proteínas que estão na base dos mesmos. O modo como duas proteínas interagem pode ser difícil de prever, sobretudo se estas estabelecerem interacções transientes. O Docking é um método computacional que permite prever o modo de ligação entre duas moléculas e que tem potencial na previsão da interacção de complexos transientes. Os métodos para prever interface de proteínas podem ser baseados unicamente nas propriedades geométricas, físico-químicas e estatísticas da superfície ou podem incorporar também informação evolucionária na forma de certas medidas de conservação derivadas de alinhamentos de múltiplas sequências (MSA). Ao longo do tempo ocorrem substituições de aminoácidos nas proteínas. Substituições que estabilizem a interface entre monómeros são favorecidas por selecção natural. Se uma mutação num monómero induz uma mutação noutro monómero do mesmo complexo, diz-se que as mutações estão correlacionadas. Estas mutações podem ser determinadas analisando as correlações entre alterações em pares de posições em MSA. Já foi demonstrado que pares de aminoácidos correlacionados estão significativamente mais perto uns dos outros do que pares não correlacionados e que estes podem ser usados para descriminar entre soluções correctas e incorrectas em métodos de docking. Neste trabalho desenvolveu-se um sistema automatizado constituído por ferramentas em Python que integraram software disponível online, tal como o BLAST, o ClustalW e algoritmos de determinação de covariações, com o objectivo de determinar dados de coevolução que permitissem filtrar soluções de docking de complexos transientes.Molecular recognition is a key process in biological systems. DNA replication and transcription, cellular adhesion, signaling cascades and metabolic cycles are some of the processes that underlie molecular recognition. In order to understand these processes it is of utmost importance to know the protein interactions that are on their origin. The way in which two proteins interact might be difficult to predict, especially if they establish transient interactions. Docking is a computational method that allows the prediction of the binding mode between two molecules and has potential in predicting transient complexes. Methods that predict protein interfaces can be based solely on geometric, statistical and physical-chemical properties of the surface or they can also incorporate evolutionary data related to amino acid conservation that is extracted from multiple sequence alignment (MSA). Throughout time amino acid substitutions occur. Substitutions that stabilize the interface between monomers are favored by natural selection. If a mutation within a monomer induces a mutation on another monomer of the same complex, it is considered that these mutations are correlated. These mutations can be determined by analysis of the correlations between a pair of amino acids in MSA. It has been demonstrated that pairs of amino acids that are correlated are significantly closer together in the structure when compared to pairs that are not correlated and correlated pairs can be used to distinguish right from wrong solutions in docking methods

Low frequency of enterohemorrhagic, enteroinvasive and diffusely adherent Escherichia coli in children under 5 years in rural Mozambique: a case-control study

BACKGROUND NlmCategory: BACKGROUND content: Diarrheagenic Escherichia coli (DEC) are among the leading pathogens associated with endemic diarrhea in low income countries. Yet, few epidemiological studies have focused the contribution of enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC) and diffusely adherent E. coli (DAEC). - Label: METHODS NlmCategory: METHODS content: "We assessed the contribution of EHEC, EIEC and DAEC isolated from stool samples from a case-control study conducted in children aged <\xE2\x80\x895\xE2\x80\x89years in Southern Mozambique between December 2007 and November 2012. The isolates were screened by conventional PCR targeting stx1 and stx2 (EHEC), ial and ipaH (EIEC), and daaE (DAEC) genes." - Label: RESULTS NlmCategory: RESULTS content: "We analyzed 297 samples from cases with less-severe diarrhea (LSD) matched to 297 controls, and 89 samples from cases with moderate-to-severe diarrhea (MSD) matched to 222 controls, collected between November 3, 2011 and November 2, 2012. DEC were more common among LSD cases (2.7%, [8/297] of cases vs. 1.3% [4/297] of controls; p\xC2\xA0=\xE2\x80\x890.243]) than in MSD cases (0%, [0/89] of cases vs. 0.4%, [1/222]\xC2\xA0of controls; p\xC2\xA0=\xE2\x80\x891.000). Detailed analysis revealed low frequency of EHEC, DAEC or EIEC and no association with diarrhea in all age strata. Although the low frequency, EIEC was predominant in LSD cases aged 24-59\xE2\x80\x89months (4.1% for cases vs. 0% for controls), followed by DAEC in similar frequency for cases and controls in infants (1.9%) and lastly EHEC from one control. Analysis of a subset of samples from previous period (December 10, 2007 and October 31, 2011) showed high frequency of DEC in controls compared to MSD cases (16.2%, [25/154] vs. 11.9%, [14/118], p\xC2\xA0=\xE2\x80\x890.383, respectively). Among these, DAEC predominated, being detected in 7.7% of cases vs. 17.6% of controls aged 24-59\xE2\x80\x89months, followed by EIEC in 7.7% of cases vs. 5.9% of controls for the same age category, although no association was observed. EHEC was detected in one sample from cases and two from controls." - Label: CONCLUSIONS NlmCategory: CONCLUSIONS content: Our data suggests that although EHEC, DAEC and EIEC are less frequent in endemic diarrhea in rural Mozambique, attention should be given to their transmission dynamics (e.g. the role on sporadic or epidemic diarrhea) considering that the role of asymptomatic individuals as source of dissemination remains unknown