Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of genetic divergence in Niger germplasm

Seventy one niger germplasm were evaluated to explore the nature and magnitude of genetic divergence for yield and its contributing traits during kharif 2015-16 using Mahalanobis’s D2 Statistics. The data were recorded on eleven important yield attributing traits from the germplasms raised in randomized complete block design (RCBD) under three replications. Highly significant differences existed among the genotypes tested for all the traits. Cluster analysis revealed wide range of diversity in the genotypes grouped in eleven clusters. Out of eleven, Cluster II was the largest among all clusters followed by cluster I, cluster IX, cluster X, cluster VII, cluster XI and cluster IV. Cluster III, V, VI and VIII were monotypic. The highest intra cluster distance was recorded by cluster X followed by cluster IX, cluster XI, cluster IV, cluster VII, cluster II and Cluster I. The highest inter cluster distance was observed between the clusters VII and XI followed by clusters IV and XI and clusters VI and VII. The characters like seed yield per plant, 1000 seed weight and number of capitula per plant exhibited major contribution towards the genetic divergence. These traits should be considered as more important and due consideration to any breeding program. On the basis of inter and intra-cluster distance coupled with cluster means of different traits, the genotypes classified in clusters IX, IV, XI, VII, II, VI and V were found to be superior and may be utilized in breeding programmes.
Inhibitory networks orchestrate the self-organization of computational function in cortical microcircuit motifs through STDP

Interneurons have diverse morphological and physiological characteristics that potentially contribute to the emergence of powerful computational properties of cortical networks. We investigate the functional role of inhibitory subnetworks in the arguably most common network motif of cortical microcircuits: ensembles of pyramidal cells (PCs) with lateral inhibition, commonly referred to as Winner-Take-All networks. Recent theoretical work has shown that spike-timing-dependent plasticity installs in this network motif an important and ubiquitously useful self-organization process: The emergence of sparse codes and Bayesian inference for repeatedly occurring high-dimensional input patterns. However, this link has so far only been established for strongly simplified models with a symbolic implementation of lateral inhibition, rather than through the interaction of PCs with known types of interneurons. We close this gap in this article, and show that the interaction of PCs with two types of inhibitory networks, that reflect salient properties of somatic-targeting neurons (e.g. basket cells) and dendritic-targeting neurons (e.g. Martinotti cells), provides a good approximation to the theoretically optimal lateral inhibition needed for the self-organization of these network motifs. We provide a step towards unraveling the functional roles of interacting networks of excitatory and inhibitory neurons from the perspective of emergent neural computation.
Identificação molecular de espécies de micobactérias por PCR-RFLP hsp65 e implicações clínicas do diagnóstico convencional

Introduction: The establishment of the therapeutic regimen for mycobacteriosis depends on the accurate identification of the species of mycobacteria and the misdiagnosis can result in inappropriate treatment and increased mortality rate of patients. Differentiation between mycobacterial species has been made by conventional tests that analyze phenotypic and biochemical characteristics after a long culture period. The molecular diagnosis of mycobacteria allows fast detection and identification of the species, although it is not available in public health programs. Objective: To standardize the use of molecular technique PCR-RFLPhs^65 in species identification of mycobacteria, test method in culture samples from patients diagnosed with mycobacteriosis compared to the conventional techniques and to determine the clinical implications of erroneous diagnosis based on symptoms, culture and bacilloscopy. Methodology: The PCR-RFLP hsp65 technique was standardized in samples already identified in reference centers and subsequently tested in 55 culture samples from patients with mycobacterial infections occurred in 2013 and 2014, comparing the results with the clinical diagnosis. Results: All patients were clinically diagnosed with tuberculosis, but only 63.7% (35/55) of culture samples were confirmed as M. tuberculosis by PCR-RFLP and the rest, 36.3% (20/55) of the patients were diagnosed by molecular method as atypical mycobacteria The molecular method identified 18 positive samples (32.7%) for non­ tuberculous mycobacteria (M avium type1, M. avium type 2, M. kansasii type1, M. intracellulare type 1, M. mucogenicum, M. chelonae, M. terrae type 3 and one NTM without pattern known in literature) and 3.7% (2 samples) were negative. Concerning to the treatment only 11% (6/55) had substitute treatment in the case of failure of the standard treatment and suspected or confirmed infection with atypical mycobacteria. Conclusion: PCR-RFLPhs^65 differentiated complex tuberculosis of non-tuberculous mycobacteria classifying them at the species level, showed be discriminatory, fast and economical. Species identification in mycobacterial infections is essential to choose the correct therapeutic regimen and the use of this technique for diagnosis can assist public health programs increasing accuracy in diagnostic and reducing inappropriate treatment.
Development of a novel Francisella tularensis Live Vaccine Strain expressing ovalbumin provides insight into Francisella tularensis-specific CD8+ T cell responses

Progress towards a safe and effective vaccine for the prevention of tularemia has been hindered by a lack of knowledge regarding the correlates of protective adaptive immunity and a lack of tools to generate this knowledge. CD8+ T cells are essential for protective immunity against virulent strains of Francisella tularensis, but to-date, it has not been possible to study these cells in a pathogen-specific manner. Here, we report the development of a tool for expression of the model antigen ovalbumin (OVA) in F. tularensis, which allows for the study of CD8+ T cell responses to the bacterium. We demonstrate that in response to intranasal infection with the F. tularensis Live Vaccine Strain, pathogen-specific CD8+ T cells expand after the first week and produce IFN-γ but not IL-17. Effector and central memory subsets develop with disparate kinetics in the lungs, draining lymph node and spleen. Notably, F. tularensis-specific cells are poorly retained in the lungs after clearance of infection. We also show that intranasal vaccination leads to more pathogen-specific CD8+ T cells in the lung-draining lymph node compared to scarification vaccination, but that an intranasal booster overcomes this difference. Together, our data show that this novel tool can be used to study multiple aspects of the CD8+ T cell response to F. tularensis. Use of this tool will enhance our understanding of immunity to this deadly pathogen.
Variations in abundance and diversity of phytoplankton in the surface waters of the Golden Horn Estuary (Sea of Marmara)

The abundance pattern and species diversity of phytoplankton in the surface waters of the Golden Horn Estuary were investigated between August 2011 and July 2012 in relation to environmental factors. Seventy-eight phytoplankton taxa (38 diatoms, 30 dinoflagellates and 10 phytoflagellates) belonging to eight taxonomic classes were identified in bottle and net samples. Phytoplankton abundance increased in spring and summer (from March to August) and reached its highest (10,429 × 103 cells L−1) during the bloom of Heterosigma akashiwo (Raphidophyceae) in the middle and upper estuary in late May. In general, phytoplankton abundance was higher in the middle estuary indicating more suitable conditions for phytoplankton growth, while species richness and diversity was higher in the lower estuary. The most abundant species were Skeletonema marinoi and Thalassiosira sp. among diatoms; Scrippsiella trochoidea among dinoflagellates; Plagioselmis prolonga and Heterosigma akashiwo among phytoflagellates. Diatoms were more abundant in the lower and middle estuary, while dinoflagellates and phytoflagellates in the upper estuary. The main factors causing the spatio-temporal variation of phytoplankton in the study area were temperature, salinity, water transparency and nutrients. Water transparency in the upper estuary is mostly influenced by organic and inorganic matter carried by two streams. As a result, this area should be considered a potential risk area for future algal blooms.
MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice

Sexual reproduction in plants underpins global food production and evolution. It is a complex process, requiring intricate signalling pathways integrating a multitude of internal and external cues. However, key players and especially non-coding genes controlling plant sexual reproduction remain elusive. We report the development of MCRiceRepGP a novel machine learning framework, which integrates genomic, transcriptomic, homology and available phenotypic evidence and employs multi-criteria decision analysis and machine learning to predict coding and non-coding genes involved in rice sexual reproduction. The rice genome was re-annotated using deep sequencing transcriptomic data from reproduction-associated tissues/cell types identifying novel putative protein coding genes, transcript isoforms and long intergenic non-coding RNAs (lincRNAs). MCRiceRepGP was used for genome-wide discovery of sexual reproduction associated genes in rice; 2,275 protein-coding and 748 lincRNA genes were predicted to be involved in sexual reproduction. The annotation performed and the genes identified, especially the ones for which mutant lines with phenotypes are available provide a valuable resource. The analysis of genes identified gives insights into the genetic architecture of plant sexual reproduction. MCRiceRepGP can be used in combination with other genome-wide studies, like GWAS, giving more confidence that the genes identified are associated with the biological process of interest. As more data, especially about mutant plant phenotypes will become available, the power of MCRiceRepGP with grow providing researchers with a tool to identify candidate genes for future experiments. MCRiceRepGP is available as a web application (http://mcgplannotator.com/MCRiceRepGP/) Significance statement Rice is a staple food crop plant for over half of the world’s population and sexual reproduction resulting in grain formation is a key process underpinning global food security. Despite considerable research efforts, much remains to be learned about the molecular mechanisms involved in rice sexual reproduction. We have developed MCRiceRepGP, a novel framework which allows prediction of sexual reproduction associated genes using multi-omics data, multicriteria decision analysis and machine learning. The genes identified and the methodology developed will become a significant resource for the plant research community.
Variation in Sterilization by Deladenus proximus on the Native Woodwasp, Sirex nigricornis, in Arkansas

Abstract: Discovery of a potentially destructive non-native woodwasp, Sirex noctilio F. (Hymenoptera: Siricidae), in pine forests of eastern North America has elicited interest in appropriate management options. A parasitic nematode, Deladenus siricidicola Bedding (Tylenchida: Neotylenchidae), was introduced as a biological control agent in the Southern Hemisphere where it has been successful in some areas and unsuccessful in others. The North American congener (D. proximus Bedding) parasitizes native Sirex woodwasps and has potential as a biological control agent of S. noctilio due to its ability to utilize the invasive woodwasp as a novel host. However, basic biology and ecology of these native nematodes are largely unknown. Sirex nigricornis females were collected from three geographic locations in Arkansas in 2009 and 2010, dissected, and examined for the presence of D. proximus. Nematodes were found within S. nigricornis collected from all locations and years. Parasitism negatively affected woodwasp body size. We found high variation in percent of eggs infected with nematodes during both years of trapping. Research is needed to investigate potential mechanisms behind this variation of parasitism.
No effect of the full moon-supermoon on the aggressive behavior of incarcerated convicts: nailing the coffin shut on the Transylvania effect (the myth of the full moon affecting human behavior)

Formal scientific investigations on paranormal topics have consistently disproven their validity (Menzel and Boyd 1963; Sagan and Page 1972; Wilson and Mather 1974; Kusche 1975; Wilson 1976; Crowe 1990). One of these paranormal topics, the subject of this paper and one that is viewed as either curious, irritating, or amusing (jokingly referred to by some in the literature as the “Transylvania Effect” (Shapiro et al. 1970), is the question of whether the full moon affects human behavior. There are various references in classical literature: from England, in Shakespeare’s Othello: “It is the very error of the moon; she comes more near the earth than she was wont, And makes men mad”. and from Austria, in Meyrink’s The Golem: “Obviously, after what I had just seen, he was an acute case of somnambulism – the kind of persons highly susceptible to the influence of the full moon”. What is puzzling with this topic is that the results do not appear 100% conclusive. There have been studies that pointed to a possible deleterious effect of the full moon: among others, Osborn (1968) found an increase in mental hospital admissions during the full moon phase, Lieber and Sherin (1972) found an increase in homicides over a 15-year period and later Lieber (1978) again found that homicides and aggravated assaults demonstrated significant clustering of cases around the full moon, while Oderda and Klein-Schwartz (1983) found that a significantly larger number of unintentional poisonings occurred in the full moon period. Templer et al. (1982) found an increase in vehicle accident injuries during the full and new moons. But, then, we have contradictory findings. For example, negative results were obtained for homicides (Pokorny and Jachimczyk 1974), emergency psychological events (Kazemi-Bajestani et al. 2011), and reported crimes to the police (Schafer et al. 2010). There were also negative results for completed suicides in Spain and Norway (Jacobsen et al. 1986; Gutiérrez-García 1997) and serious crimes of battery in Germany (Biermann et al. 2009). Russell and de Graaf (1985), found no evidence in Canada for aggression during hockey games. Sanduleak (1985) found no relationship between lunar cycles and homicides in Cleveland. In a prison setting, Pettigrew (1985) did find an increase in violent incidents in a correctional setting. However, Simón (1998), found no relationship in records of aggressive acts by convicts during the full moon. In regards to medical problems, uniformly negative results have been the rule in the United States (Alves et al. 2003; Wende et al. 2013; Komann et al. 2014), Holland (Nijsten and Willemsen 1991) and Turkey (Arai et al. 2015). And for good measure, Schuld et al. (2011) found that moon phases, zodiac signs, and Friday the 13th had no influence on blood loss, emergency frequency, and intestinal perforations.
Commentary: Forest Cover Is Critical for Biodiversity Conservation in Tropical Livestock-Dominated Landscapes

Balancing meat production and biodiversity conservation is a major challenge. To address this challenge, we must understand the independent effects of land-use change and production practices on biodiversity across spatial scales. A key question is whether biodiversity will benefit more from habitats embedded in farmland (“land sharing”) or preserved elsewhere (“land sparing”). Our multiscale assessment of dung beetle communities in livestock-dominated landscapes from the Yucatan Peninsula, Mexico, supports the latter strategy. New results from phylogenetic analyses and unpublished results from dung removal experiments also highlight the importance of forest cover for preserving dung beetles and their key ecological roles. Both landscape-scale forest cover and macrocyclic lactones (commonly used veterinary drugs) shape dung beetle communities in the Yucatan Peninsula, thus suggesting that a land sparing approach, which maximizes forest protection, may minimize the damage of beef production to biodiversity. However, maximizing yields through macrocyclic lactone use will likely reduce on-farm ecosystem service provision. These surprising results have important implications for the conservation of biodiversity and ecological functions, as they suggest that the best strategies for conserving biodiversity may differ from those focused on delivering ecosystem services. We must therefore consider factors other than just food production and biodiversity conservation when designing land-use strategies.
Loma salmonae in Chinook salmon (Oncorhynchus tshawytscha): improving detection, preventing infection, and increasing our understanding of the host response to a microsporidian parasite

Supervisory Committee Dr. Ben Koop, (Department of Biology) Co-Supervisor Dr. Simon Jones, (Department of Biology) Co-Supervisor Dr. Nancy Sherwood, (Department of Biology) Departmental Member Dr. Terry Pearson, (Department of Biochemistry) Outside Member Loma salmonae is a microsporidian parasite that infects economically important Chinook salmon (Oncorhynchus tshawytscha) farmed in British Columbia, Canada. Here a variety of research efforts aimed at improving early detection and diagnostic tools, developing preventative strategies, and increasing understanding of the parasite/host interactions are presented. First, the development of chicken-derived polyclonal antibodies (IgY) specific for L. salmonae is described. These antibodies have proven useful for immunohistochemical detection of parasites very early in the infection process. Next, the immune-modulating effects of intra-peritoneal β-glucan inoculation of Chinook salmon are presented. Intensity of L. salmonae infection was significantly reduced in fish inoculated with β-glucan 3 weeks prior to parasite exposure, although prevalence was not reduced in these fish. Gene expression analysis of head kidney from glucan-inoculated fish measured at 1, 2 and 3 weeks post-inoculation (PI) revealed that the majority of differential expression occurred at 1 week. Pathways related to antioxidant defence, innate immune responses, antigen presentation, as well as oxidative metabolism were upregulated in glucan-inoculated fish at 1 week PI. Finally, temporal gene-expression iv analysis on gill and kidney tissue from Chinook salmon infected with L. salmonae is described. Analysis at 4 weeks post-exposure (PE) in the gill revealed an early upregulation of gas transport, whereas numerous pathways including oxidative metabolism, antioxidant defences, monooxygenases and immune receptors were down-regulated in the gill at the same time point. Similarly, oxidative metabolism, antioxidant defences, and monooxygenases were down-regulated in the kidney at 4 weeks PE. However, there is evidence for a developing immune response over time. Antigen processing and presentation pathways were up-regulated in the kidney at 4 weeks and in both tissues at 8 weeks PE. In addition a number of immune receptors and genes involved with innate immune functions were also up-regulated at 4 and 8 weeks PE in the kidney.
Anatomy and affinities of a new 535‐million‐year‐old medusozoan from the Kuanchuanpu Formation, South China

We describe here Sinaster petalon gen. et sp. nov., a new embryonic form from the c. 535 million‐year‐old Kuanchuanpu Formation of South China (Ningqiang, Shaanxi Province). The excellent three‐dimensional, phosphatic preservation of these microfossils allowed us to use x‐ray microtomographic techniques to make accurate reconstructions of their internal structures and to compare their anatomy point‐by‐point with that of extant cnidarians and other animal groups. Sinaster petalon has anatomical features typical of extant Medusozoa (Cnidaria), such as coronal muscles, perradial and adradial frenula, interradial septa, accessory septa, gonad‐lamellae, tentacle buds and perradial pockets. Although Sinaster cannot be straightforwardly assigned to any crown‐group within Medusozoa, the presence of marginal lappets and endodermal lamellae suggests that it is closer to Cubozoa and Scyphozoa than to any other group of modern cnidarians. The tentative placement of Sinaster within the stem‐group Cubozoa is justified by the presence of a velarium supported by a frenulum. The cubozoan affinities of Sinaster are also supported by cladistic analysis.
Análise comparativa de vegetação lenhosa do ecossistema campina na Amazônia brasileira

As campinas amazonicas sao formacoes vegetais esclerofilas que se desenvolvem em solos de areia branca. Apesar de inicialmente citadas apenas para a bacia do Rio Negro, sabe-se atualmente que as campinas estao amplamente distribuidas na Amazonia e em outras areas da America Tropical. As campinas ocorrem como enclaves em areas com matriz de floresta ombrofila, cerrado ou campinarana. Os substratos arenosos colonizados pelas plantas de campina podem ser de diferente natureza, tais como: (a) leitos de antigos corpos de agua que secaram, (b) perfis arenosos oriundos da decomposicao de arenitos do Escudo Guianense e do Escudo Brasileiro, e (c) antigas dunas arenosas de origem heolica. O presente trabalho teve como objetivo descrever e comparar, do ponto de vista floristico e fitossociologico, nove campinas na Amazonia Brasileira. Foram estudadas apenas as especies arboreas e arbustivas com diâmetro na altura do peito (DAP)  5 cm. Foram registradas, nas nove campinas estudadas, 252 especies pertencentes a 121 generos e 44 familias. As familias de maior riqueza floristica foram Fabaceae, Myrtaceae, Rubiaceae, Clusiaceae, Malpighiaceae e Annonaceae. Os generos de maior importância foram Clusia, Emmotum, Pagamea, Tapirira, Eugenia, Matayba, Myrcia e Ouratea. As nove campinas amostradas exibiram uma alta proporcao de especies exclusivas: 72,6% das especies foi registrada apenas em uma das campinas. A alta proporcao de especies exclusivas resultou em grande distância floristica entre as campinas estudadas (distância de Jaccard variando de 0,471 a 0,942). Em contraste, sete especies (2,8% do total) ocorreram em mais de cinco campinas. Estas especies, de ampla distribuicao neotropical e de ocorrencia em diferentes fisionomias, sao: Humiria balsamifera Aubl. , Emmotum nitens Miers, Pagamea guianensis Aubl. , Tapirira guianensis Aubl. , Byrsonima crassifolia (L.) Kunth. , Ouratea spruceana Engl. e Alchornea discolor Poepp. A analise de distribuicao das especies, juntamente com analises de similaridade floristica e de ordenamento MDS (Escalonamento multi-dimensional nao-metrico) indicam alguns padroes fitogeograficos para as campinas, tais quais: (a) grande afinidade floristica entre as campinas amazonicas e a vegetacao do Escudo Guianense e dos Llanos Venezuelanos/Colombianos; (b) campinas no contato da bacia amazonica com o Escudo Brasileiro – como as da Serra do Cachimbo - apresentam maior influencia da vegetacao do cerrado; (c) campinas do leste amazonico apresentam influencia mista das floras do Escudo Guianense e do Escudo Brasileiro; (d) baixa afinidade da flora das campinas com a da Restinga Atlântica; (e) campinas do extremo oeste da Amazonia brasileira – como a de Cruzeiro do Sul (Acre) - sao altamente diferenciadas das demais. Os resultados aqui apresentados reforcam a necessidade de programas de conservacao da biodiversidade das campinas amazonicos, dada a alta diferenciacao floristica observada entre elas, a grande concentracao de endemismos e sua ocorrencia em manchas restritas e isoladas.