O Brasil, como país detentor da maior biodiversidade mundial de plantas, possui um importante papel no desenvolvimento de pesquisas que auxiliem ou viabilizem a identificação de sua diversidade vegetal, como o estudo de marcadores moleculares adequados a esta tarefa. Fabaceae, Lauraceae e Myrtaceae são as famílias mais importantes da Flora Brasileira por apresentarem grande diversidade de gêneros e espécies e serem consideradas de difícil identificação pela taxonomia tradicional. Tendo em vista o potencial do rbcL na identificação molecular de plantas, este trabalho propôs estudar a eficiência deste marcador em identificar gêneros e espécies das três principais famílias de árvores da Flora do Estado de São Paulo. Foi criado um banco de sequências de rbcL contendo 160 espécies, o qual foi testado quanto sua eficiência de identificação através de um teste cego contendo as sequências inteiras (maior que 400 pares de base) e as sequências de tamanho reduzido em 300, 200 e 100 pb. O teste cego também foi realizado no banco de sequências mundial Boldsystems. Para a análise dos resultados foi utilizado o programa BLAST que busca similaridades entre as sequências. Os resultados evidenciaram a viabilidade do método ao mostrar que o rbcL identificou 100% dos gêneros arbóreos de Fabaceae e Myrtaceae, porém não podemos dizer o mesmo para identificar gêneros de Lauraceae e nem em nível específico para qualquer uma das famílias, já o teste de identificação com as sequências reduzidas mostrou que a sequência de rbcL da espécie a ser analisada deve conter mais que 400 pares de base para não comprometer a correta identificação de gênero. / Brazil, as the country with the greatest biodiversity in the world, has an important role in the development of research to help or enables the identification of its plant diversity, such as the study of suitable molecular markers for this task. Fabaceae, Lauraceae and Myrtaceae are the most important families of the Brazilian Flora because they present a large diversity of genera and species and are considered difficult to identify by the traditional taxonomy. Considering the potential of rbcL in the molecular identification of plants, this work aims to study the efficiency of this marker in identifying genera and species of the three main tree families of São Paulo State\'s Flora. A rbcL sequence Bank containing 160 tree species was created in order to test its efficiency through a blind test with whole and reduced sequences using the BLAST program that searches for similarities between sequences. The blind identification test was also performed using the Boldsystems database. The results showed that the rbcL can´t be indicated to identify Lauraceae tree genera, but can be indicated to successfully identify tree genera of Fabaceae and Myrtaceae. The test identification with reduced sequences showed that the analized specie must have at least 400pb to not compromise the correct genera identification.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2018-05-04T17:50:45Z No. of bitstreams: 1 2014 - Paloma Martins Mendon?a.pdf: 5837915 bytes, checksum: 4380ed0e7adefff59205996c112ae7af (MD5) / Made available in DSpace on 2018-05-04T17:50:46Z (GMT). No. of bitstreams: 1 2014 - Paloma Martins Mendon?a.pdf: 5837915 bytes, checksum: 4380ed0e7adefff59205996c112ae7af (MD5) Previous issue date: 2014-10-16 / CNPq / The Order Diptera is composed by about 153 thousand described species, but it is believed that the number of unknown species is much bigger. Adults and immature of some muscoid dipteran groups have little morphological differences, making the identification process more difficult. Besides, the available dichotomous keys are based on adults, but in the case of myiasis and cadaver colonization, only immature are found. These insects are known pathogen vectors, their larvae parasite humans and animais and they play an important role in forensic entomology. Therefore, the correct identification of these species is very important. This study aims to characterize features of medical, veterinary and forensic important dipteran species using two new approaches. The first chapter uses scanning electron microscopy which gives detailed information on the morphological characters that can help identify the immature forms of the flies. Immatures belonging to three muscoids with forensic and sanitary importance were studied using this methodology: Peckia (Eubaettcheria) cal/usar (Diptera: Sarcophagidae) (larvae and puparia), Luc?lia cuprina (larvae and puparia) e Cachliamyia macellaria (eggs, larvae and puparia) (Diptera: Calliphoridae). The size ofthe chorionic cells as well as the absence of spines at the posterior spiracle allowed to differentiate C. mace/faria from C. haminivarax, both myiasis causing species. The maxillary palp complex composed by a group of papillae inside a cavity seem to be specific to the subgenus Eubaeucheria. The anterior spiracular openings displaced in an irregular row are found exclusively in Sarcophagidae. The filiform spines at the anal segments are found only in the genus Lucilia. In the second chapter, barcading is used to provide a gene sequence database of medical, veterinary and forensically important Calliphoridae flies. This technique is based on the sequencing of a portion of the genome of the mitochondrial cytochrome oxidase l (cal) gene. Nine species of flies were collected in four regions in Brazil, corresponding to 346 specimens. Two other gene fragments ( elongation factor 1 alpha and white) were sequenced for the first time for some species. The barcade proposal was successfully achieved for Hemilucilia segmentaria, Hemi/ucilia semidiaphana, Chlarapracla idiaidea, Cachliamyia macellaria, Chrysamya megacephala and Chrysamya albiceps, for which the intraspecific variation was less than 3%. However, for Lucilia eximia, Chrysamya putaria and Chrysamya rufifacies, this methodology brought incipient results. Intraspecific variation among Lucilia eximia samples was 4.6%, suggesting that the threshold proposed should not be used for ali dipteran species without previous analysis of the studied group. Chrysamya putaria is polyphyletic according to nuclear and mitochondrial genes. In addition, a set of samples grouped with samples of C. albiceps and C. rufifacies. Therefore, more studies need to be clone to better explain these taxonomic problems. / A ordem Diptera ? composta por aproximadamente 153 mil esp?cies descritas, mas acredita-se que o n?mero de esp?cies ainda desconhecidas ? muito grande. Alguns grupos de d?pteros musc?ides possuem imaturos e adultos com poucas varia??es morfol?gicas, dificultando muito o processo de identifica??o. Al?m disso, as chaves dicot?micas existentes s?o baseadas nos adultos, entretanto, s?o os imaturos mais encontrados causando mi?ases ou colonizando cad?veres. Estes inselos s?o conhecidos vetores de pat?genos, suas larvas s?o parasitas de humanos e animais e apresentam papel importante como auxilio a entomologia forense. Assim, a correta identifica??o das esp?cies que desempenham estas fun??es ? muito importante. O presente estudo tem como objetivo principal caracterizar esp?cies de d?ptcros mnscoidcs de import?ncia m?dica-veterin?ria e forense, atrav?s da utiliza??o de duas t?cnicas modernas de identifica??o. O primeiro cap?tulo utiliza a microscopia eletr?nica de varredura que permite a visualiza??o e a determina??o de caracteres que possam ser utilizados na identifica??o das esp?cies. Foram estudados imaturos de tr?s esp?cies de d?pteros de duas fam?lias diferentes: Peckia (Eubaettcheria) callusar (Diptera: Sarcophagidae) (larvas e pup?rios), Lucilia cuprina (larvas e pup?rios) e Cachliamyia macellaria (ovos, larvas e pup?rios) (Diptera: Calliphoridae) atrav?s desta t?cnica. O tamanho das c?lulas do exoc?rion permitiu diferenciar entre C. macellaria e C. haminivarax, duas esp?cies causadoras de mi?ases. A aus?ncia de espinhos no espir?culo posterior das larvas de C. macellaria tamb?m a diferencia de C. haminivarax. As papilas do complexo do palpo maxilar em uma cavidade parecem ser espec?ficas do subg?nero Eubaettcheria. As aberturas respirat?rias do espir?culo anterior dispostas em fileiras irregulares s?o exclusivas da fam?lia Sarcophagidae. A presen?a de espinhos filamentosos no ?ltimo segmento larval ? caracter?stica espec?fica do g?nero Lucilia. No segundo cap?tulo, a t?cnica de harcade ? utilizada para a forma??o de um banco de dados contendo sequ?ncias g?nicas de esp?cies de import?ncia m?dica-veterin?ria e forense da fam?lia Calliphoridae. Esta t?cnica baseia-se no sequenciamento de uma por??o do gene mitocondrial citocromo oxidase I (cal). Foram analisadas nove esp?cies de d?pteros, coletadas em quatro regi?es do Brasil, em um total de 346 esp?cimes utilizados. Dois segmentos do genoma nuclear (fator de elonga??o 1 alfa e white) tamb?m foram sequenciados pela primeira vez para algumas esp?cies. A proposta de barcade foi bem sucedida em Hemilucilia segmentaria, Hemilucilia semidiaphana, Chlaraprocta idiaidea, Cachliamyia macellaria, Chrysamya megacephala e Chrysamya albiceps, onde a varia??o intraespec?fica foi menor do que 3%. Entretanto, em Lucilia eximia, Chrysamya putaria e Ch1ysamya rufifacies esta metodologia trouxe resultados incipientes. A varia??o intraespec?fica em Lucilia eximia foi 4,6%, sugerindo que o limiar proposto n?o deve ser aplicado em todos os d?pteros sem an?lise pr?via do grupo estudado. Chrysamya pularia ? uma esp?cie polifi!?tica comprovada tanto pelos genes nucleares quanto mitocondrial, al?m isso, uma parte das amostras forma um agrupamento com as amostras de C. albiceps e C. nijifacies. Assim, acrcditase que mais estudos precisam ser conduzidos com o objetivo de esclarecer melhor estas quest?es taxon?micas.

Changes to traditional taxonomic methods to incorporate new technologies and methods have already improved the quality of species hypotheses, but more work can be done to improve the speed of new species documentation. The mitochondrial COI DNA barcode has been successfully used to identify species with high accuracy since the early 2000s, and has been used in conjunction with morphological examinations and other DNA markers to discover and delimit new species. This thesis explores the application of DNA barcodes as the primary data for delimitation and diagnosis of new species of ichneumonoids. The genera Zelomorpha and Hemichoma are revised and 18 new species from the Área de Conservación Guanacaste in Costa Rica are diagnosed based on COI barcodes. Two additional species are described based on morphology. An illustrated morphological key and morphological diagnoses for each species are also included.

Adverse drug events, resulting in preventable patient harm or death, are of great concern. To keep patients safe, hospitals have implemented barcode medication administration (BCMA) technology for RNs who have accepted this technology with varying levels of satisfaction. When nurses are dissatisfied with a BCMA system, they may find alternative methods to complete their work. Framed by the Technology Acceptance Model (Davis, 1989), this analytic, cross-sectional study aimed to understand the relationship between BCMA satisfaction and workarounds, perceived ease of use (PEOU) and perceived usefulness (PU) of a BCMA system by 80 hospital-based RNs in northeastern US. Data were collected using the Workaround Usage and Satisfaction with Barcoding Instrument for Nurses (WUSBIN), which was adapted from Hurley's (2006) Medication Administration System-Nurses Assessment of Satisfaction Scale (MAS-NAS) Halbesleben and Rathert's (2010) Workaround Assessment. Results suggested that RNs who were more satisfied with the BCMA system were less likely to use workarounds than nurses who were less satisfied (r2(78)= -.681, p < .05). Significant relationships were noted among BCMA Satisfaction and PEOU (r2(78) = -.725, p < .05), Workaround Usage and PEOU (r2(78) =.943, p < .05) and Workaround Usage and PU (r2(78)=.501, p < .05). RNs perceived the BCMA system to be easy to use (PEOU), but not very useful (PU). BCMA Satisfaction was significantly related to the use of six workarounds, while Workaround Usage was significantly related to five. Significant relationships were also noted among both BCMA Satisfaction (r2(78) = -.393, p < .01), and Workaround Usage (r2(78) = .423, p < .01) with the total number of workarounds used. Significant relationships were found among demographic variables, BCMA Satisfaction, and Workaround Usage. Since admitting to the use of workarounds may be a sensitive matter for RNs, measuring BCMA satisfaction may help understand the state of patient safety related to medication administration. Based on high satisfaction scores and low workaround usage, a profile may be developed to identify nurse champions to improve quality of care. Further research is indicated to fully understand these possibilities. / School of Nursing / Nursing / PhD / Dissertation

A new era of malaria eradication programs relies on increased knowledge of the parasite through sequencing of the Plasmodium genome. Programs call for re-orientation at specific epidemiological markers as regions move from control towards pre- and total elimination. However, relatively little is known about the effects of intervention strategies on the parasite population or if the epidemiological cues correspond to effects on the parasite population. We hypothesized that genomic tools could be used to track population changes in Plasmodium falciparum to detect significant shifts as eradication programs apply interventions. Making use of new whole-genome sequencing data as well as GWAS and other studies, we used SNPs as biological markers for regions associated with drug resistance as well as a set of neutral SNPs to identify individual parasites. By utilizing tools developed as proxy for full genomic sequencing of the human pathogen Plasmodium falciparum, we characterized and tracked parasite populations to test for changes over time and between populations. When applied to markers under selection - those associated with reduced antimalarial drug sensitivity - we were able to track migration of resistance-associated mutations in the population and identify new mutations with potential implications for resistance. Using a population genetic analysis toolbox to study changes in neutral allele frequencies in samples from the field, we found significant population changes over time that included restricted effective population size, reduced complexity of infections, and evidence for both clonal and epidemic propagation of parasites.

Στην παρούσα μεταπτυχιακή εργασία παρουσιάζονται και συγκρίνονται οι νέες τεχνολογίες που συνδέονται με τη διαχείριση της εφοδιαστικής αλυσίδας. Αρχικά αναλύονται οι έννοιες της διαχείρισης της εφοδιαστικής αλυσίδας και της επιστήμης των Logistics. Στη συνέχεια παρουσιάζονται τα σύγχρονα συστήματα ιχνηλασιμότητας και κωδικοποίησης των προϊόντων που εμπλέκονται στην παραγωγική διαδικασία. Κατόπιν αναλύονται οι πιο εφαρμόσιμες μορφές τεχνολογίας στην ταυτοποίηση των προϊόντων, δηλαδή των barcodes και του RFID. Τέλος, περιγράφεται και τονίζεται η σημασία της μεθόδου DDSN, μεθόδου πρόγνωσης της ζήτησης με βάση τις απαιτήσεις των πελατών. / In this paper are presented and compared the new technologies which are related with the Supply Chain Management. At first, there are analyzed the definitions of the Supply Chain Management and the Science of Logistics. Furthermore, there is a presentation of the modern products’ tracking and encoding systems related with the process of production. Moreover, there are analyzed the most applicable forms of technology in the identification of products, namely barcodes and RFID. Finally, is described and stressed the importance of method DDSN, method of forecast of demand with base the requirements of customers.

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

Main goal of graduation theses is analysis possibilities to use logistic technologies in food company Fontea. This analysis is focused on material and informative flows in her logistic chain including analysis of key factors. These factors are important for implementation of chosen technologies. Subsequently were analyzed customer department, sales department, production department, purchasing department and shipping department. There were found several principal problems. Customer department staffs have a problem with finding actual quantity of manufactured finished goods, because up-dating of computer system is provided only once a day. Most of orders are inserted manually in computer system. Staffs are not able to find out charges of manufactured finished goods. Similar problems were discovered also in the next departments. To fix the problem were suggested implementation of Quick Response and automatic identification of barcodes and Radio Frequency Identification (RFID).

Abnormal activation of brain microglial cells is widely implicated in the pathogenesis of schizophrenia. The disrupted balance of microglia phenotypes has been hypothesized to influence the clinical course of the disease and affect symptom severity. Previously, the pathophysiology of microglial activation was considered to be intrinsic to the central nervous system. We hypothesised that due to their perivascular localization, microglia can also be activated by factors present in circulating blood. We applied a high-content functional screening platform, to characterize alterations in microglial intracellular signalling cascades induced by schizophrenia patient serum relative to control serum. Using automated sample preparation, fluorescent cellular barcoding and flow cytometry, the applied platform is capable of detecting multiple parallel cell signalling responses in microglia. First, we exposed a human microglia cell line to serum isolated from first-onset drug-naïve schizophrenia patients (n=60) and healthy controls (n=79). We were able to show that peripheral blood serum obtained from schizophrenia patients induced differential microglial cell signalling network responses in vitro. We subsequently assessed whether antipsychotic drug-treatment can normalise the abnormal microglial signalling responses previously identified by exposing microglia cells to serum from antipsychotic treated schizophrenia patients (n=15) and controls (n=17). In addition, in order to assess microglia activation in vivo, we obtained positron emission tomography (PET) imaging data from collaborators, who used a radiotracer to assess potential altered microglia activation in patients suffering from schizophrenia. Finally, as a proof of concept study, we attempted to validate these findings by assessing the effect of serum collected from first-onset drug-naïve schizophrenia patients (n=9), controls (n=12) as well as serum isolated from the same patients subjected to six weeks of clinical treatment with the antipsychotic olanzapine (n=9). This study aimed to identify normalisation of previously detected differences in microglia signalling pathways based on successful in vivo treatment. We demonstrate that peripheral blood serum isolated from schizophrenia patients, independent of their treatment status, is sufficient to trigger microglial cell signalling network responses in vitro, which are indicative of altered STAT3 signalling. We further explored the composition of the serum for differential expression of analytes, previously associated with neuropsychiatric disorders, and the utility of the detected microglial cellular phenotype as a target for novel drug discovery.