Miracle-dz/UniFAR-FTUs huggingface dataset:
Significance of epigenetic data in environmental risk assessment

ASSESSMENT: USING HUMAN HEALTH AND ECOLOGICAL MODELS by RAMYA TULASI KOLLI (Under the Direction of Brian S. Cummings) ABSTRACT The role of epigenetic mechanisms in gene regulation is well studied in basic science and cancer pathology. However, our knowledge on toxicant-induced alterations of gene expression via epigenetic alterations is meager. Having this knowledge is key to estimating the risk of adverse and long-term effects of toxicants on human health and ecosystem. This series of studies tested the epigenetic effects of sub-chronic exposure to low-dose bromate (BrO3) on human and rat renal cells. BrO3 is a drinking water disinfection byproduct regulated by the US EPA. Based on our previous data, we tested the hypothesis that BrO3-induced renal p21 expression is mediated by epigenetic mechanisms.
Short Communication Construction and use of new cloning vectors for the rapid isolation of recombinant proteins from Escherichia coli

We describe the construction and use of two sets of vectors for the over-expression and purification of protein from Escherichia coli. The set of pTEV plasmids (pTEV3, 4, 5) directs the synthesis of a recombinant protein with a N-terminal hexahistidine (His6) tag that is removable by the tobacco etch virus (TEV) protease. The set of pKLD plasmids (pKLD66, 116) directs the synthesis of a recombinant protein that contains a N-terminal His6 and maltose-binding protein tag in tandem, which can also be removed with TEV protease. The usefulness of these plasmids is illustrated by the rapid, high-yield purification of the 2-methylcitrate dehydratase (PrpD) protein of Salmonella enterica, and the 2-methylaconitate isomerase (PrpF) protein of Shewanella oneidensis, two enzymes involved in the catabolism of propionate to pyruvate via the 2-methylcitric acid cycle.
Global convergence and ascent property of a cyclic algorithm used for statistical analysis of crash data

In this paper, we consider an estimation algorithm called cyclic iterative algorithm (CA) that is used in statistics to estimate the unknown vector parameter of a crash data model. We provide a theoretical proof of the global convergence of the CA that justifies the good numerical results obtained in early numerical studies of this algorithm. We also prove that the CA is an ascent algorithm, what ensures its numerical stability. Keywords: Iterative method, Maximum likelihood, cyclic algorithm, global convergence, road safety AMS 2010 Mathematics Subject Classification : 62-04, 62F10, 62H12, 62P99
STRUCTURAL MODELS FOR DISCRETE DATA: THE ANALYSIS OF DISCRETE CHOICE

The Prologue to the 1979 volume of Sociological Methodology noted both the recent preoccupation of sociologists with categorical data and their growing interest in structural equation theory. Ironically the various chapters in the volume indicate that these two important trends are progressing largely in mutual isolation. ' On the one hand, the structural equation models that have received attention to date presume continuous endogenous variables. On the other hand, an empirical data-analytic approach has characterized the handling of discrete data. In many contexts involving discrete data a structural model of the process generating the observations can be specified. One such context is that of discrete choice, in which the data are observations of
Effects of Global Risks — Nitrogen Additions on Growth and Competitive Relations among Invasive and Native Congeneric Species — Bidens frondosa

ABSTRACT Human activity has greatly increased the amount of biologically available nitrogen entering the natural environment. Addition of N can affect growth of and competitive interactions between native and invasive plants, thus increasing or decreasing the risk of invasion by alien species. Bidens frondosa is an invasive weed native to North America that recently has begun to spread in China. The influence of soil nutrient content on B. frondosa invasion has not yet been reported. In a common garden experiment, we compared the growth and competitive effects between B. frondosa and its co-occurring native congeners — B. tripartita and B. biternata — under three N levels (0 g m-2, 1 g m-2, 5 g m-2) to assess whether increased levels of N modifies risk of B. frondosa invasion. Our results showed that while N additions increased both the growth and competitive advantage of B. frondosa as compared with that of the native congener species, results are particularly pronounced under high N levels. While growth responses to N addition varied little among invasive populations under high N levels, the competitive effect of B. frondosa did vary among populations and was significantly greater than that of the congeners. Anthropogenic N additions are likely to increase risks of B. frondosa invasions. Thus, management efforts should focus on the reduction of N input to ecosystems to mitigate invasions by B. frondosa.
Aiptasia as a model to study metabolic diversity and specificity in cnidarian-dinoflagellate symbioses

The symbiosis between cnidarian hosts and microalgae of the genus Symbiodinium provides the foundation of coral reefs in oligotrophic waters. Understanding the nutrient-exchange between these partners is key to identifying the fundamental mechanisms behind this symbiosis. However, deciphering the individual role of host and algal partners in the uptake and cycling of nutrients has proven difficult, given the endosymbiotic nature of this relationship. In this study, we highlight the advantages of the emerging model system Aiptasia to investigate the metabolic diversity and specificity of cnidarian – dinoflagellate symbiosis. For this, we combined traditional measurements with nano-scale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling to investigate carbon and nitrogen cycling both at the organismal scale and the cellular scale. Our results suggest that the individual nutrient assimilation by hosts and symbionts depends on the identity of their respective symbiotic partner. Further, δ13C enrichment patterns revealed that alterations in carbon fixation rates only affected carbon assimilation in the cnidarian host but not the algal symbiont, suggesting a ‘selfish’ character of this symbiotic association. Based on our findings, we identify new venues for future research regarding the role and regulation of nutrient exchange in the cnidarian - dinoflagellate symbiosis. In this context, the model system approach outlined in this study constitutes a powerful tool set to address these questions.
Alessioporus rubriflavus (Boletaceae), a new species from the eastern United States

In 2014 Alessioporus was erected as a monotypic genus. Here we describe a new species from the eastern United States, Alessioporus rubriflavus, based on unique morphology and molecular data (ITS and LSU nrDNA genes). Ecology, geographical distribution and comparison to other closely allied taxa are discussed.
Characterizing Subpopulations with Better Response to Treatment Using Observational Data – an Epilepsy Case Study

Electronic health records and health insurance claims, providing observational data on millions of patients, offer great opportunities, and challenges, for population health studies. The objective of this study is identifying subpopulations that are likely to benefit from a given treatment using observational data. We refer to these subpopulations as “better responders” and focus on characterizing these using linear scores with a limited number of variables. Building upon well-established causal inference techniques for analyzing observational data, we propose two algorithms that generate such scores for identifying better responders, as well as methods for evaluating and comparing these scores. We applied our methodology to a large dataset of ~135,000 epilepsy patients derived from claims data. Out of this sample, 85,000 were used to characterize subpopulations with better response to next-generation (“Newer”) anti-epileptic drugs (AEDs), compared to an alternative treatment by first-generation (“Older”) AEDs. The remaining 50,000 epilepsy patients were then used to evaluate our scores. Our results demonstrate the ability of our scores to identify large subpopulations of epilepsy patients with significantly better response to newer AEDs.
On the Social Structure behind Biological Collections

In this paper we describe two network models as a base for understanding the relevance of social processes involving collectors for shaping the composition of biological collections. Species-Collector Networks (SCNs) represent the interests of collectors towards particular species, while Collector CoWorking Networks (CWNs) represent collaborative ties between collectors during fieldwork. We demonstrate the practical use of our models with species occurrence data from the University of Brasília Herbarium.
First record of the genus Tropidia Lindl. (Orchidaceae) for Brazil

The genus Tropidia is composed of ca. 20-30 species distributed in southern Asia, South Pacific islands and northern Australia, and a single species occurring in America, from United States to Ecuador. The first record of the genus Tropidia for Brazil is presented here. It consists of Tropidia polystachya, a species found in the Cerrado biome, Midwestern Brazil. Description, illustration, photos, and distribution map of the species are provided. Additionally, the leaf anatomy of the species was studied and it is very similar to the leaves of other species of Tropidieae described so far. DNA sequences of T. polystachya are presented (plastid matK and rbcL and nuclear ITS) in order to assist future phylogenetic studies with the genus.
Mangiferin content, carotenoids, tannins and oxygen radical absorbance capacity (ORAC) values of six mango (Mangifera indica) cultivars from the Colombian Caribbean

Mango is one of the tropical fruits of greater production and consumption in the world, and a rich source of bioactive compounds, with various functional properties such as antioxidant activity. In Colombia, mango’s market is very broad and diverse. However, there are very few studies that determined the content of bioactive secondary metabolites. The objective of this study was to evaluated the content of different metabolites like Mangiferin, carotenoids, tannins, and the antioxidant capacity by oxygen radical absorbance capacity (ORAC) methodology of six cultivars from the Colombian Caribbean region, with total carotenoid values ​​ranging from 24.67 to 196.15 mg of β-carotene/100 g dry pulp; 84.30 to 161.49 mg Catequine eq./100 g dry pulp for the content of condensed tannins, and 91.80 to 259.23 mg/100 g dry pulp for mangiferin content. The ORAC methodology showed important antioxidant activity results, such as the Chancleta variety with the highest value (2163.78 μmol Trolox/100 g dry pulp). In conclusion, the evaluated mango varieties had promising results as functional food of high nutraceutical value, being Chancleta, Criollo and Jobo varieties, the fruits with highest content in bioactive compounds that expressed the best antioxidant activity. Key words: Mangiferin, antioxidant activity, mango, nutraceutical.
Regulation of Muscle Stem Cell Function by the Transcription Factor Pax7

Pax7 is a paired box transcription factor expressed by all satellite cells which are critically required for muscle regeneration and growth. The absolute requirements of Pax7 in the maintenance of the satellite cell pool are widely acknowledged. However the mechanisms by which Pax7 executes muscle regeneration or contributes to satellite cell homeostasis remain elusive. We performed cell and molecular analysis of Pax7 null satellite cells to investigate muscle stem cell function. Through genome wide studies, we found that genes involved in cellcell interactions, regulation of migration, control of lipid metabolism and inhibition of myogenic differentiation were significantly perturbed in Pax7 null satellite cells. Analysis of satellite cells in vitro showed that Pax7 null satellite cells undergo precocious myogenic differentiation and have perturbed expression of genes involved in the Notch signaling pathway. We showed that Notch 1 is a novel Pax7 target gene and by using a genetic approach we demonstrate that ectopic expression of the constitutively active intracellular domain of Notch1 (NICD1) in Pax7 null satellite cells is sufficient to maintain the satellite cell pool as well as to restore their proliferation. Instead of differentiating into myogenic cells and in the absence of a myogenic cue, NICD1 Pax7 null satellite cells become a source of ectopic brown fat within muscles and give rise to brown adipocytes both in vivo and in vitro. In conclusion we showed that Notch 1 partially rescues Pax7 deficient satellite cells loss and proliferation. Additionally we provide the first evidence that Notch signalling contributes to satellite cell fate by inhibiting terminal myogenic differentiation and inducing brown
Detection of a Brucella-like (Alphaproteobacteria) Bacterium in Boophilus spp. (Acari: Ixodidae) from Iran

1Department of Plant Protection, Faculty of Agriculture, University of Lorestan, Khorramabad, Iran; 2Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; 3Lorestan Agricultural and Natural Resources Research Center, Khorramabad, Iran; 4Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; 5Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
The complete mitochondrial genomes of hycleus cichorii and hycleus phaleratus (Coleoptera: Meloidae)

Abstract The Hycleus cichorii and Hycleus phaleratus are two species of medicinal meloids widely distributed in southwest of China. We sequenced an annotated the complete mitochondrial genomes of H. cichorii and H. phaleratus, and the mitogenomes are 15,847 and 16,004 bp in length, respectively. Every mitochondrial genome encodes 13 proteins, 2 ribosomal RNAs, 22 tRNAs, and a control region with the identical arrangement to other beetles. The preliminary phylogenetic analysis with mitochondrial genomes of nine meloid species further confirmed the status of these two species.
Ecophysiological performance and life cycle strategies of North Sea shrimps

Environmental fluctuations can impose energetic constraints on organisms in terms of food shortage or compensation for metabolic stress. To better understand the biochemical strategies that support adaptive physiological processes in variable environments, we studied the lipid dynamics of the brown shrimp Crangon crangon and the pink shrimp Pandalus montagui by analysing their midgut glands during an annual cycle. Both species have an overlapping distribution range in the southern North Sea, but differ in their habitat preferences, reproductive strategies, and life-history traits. C. crangon showed minor total lipid accumulation in their midgut glands, ranging between 14 and 17% of dry mass (DM), dominated by phospholipids. In contrast, P. montagui stored significantly larger amounts of total lipid (47−70% DM, mainly triacylglycerols) and showed a distinct seasonal cycle in lipid accumulation with a maximum in summer. Fatty acid trophic markers indicated a wide food spectrum for both species, with higher preferences of P. montagui for microalgae. In C. crangon, feeding preferences were less distinct due the low total lipid levels in the midgut gland. PCA based on fatty acid compositions of both species suggested that C. crangon has a broader dietary spectrum than P. montagui. C. crangon seems to have the capacity to use sufficient energy directly from ingested food to fuel all metabolic requirements, including multiple spawnings, without building up large lipid reserves in the midgut gland. P. montagui, in contrast, relies more on the energy storage function of the midgut gland to overcome food scarcity and to allocate lipids for reproduction.
Venation Patterns in Mimosa Subseries Dolentes and Brevipedes (Leguminosae) and their Taxonomical Inferences

Abstract Mimosa is a megadiverse genus of pantropical and subpantropical distribution. High morphological variability at infraspecific levels has often led to problems in the delimitation of taxa and the formation of taxonomic complexes. Here, on cleared leaflets of 20 taxa of the Dolentes-Brevipedes taxonomic complex, we describe three major venation types: acrodromous, parallelodromous, and brochidodromous. We provide a detailed description of variability among each one, leading to the establishment of two and five subtypes within the acrodromous and brochidodromous taxa, respectively. Venation architecture clearly differentiates three species within Mimosa subseries Brevipedes: M. brevipes with acrodromous, M. fernandez-casasii with parallelodromous venation, and M. diversipila by its brochidodromous weak pattern. Three varieties are also recognizable in brochidodromous subseries Dolentes: M. dolens var. anisitsii with round pattern, M. dolens var. eriophylla and M. dolens var. rudis with ample pattern.
Isolation and Identification of the Pathogen of Cardamine violifolia Bacterial Blight Disease in China

Cardamine violifolia is found in Yutangba, Shuanghe Town (an area rich in Se) of Enshi city, Hubei province, China, has strong capacity of accumulating Se . The Se content in seedling leaves exceeds 1000 mg/kg, which is the international standard of Sehyperaccumulator (Karol et al., 2015). So Cardamine violifolia was artificial cultivation. A bacterial disease was found on leaves of Cardamine violifolia grown under greenhouse in winter of 2014 and 2015. The disease usually started from leaf edges near hydathodes and quickly enlarged to form Vshaped lesions frequently surrounded by chlorotic areas. These lesions finally coalesced to form the severe blight along the whole leaves. The objective of this research was to identify the causal agent of Cardamine violifolia disease suspected to be bacterial blight disease.
Diet Selection of Leopards (Panthera pardus) in a Human-Use Landscape in North-Eastern India

There is increasing evidence of large carnivores using human-use areas, but our understanding of their ecology in such landscapes is limited. The role of wild and domestic prey in sustaining populations of carnivores in human-use landscapes could be significant but is currently poorly documented. We studied the prey composition and diet selection of leopards (Panthera pardus) in a forest and tea-garden landscape in north-eastern India where the population density is greater than 700 people per km2 and average domestic animal density is 340 animals per km2. Wild prey density in the landscape was 56 animals per km2. Both wild and domestic prey were used by leopards in proportion to their availability with no selectivity toward either (χ2 = 87.17, p = .99, SE = 0.001). Among wild prey, Rhesus macaque (Macaca mulatta) was found in high densities (24 animals per km2) and was preyed by leopards more frequently that the proportional availability. High use of domestic prey by leopard, with 60% of the prey biomass comprising cattle and goats has the potential for negative impact on conservation support for the species. While on one hand, there is great scope for the persistence of large cats in dense human-use landscapes due to the availability of domestic prey, on the other hand, the study highlights the problems of livestock loss especially to poorer sections of the society which need to be reconciled for achieving long-term and sustainable conservation goals.
Cardinalfish of the genus Apogonichthyoides Smith, 1949 (Apogonidae) with a description of a new species from the West-Pacific region

Apogonichthyoides is resurrected from Apogon (Ostorhinchus) as a valid genus with 19 species. Members of this genus are mostly tannish brown to brownish-black in body color. The head and body usually have brownish to blackish spots (sometimes stripe-like), a darkish cheek line and usually two body bars. An ocellus may be present below the lateral line on the body or absent. One or more caudal-peduncular bars and/or a basicaudal spot are often present. Insertion patterns of supraneurals and pterygiophores are given for 11 species. Apogonichthyoides umbratilis, a new species, has 14 pectoral rays and five bars (three faint) on the body and caudal peduncle. Color pattern of the new species suggest relationships with Apogonichthyoides gardineri, A. timorensis and A. opercularis. Descriptions and illustrations of the latter two species are provided for comparison. Apogonichthyoides gardineri, a rare, deep-water species is characterized by 14 pectoral rays, two bars on the body and one wide bar near the base of the caudal peduncle. Specimens of Apogonichthyoides timorensis usually have 15–16 pectoral rays and two or three bars on the body and caudal peduncle. Specimens of Apogonichthyoides opercularis have nine soft anal rays and 10 soft dorsal rays. A key to eight species included in the timorensis species group is provided. A lectotype and paralectotypes are designated for the syntype series of Apogon opercularis. New name combinations follow: Apogonichthyoides atripes, A. brevicaudatus, A. cantoris, A. chrysurus, A. euspilotus, A. gardineri, A. heptastygma, A. niger, A. opercularis, A. pharaonis, A. pseudotaeniatus, A. regani, A. sialis and A. timorensis. Previous usage includes: Apogonichthyoides enigmaticus, A. nigripinnis, A. taeniatus and A. uninotatus
Morphometric Differences Between Sexes of Two Subspecies of Black-crowned Night-Heron (Nycticorax nycticorax) Using Discriminant Function Analysis

Abstract. The objective of this study was to develop tools for distinguishing between sexes of the two Black-crowned Night-Heron (Nycticorax nycticorax) subspecies (N. n. obscurus and N. n. hoactli) using discriminant function analysis. Significant differences were found in length of the culmen, length of the bill from the gape, and length of the wing chord between the sexes of each subspecies, with males being larger than females. The resulting discriminant functions were able to differentiate between the sexes of each studied subspecies and between subspecies after determining the sex of the individuals (with a correct classification of 77.8% for females and 97.8% for males). In females, all morphometrics were greater for N. n. obscurus than N. n. hoactli; this was also the case for males, except for bill width, which was greater in N. n. hoactli. Wing chord length was the most useful measurement for constructing the discriminant functions. External morphometrics are a valuable tool not only for discriminating between N. n. hoactli and N. n. obscurus but also for sexing these subspecies.
Antimicrobial activity of various extracts of Plectranthus ambionicus and Phyllanthus amarus

Hexane, chloroform, ethyl acetate and methanol extracts of leaves of Plectranthus ambionicus and Phyllanthus amarus were screened for their antimicrobial activity against human pathogenic bacterial and fungal strains. Antimicrobial activity was carried out by disc diffusion method, determination of minimum inhibitory concentrations (MIC), minimum bactericidal concentrations (MBC) and minimum fungicidal concentrations (MFC) against four strains of Gram positive bacteria, three strains of Gram negative bacteria and three species of fungi. The antimicrobial activity of various extracts of Plectranthus ambionicus and Phyllanthus amarus showed varied levels of antimicrobial activity against the studied bacterial and fungal pathogens. The mean zone of inhibition produced by all the tested extracts ranged from 7.0 ± 0.50 mm to 29.5 ± 0.50 mm. The MIC, MBC and MFC values were between 15.62 and 1000 μg/mL. The ethyl acetate extract of Plectranthus ambionicus showed good antimicrobial activity with the highest mean zone of inhibition (29.5±0.5 mm), lowest MIC (15.62 μg/mL) and MBC (31.25 μg/mL) values followed by ethyl acetate extract of Phyllanthus amarus (23.6±0.50 mm; MIC=62.5; MBC=125 μg/mL) against Aspergillus fumigates .