Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisionary systematics and evolutionary ecology of Neophylidorea (Diptera: Tipuloidea)

VII CHAPTER ONE: DISSERTATION OVERVIEW . 1 Crane Flies . 3 Dissertation Organization . 5 References . 6 CHAPTER TWO: BOTTOM-UP SOLUTION TO THE CRANE FLY CONFUSION: DESCRIPTION OF A NEW GENUS NEOPHYLIDOREA (DIPTERA: TIPULOIDEA) . 12 Abstract . 12 Introduction . 12 Classification of “Limnophilinae” . 13 Taxonomic History of Euphylidorea . 15. 12 Introduction . 12 Classification of “Limnophilinae” . 13 Taxonomic History of Euphylidorea . 15 Possible Solutions . 16 Methods . 17 Taxonomy . 18 Discussion . 22 References . 24 Acknowledgements . 27 Figures . 28 Tables . 31 CHAPTER THREE: INTEGRATING MORPHOLOGY, MOLECULAR AND ECOLOGICAL DATA TO DELIMIT SPECIES: SUPPORT FOR NEW COMBINATIONS OF NEOPHYLIDOREA (DIPTERA: TIPULOIDEA) . 34
Alternatives for forage evaluation in ruminants

The objective of this thesis was to validate and to compare in situ and in vitro techniques with in vivo data. These techniques were also evaluated for future and practical use in feed evaluation for ruminants. The techniques were compared using the digestion data of 98 forages and the energy values: in vivo total tract organic matter digestibility (OMD) and rumen fermentable organic matter (FOM), and the protein values: microbial nitrogen synthesised in the rumen (MNS) and rumen escape N (REN). The in situ nylon bag technique, the pepsin-cellulase technique, the gas production technique (GPT) and the Tilley and Terry technique showed good potency to predict OMD and the in situ technique and GPT gave most accurate FOM predictions. MNS was evaluated using in vivo data from the literature and showed a significant relationship with the content of crude protein in forages. The method of conservation of forages had an extra effect on MNS. REN was determined using in situ and different in vitro techniques, but only ADIN (fibre attached N) had a good relationship with in vivo
Altered calcium handling in cerebellar Purkinje neurons with the malignant hyperthermia mutation, RyR1Y522S/+

To investigate the etiology of malignant hyperthermia and central core dis ease, mouse models have recently been generated and characterized (Chelu et al., 2006). These RyR knock-in mutant mice provide an excellent tool to investigate calcium dysregulation, its pathological consequences, and potential therapeutic approac hes. Skeletal muscle harboring this mutation exhibits calcium leak from internal stores and an increased sensitivity to activation by caffeine, voltage, and temperature (D ham et al., 2008). Although alterations in RyR1 channel function and resultant changes in cellular function have been characterized in skeletal muscle, the effects of MH mutations in RyR1 on central nervous system function have not been investigated. Since RyR1 is highly expressed in cerebellar Purkinje neurons, our goal is to investigate whether the RyR mutation causes altered calcium handling and whether potential calcium dysreg ulation alters cellular function.
Detecção de genes codificadores de resistência a antimicrobianos de importância clínica em amostras de carne de frango

COAN, M. M. Detecção de genes codificadores de resistência a antimicrobianos de importância clínica em amostras de carne de frango [Dissertação de Mestrado]. São Paulo: Faculdade de Saúde Pública da USP; 2014/ Detection of genes encoding resistance to clinically important antibiotics in samples of chicken. São Paulo (BR): Faculdade de Saúde Pública da USP; 2014. Introduction. The introduction of antibiotics in clinical practice in the twentieth century was a breakthrough for medicine. However, their indiscriminate use in both medicine (human and animal) as in agriculture and livestock, enabled the selection and spread of resistant microorganisms. Horizontal gene transfer is a major mechanism responsible for the spread of genes encoding antimicrobial resistance, since it allows the transmission of resistance from one bacteria to another. Genes encoding resistance to antimicrobials of clinical importance are found in microorganisms present in food, environment and clinical sources. Objective. The aim of this study was to detect genes encoding resistance to β -lactam antibiotics, tetracyclines and quinolones in meat samples from chicken samples, to study the occurrence of antimicrobial resistance in this product considered a common food in human diet. Materials and Methods. Thirty samples of chicken were used. After inoculation of chicken meat in Luria broth 0.5 %, the total DNA of the bacteria cultured was extracted by heat shock and used to search resistance genes by PCR followed by agarose gel electrophoresis. The search for thermotolerant coliforms was also conducted using the technique of multiple tubes in order to estimate the sanitary quality of the samples. Results: Eight (26,7 %) of the samples had one or more genes encoding for resistance to β -lactam antimicrobials, 28 (93,3%) had one or more genes encoding resistance to tetracyclines and 27 (93,3 %) samples had one or more genes encoding resistance to quinolones. Conclusions: This study contributes to the scientific community and sanitary agencies, bringing information regarding the occurrence and distribution of resistance genes in chicken, alerting the Public Health authorities in Brazil about the spread of bacterial resistance and the need for more studies in this field, as these are rare or nonexistent in the country.
Ophiocordyceps sinensis, the flagship fungus of China: terminology, life strategy and ecology

The Chinese caterpillar fungus, Ophiocordyceps sinensis (syn. Cordyceps sinensis), is one of the most famous and perhaps the most expensive fungal species in the world. Its biology largely remains a secret, and its commercial cultivation is still a dream. Owing to its medicinal, economic, social and ecological importance, and its limited distribution mainly in China, O. sinensis is herein nominated as the national fungus of China and the fungus of the year (2012) for the journal Mycology. To clarify the confusion, a standard nomenclature is proposed and recommended in this paper for a comprehensive understanding of the terms related to Cordyceps sensu lato and O. sinensis. We also review recent research on the life cycle and distribution of this fungus, parasitism of ghost moths by the fungus, the microbial community of natural Chinese cordyceps and its insect hosts, as well as the secondary metabolites produced by the fungi isolated from natural Chinese cordyceps. By taking advantage of various expertises as well as the government support, we believe that the biological secrets of O. sinensis will be unravelled gradually, and the sustainable development and utilization of this traditional medicine will be fully achieved in the future.
A Cladistic Analysis and Taxonomic Revision of the Plesiosauria (Reptilia: Sauropterygia)

The Plesiosauria (Reptilia: Sauropterygia) is a group of Mesozoic marine reptiles known from abundant material, with specimens described from all continents. The group originated very near the Triassic–Jurassic boundary and persisted to the endCretaceous mass extinction. This study describes the results of a specimen-based cladistic study of the Plesiosauria, based on examination of 34 taxa scored for 166 morphological characters. The Pliosauroidea is found to by polyphyletic due to the inclusion of the Polycotylidae; this second clade is instead a member of the Plesiosauroidea, and thus more closely related to elasmosaurs than to other ‘pliosaurs’. Characters of body proportion such as neck length and head size are very labile, with the ‘pliosauromorph’ body plan evolving three times, while extremely long necks evolved in two clades. Characters from the entire skeleton support these relationships, although characters of the skull roof and palate are especially useful. Lastly, a new genus and species, Hauffiosaurus zanoni, is named based on German material of Toarcian age.
Modifikasi Portofolio Mean-Variance dengan Melibatkan Model Keasimetrian Distribusi

Portofolio mean-variance adalah salah satu metode yang digunakan dalam pembentukan portofolio. Portofolio mean-variance menekankan pada usaha memaksimalkan expected return dan meminimalkan ketidakpastian/ risiko (variance) untuk membentuk dan menyusun portofolio. Akan tetapi, metode mean-variance memiliki kekurangan. Copula merupakan salah satu metode estimasi pemodelan distribusi yang memiliki keunggulan dalam membentuk portofolio. Parameter 𝜌 merupakan salah satu yang digunakan dalam metode copula. Dengan 𝜌 maka dapat dibentuk portofolio. Copula yang digunakan pada tugas akhir ini adalah gaussian copula. Kinerja portofolio mean-variance classic dan portofolio mean-variance dengan gaussian copula diukur menggunakan Sharpe Ratio. Kata Kunci : mean-variance, copula, gaussian copula, sharpe ratio
Recombinant expression and initial characterisation of two Plasmodium copper binding proteins.

Plasmodium falciparum is a protozoan parasite responsible for the most severe form of human malaria, with infection often resulting in death. Efforts to control malaria have been hindered by an increased spread of parasite resistance to previously effective antimalarial drugs, leading to an intensified search for novel antimalarial drug targets. A group of proteins suggested as potentially effective targets are the integral membrane transport proteins, since they play key roles in Plasmodium parasite growth and replication. One such membrane protein recently characterised was the P. falciparum copper efflux transporter. Treatment of cultured P. falciparum parasites with the intracellular copper chelator neocuproine inhibited parasite growth, suggesting that additional mechanisms for malaria parasite copper homoeostasis are likely to be present. Copper is an essential trace element involved in enzymatic processes requiring redox-chemistry. In higher eukaryotes copper is transported across the plasma membrane via the copper transport protein, Ctr1, and distributed intracellularly by copper metallochaperones. The mechanisms for copper acquisition and distribution in the Plasmodium parasite are, however, yet to be characterised. An in silico Basic Local Alignment Search Tool for protein (BLASTp) screen of the Plasmodium database (www.plasmodb.org) identified sequences corresponding to a putative copper transporter, and associated copper metallochaperones, in eight species of the Plasmodium parasite. Each of the Plasmodium copper transport protein sequences was found to contain features common to the well characterised copper transporters. These features included predicted copper-binding motifs in the protein's amino terminus, three membrane spanning domains and the characteristic MxxxM and GxxxG motifs located in the second and third transmembrane domains, respectively. Affinity purified anti-peptide antibodies, generated against an immunogenic peptide (CSDKQSGDDECKPILD) in the amino terminus of a putative malaria parasite copper transporter (PY00413), detected the target protein in murine malaria parasites in association with a parasite membrane. The open reading frames corresponding to the amino terminal domains of one P. berghei [PBANKA_130290 (447 bp)] and two P. falciparum [PF14_0211 (132 bp) and PF14_0369 (282 bp)] putative copper transport proteins were PCR amplified, ligated into pGEM®-T and then expressed as recombinant fusion proteins with maltose binding protein (MBP). The resulting sizes for the recombinant proteins were 61kDa for MBP-PbCtrNt, 48kDa for MBP-PfCtr211NtTD and 55kDa for MBP-PfCtr369NtTD, with each protein being recognised by a corresponding anti-peptide antibody. All three recombinant proteins bound copper in vitro and in vivo, with each having a binding preference for the reduced cuprous ion. This preference has been similarly established for the characterised copper transporters. Although the results supported the expression and copper binding ability of
New 3D scaffolds and adequate mesenchymal stem cells culture methodologies for engineering an articular cartilage transplant

Cartilage is a type of dense connective tissue that possesses interesting features in terms of organization and functionality. It has only one type of cells – the chondrocytes – which are embedded in an extensive network constituted mostly of collagens and proteoglycans. It is also avascular, exhibiting a low metabolic rate and a subsequent low regenerative potential. Articular cartilage is a particular type of hyaline cartilage that has an important structural function in the skeletal system as a weight bearing tissue, creating smooth gliding areas that can absorb both shocks and loads in an efficient way. Due to its nature, articular cartilage function may be severely affected by trauma events, aging related degeneration such as osteoarthritis, or developmental disorders, since no efficient regeneration of the damaged tissue is performed. A direct result of this is chronic pain and disability conditions that seriously limit normal everyday life. Different possible solutions have been experimented to solve these conditions, such as prosthetic joint replacement, arthroplasty, and drilling, but the outcomes are still not satisfactory which imposed the need for alternative approaches. Tissue engineering has been proposed as a new method to address these problems, being widely studied as a promising therapeutic tool. The tissue engineering strategy usually implies the use of a 3D structure that is able to support cells growth and differentiation in an adequate environment towards the development of a functional tissue engineered system. The support systems fabricated for these purposes can be of natural or synthetic origin, or either a combination of both. Different materials have been produced and processed in various ways with the aim of conferring specific properties that are expected to render the best performances. The main goal of the work described in this thesis was to develop a system that can be easily, efficiently, and successfully applied in the treatment of articular cartilage lesions. Due to its potential, the concept of tissue engineering was applied by using natural origin based structures combined with different cell types (cell lines, primary culture differentiated and undifferentiated cells) in adequate culturing environments. Among the several support structures studied, the emphasis of the work was put on the development and application of a minimally invasive
Associação de anfípodes herbívoros com a alga parda Sargassum filipendula e suas epífitas : variação temporal e efeito da dieta sobre a aptidão

Macroalgas oferecem alimento e habitat para pequenos herbivoros, como anfipodes. O papel da macroalga como alimento e um dos principais fatores que influencia a interacao herbivoro-macroalga. Dessa forma, para compreender essa interacao, e imprescindivel conhecer as consequencias da dieta sobre a aptidao de pequenos herbivoros e a associacao desses animais com as macroalgas em campo. Nesse estudo, avaliamos a variacao temporal de anfipodes herbivoros da familia Ampithoidae e da alga parda Sargassum filipendula e suas epifitas. Em complemento, investigamos o efeito do consumo de algas com diferentes caracteristicas (Sargassum filipendula e duas algas epifitas, Dictyota cervicornis e Hypnea musciformis) sobre a aptidao de dois ampitoideos, Cymadusa filosa e Sunampithoe pelagica, bem como a preferencia e taxa alimentar desses anfipodes. A composicao das especies de Ampithoidae variou quanto ao tempo e foi influenciada pela biomassa de Sargassum e pela intensidade de epifitismo. Sunampithoe pelagica destacou-se como a especie de ampitoideo mais abundante, apresentando forte associacao com a biomassa de Sargassum. As especies C. filosa, Ampithoe marcuzzi e A. ramondi ocorreram em menor abundância e acompanharam a variacao da biomassa de epifitas. Nos experimentos de aptidao, jovens de S. pelagica alimentados com Sargassum, em comparacao aqueles nos tratamentos com Hypnea e Dictyota, apresentaram maior sobrevivencia, o que sugere uma dieta restrita apresentada por essa especie. Para C. filosa, a sobrevivencia foi semelhante entre jovens submetidos as tres dietas, porem, aqueles alimentados com Sargassum apresentaram maior crescimento e sucesso reprodutivo. Em um experimento de multipla escolha de algas, adultos de C. filosa e S. pelagica apresentaram maior preferencia de consumo pela alga Sargassum. Quando nao oferecida escolha quanto ao alimento, as tres algas foram consumidas por adultos de C. filosa a uma mesma taxa. Em contraste, Sargassum foi a alga mais consumida por adultos de S. pelagica no experimento de taxa alimentar. Apesar de ambas as especies de anfipodes apresentarem maior preferencia e sucesso ao consumirem Sargassum, elas responderam de maneiras distintas quando oferecidas outras algas, o que pode refletir as diferencas observadas entre essas especies quanto aos seus padroes de ocorrencia em campo. Nesse sentido, enquanto um importante componente na interacao entre pequenos herbivoros e macroalgas, a dieta pode influenciar as respostas de anfipodes herbivoros as variacoes de biomassa das macroalgas. Alem disso, nossos resultados reforcam a importância de se considerar as especificidades de cada herbivoro para compreensao do impacto desses animais sobre a comunidade de algas. Abstract
Oxidative stress in neonatology: Role of reactive oxygen species

Abstract Oxygen is one of the most abundant elements on Earth and plays a central role in the evolution of complex life by maintaining a homeostasis within our planet biosphere. However, oxygen can also produce toxic molecules such as reactive oxygen species (ROS). ROS is a collective term that includes both free oxygen radicals and certain oxidizing agents that are easily converted into free radicals. ROS can be produced from both endogenous and exogenous substances and play a dual role in different biological systems, either harmful or beneficial to living organisms. On one hand, oxygen-dependent reactions and aerobic respiration have significant advantages but, on the other, overproduction of ROS has the potential to cause tissue damage. Living organisms have developed different ways of counteracting the harmful effects of ROS: by preventive mechanisms; repair; and physical and antioxidant defenses. The study of the interplay of the generation of ROS and their counteracting antioxidant defense systems during fetal and neonatal life is constantly changing and still not understood fully. New studies are being carried out to define the biological roles of these highly reactive species and in-vivo maintenance of optimal oxidant/antioxidant balance in neonates. It is now known that preterm birth, itself, is associated with an increased oxidant burden, which places these infants at much higher risk of tissue injury. In this article, we discuss the biochemical and physiological aspects of ROS-mediated injury in neonates.
BODY COMPOSITION OF CHILDREN AGED 5-18 YEARS WITH SICKLE CELL ANAEMIA IN LAGOS, NIGERIA

Assessment of body composition provides a more useful and complete data relating to nutritional status. Most studies on the size of children with Sickle cell anaemia (SCA) are limited to composite measures of weight, height, and BMI without reference to body composition. This has left a gap in the knowledge of the relative impact of the disease on body composition in terms of Percentage Body Fat, Fat Mass and Fat Free Mass (PBF, FM and FFM). The aim of the current study was to evaluate body composition of children with sickle cell anaemia aged 5 – 18 years who attend the Haematology clinics of General Hospital Gbagada and Massey Street Children’s Hospital. The present study was descriptive, comparative and cross sectional. It was carried out over a period of six months (February 2016 to July 2016). A total of 480 children aged five to eighteen years were recruited following parental consent and assent from the children seven years and above. Two hundred forty children with SCA in steady state and 240 age and sex matched children with HbAA controls were studied. All subjects and controls had body composition measured by bioelectrical impedance analysis (BIA) and from two skin fold thicknesses (subscapular SFT and triceps SFT). Percentage body fat (PBF), fat free mass (FFM) and fat mass (FM) were estimated from both methods. Female children with SCA had significantly higher overall mean PBF (17.64 ± 3.4% vs. 13.45 ± 5.7%: t = 6.916, p < 0.001 –BIA; 13.10 ± 2.1% vs. 7.90 ± 2.1%: t = 11.470, p < 0.0001-SFT) and mean FM (5.62 ± 2.9kg vs. 3.62 ± 1.3kg: t =15.369, p < 0.0001 - BIA; 4.39 ± 2.9kg vs.2.22 ± 0.6kg: t = 11.384, p < 0.0001-SFT) than their male counterparts for both methods. Male children with SCA had higher values of overall mean FFM than females with SCA, (25.64 ± 8.7kg vs. 25.20 ± 8.3kg: t = 0.400, p = 0.689 –BIA; 27.04 ± 8.3kg vs. 26.43 ± 8.4kg: t = 0.566, p = 0.572 – SFT) but the difference was not significant by both methods. 2 The mean PBF and mean FM were directly related to age in female children with SCA by both methods. In male children with SCA mean PBF was inversely related to age by both methods. Mean FM was inversely related to age using BIA and directly related with age using SFT in male children with SCA. Mean FFM was directly related to age in female and male children with SCA by both methods. Male children with SCA had comparable mean FFM with their female counterparts. Children with SCA had significantly lower PBF, FM and FFM compared to HbAA controls by both methods. The difference was significant (p < 0.05). In conclusion the age related mean PBF, FM and FFM in male and female children with SCA followed expected physiologic trend. Children with SCA have a deficit in body composition parameters compared to age and sex matched HbAA children. It is therefore recommended that body composition monitoring be a part of the comprehensive care of children with SCA for identification of body composition deficit.
CRECIMIENTO DE Brachiaria decumbens Stapf Y Cynodon nlemfuensis Vanderyst EN SUELOS SULFATADOS ÁCIDOS DE CÓRDOBA

Objetivo. Evaluar el efecto quimico de dosis de cal en suelos sulfatados acidos (SSA) y las respuestas fisiologicas de Cynodon nlemfuensis Vanderyst y Brachiaria decumbens Stapf. Materiales y metodos. El trabajo se desarrollo durante 2006 en suelos sulfatados acidos de la finca “El Deseo” (Cienaga de Oro - Cordoba), donde se aplicaron 3, 6 y 9 toneladas de cal agricola por hectarea y se establecieron dos especies de pasto, Cynodon nlemfuensis Vanderyst (pasto estrella) y Brachiaria decumbens Stapf (pasto brachiaria). Las respuestas consideradas fueron las propiedades quimicas del suelo, peso fresco y seco de genotipos y relacion hoja/tallo. Se diseno un experimento de bloques completamente randomizados con estructura de parcelas divididas, donde las parcelas principales correspondieron a los pastos y las subparcelas a las dosis de encalamiento. Resultados. Los valores del pH del suelo aumentaron y las concentraciones de aluminio decrecieron significativamente con la dosis de cal reduciendose hasta en un 80%. Las bases intercambiables aumentaron con la aplicacion de cal y los microelementos disminuyeron en funcion del tiempo, aunque no con el encalamiento. Por su parte, independientemente del genotipo, la produccion de biomasa fresca mostro una relacion lineal con el nivel de encalamiento (y=0.656x + 11.99; r2=0.92); la materia seca y la relacion hoja/tallo fueron mayores siempre para B. decumbens respecto a C. nlemfuensis, de manera independiente al nivel de encalamiento. Conclusiones. La aplicacion de dosis crecientes de cal en SSA incremento los valores de pH y la produccion de biomasa en la pastura independientemente de la especie forrajera.