The Likelihood Ratio Test and Full Bayesian Significance Test under small sample sizes for contingency tables

Hypothesis testing in contingency tables is usually based on asymptotic results, thereby restricting its proper use to large samples. To study these tests in small samples, we consider the likelihood ratio test and define an accurate index, the P-value, for the celebrated hypotheses of homogeneity, independence, and Hardy-Weinberg equilibrium. The aim is to understand the use of the asymptotic results of the frequentist Likelihood Ratio Test and the Bayesian FBST -- Full Bayesian Significance Test -- under small-sample scenarios. The proposed exact P-value is used as a benchmark to understand the other indices. We perform analysis in different scenarios, considering different sample sizes and different table dimensions. The exact Fisher test for $2 \times 2$ tables that drastically reduces the sample space is also discussed. The main message of this paper is that all indices have very similar behavior, so the tests based on asymptotic results are very good to be used in any circumstance, even with small sample sizes

Repurposing benzimidazoles to fight Cryptococcus

As doenças humanas causadas pelos patógenos fúngicos Cryptococcus neoformans e Cryptococcus gattii estão associadas a altas taxas de mortalidade e protocolos terapêuticos tóxicos ou de custo proibitivo. A necessidade de antifúngicos acessíveis para combater a doença criptocócica é inquestionável. Os benzimidazóis são compostos antifúngicos potencialmente atraentes que foram introduzidos na prática clínica há quase 60 anos para tratar infecções helmínticas. Além de serem seguros, seu custo de tratamento é extraordinariamente baixo. Vários estudos sugeriram os benzimidazóis como agentes anticriptocócicos promissores que combinam baixo custo e alta eficácia antifúngica. Até agora, atividades anticriptocócicas foram demonstradas para 16 benzimidazóis diferentes. Em particular, albendazol, mebendazol, flubendazol e fenbendazol têm potente atividade antifúngica in vitro contra C. neoformans e C. gattii. Camundongos letalmente infectados com C. neoformans e tratados com fenbendazol tiveram 100% de sobrevivência quando o medicamento foi administrado intranasalmente. Nesta revisão, discutimos o potencial dos benzimidazóis como potenciais agentes anticriptocócicos, incluindo uma visão geral da literatura, descobertas mais recentes, mecanismo de ação antifúngica, custos, toxicidade e potencial antifúngico in vivo.The human diseases caused by the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii are associated with high rates of mortality and toxic or cost-prohibitive therapeutic protocols. The need for affordable antifungals to combat cryptococcal disease is unquestionable. Benzimidazoles are potentially attractive antifungal compounds that were introduced in clinical practice nearly 60 years ago to treat helminthic infections. In addition to being safe, their cost of treatment is extraordinarily low. Several studies suggested benzimidazoles as promising anticryptococcal agents combining low-cost and high antifungal efficacy. So far, anti-cryptococcal activities were demonstrated for 16 different benzimidazoles. In particular, albendazole, mebendazole, flubendazole, and fenbendazole have potent in vitro antifungal activity against C. neoformans and C. gattii. Mice lethally infected with C. neoformans and treated with fenbendazole had 100 % survival when the drug was administered intranasally. In this review, we discuss the potential of benzimidazoles as potential anti-cryptococcal agents, including a general literature overview, most recent findings, mechanism of antifungal action, costs, toxicity, and antifungal potential in vivo

Accurate Atmospheric Parameters at Moderate Resolution Using Spectral Indices: Preliminary Application to the MARVELS Survey

Studies of Galactic chemical and dynamical evolution in the solar neighborhood depend on the availability of precise atmospheric parameters (Teff, [Fe/H] and log g) for solar-type stars. Many large-scale spectroscopic surveys operate at low to moderate spectral resolution for efficiency in observing large samples, which makes the stellar characterization difficult due to the high degree of blending of spectral features. While most surveys use spectral synthesis, in this work we employ an alternative method based on spectral indices to determine the atmospheric parameters of a sample of nearby FGK dwarfs and subgiants observed by the MARVELS survey at moderate resolving power (R~12,000). We have developed three codes to automatically normalize the observed spectra, measure the equivalent widths of the indices and, through the comparison of those with values calculated with pre-determined calibrations, derive the atmospheric parameters of the stars. The calibrations were built using a sample of 309 stars with precise stellar parameters obtained from the analysis of high-resolution FEROS spectra. A validation test of the method was conducted with a sample of 30 MARVELS targets that also have reliable atmospheric parameters from high-resolution spectroscopic analysis. Our approach was able to recover the parameters within 80 K for Teff, 0.05 dex for [Fe/H] and 0.15 dex for log g, values that are lower or equal to the typical external uncertainties found between different high-resolution analyzes. An additional test was performed with a subsample of 138 stars from the ELODIE stellar library and the literature atmospheric parameters were recovered within 125 K for Teff, 0.10 dex for [Fe/H] and 0.29 dex for log g. These results show that the spectral indices are a competitive tool to characterize stars with the intermediate resolution spectra.Comment: Accepted for publication in AJ. Abstract edited to comply with arXiv standards regarding the number of character

Prime Focus Spectrograph - Subaru's future -

The Prime Focus Spectrograph (PFS) of the Subaru Measurement of Images and Redshifts (SuMIRe) project has been endorsed by Japanese community as one of the main future instruments of the Subaru 8.2-meter telescope at Mauna Kea, Hawaii. This optical/near-infrared multi-fiber spectrograph targets cosmology with galaxy surveys, Galactic archaeology, and studies of galaxy/AGN evolution. Taking advantage of Subaru's wide field of view, which is further extended with the recently completed Wide Field Corrector, PFS will enable us to carry out multi-fiber spectroscopy of 2400 targets within 1.3 degree diameter. A microlens is attached at each fiber entrance for F-ratio transformation into a larger one so that difficulties of spectrograph design are eased. Fibers are accurately placed onto target positions by positioners, each of which consists of two stages of piezo-electric rotary motors, through iterations by using back-illuminated fiber position measurements with a wide-field metrology camera. Fibers then carry light to a set of four identical fast-Schmidt spectrographs with three color arms each: the wavelength ranges from 0.38 {\mu}m to 1.3 {\mu}m will be simultaneously observed with an average resolving power of 3000. Before and during the era of extremely large telescopes, PFS will provide the unique capability of obtaining spectra of 2400 cosmological/astrophysical targets simultaneously with an 8-10 meter class telescope. The PFS collaboration, led by IPMU, consists of USP/LNA in Brazil, Caltech/JPL, Princeton, & JHU in USA, LAM in France, ASIAA in Taiwan, and NAOJ/Subaru.Comment: 13 pages, 11 figures, submitted to "Ground-based and Airborne Instrumentation for Astronomy IV, Ian S. McLean, Suzanne K. Ramsay, Hideki Takami, Editors, Proc. SPIE 8446 (2012)

The characterization of RNA-binding proteins and RNA metabolism-related proteins in fungal extracellular vesicles

RNA-binding proteins (RBPs) are essential for regulating RNA metabolism, stability, and translation within cells. Recent studies have shown that RBPs are not restricted to intracellular functions and can be found in extracellular vesicles (EVs) in different mammalian cells. EVs released by fungi contain a variety of proteins involved in RNA metabolism. These include RNA helicases, which play essential roles in RNA synthesis, folding, and degradation. Aminoacyl-tRNA synthetases, responsible for acetylating tRNA molecules, are also enriched in EVs, suggesting a possible link between these enzymes and tRNA fragments detected in EVs. Proteins with canonical RNA-binding domains interact with proteins and RNA, such as the RNA Recognition Motif (RRM), Zinc finger, and hnRNP K-homology (KH) domains. Polyadenylate-binding protein (PABP) plays a critical role in the regulation of gene expression by binding the poly(A) tail of messenger RNA (mRNA) and facilitating its translation, stability, and localization, making it a key factor in post-transcriptional control of gene expression. The presence of proteins related to the RNA life cycle in EVs from different fungal species suggests a conserved mechanism of EV cargo packing. Various models have been proposed for selecting RNA molecules for release into EVs. Still, the actual loading processes are unknown, and further molecular characterization of these proteins may provide insight into the mechanism of RNA sorting into EVs. This work reviews the current knowledge of RBPs and proteins related to RNA metabolism in EVs derived from distinct fungi species, and presents an analysis of proteomic datasets through GO term and orthology analysis, Our investigation identified orthologous proteins in fungal EVs on different fungal species

EQUATIONS TO ESTIMATE THE CARBON STOCK PER HECTARE IN STEMS OF TREES IN SEASONAL SEMIDECIDUAL FOREST

The aim of this study was to adjust equations to estimate the carbon stock per hectare in stems of trees in function of forest variables, obtained by horizontal point sampling (Bitterlich method). Were sampled 55 points with a basal area factor K = 1, in natural forest fragments, located at Vi\ue7osa, Minas Gerais. After adjustment and evaluation of different regression models, was verified that the model 8 (non-linear) were the most precise to estimate the carbon stock per hectare in the stems of trees.Este trabalho teve por objetivo ajustar equa\ue7\uf5es para estimar o estoque de carbono por hectare nos fustes das \ue1rvores, em fun\ue7\ue3o de vari\ue1veis da floresta obtidas por meio da amostragem por ponto horizontal (m\ue9todo de Bitterlich). Foram amostrados 55 pontos, com um fator de \ue1rea basal igual a 1, em fragmentos de floresta estacional semidecidual, no munic\uedpio de Vi\ue7osa, Minas Gerais. Ap\uf3s o ajuste e a avalia\ue7\ue3o de diferentes modelos de regress\ue3o lineares e n\ue3o lineares, verificou-se que as equa\ue7\uf5es referentes ao modelo 8 (n\ue3o linear) foram as mais precisas para estimar o estoque de carbono por hectare nos fustes das \ue1rvores

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Animal production in tropical pastures of Latin America

Animal production in Latin America based on tropical pastures contributes significantly to the Agricultural Gross Domestic Product (GDP). Edapho-climatic conditions and the land tenure system are among the determining factors of different types of animal production in various countries. Based on climatic characteristics, it is possible to divide Latin American tropical livestock production systems into those of dry areas, savannahs and humid areas. Dual-purpose animals account for the bulk of total livestock in tropical Latin America, with management in native pastures predominating. Measures to increase animal production in the region should include the use of more productive forage varieties adapted to different areas, appropriate pasture and herd management procedures and animal and plant genetic improvement, among others. Two of the main obstacles to greater livestock production are the degraded state of many pastures and the need to control the emission of greenhouse gases. In order to meet the increased demand for food, especially those of animal origin, efforts to increase production should prioritize the recovery of degraded pastures, greater use of integrated systems incorporating legumes and proper management practices, aimed at reducing the emission of greenhouse gase

Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem

Rare variants are becoming the new candidates in the search for genetic variants that predispose individuals to a phenotype of interest. Their low prevalence in a population requires the development of dedicated detection and analytical methods. A family-based approach could greatly enhance their detection and interpretation because rare variants are nearly family specific. In this report, we test several distinct approaches for analyzing the information provided by rare and common variants and how they can be effectively used to pinpoint putative candidate genes for follow-up studies. The analyses were performed on the mini-exome data set provided by Genetic Analysis Workshop 17. Eight approaches were tested, four using the trait’s heritability estimates and four using QTDT models. These methods had their sensitivity, specificity, and positive and negative predictive values compared in light of the simulation parameters. Our results highlight important limitations of current methods to deal with rare and common variants, all methods presented a reduced specificity and, consequently, prone to false positive associations. Methods analyzing common variants information showed an enhanced sensibility when compared to rare variants methods. Furthermore, our limited knowledge of the use of biological databases for gene annotations, possibly for use as covariates in regression models, imposes a barrier to further research

Transcriptome analysis of Gossypium hirsutum flower buds infested by cotton boll weevil (Anthonomus grandis) larvae

Background\ud Cotton is a major fibre crop grown worldwide that suffers extensive damage from chewing insects, including the cotton boll weevil larvae (Anthonomus grandis). Transcriptome analysis was performed to understand the molecular interactions between Gossypium hirsutum L. and cotton boll weevil larvae. The Illumina HiSeq 2000 platform was used to sequence the transcriptome of cotton flower buds infested with boll weevil larvae.\ud \ud \ud Results\ud The analysis generated a total of 327,489,418 sequence reads that were aligned to the G. hirsutum reference transcriptome. The total number of expressed genes was over 21,697 per sample with an average length of 1,063 bp. The DEGseq analysis identified 443 differentially expressed genes (DEG) in cotton flower buds infected with boll weevil larvae. Among them, 402 (90.7%) were up-regulated, 41 (9.3%) were down-regulated and 432 (97.5%) were identified as orthologues of A. thaliana genes using Blastx. Mapman analysis of DEG indicated that many genes were involved in the biotic stress response spanning a range of functions, from a gene encoding a receptor-like kinase to genes involved in triggering defensive responses such as MAPK, transcription factors (WRKY and ERF) and signalling by ethylene (ET) and jasmonic acid (JA) hormones. Furthermore, the spatial expression pattern of 32 of the genes responsive to boll weevil larvae feeding was determined by “in situ” qPCR analysis from RNA isolated from two flower structures, the stamen and the carpel, by laser microdissection (LMD).\ud \ud \ud Conclusion\ud A large number of cotton transcripts were significantly altered upon infestation by larvae. Among the changes in gene expression, we highlighted the transcription of receptors/sensors that recognise chitin or insect oral secretions; the altered regulation of transcripts encoding enzymes related to kinase cascades, transcription factors, Ca2+ influxes, and reactive oxygen species; and the modulation of transcripts encoding enzymes from phytohormone signalling pathways. These data will aid in the selection of target genes to genetically engineer cotton to control the cotton boll weevil.FAPESP [2009/53998-3]CNPq [310.612/2011-0, 306025/2010-8]Fundação de Amparo à Pesquisa do Rio de Janeiro (FAPERJ