Phylogenetic and taxonomic studies in Myrcia DC. sensu lato (Myrtaceae), with emphasis on the Guianensis clade

Orientadores: Renato Goldenberg, Evelyne Jill LucasTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: Myrcia s.l. é um grande grupo exclusivamente neotropical (ca. 750 espécies) que inclui em sua circunscrição os tradicionais gêneros Myrcia, Marlierea e Calyptranthes. Estudos filogenéticos recentes baseados em dados moleculares mostram estes três gêneros para- ou polifiléticos em relação uns aos outros e, desta forma, a sinonimização de Marlierea e Calyptranthes sob Myrcia é necessária para o reconhecimento de um grupo monofilético. Mrycia s.l. tem sido dividido em nove clados que servem de base para uma futura classificação sub-genérica formal, e um destes clados é o principal foco dos estudos filogenéticos e taxonômicos apresentados nesta tese. Como base para os estudos filogenéticos, uma lista incluindo 36 possíveis espécies pertencentes ao clado Guianensis foi construída. Destas espécies, 26 foram amostradas. Os estudos filogenéticos foram realizados a partir de sequências de cloroplasto e núcleo obtidas através de técnicas modernas de next-generation sequencing (sequenciamento de nova geração) e também a partir de sequências específicas (ITS, psbA-trnH, trnL-trnF, trnQ-rpl16, ndhF) obtidas por técnicas clássicas de sequenciamento de Sanger, e análises de Máxima Verossimilhança e Bayesiana foram empregadas. As relações específicas dentro do clado Guianensis e as relações entre este e os outros clados de Myrcia s.l. são discutidas em relação aos aspectos geográficos e morfológicos. De acordo com os dados moleculares, sete espécies da lista preliminar não pertencem ao clado Guianensis e uma caracterização morfológica precisa do grupo é apresentada. O grupo é composto por 29 espécies, sendo que 3 destas são novas para a ciência. As características diagnósticas mais importantes são a panícula triangular e simétrica, o hipanto glabro elevado acima do ovário, o disco estaminal glabro e o ovário 3-locular. O grupo tem ampla distribuição, desde o Caribe até o sul do Brasil e Paraguai, com centros de distribuição no Cerrado e Mata Atlântica brasileiros. Baseada nesta delimitação do grupo, uma completa revisão taxonômica e nomenclatural das 29 espécies é apresentada, incluindo descrições, ilustrações, comentários sobre morfologia, afinidades taxonômicas, fenologia, distribuição geográfica e status de conservação, e chave de identificação. Trinta e seis novos sinônimos foram propostos e 95 lectotipficações e cinco neotipificações foram feitas. Por último, uma nova espécie e notas taxonômicas em Myrcia seção Aulomyrcia (clado 9 de Myrcia s.l.) são apresentadas com descrições, ilustrações e comentáriosAbstract: Myrcia s.l. is a large exclusively Neotropical group (ca. 750 species) that includes the traditional genera Myrcia, Marlierea and Calyptranthes. Recent phylogenetic studies based on molecular data have shown these three genera para- or poly-phyletic in respect to each other and, consequently, the synonymization of Marlierea and Calyptranthes under Myrcia is necessary to recognize a monophyletic group. Myrcia s.l. has been divided in nine clades that are the basis for a future formal sub-generic classification, and one of these clades is the main focus of the phylogenetic and taxonomic studies presented herein. As a basis for the phylogenetic studies, a list of 36 species inferred to belong to the Guianensis clade was built. Twenty-six of which were sampled for molecular purposes. The phylogenetic studies were carried out with plastid and nuclear sequences obtained from modern techniques of next-generation sequencing, and also with target DNA sequences (ITS, psbA-trnH, trnL-trnF, trnQ-rpl16, ndhF) obtained from the classical Sanger sequencing. Maximum Likelihood and Bayesian analyses were employed. Specific relationships inside the Guianensis clade and relationships between this and other Myrcia s.l. clades are discussed in light of geography and morphology. According to the molecular data, seven species of the preliminary list do not belong to the Guianensis clade and a precise morphological circumscription is presented for the group. The Guianensis clade comprises 29 species, three of which are new to science. The main diagnostic characters are the symmetrical and triangular panicle, the glabrous hypanthium prolonged beyond the ovary, the glabrous staminal ring and the 3-locular ovary. The group has a wide geographic distribution, from Caribbean to southern Brazil and Paraguay, with distribution centers in the Brazilian Cerrado and Atlantic Forest. Based on the phylogenetic results, a complete taxonomic and nomenclatural revision is presented, including descriptions, illustrations, comments regarding morphology, taxonomic affinities, phenology, geographical distribution and conservation status, and identification key. Thirty-six new synonyms are proposed and 95 lectotypifications and five neotypifications are made. Lastly, a new species and taxonomic notes of Myrcia section Aulomyrcia (clade 9 of Myrcia s.l.) are presentedDoutoradoBiologia VegetalDoutora em Biologia Vegeta

A família Myrtaceae Juss. nas áreas de planície da Ilha do Mel, Paraná

Orientador: Renato GoldenbergCoorientador: Marcos SobralMonografia (Bacharelado) - Universidade Federal do Paraná. Setor de Ciências Biológicas. Curso de Graduação em Ciências BiológicasResumo : A família Myrtaceae conta com aproximadamente 132 gêneros e 5600 espécies. É dividida em duas subfamílias monofiléticas, Psiloxyloideae e Myrtoideae, esta última com 15 tribos. Dentre essas tribos, a mais rica é Myrteae, que compreende todas as mirtáceas americanas, exceto o gênero Tepualia. As plantas pertencentes a essa tribo são caracterizadas principalmente pelas folhas simples e opostas, com numerosas glândulas translúcidas, e geralmente com uma nervura marginal. A Ilha do Mel pertence ao município de Paranaguá e está localizada no centro do litoral paranaense, a aproximadamente 2800 metros do continente. É constituída de morros e planícies, sendo que estas totalizam 93,8% da área total da ilha. A vegetação da planície pode ser dividida em três tipos vegetacionais: florestas, fruticetos (formações arbustivas com elementos arbóreos isolados) e formações campestres. O estado do Paraná apresenta escassez de estudos relacionados à Myrtaceae. Visto isto, este trabalho tem por objetivo fornecer subsídios para futuros estudos relacionados com a Flora Paranaense, especialmente a flora do litoral do estado, através da chave de identificação e das descrições das espécies de Myrtaceae ocorrentes na Ilha do Mel. O trabalho foi realizado através da análise de exsicatas provenientes da Ilha do Mel depositadas nos herbários MBM, UEC e UPCB, e de material coletado nas saídas a campo. Quando preciso, para complementação das descrições, foram realizadas análises de outros materiais, sempre dando preferência ao litoral paranaense. Os dados de floração, frutificação e distribuições foram descritos com base nas coleções visitadas e em literatura. Táxons infra-específicos não foram considerados neste trabalho. A família está representada por 31 espécies na Ilha do Mel, distribuídas em nove gêneros: Myrcia (11 spp.), Eugenia (7 spp.), Calyptranthes (3 spp.), Marlierea (3 spp.), Psidium (2 spp.) Syzygium (2 spp.), Blepharocalyx (1 sp.), Neomitranthes (1 sp.) e Siphoneugena (1sp.). Estas espécies estão distribuídas em dois dos três tipos vegetacionais da Ilha do Mel, sendo que as florestas são mais representativas (27 spp.), seguidas dos fruticetos (12 spp.). Além disso, cinco espécies ainda ocorrem nas regiões das vilas, sendo que três delas são restritas a estas áreas. Três espécies (Psidium guajava, Syzygium cumini e S. jambos) são introduzidas. O estado é limite sul de ocorrência no Brasil para cinco espécies (Eugenia cuprea, E. neoglomerata, Myrcia hexasticha, M. isaiana, Siphoneugena guilfoyleiana). Myrcia dichrophylla teve seu primeiro registro para o estado do Paraná e tem limite norte de distribuição brasileira no estado

Ambient Laboratory Coater for Advanced Gas Reactor Fuel Development

this research is targeted at developing improved experimentally-based scaling relationships for the hydrodynamics of shallow, gas-spouted beds of dense particles. The work is motivated by the need to more effctively scale up shallow spouted beds used in processes such as in the coating of nuclear fuel particles where precise control of solids and gas circulation is critically important. Experimental results reported here are for a 50 mm diameter spouted bed containing two different types of bed solids (alumina and zirconia) at different static bed depths and fluidized by air and helium. Measurements of multiple local average pressures, inlet gas pressure fluctuations, and spout height were used to characterize the bed hydrodynamics for each operating condition. Follow-on studies are planned that include additional variations in bed size, particle properties, and fluidizing gas. The ultimate objective is to identify the most important non-dimensional hydrodynamic scaling groups and possible spouted-bed design correlations based on these groups

Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination

Network inference deals with the reconstruction of biological networks from experimental data. A variety of different reverse engineering techniques are available; they differ in the underlying assumptions and mathematical models used. One common problem for all approaches stems from the complexity of the task, due to the combinatorial explosion of different network topologies for increasing network size. To handle this problem, constraints are frequently used, for example on the node degree, number of edges, or constraints on regulation functions between network components. We propose to exploit topological considerations in the inference of gene regulatory networks. Such systems are often controlled by a small number of hub genes, while most other genes have only limited influence on the network's dynamic. We model gene regulation using a Bayesian network with discrete, Boolean nodes. A hierarchical prior is employed to identify hub genes. The first layer of the prior is used to regularize weights on edges emanating from one specific node. A second prior on hyperparameters controls the magnitude of the former regularization for different nodes. The net effect is that central nodes tend to form in reconstructed networks. Network reconstruction is then performed by maximization of or sampling from the posterior distribution. We evaluate our approach on simulated and real experimental data, indicating that we can reconstruct main regulatory interactions from the data. We furthermore compare our approach to other state-of-the art methods, showing superior performance in identifying hubs. Using a large publicly available dataset of over 800 cell cycle regulated genes, we are able to identify several main hub genes. Our method may thus provide a valuable tool to identify interesting candidate genes for further study. Furthermore, the approach presented may stimulate further developments in regularization methods for network reconstruction from data

The impact of surgical delay on resectability of colorectal cancer: An international prospective cohort study

AIM: The SARS-CoV-2 pandemic has provided a unique opportunity to explore the impact of surgical delays on cancer resectability. This study aimed to compare resectability for colorectal cancer patients undergoing delayed versus non-delayed surgery. METHODS: This was an international prospective cohort study of consecutive colorectal cancer patients with a decision for curative surgery (January-April 2020). Surgical delay was defined as an operation taking place more than 4 weeks after treatment decision, in a patient who did not receive neoadjuvant therapy. A subgroup analysis explored the effects of delay in elective patients only. The impact of longer delays was explored in a sensitivity analysis. The primary outcome was complete resection, defined as curative resection with an R0 margin. RESULTS: Overall, 5453 patients from 304 hospitals in 47 countries were included, of whom 6.6% (358/5453) did not receive their planned operation. Of the 4304 operated patients without neoadjuvant therapy, 40.5% (1744/4304) were delayed beyond 4 weeks. Delayed patients were more likely to be older, men, more comorbid, have higher body mass index and have rectal cancer and early stage disease. Delayed patients had higher unadjusted rates of complete resection (93.7% vs. 91.9%, P = 0.032) and lower rates of emergency surgery (4.5% vs. 22.5%, P < 0.001). After adjustment, delay was not associated with a lower rate of complete resection (OR 1.18, 95% CI 0.90-1.55, P = 0.224), which was consistent in elective patients only (OR 0.94, 95% CI 0.69-1.27, P = 0.672). Longer delays were not associated with poorer outcomes. CONCLUSION: One in 15 colorectal cancer patients did not receive their planned operation during the first wave of COVID-19. Surgical delay did not appear to compromise resectability, raising the hypothesis that any reduction in long-term survival attributable to delays is likely to be due to micro-metastatic disease

Global wealth disparities drive adherence to COVID-safe pathways in head and neck cancer surgery

Peer reviewe

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone

Biosystematic and taxonomic studies on the Myrcia laruotteana Cambess. complex (Myrtaceae)

Orientadores: Renato Goldenberg, Eric de Camargo SmidtDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: Myrtaceae é conhecida como uma das mais complexas famílias de angiospermas. Myrcia teve sua última revisão taxonômica realizada há 153 anos e desde então inúmeras espécies novas foram descritas, deixando Myrcia como o segundo maior gênero da tribo Myrteae. O elevado número de espécies no gênero e a falta de uma revisão taxonômica completa e atualizada fez com que vários complexos de espécies mal delimitadas fossem formados em Myrcia. Um destes complexos é abordado no presente trabalho e inclui quatro espécies (M. laruotteana, M. lajeana, M. selloi e M. tomentosa) de ampla distribuição e grande variação morfológica, tornando difícil a separação entre os táxons. Neste estudo foram usados marcadores ISSR para investigar a correlação entre a variabilidade genética de populações destas espécies com aspectos morfológicos, geográficos, fitogeográficos e taxonômicos, a fim de esclarecer a delimitação das espécies. Levando em conta os resultados obtidos nestas análises, uma nova proposta de classificação específica é apresentada, com descrições dos táxons aceitos, dados de distribuição geográfica, floração e frutificação, e chave de identificação. No estudo de genética de populações com ISSR, o valor de diversidade genética encontrado (He = 0,215) foi mais baixo que o valor para espécies perenes, de distribuição ampla e fecundação cruzada. Isto pode ser explicado em partes pela auto-compatibilidade que as espécies do complexo M. laruotteana podem apresentar, como já relatado na literatura. Nenhum dos grupos que refletem aspectos morfológicos, geográficos e fitogeográficos testados apresentou boa estruturação genética, ou seja, nenhum deles mostrou alguma descontinuidade genética que pudesse representar os táxons envolvidos no complexo. Os grupos testados que representam a circunscrição taxonômica atual do complexo também não apresentaram boa estruturação genética. Os grupos formados a partir da análise Bayesiana mostraram melhor estruturação genética a partir da AMOVA (12% de variação entre as populações dentro dos grupos e 27% de variação entre os grupos). A análise Bayesiana juntamente com o dendrograma formado demonstra uma separação em dois grandes grupos, o primeiro formado por todas as populações de M. tomentosa, e o segundo contendo as populações das outras espécies misturadas. A partir destes resultados e levando em consideração toda a variação existente entre os extremos morfológicos das espécies, é proposta uma nova classificação para o complexo, com sinonimização de M. lajeana sob M. laruotteana. Myrcia tomentosa e M. laruotteana podem ser reconhecidas principalmente pelo indumento, geralmente denso na primeira e quase ausente na segunda. Myrcia selloi pode ser reconhecida pela queda dos remanescentes do hipanto e do cálice, deixando os frutos com uma cicatriz circular apicalAbstract: Myrtaceae is known as one of the most complex families of angiosperms. The last taxonomic revision of Myrcia was made 153 years ago and since then many new species were described, leaving Myrcia as the second largest genus of the tribe Myrteae. The high number of species in the genus and the lack of a complete and updated taxonomic revision resulted in many species complexes in Myrcia. One of these complexes is investigated in this work and includes four species (M. laruotteana, M. lajeana, M. selloi and M. tomentosa) with wide distribution and a lot of morphological variation, making it difficult to distinguish these taxa. This study used ISSR markers to investigate the correlation between the genetic variability of populations of these species with morphological, geographical, phytogeographic and taxonomic aspects, in order to clarify the delimitation of species. Taking into account the results obtained in these analyzes, a new proposal of specific classification is presented with descriptions of accepted taxa, geographical, flowering and fruiting data, and identification key. In the study of population genetics with ISSR, the value of genetic diversity (He = 0.215) was lower than the value for perennial, widely distributed and cross-fertilization species. This can be explained in part by self-compatibility that species within M. laruotteana complex apparently present, as previously reported in the literature. None of the groups that reflect morphological, geographical and phytogeographic aspects showed good genetic structure, i.e., none of them showed any genetic discontinuity that could represent the taxa involved in the complex. The groups represented by the current taxonomic circumscription of the complex also did not show good genetic structure. The groups formed from the Bayesian analysis showed better genetic structure from the AMOVA (12% variation among populations within groups and 27% variation between groups). The Bayesian analysis with the dendrogram formed showed two major groups, the first with all populations of M. tomentosa, and the second containing mixed populations from other species. From these results and taking into account the large amount of variation between the morphological extremes of the species, we propose a new classification for the complex, with the synonymization of M. lajeana under M. laruotteana. Myrcia tomentosa and M. laruotteana differ from each other mainly by the indumenta, which is dense in the former and almost absent in the latter. Myrcia selloi differs from the others by the caduceus remnants of the hypanthium and calyx, leaving circular apical scar on the fruitMestradoBiologia VegetalMestra em Biologia Vegeta