Aerospace medicine and biology: A continuing bibliography with indexes (supplement 333)

This bibliography lists 122 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during January, 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Bond Additive Modeling 1. Adriatic Indices

Some of the most famous molecular descriptors are bond additive, i.e. they are calculated as the sum of edge contributions (Randić-type indices, Balaban-type indices, Wiener index and its modifications, Szeged index...). In this paper, the methods of calculations of bond contributions of these descriptors are analyzed. The general concepts are extracted, and based on these concepts a large class of molecular descriptors is defined. These descriptors are named Adriatic indices. An especially interesting subclass of these descriptors consists of 148 discrete Adriatic indices. They are analyzed on the testing sets provided by the International Academy of Mathematical Chemistry, and it has been shown that they have good predictive properties in many cases. They can be easily encoded in the computer and it may be of interest to incorporate them in the existing software packages for chemical modeling. It is possible that they could improve various QSAR and QSPR studies

Wastewater treatment improvement through an intelligent integrated supervisory system

Aquest article mostra el resultat de la col·laboració portada a terme durant els darrers anys entre grups d'enginyeria química, enginyeria ambiental i intel·ligència artificial. El treball se centra en el desenvolupament de tècniques per a la millora i supervisió de processos complexos, especialment del tractament biològic d'aigües residuals. L'experiència demostra que la millor opció requereix desenvolupar un sistema supervisor que combini i integri tècniques de control clàssic (controlador automàtic del nivell d'oxigen dissolt en el reactor biològic, ús de models descriptius del procés, etc.) amb sistemes basats en el coneixement (concretament sistemes experts i sistemes basats en casos). El present article descriu la complexitat de la gestió del procés de tractament de les aigües residuals, l'arquitectura integrada que es proposa i el desenvolupament i la construcció de cadascun dels mòduls d'aquesta proposta per a la implementació real a l'estació depuradora d'aigües residuals de Granollers. Finalment, es detallen alguns resultats del procés de validació del seu funcionament enfront de situacions quotidianes de la planta.This paper shows the result of years of work by a cooperative research group including chemical engineers, environmental scientists and computer scientists. This research has been focused on the development and implementation of new techniques for the optimisation of complex process management, mainly related to wastewater treatment plants (WWTP). The experience obtained indicates that the best approach is a Supervisory System that combines and integrates classical control of WWTP (automatic controller for maintaining a fixed dissolved oxygen level in the aeration tank, use of mathematical models to describe the process...) with the application of knowledge-based systems (mainly expert systems and case-based systems). The first part is an introduction to wastewater treatment processes and an explanation of the complexity of the management and control of such complex processes. The next section illustrates the architecture of the supervisory system and the work carried out to develop and build the expert system, the casebased system and the simulation model for implementation in a real plant (the Granollers WWTP). Finally, some results of the field validation phase of the Supervisory System when dealing with real situations in the plant are described

A treatment of stereochemistry in computer aided organic synthesis

This thesis describes the author’s contributions to a new stereochemical processing module constructed for the ARChem retrosynthesis program. The purpose of the module is to add the ability to perform enantioselective and diastereoselective retrosynthetic disconnections and generate appropriate precursor molecules. The module uses evidence based rules generated from a large database of literature reactions. Chapter 1 provides an introduction and critical review of the published body of work for computer aided synthesis design. The role of computer perception of key structural features (rings, functions groups etc.) and the construction and use of reaction transforms for generating precursors is discussed. Emphasis is also given to the application of strategies in retrosynthetic analysis. The availability of large reaction databases has enabled a new generation of retrosynthesis design programs to be developed that use automatically generated transforms assembled from published reactions. A brief description of the transform generation method employed by ARChem is given. Chapter 2 describes the algorithms devised by the author for handling the computer recognition and representation of the stereochemical features found in molecule and reaction scheme diagrams. The approach is generalised and uses flexible recognition patterns to transform information found in chemical diagrams into concise stereo descriptors for computer processing. An algorithm for efficiently comparing and classifying pairs of stereo descriptors is described. This algorithm is central for solving the stereochemical constraints in a variety of substructure matching problems addressed in chapter 3. The concise representation of reactions and transform rules as hyperstructure graphs is described. Chapter 3 is concerned with the efficient and reliable detection of stereochemical symmetry in both molecules, reactions and rules. A novel symmetry perception algorithm, based on a constraints satisfaction problem (CSP) solver, is described. The use of a CSP solver to implement an isomorph‐free matching algorithm for stereochemical substructure matching is detailed. The prime function of this algorithm is to seek out unique retron locations in target molecules and then to generate precursor molecules without duplications due to symmetry. Novel algorithms for classifying asymmetric, pseudo‐asymmetric and symmetric stereocentres; meso, centro, and C2 symmetric molecules; and the stereotopicity of trigonal (sp2) centres are described. Chapter 4 introduces and formalises the annotated structural language used to create both retrosynthetic rules and the patterns used for functional group recognition. A novel functional group recognition package is described along with its use to detect important electronic features such as electron‐withdrawing or donating groups and leaving groups. The functional groups and electronic features are used as constraints in retron rules to improve transform relevance. Chapter 5 details the approach taken to design detailed stereoselective and substrate controlled transforms from organised hierarchies of rules. The rules employ a rich set of constraints annotations that concisely describe the keying retrons. The application of the transforms for collating evidence based scoring parameters from published reaction examples is described. A survey of available reaction databases and the techniques for mining stereoselective reactions is demonstrated. A data mining tool was developed for finding the best reputable stereoselective reaction types for coding as transforms. For various reasons it was not possible during the research period to fully integrate this work with the ARChem program. Instead, Chapter 6 introduces a novel one‐step retrosynthesis module to test the developed transforms. The retrosynthesis algorithms use the organisation of the transform rule hierarchy to efficiently locate the best retron matches using all applicable stereoselective transforms. This module was tested using a small set of selected target molecules and the generated routes were ranked using a series of measured parameters including: stereocentre clearance and bond cleavage; example reputation; estimated stereoselectivity with reliability; and evidence of tolerated functional groups. In addition a method for detecting regioselectivity issues is presented. This work presents a number of algorithms using common set and graph theory operations and notations. Appendix A lists the set theory symbols and meanings. Appendix B summarises and defines the common graph theory terminology used throughout this thesis

Novel methods for the analysis of small molecule fragmentation mass spectra

The identification of small molecules, such as metabolites, in a high throughput manner plays an important in many research areas. Mass spectrometry (MS) is one of the predominant analysis technologies and is much more sensitive than nuclear magnetic resonance spectroscopy. Fragmentation of the molecules is used to obtain information beyond its mass. Gas chromatography-MS is one of the oldest and most widespread techniques for the analysis of small molecules. Commonly, the molecule is fragmented using electron ionization (EI). Using this technique, the molecular ion peak is often barely visible in the mass spectrum or even absent. We present a method to calculate fragmentation trees from high mass accuracy EI spectra, which annotate the peaks in the mass spectrum with molecular formulas of fragments and explain relevant fragmentation pathways. Fragmentation trees enable the identification of the molecular ion and its molecular formula if the molecular ion is present in the spectrum. The method works even if the molecular ion is of very low abundance. MS experts confirm that the calculated trees correspond very well to known fragmentation mechanisms.Using pairwise local alignments of fragmentation trees, structural and chemical similarities to already-known molecules can be determined. In order to compare a fragmentation tree of an unknown metabolite to a huge database of fragmentation trees, fast algorithms for solving the tree alignment problem are required. Unfortunately the alignment of unordered trees, such as fragmentation trees, is NP-hard. We present three exact algorithms for the problem. Evaluation of our methods showed that thousands of alignments can be computed in a matter of minutes. Both the computation and the comparison of fragmentation trees are rule-free approaches that require no chemical knowledge about the unknown molecule and thus will be very helpful in the automated analysis of metabolites that are not included in common libraries

Wastewater treatment improvement through an intelligent integrated supervisory system

This paper shows the result of years of work by a cooperative research group including chemical engineers, environmental scientists and computer scientists. This research has been focused on the development and implementation of new techniques for the optimisation of complex process management, mainly related to wastewater treatment plants (WWTP). The experience obtained indicates that the best approach is a Supervisory System that combines and integrates classical control of WWTP (automatic controller for maintaining a fixed dissolved oxygen level in the aeration tank, use of mathematical models to describe the process...) with the application of knowledge-based systems (mainly expert systems and case-based systems). The first part is an introduction to wastewater treatment processes and an explanation of the complexity of the management and control of such complex processes. The next section illustrates the architecture of the supervisory system and the work carried out to develop and build the expert system, the casebased system and the simulation model for implementation in a real plant (the Granollers WWTP). Finally, some results of the field validation phase of the Supervisory System when dealing with real situations in the plant are described.Aquest article mostra el resultat de la col·laboració portada a terme durant els darrers anys entre grups d'enginyeria química, enginyeria ambiental i intel·ligència artificial. El treball se centra en el desenvolupament de tècniques per a la millora i supervisió de processos complexos, especialment del tractament biològic d'aigües residuals. L'experiència demostra que la millor opció requereix desenvolupar un sistema supervisor que combini i integri tècniques de control clàssic (controlador automàtic del nivell d'oxigen dissolt en el reactor biològic, ús de models descriptius del procés, etc.) amb sistemes basats en el coneixement (concretament sistemes experts i sistemes basats en casos). El present article descriu la complexitat de la gestió del procés de tractament de les aigües residuals, l'arquitectura integrada que es proposa i el desenvolupament i la construcció de cadascun dels mòduls d'aquesta proposta per a la implementació real a l'estació depuradora d'aigües residuals de Granollers. Finalment, es detallen alguns resultats del procés de validació del seu funcionament enfront de situacions quotidianes de la planta

A review of the meteorological parameters which affect aerial application

The ambient wind field and temperature gradient were found to be the most important parameters. Investigation results indicated that the majority of meteorological parameters affecting dispersion were interdependent and the exact mechanism by which these factors influence the particle dispersion was largely unknown. The types and approximately ranges of instrumented capabilities for a systematic study of the significant meteorological parameters influencing aerial applications were defined. Current mathematical dispersion models were also briefly reviewed. Unfortunately, a rigorous dispersion model which could be applied to aerial application was not available

Alternative splicing detection across different tissues in cork oak

Tese de mestrado, Bioinformática e Biologia Computacional (Bioinformática) Universidade de Lisboa, Faculdade de Ciências, 2017As florestas de sobreiro (Quercus suber L.) são recursos únicos e emblemáticos em Portugal, com elevado impacto económico, ecológico e social. A disponibilidade recente da sequência do genoma de sobreiro forneceu um importante contributo para revitalizar a pesquisa em temas como desenvolvimento de cortiça e melhoramento da planta, assim como promover a competitividade da indústria da cortiça. No entanto, é ainda necessário adicionar mais detalhe à anotação estrutural do genoma, nomeadamente ao nível dos transcritos, incluindo previsão de eventos de splicing alternativo. O splicing alternativo (AS) é um processo usado durante a expressão génica que origina diferentes variantes de transcritos (isoformas) e produtos proteicos a partir um único gene. No presente estudo, procedemos à análise de dezasseis bibliotecas de RNA-seq, preparadas a partir de quatro tecidos de sobreiro (folhas, felema, entrecasco e xilema), de modo a prever novas formas de AS para genes já previstos e melhorar a anotação estrutural do genoma. Um protocolo bioinformático foi definido para testar o desempenho do software HISAT2 e STAR para mapeamento de reads de RNAseq no genoma de referência, e do software Cufflinks e StringTie para (re)construção de transcritos. O alinhamento de reads no genoma efetuado com STAR resultou em taxas de mapeamento (de 84,22% a 86,86%) superiores aos resultados atingidos com HISAT2 (73,88% a 76,55%). Assim, os resultados de mapeamento com STAR foram utilizados para a (re)construção de transcritos. O uso do StringTie para este processo foi globalmente mais conservador do que com Cufflinks, gerando menos transcritos novos, mas com melhor cobertura de reads por pares de base. Para melhorar a precisão da anotação e reduzir falsos positivos, foi realizado um passo adicional de otimização com StringTie. Desta otimização resultou uma anotação que prevê a ocorrência de 7 958 novos transcritos (8% dos transcritos totais), dos quais 5 453 são novas isoformas para genes previstos na anotação de referência. Esta nova anotação foi utilizada como referência para estimar a abundância dos transcritos em cada um dos tecidos estudados e efetuar a análise de expressão diferencial. Cerca de 16% de todos os genes expressos nos quatro tecidos e que contêm intrões apresentaram splicing alternativo, e os principais eventos de splicing foram alternative acceptor site e intron retention. Grupos de transcritos com expressão diferencial entre os quatro tecidos foram identificados e a análise de enriquecimento funcional confirmou os principais processos biológicos esperados para cada tecido: os transcritos mais expressos nas folhas e no xilema estavam relacionados com a fotossíntese e com transporte, respetivamente; transcritos mais expressos na periderme (felema e entrecasco) mostraram um enriquecimento em categorias funcionais relacionadas com a síntese de suberina e outros componentes de parede celular presentes nas células de cortiça. Estes grupos específicos mostraram também um enriquecimento em transcritos envolvidos na resposta ao stresse (biótico ou abiótico). Nos tecidos que compõem a periderme, este enriquecimento foi observado principalmente no entrecasco, enquanto que no felema foi detetado um enriquecimento em transcritos envolvidos no metabolismo secundário. A presente tese permitiu a definição de um protocolo padrão que poderá ser usado para estudar o splicing alternativo no sobreiro e para uma análise mais aprofundada na nova versão do genoma, que estará disponível em breve.Cork oak (Quercus suber L.) forests are unique and emblematic resources for Portugal, with high economical, ecological and social significance. The recent availability of the cork oak genome sequence provided an important contribution to reinvigorate research in fundamental topics such as cork development and plant improvement, and to promote the competitiveness of cork industry. Yet, further analysis is required to add detail to genome structure annotation, namely at the transcript level, also taking into account alternative splicing. Alternative splicing (AS) is a process used during gene expression to yield different transcript variants and protein products derived from a single gene. In the present study, we analyzed sixteen RNA-seq libraries prepared from four cork oak tissues (leaf, xylem, phellem and inner bark), in order to predict new AS forms for the already predicted genes and improve genome structural annotation. A bioinformatics pipeline was defined in order to test the performance of HISAT2 and STAR for read mapping against the reference genome, and Cufflinks and StringTie for transcript assembly. STAR yielded higher mapping efficiencies (84.22% to 86.86%) for the cork oak datasets, as compared to HISAT2 (73.88% to 76.55%), and the corresponding mapping data was selected for transcript assembly. The use of StringTie for this step was globally more conservative than Cufflinks, generating less novel transcripts, but with better support by read per base coverage. A further optimization step was performed using StringTie in order to improve annotation precision. The final transcript annotation was selected from this optimization step, predicting 7,958 novel transcripts (8% of total transcripts in the new annotation), 5,453 of which were novel isoforms for genes in reference annotation. This new annotation was used as reference to estimate transcript abundance in each tissue and differential expression analysis. Approximately 16% of all intron-containing genes expressed in the four tissues were alternatively spliced and the main event found in the four cork oak tissues was alternative acceptor site, followed by intron retention. Transcript clusters showing differential expression among the four tissues were identified and functional enrichment analysis confirmed the main biological processes expected for each tissue: transcripts highly expressed in leaves and xylem were mostly related to photosynthesis and transport, respectively; transcripts highly expressed in peridermis (phellem and inner bark) showed an enrichment in functional categories related to the synthesis of suberin and other component of cork cell walls. These tissue-specific clusters also showed an enrichment in transcripts involved in the response to stress (biotic or abiotic). Yet, in peridermis, this enrichment was mostly observed in inner bark samples, while phellem samples showed an enrichment in transcripts related to secondary metabolism. This thesis allowed the definition of a standard workflow that can be used to study alternative splicing in cork oak and used for further analysis on the new improved genome version that will be available soon