Miracle-dz/UniFAR-FTUs huggingface dataset:
DiGeorge syndrome and related birth defects

Abstract Classically, DiGeorge syndrome patients have congenital heart defects, particularly involving the outflow tract, hypocalcaemia, cell-mediated immune deficiency, learning or behavioural problems, craniofacial dysmorphism and hemizygosity for a region of human chromosome 22q11. This chromosomal abnormality is now known to cause other syndromal defects and apparently isolated congenital heart disease. Although most patients have a large deletion, at least 2 Mb, a critical region of 300 kbp has been defined. Within this region a putative transcriptional regulator called TUPLE-1 has been identified. TUPLE-1 is proposed as a candidate gene for the 22q11 haploinsufficiency syndromes.
Manufacture of acid urease by lactobacillus fermentumfermentation

Ethyl carbamate can be found in fermented foods and alcoholic beverages, such as sake, beer and wine. It is considered as a carcinogenic compound for some animals, and probably carcinogenic to humans, as well. Ethyl carbamate is formed by a chemical reaction of ethanol and urea. The urea content should be reduced to less than 1 mg/l to prevent the formation of ethyl carbamate. Urease is an enzyme, which hydrolyzes urea into ammonia and carbon dioxide. The acidic condition of fermented beverages is optimal for these types of ureases, which show high activity at low pH. Acid urease is an intracellular enzymeproduced by Gram positive bacteria like Lactobacillus fermentum. It is commercially not easily available, hence it has to be produced by fermentation, extracted from the bacteria and purified properly.
Gall morpho-type corresponds to separate species of gall-inducing thrips (Thysanoptera: Phlaeothripidae)

CSIRO Entomology, GPO Box 1700, Canberra ACT 2601, AustraliaReceived 13 December 2004; accepted for publication 5 December 2005Kladothrips rugosus Froggatt has previously been considered a single polyphagous species that, in Australia,induces galls on several species of Acacia, with the gall structure varying both within and between hosts. On Acaciapapyrocarpa, two types of gall are induced by this species, one with the surface ridged but the other with the surfacesmooth. Using sequence data from cytochrome oxidase subunit I (CO I) and elongation factor-1 alpha gene frag-ments, we show that the thrips inducing these two gall-types are genetically distinct and comprise separate lineages.Uncorrected ‘ p’ distances calculated from CO I gene fragments were 0.000 and 0.006 within lineages and 0.074 and0.078 between lineages. The between-lineage distances are comparable with distances between morphologically dis-tinct species of other Acacia gall-thrips. Re-examination of adult thrips from the two gall types revealed consistentdifferences in body colour, as well as in body sculpture. Together with observations on gall founding behaviour, thesedata indicate that the thrips populations in the two gall types on A. papyrocarpa are reproductively isolated andshould be considered as separate species. The form from smooth galls on A. papyrocarpa is therefore described asKladothrips nicolsoni sp. nov., although the form from ridged galls can be considered only as ‘K. rugosus agg. ’. These inconsistencies in the taxonomic status of the various units within the K. rugosus species complex are dis-cussed, although most of them cannot be distinguished morphologically at present. © 2006 The Linnean Society ofLondon, Biological Journal of the Linnean Society, 2006, 88, 555–563.
Genetic variation and phylogenetic relationships of a pantropical species group in Polystachya (Orchidaceae)

Amplified fragment length polymorphism (AFLP) markers were used to investigate the relationships among Polystachya accessions from a group of closely related pantropical tetraploids. Before starting with the fingerprinting analyses, the polyploid accessions were first included in a phylogenetic analysis using low-copy nuclear DNA data to establish their relationships, which confirmed that they belonged to a species group of closely related allotetraploids. Neo- and Palaeotropical polyploid accessions formed two hybrid clades with apparently independent origins. Sampling for the AFLP analyses included single accessions from much of the range of the genus and populations from Costa Rica (CR) and Sri Lanka (SL) to compare population structure and genetic diversity in these two areas in more detail. A splits graph of the complete AFLP data showed three major clusters corresponding to three sources of population sampling (P. concreta, SL; P. foliosa ,C R;P. masayensis, CR), with individual accessions from Africa and Indian Ocean islands showing a closer relationship to P. concreta from SL than to the two CR species. Individual accessions from the Neotropics occurred in more isolated positions in the splits network, with little resolution. Some P. foliosa accessions clustered with P. masayensis, suggesting some hybridization between the two species, and this was confirmed by Bayesian structure analysis. However, the splits network, structure and analyses of molecular variance indicated a generally high level of genetic divergence between the two CR species, despite their recent hybrid origin, occurrence in largely the same localities and occasional hybridization. Polystachya foliosa from CR had a higher degree of population-level genetic structure (FST = 0.291) than P. masayensis from CR (FST = 0.161) and P. concreta from SL (FST = 0.138), possibly because of its occurrence within a larger and more environmentally diverse continuous range than the other two species. Genetic divergence between Neo- and Palaeotropical members of the pantropical tetraploid group of Polystachya and the nonmonophyly of P. concreta suggested that P. concreta s.l. should be split and the use of this epithet should be confined to the Neotropics (the type is from Martinique). Other names should be used in Africa and the Asian tropics. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165, 235–250.
Epigean Spiders at Abisko Scientific Research Station in Swedish Lapland (Arachnida: Araneae)

Summary The Torneträsk area, including the Abisko National Park, Sweden, is arachnologically one of the best explored sites of Fennoscandia. Here, we report the results of pitfall trapping at Abisko Scientific Research Station during the summers of 2004 and 2005, recording 791 individuals of 62 species of spiders. As expected, at the species level, samples were dominated by members of the Linyphiidae, while at the level of individuals Pardosa hyperborea and other lycosids were dominant. Two subsites, on heath and bog, differed substantially in their species profile: seven species were statistically overrepresented on the drier heath site, while two showed a strong preference for the wetter bog site. The samples also contained the first reported lateral gynandromorph of Archaeodictyna consecuta (Dictynidae). This study, from 195 km north of the Arctic Circle, provides important reference data for continued studies on the long-term effects of climate change on Arctic ecosystems.
Quaternary and pre-Quaternary historical legacies in the global distribution of a major tropical plant lineage

Aim The relative importance of current climate and past historical legacies is hotly debated. Here, we assess their role in determining the global distribution and diversity patterns of palms (Arecaceae), a widespread, species-rich group of keystone ecological importance in tropical ecosystems. Location Global. Methods We assembled country-level species lists world-wide and compiled associated data on potential contemporary environmental drivers (current climate, habitat heterogeneity, area, and insularity), Quaternary glacial–interglacial climate change and major biogeographic regions to evaluate to what extent the global distribution and species richness patterns in palms reflect Quaternary climatic oscillations or regional effects reflecting pre-Quaternary legacies. We also assessed for the first time if historical legacies differ between continents and islands, providing novel insights into determinants of insular species richness. Results Palm species richness was significantly affected by Quaternary climate changes and further differed between biogeographic regions even when both current environmental conditions and Quaternary climate changes were accounted for. In contrast, global limits to the distribution of the palm family were best explained by current temperature while biogeographic regional differences were unimportant and Quaternary climate change caused only a small constraint. Historical legacies were weak on islands, with only a small regional effect and no effect of Quaternary climate changes. Main conclusions Strong historical legacies supplement current environment as determinants of palm species richness. These primarily comprise pre-Quaternary historical effects, reflected in low African species richness (possibly linked to pre-Quaternary extinctions) and outstandingly high Neotropical and Indomalayan palm species richness (possibly linked to these regions' long-term climatic suitability for palms). In contrast to species richness, the global distribution of the family range is largely in equilibrium with current climate. The small historical effects on islands are consistent with climatic buffering from their oceanic environment.
Comparative Efficacy of Enrofloxacin and Oxytetracycline by Different Administration Methods in Broilers after Experimental Infection with Avian Pathogenic Escherichia coli

The aims of this study were to compare the efficacy of 2 kinds of antibiotics that are commonly used in the Thai broiler industry and to determine the optimal times of drug administration. One hundred and sixty, 21-day-old broilers were divided into eight groups. Chickens in groups 1, 2 and 3 were challenged with avian pathogenic E. coli (APEC) and received oxytetracycline for the first 3 days after infection via oral, drinking water within 2 h and drinking water throughout the day, respectively. The chickens in groups 4, 5 and 6 were challenged with APEC and received enrofloxacin for the first 3 days after infection via oral, drinking water within 2 h and drinking water throughout the day, respectively. The chickens in group 7 and 8 served as positive and negative control groups. Enrofloxacin treated chickens showed better results in feed conversion ratio, mortality, gross pathology and bacterial isolation than those treated with oxytetracycline (p<0.05). Infections of chickens with APEC can be treated with the enrofloxacin. Oral administration provided a better protection than drinking water within 2 h and drinking water throughout the day, respectively.
Bioenrichment of trace elements in a series of ponds near a northern fulmar (Fulmarus glacialis) colony at Cape Vera, Devon Island

Seabirds are an important link between their marine feeding areas and their terrestrial breeding environments, transporting both marine-derived nutrients and contaminants and then depositing them on land in their guano. In this study, the impact of a large northern fulmar (Fulmarus glacialis) colony on the water chemistry of 26 nearby ponds spanning a gradient of seabird influence was investigated at Cape Vera, Devon Island, in the Canadian High Arctic. The presence of the fulmar colony has led to nutrient and trace element enrichment in the ponds, as evidenced by the close association among As, Cd, Co, Cu, Li, Mn, Mo, Ni, Sb, and Sr and the ornithogenic gradient. The ponds most affected by the fulmar colony were characterized by increased primary production, high organic carbon concentrations, and elevated pH — condi- tions favorable for the in situ removal of metals from the water column. Despite this, the highest trace element concentra- tions were observed in the seabird-influenced ponds, suggesting that these elements have undergone biotransport. Resume´ : Les oiseaux marins constituent un lien important entre leurs sites marins d'alimentation et leurs environnements terrestres de reproduction, car ils transportent ala fois des nutriments et des contaminants d'origine marine et les deposent sur terre dans leur guano. Nous evaluons, dans notre etude, l'impact d'une grande colonie de fulmars boreaux (Fulmarus glacialis) sur la chimie de l'eau de 26 etangs adjacents formant un gradient d'influence des oiseaux marins au cap Vera, ole Devon, dans le haut-arctique canadien. La presence de la colonie de fulmars boreaux provoque un enrichissement des etangs en nutriments et en elements en trace, comme le demontre l'association etroite entre As, Cd, Co, Cu, Li, Mn, Mo, Ni, Sb et Sr et le gradient ornithogene. Les etangs les plus affectes par la colonie de fulmars boreaux se caracterisent par une production primaire accrue, de fortes concentrations de carbone organique et un pH eleve ´ — des conditions favorables au retrait in situ des metaux de la colonne d'eau. Malgrecela, les concentrations les plus elevees de metaux en trace s'ob- servent dans les etangs influences par les oiseaux marins, ce qui laisse croire que ces elements subissent un transport biol- ogique. (Traduit par la Redaction)
Changes in the abundance and distribution of a montane specialist bird, the Dotterel Charadrius morinellus, in the UK over 25 years

Capsule The number of Dotterel breeding in the UK declined by 57% between 1987/88 and 2011, from 980 to 423 breeding males; there has been a contraction of the species’ geographical range as well as declining numbers on core sites. Aims To estimate the number of Dotterel breeding in the UK in 2011, the changes since surveys in 1987–88 and 1999, and to document broad patterns of change in distribution. Methods Two survey visits were carried out at montane sites (protected areas designated for Dotterel; and a stratified random sample of other sites >600 m altitude) across the Dotterel's breeding range using a standardized protocol as used in previous surveys. The first visit was to assess numbers in the pre-breeding period, and the second visit, comparable to those made in previous national surveys, provided data to calculate population estimates through extrapolation to unsurveyed sites and 95% confidence intervals by bootstrapping. Results In 2011, the number of Dotterel in the UK was estimated to be 423 breeding males (95% CI 279–644), a decline of 57% since 1987/88 and 43% since 1999. As in previous surveys, the majority of the population (61%) was found in the East Highlands, but large declines were recorded in this region. Dotterels were largely absent from previously occupied sites in North and West Highlands. Conclusions Numbers of Dotterel breeding in the UK declined by more than half between 1987 and 2011. Long-term monitoring data are rare for montane environments in the UK, but these findings may signify the occurrence of important ecological changes, with possible drivers including land-use/habitat change, nitrogen deposition and climate change.
Specialized predation on Oribatid mites by two species of the ant genus Myrmecina (Hymenoptera: Formicidae)

Specialized predation on oribatid mites was confirmed in two Japanese species of the myrmicine genus Myrmecina, the first instance in the Formicidae. Using the mouthparts and legs, a worker skillfully tears a hole in the oribatid body and gives the partly dismembered prey to a larva. During food preparation workers bend the gaster forward deeply and raise their anterior body thus making the working posture stable; both seem necessary for handling such round slippery prey as oribatid mites. The larva of Myrmecina has a peculiarly elongate head which it inserts into an oribatid body and consumes the contents.
Are We Misinterpreting Seed Predation in Palms?

The inadvertent inclusion of weevil‐infested seeds when evaluating seed predation by vertebrates, and particularly rodents, may lead to an overestimation of predation rates, thereby confusing the roles of rodents and invertebrates as ecological filters. A study of weevils, rodents and Syagrus romanzoffiana palm seeds indicates the usefulness of X‐rays to improve evaluation of invertebrate seed predation.
Molecular cloning, genomic organization and functional analysis of the ribosomal protein L4/L1 (RPL4) gene from Arachis hypogaea

Wu, Q. , Wang, X. Z. , Tang, Y. Y. , Yu, H. T. , Cui, F. G. , Zhang, J. C. and Wang, C. T. 2014. Molecular cloning, genomic organization and functional analysis of the ribosomal protein L4/L1 (RPL4) gene from Arachis hypogaea. Can. J. Plant Sci. 94: 85-97. The ribosomal proteins have been shown to be important in plant polarity establishment, cell proliferation, leaf shape and auxin-related development. The RPL4 protein is crucial for the maintenance of ribosomal translational efficiency and fidelity. This study concerns the RPL4 gene from Arachis hypogaea. The full-length cDNA (1538 bp) of RPL4 consisted of an open-reading frame of 1221 bp encoding 406 amino acids. The genomic DNA sequence of RPL4 gene consisted of 1491 bp containing two exons and one 270-bp intron. The RPL4 mRNA transcript was mainly expressed in roots and leaves, and fewer signals were detected in stems. The sequence data revealed that RPL4 encoded a typical ribosomal protein L4/L1e domain. Phylogenetic analysis for genes encoding proteins showed that RPL4 were conserved within dicotyledonous and monocotyledonous plants. The ratios of nonsynonymous/synonymous substitution rate (ω=d N/d S) were analyzed. No sites were identified under positive selection. In the whole RPL4 sequence, d S greatly exceeded d N in all branches of the tree (d N/d S<< 1.0), indicating that functional constraints (purifying selection) have acted on RPL4 throughout evolution. The differences among plants and animals and Caenorhabditis elegans may indicate functional differentiation during species evolution.
The taxonomy and systematics of New Zealand lycosidae (wolf spiders)

The 27 species of Lycosidae found in New Zealand were revised. One species in the genus Allotrochosina Roewer, 1960; twenty species in the genus Anoteropsis L. Koch, 1878, of which 11 were new species (alpina, hlesti, cantuaria,forsteri, halli, insularis, lacustris, litoralis, montana, okalainae, and westlandica); three new species in the genus Artoria Thorell, 1877 (hospita, segrega, and separata); one species in the genus Geolycosa Montgomery, 1904; one species in the new genus Notocosa; one species in the genus Venatrix Roewer, 1960. All genera and species were described, with information on synonymy, type data, material examined, geographical distribution and sub familial status. A key to adults was constructed and habitus images of adults, illustrations of important structural features and distribution maps have been provided. A phylogeny for the genus Anoteropsis was inferred using parsimony analysis of morphological characters and contained significant phylogenetic structure. The phylogeny of Anoteropsis was further investigated using molecular data to test for congruence with the morphological data and the monophyly of widespread species. Data sets from the mitochondrial gene regions NADH dehydrogenase subunit I (ND1) and cytochrome c oxidase I (COI) of the 20 species in the New Zealand genus Anoteropsis were generated. Two species of Artoria were also sequenced and used as an outgroup. Species with a large distribution within New Zealand were represented by two or more specimens to test for monophyly or cryptic species. Sequence data were phylogenetically analysed using parsimony and maximum likelihood analyses. Sequence data was combined with a previously generated morphological data set and phylogenetic ally analysed using parsimony. The ND1 region sequenced included part of tRNA Leu(CUN), which appears to have an unstable amino-acyl arm and no TψC arm in lycosids. Analyses supported the existence of five main species groups within Anoteropsis and the monophyly of the species. Maximum likelihood analyses appears to provide better resolution of the deeper phylogenetic structure within Anoteropsis. Phylogenies generated from the COI data set show inconsistencies with the ND1 and morphological trees and caution is advised when using COI to estimate spider phylogenies. A radiation of Anoteropsis species within the last five million years is inferred from the ND1 likelihood phylogram, habitat and geological data. The relationship of New Zealand wolf spiders to Australian, Asian and Holarctic genera was investigated to ensure the correct generic placement of New Zealand species. A data set from the mitochondrial12S rRNA gene subunit of 11 Australasian lycosid species (six New Zealand species and five Australian species), three North American lycosid species, one European lycosid species and one New Zealand pisaurid (outgroup) were generated. They were combined with the published sequences of 12 European lycosids, two Asian lycosids and one Asian pisaurid and were phylogenetic ally analysed using parsimony and…
Association of Serum Thyroid Hormones with the Risk and Severity of Chronic Kidney Disease Among 3563 Chinese Adults

Background Chronic kidney disease (CKD) is a global health problem with an increasing prevalence. We explored the association of serum thyroid hormones with the risk and severity of CKD among Chinese adults. Material/Methods This retrospective study involved 3563 participants. CKD was diagnosed according to the clinical practice guidelines of the 2012 Kidney Disease Improving Global Outcomes guidelines. Effect-size estimates are expressed as odds ratio (OR) and 95% confidence interval (CI). Results Given the strong magnitude of correlation, only 3 thyroid hormones were analyzed: free triiodothyronine (FT3), free thyroxin (FT4), and thyroid-stimulating hormone (TSH). After propensity score matching on age, sex, diabetes, and hypertension, per 0.2 pg/mL increase in FT3 was significantly associated with 35–38% reduced risk of CKD at stage 1–4, and per 0.3 ng/dL increase in FT4 was only significantly associated with 21% reduced risk of CKD at stage 5 (OR, 95% CI: 0.79, 0.69–0.89), and per 0.5 μIU/mL increment in TSH increased the risk of CKD stage 5 by 8% (1.08, 1.02–1.14). Importantly, 3 thyroid hormones acted interactively, particularly for the interaction between FT3 and FT4 in predicting CKD at stage 5 (OR, 95% CI: 1.81, 1.30–2.55 for high FT3-low FT4, 17.72, 7.18–43.74 for low FT3-high FT4, and 22.28, 9.68–51.30 for low FT3-low FT4). Conclusions Our findings indicate that serum FT3 can be used as an early-stage biomarker for CKD, and FT4 and TSH can be used as advanced-stage biomarkers among Chinese adults.
Regulation by phytoestrogens of migration, actin cytoskeleton, and signaling cascades relevant to cancer cell motility

vi List of Figures xii Abbreviations xv Overview 1 Goals and Objectives 1 Significance and Relevance 2 Chapter 1: Introduction 5 Genomic E2 signaling and nuclear ERs 5 Genomic function of ERα versus ERβ in breast cancer 8 E2/ER function in cancer cell motility, invasion, and metastasis.10 Non-genomic E2 signaling and PM ERs 12 PM ER cross-talk with other PM-associated receptors 13 EGFR signaling 15 Relevance of E2 and PEs in postmenopausal HRT 17 Phytoestrogens 18 Structure of genistein and daidzein 18 Function of genistein and daidzein in plants 19 Structure of resveratrol 20 Function of resveratrol in plants 20 PEs and breast cancer 21 Metabolism and Bioavailability of PEs 23 PEs as Antioxidants 24 Genistein/Daidzein and Breast Cancer 26 Genistein/Daidzein effects on cell proliferation/cell cycle progression 28 Genistein/Daidzein effects on apoptosis 29 Genistein/Daidzein effects on cell invasion/metastasis 31