Miracle-dz/UniFAR-FTUs huggingface dataset:
Sample size estimation for genomics experiments with dependent end points

In typical genomics studies involving numerous association tests of gene mutations with a disease, error rate control via multiplicity adjustment is paramount because even if all genes were to be non-differentially associated, we would still make some false positives. Many methods exist that incorporate the control of multiplicity for normally distributed endpoints in sample size estimation, but none addresses the issue for non-normally correlated endpoints. One common practice in the literature is to assume an equal correlation among all differentially associated or expressed genes, thereby using the generalized binomial or beta-binomial model to compute the comparison-wise power of detecting these genes. We present a fast and simple novel approach for estimating sample size which focuses on controlling the family-wise error rate using Hunter and Worsley’s method for normally, t and chi-square distributed endpoints of any correlation structure. The sample size needed are computed using either a two-sample z-test or chi-square test formula depending on whether the response variable is continuous or binary at the desired comparison-wise power (using the binomial model), adjusted family-wise error rate and standardized effect size. These modifications would provide sample size estimates that are close to their exact values under more general correlation structures, where the generalized binomial or beta-binomial model may fail to perform.
Are tourism and conservation compatible for ‘island tame’ species?

Islands play an important conservation role due to high rates of speciation as well as providing a predator‐free refuge environment for species that are vulnerable to terrestrial predation on the mainland. Many animals show marked ‘island tameness’ on predator‐free islands, reducing costly escape responses in the absence of predation threat. Island tameness also translates to altered responses toward humans, making many island species attractive for wildlife tourism. We explored temporal and spatial differences in behavioral responses in the Rottnest Island quokka Setonix brachyurus. This marsupial is an excellent species to test for the effects of ecotourism, as well as of being conservation significance (IUCN‐listed as vulnerable). Comparing escape responses for n = 339 individuals in high tourism and low tourism seasons, quokkas at tourism sites allowed a person to approach closer before moving away compared with non‐tourisms sites, and two‐thirds of individuals around tourism sites allowed a person to approach within 1 m (compared with 14% of individuals at non‐tourism sites). For n = 67 ad hoc interactions with tourists, quokkas would only move away from an interaction with a tourist when the tourist group was noisy or there was an attempt to touch the animal. Time budgets (n = 379 individuals) showed that quokkas spent more time in group behavior and locomotion, but less in vigilance and feeding for tourism sites compared with non‐tourism sites. Understanding the impact of ecotourism on animal behavior will help to frame conservation management actions to ensure persistence of threatened wildlife species. We propose two models describing animal responses toward ecotourism: spatial separation according to animal temperament or temporal adjustment due to learned habituation. These models are not mutually exclusive and we suggest that both spatial separation and habitation are likely evident for Rottnest quokkas. We discuss the implications of these results for protection of animals on the island as well as for species conservation.
Height structure and spatial pattern of five tropical tree species in two seasonal semideciduous forest fragments with different conservation histories.

Anthropogenic disturbances in forests modify survival conditions and development of plants, which has direct effect on the height and spatial structure of tree populations. This study aimed to compare the height structure and spatial pattern of five tree species in two distinct fragments of seasonal semideciduous forest with different histories of conservation. We studied shade-intolerant (Astronium graveolens Jacq., Gallesia integrifolia (Spreng.) Harms) and shade-tolerant species (Chrysophyllum gonocarpum (Mart. & Eichler ex Miq.) Engl. , Euterpe edulis Mart. and Holocalyx balansae Micheli). Sixty plots of 100 m2 (10 m x 10 m) were allocated, being 30 contiguous plots in each fragment. All individuals of five species were marked, assessed for total height data and mapped using Cartesian coordinates. We observed differences in height structure between fragments. All populations had a random spatial pattern, except to H. balansae in the less conserved fragment and E. edulis in the conserved fragment that showed a clumped spatial pattern. There were evidences of forest regeneration due to the establishment of shade-tolerant species in less conserved fragment and coexistence of functional groups in both fragments. The height structure and spatial pattern analyses indicating that anthropogenic exploitation changed the environment and population structure in the less conserved area when compared to conserved area. The anthropic exploitation was ceased few years ago, so it is expected that the less conserved fragment reach the stability of an old-growth forest.
Exploring a fish model of developmental neurotoxicity using the Japanese medaka fish (Oryzias latipes)

SHARON L. OXENDINE: Exploring a fish model of developmental neurotoxicity using the Japanese medaka fish (Oryzias latipes) Ethanol exposure induces profound disruptions in developing organisms, but the period(s) of maximal susceptibility for these effects are not clearly defined. The overall hypothesis of this dissertation was that the timing of developmental ethanol exposure would influence manifestations of ethanol toxicity in medaka. Hatching success and morphometric measures of medaka growth and development were used to assess the doseresponse for developmental ethanol toxicity. Specifically, medaka embryos were exposed to a range of sublethal ethanol concentrations (0.1, 0.5, ot 1.0 % ≡ 17.2, 86, or 172 mM) during early, middle or late development in order to address temporal variations in sensitivity. Ethanol-induced decreases in total body length were found to be most severe with increasing ethanol concentrations that occurred either early or late in embryonic development, whereas head width was consistently decreased at all ethanol concentrations, regardless of developmental timing. These effects were accompanied by dose-related decreases in hatching success which were more pronounced with ethanol exposures that occurred early in development. Subsequent analyses of time-dependent changes in brain growth and caspase-3/7 activation were used to address the neurodevelopmental consequences of ethanol exposure. In these studies, medaka embryos were exposed to 1% ethanol during early, middle or late development and evaluated for treatment-related changes in brain volume and caspase-3/7 activation on day 9 postfertilization. Interestingly, the pattern of sensitivity observed for ethanol-induced decreases in total brain volume was similar to that seen with ethanol-induced decreases in somatic growth; embryos treated either early or late in development were most severely affected. Treatment-related decreases in caspase-3/7 activity were independent of
Impact of bad weather on the development of the broodnest and pollen stores in a honeybee colony (Hymenoptera: Apidae)

A honeybee colony of the race Apis mellifera carnica Pollmann 1879 with about 12.300-13.100 individuals, housed in an eight-frame observation hive (2 x 4 vertically arranged frames), was observed in summer 1997. The amounts of food stores and brood were measured during alternating periods of good weather (3 periods of 6 days each) and bad weather (3 periods of 5 days each), which was simulated by intense artificial rain. The amount of stored pollen typically increased during periods of good weather and decreased during phases of bad weather. The honey reserves were plentiful during the entire experiment. The larvae were classified into 2 categories according to their size: 'small' larvae (estimated fresh weight 140 mg). The total number of larvae increased slightly and fairly consistently over the course of the whole study, but under different weather conditions there were significant differences in the amounts of small and large larvae. During bad weather periods, the number of large larvae decreased significantly and heavily, while the number of small larvae increased. In contrast, during good weather conditions, the number of large larvae significantly increased, and the number of small larvae did not change. The changes in the number of large larvae correlated well with the changes in the amount of pollen in the colony. It seems that, during bad weather, a decline in the pollen stores might alter the brood-feeding behaviour of nurse bees, and this can result in underfed larvae, which may be sealed at a lighter weight. As the decreases in the number of large larvae started early in the rainy period, when pollen was still available, the bees seem to switch very rapidly to a 'save resources' strategy when a period of lack arises. The results do not suggest that brood cannibalism was prevalent, although this behaviour is known to occur under bad weather conditions.
Modern Computing Techniques for Solving Genomic Problems

With the advent of high-throughput genomics, biological big data brings challenges to scientists in handling, analyzing, processing and mining this massive data. In this new interdisciplinary field, diverse theories, methods, tools and knowledge are utilized to solve a wide variety of problems. As an exploration, this dissertation project is designed to combine concepts and principles in multiple areas, including signal processing, information-coding theory, artificial intelligence and cloud computing, in order to solve the following problems in computational biology: (1) comparative gene structure detection, (2) DNA sequence annotation, (3) investigation of CpG islands (CGIs) for epigenetic studies. Briefly, in problem #1, sequences are transformed into signal series or binary codes. Similar to the speech/voice recognition, similarity is calculated between two signal series and subsequently signals are stitched/matched into a temporal sequence. In the nature of binary operation, all calculations/steps can be performed in an efficient and accurate way. Improving performance in terms of accuracy and specificity is the key for a comparative method. In problem #2, DNA sequences are encoded and transformed into numeric representations for deep learning methods. Encoding schemes greatly influence the performance of deep learning algorithms. Finding the best encoding scheme for a particular application of deep learning is significant. Three applications (detection of protein-coding splicing sites, detection of lincRNA splicing sites and improvement of comparative gene structure identification) are used to show the computing power of deep neural networks. In problem #3, CpG sites are assigned certain energy and a Gaussian filter is applied to detection of CpG islands. By using the CpG box and Markov model, we investigate the properties of CGIs and redefine the CGIs using the emerging epigenetic data. In summary, these three problems and their solutions are not isolated; they are linked to modern techniques in such diverse areas as signal processing, information-coding theory, artificial intelligence and cloud computing. These novel methods are expected to improve the efficiency and accuracy of computational tools and bridge the gap between biology and scientific computing. INDEX WORDS: Signal processing, Deep learning, Cloud computing, Biological big data, DNA annotation, Epigenetics, CpG island, CpG box, Markov model MODERN COMPUTING TECHNIQUES FOR SOLVING GENOMIC PROBLEMS
Characterization of the complete mitochondrial genome and phylogenetic relationship of Pomatorhinus ruficollis (Passeriformes, Timaliinae)

Abstract In our study, we first report complete mitogenome for P. ruficollis and obtain basic genetic information. The genome of P. ruficollis is 17 009 bp which contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. Overall bases composition of the complete mitochondrial genome is 29.70%A, 14.47%G, 23.31% T, 32.52%C. Twelve PCGs and 14 tRNA genes are distributed on the H-strand, ND6 and eight tRNA genes are encoded on the L-strand.
COURTSHIP AND PARENTAL BEHAVIOR IN A PANAMANIAN POISON-ARROW FROG (DENDROBATES AURATUS)

Courtship and parental behavior of Dendrobates auratus were studied in the field and in captivity. Males are nonterritorial, but occasionally engage in aggressive competition. Males call to attract 9 9 and lead them to oviposition sites in leaf litter. Court- ship includes elaborate tactile interactions between partners, with the 9 taking the more active role. Parental care is performed by the 8 and includes tending of eggs and transport of tadpoles to water. Males can care for >1 clutch simultaneously. High 8 parental investment may lead to a shortage of 8 8, limiting 9 reproductive success. This may result in interfemale competition and a partial reversal of the usual sex roles in courtship.
The complete chloroplast genome sequences of Pogostemon stellatus and Pogostemon yatabeanus (Lamiaceae)

Abstract The nucleotide sequences of the two chloroplast (cp) genomes from Pogostemon stellatus and Pogostemon yatabeanus are the first to be completed in genus Pogostemon of family Lamiaceae. The structure of two Pogostemon cp genomes shows similar characteristic to the typical cp genome of angiosperms. The lengths of two cp genomes are 151,825bp and 152,707 bp, respectively. Two cp genomes are divided into LSC region (83,012 bp and 83,791 bp) and SSC region (17,524 bp and 17,568 bp) by two IR regions (25,644 bp and 25,674 bp). Both of two cp genomes contain 114 genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes), 10 protein-coding genes and 7 tRNA genes duplicated in the IR regions. Similar to the typical cp genome of angiosperms, 18 of the genes in the Pogostemon cp genome have one or two introns. The overall A-T contents of two genomes are 61.8% which is also similar to general angiosperms. The A-T content in the non-coding (64.4%) is higher than in the coding (59.9%) regions. Sixty-seven and seventy-three simple sequence repeat (SSR) loci were identified in the P. stellatus and P. yatabeanus cp genomes, respectively. In phylogenetic analysis, genus Pogostemon shows closed relationship with Scutellaria baicalensis of Scutellarioideae
Nitrous oxide emissions from drained peat soil beneath pasture

ABSTRACT Nitrous oxide (N2O) emissions (EN2O) from drained peat soils used for pastoral agriculture have not been measured throughout the year in New Zealand. In response to this research gap, EN2O was measured fortnightly for 1 year in the Waikato region in a plot that was not grazed or nitrogen (N) fertilised. The time series was variable, the frequency distribution skewed and the fortnightly means correlated. To account for these factors, the data were loge transformed and an order 2 autoregressive model used to estimate a mean EN2O of 4.3 g N ha−1 d−1 and 95% confidence limits of 0.6–29.1 g N ha−1 d−1. There was a statistically significant, inverse relationship between EN2O and the depth to groundwater. In winter, when rainfall totalled 393 mm, EN2O and soil N content were significantly greater under a rain shelter designed to minimise N loss by leaching, than in an uncovered plot.
The Structures of Shellfish Glycogens I

Gel filtration profile and ultracentrifugation analysis showed that the molecular weight of the commercial glycogen or the glycogen extracted with trichloroacetic acid (TCA) from whole oyster tissue was smaller than that of the glycogen extracted with dimethyl sulfoxide (DMSO). The degradation extents of glycogens extracted with DMSO and TCA on pullulanase treatment were 6.3% and 10.8 and that of commercial glycogen was 24.8%. Gel filtration profile or paper chromatogram of the pullulanase digest of the glycogen extracted with DMSO (DMSO-glycogen) was similar to those of the glycogen extracted with TCA (TCA-glycogen) and commercial glycogen. These results suggested that TCA-glycogen or commercial glycogen was degraded to some extent during the extraction of glycogen and became more susceptible to pullulanase keeping fundamental structure of the glycogen naltered. Electron microscopic study showed that the particle size (diameter) of DMSO-glycogen ranged 20-180 nm while the particle size of TCA-glycogen or commercial glycogen ranged 10-130 or 10-40 nm, respectively.
Partial support for the classical ring species hypothesis in the Chaerephon pumilus species complex (Chiroptera: Molossidae) from southeastern Africa and western Indian Ocean islands

Abstract We examined phylogenetic and phylogeographic relationships (cyt b, control region, Rag2) among members of the Chaerephon pumilus species complex from islands in the western Indian Ocean, and eastern and southeastern Africa. The sampling also includes material from the topotype of C. naivashae, holotypes of C. elphicki and C. langi, and syntypes of C. limbatus, all considered junior synonyms of C. pumilus. We found that the nominate C. pumilus sensu stricto (s.s.) from Massawa, Eritrea, is specifically distinct from the following taxa/samples, all of which form part of the C. pumilus species complex defined by Goodman et al. (2010): C. pumilus from southeastern Africa, the syntype of C. limbatus, the holotypes of C. elphicki and C. langi, and the topotype of C. naivashae. The conclusions relating to the type material are based on only 57 informative sites present within the 206 nucleotides of cytochrome b sequence obtainable. Chaerephon pumilus s.s. (Eritrea and Yemen) diverged from the other members of the C. pumilus species complex about 6.24 million years ago (MYA); Chaerephon atsinanana diverged approximately 5.01 MYA from a well-supported but unresolved clade comprising subclades, which appear to have arisen between 0.88 and 2.39 MYA and include: C. pusillus (Comoros and Aldabra); C. leucogaster (western Madagascar, Pemba, Zanzibar, Comoros); C. pumilus s.l. (southeastern Africa); and C. pumilus s.l. (Tanzania). There is evidence of introgression of both C. pusillus and C. pumilus s.l. (southeastern Africa) mitochondrial control region haplotypes into C. leucogaster. Clade B1 (network 7) of the C. pumilus species complex has several attributes of a ring species, but appears to differ from this model in several aspects. We propose that a source population on mainland Africa may have migrated in two directions across the Mozambique Channel, a potential barrier to gene flow, differentiating into C. pusillus on the Comoros and into C. leucogaster on Madagascar. Chaerephon leucogaster may then have migrated to the Comoros, where it occurs in sympatry with C. pusillus, completing the ring. In support of the hypothesis, there is evidence of isolation by distance around the ring, although there is also a relatively high degree of genetic structure and limited gene flow. It appears that the island-based component species may have differentiated in allopatry, with some gene flow by over water dispersal, whereas the African mainland species may have differentiated through isolation by distance.
Inhibition of the Mex Pumps of Pseudomonas aeruginosa with a Newly Characterized Member of Peptidomimetic Family

Aims: Efflux pumps, particularly resistance-nodulation-division family such as Mex pumps in Pseudomonas aeruginosa, are the major contributors to multidrug resistance in Gram-negative bacteria. Since the well-known efflux pump inhibitor (EPI), phenylalanine-arginine β-naphthylamide (PAβN), is a substrate of cathepsin C (a proteolytic enzyme), inhibitory effects of similar substrates of this enzyme, proline-arginine 4-methoxy-β-naphthylamide (PA4MβN) and Nα-Benzoyl-DL-arginine β-naphthylamide (BAN), were investigated as possible new EPIs. Additionally, the probable EPI activities of three different alkaloids (noscapine, caffeine and ergotamine) against Mex-pump expressing strains were also evaluated mainly based on their structural similarities to major EPIs. Methodology: MPC8 (minimum potentiating concentrations) of mentioned compounds in combination with levofloxacin (LVX) were screened against a wild type (PAO1) and two different Mex-pump overexpressing P. aeruginosa strains (nalB and nfxB). The most synergizing compound was further validated by the checkerboard assay for its EPI potency against strains overexpressing Original Research Article Avakh and Rezaei; BMRJ, 16(2): 1-13, 2016; Article no.BMRJ. 27374 2 or lacking different Mex-pumps. The frequencies of emergence of LVX-resistance strains when it was used either alone or in combination with the suggested EPI were also compared against each other. Results: PA4MβN caused significant increase in LVX activity against PAO1 and different Mexpump overexpressing P. aeruginosa strains showing a significant decrease in the intrinsic (8-fold) and acquired (16-fold) resistances. Interestingly, PA4MβN fully prevented further emergence of P. aeruginosa mutants highly resistant to fluoroquinolones. Conclusion: A new compound from peptidomimetic family (PA4MβN), which is also a substrate of cathepsin C, was introduced in the current study as an effective EPI against Mex pumps from P. aeruginosa.
Distribution of mating types, metalaxyl sensitivity and virulence races of Phytophthora infestans in Estonia.

Potato late blight, caused by the oomycete Phytophthora infestans, is a destructive potato disease, causing considerable crop loss worldwide. As the late blight pathogen population is diverse and variable in Estonia, changes in the population should be monitored regularly. In this study, the Estonian population of P. infestans was characterised with mating type, sensitivity to metalaxyl and virulence on potato R-gene differentials. During the growing season 2013, 110 isolates were collected from nine potato fields. The frequency of A2 mating type was on average 29%, and varied significantly between different fields from 7% to 78% (p = 0.001). On all studied potato fields, both mating types were recorded, suggesting continuous sexual reproduction of P. infestans and possible risk of oospore production and early attacks of late blight in Estonian potato fields. The prevalence of metalaxyl sensitive isolates in the population (64%) differed from results from previous research. Thus changes have occurred in the P. infestans Estonian population. There were no significant differences in metalaxyl sensitivity between studied fields (p = 0.073). The Estonian race structure was highly diverse and complex, on average 7.2 virulence factors per isolate, but varied between fields from 5.6 to 9.0. 42 virulence races were found; the four most common were 1.2. 3.4. 5.6.7.8.10.11, 1.2. 3.4. 6.7.8.10.11, 1.2. 3.4. 7.10.11 and 1.2. 3.4. 7.8.10.11, which comprised 46% of the population. The overall normalized Shannon’s diversity index was 0.69, confirming the high diversity of the population. Continuous pathogen population studies describing the contemporary P. infestans population are essential in order to advise potato breeders and growers accordingly.