Miracle-dz/UniFAR-FTUs huggingface dataset:
Contribution of mitochondrial cox1 intron sequences to the phylogenetics of tribe Orchideae (Orchidaceae): do the distribution and sequence of this intron in orchids also tell us something about its evolution?

In this paper, we use the mitochondrial region cox1 to assess the usefulness of this marker in addressing evolutionary relationships within the tribe Orchideae. Despite the low overall variation uncovered in this region, one good phylogenetic marker was identified. A large group I intron was shared across subtribe Orchidinae and some species ofHabenariinae sensu Dressler. The clades identified in the cox1 tree were weakly supported, but consistent with previous studies based on nuclear ribosomal spacers (nrITS). Moreover, the phylogenetic analysis of the combined cox1/ITS data matrix allowed us to highly improve the resolution of the ITS-only analysis and confirm several previously controversial relationships. A second purpose of this study was to analyse the evolution of the group I cox1 intron in Orchideae. This intron has a patchy distribution in angiosperms that has been claimed to be mostly due to horizontal transfer events. Our results suggest that, despite the differences observed in the co-conversion tracts in the tribe, vertical transfer is more consistent with the observed phylogenetic trees.
Variation Genetics of Extinct Animals

Many aspects of variation genetics are reviewed, especially but by no means exclusively with reference to extinct animals. The major topics covered are: polymorphism; the causes of variation; the relation of variation to evolutionary rate, stage of evolution, and niche width; changes of variation in time; range of reaction; parthenogenesis and variation; evolution of correlations; and ontogeny of variation.
COMBINED EFFECT OF STRONTIUM CONTENT AND ELECTRODE TYPE ON ELECTRICAL PROPERTIES OF BaXSr1‐X TiO3 THIN‐FILMS by OMID

Ferroelectric thin films have been on agenda of many research groups and the semiconductor industry for applications ranging from non‐volatile data storage to tunable capacitors and antennas. In much of these works, the fact that ferroelectrics can be sensitive to the electrical boundary conditions, namely the type of the electrodes employed, is often taken for granted without an in‐depth analysis. In this thesis work, we focus on BaxSr1‐xTiO3 compositions, a well‐known system, grown via a sol‐gel method on conducting Nb:SrTiO3 bottom electrodes to explore the effect of the Sr content and the top/bottom electrode asymmetry on the electrical characteristics of these systems. Following structural and morhphological characterization for quality check of the films, we extensively focus on a process called “resistive switching”, which we repeatedly observed in our samples. Resistive switching phenomena is a topic of interest as the direction of the ferroelectric polarization determines whether there will be carrier depletion or accumulation in the semiconducting electrode (the conducting oxide bottom electrode in this thesis), upon which various novel device and transistor designs have been recently proposed by a number of groups. In this work, we focus on the experimental evidence for resistive switching in the light of thermodynamic theory of these systems and discuss the effect of Sr content on current‐voltage characteristics of our samples.
An Empirical Application of Optimal Tax Approach

We examine empirically the relationship between the extent of redistribution and the components of the Mirrlees framework, with a focus on inherent inequality and government’s redistributive preferences. We have constructed our income distribution variables from the Luxembourg Income Study (LIS) database, which provides information on both factor and disposable incomes. Our redistributive preference measure is constructed using the optimal tax formula for which we have collected data from various sources. In addition to traditional linear specifications, we use flexible methods to allow nonlinearities because pre-specified functional forms are not easy to justify in empirical investigations of the optimal tax framework. We study 14 advanced countries for approximately four decades and find support for the Mirrlees model: There is a positive relationship between factor-income inequality and the extent of redistribution. We also find a link between our redistributive preference measure and the extent of redistribution.
Foraging Habitat and Home-Range Characteristics of California Spotted Owls in the Sierra Nevada

We examined habitat use patterns at two spatial scales among six radio-tagged California Spotted Owls (Strix occidentalis occidentalis) in the Sierra Nevada. Foraging owls selected macrohabitats composed of larger trees (> 52 cm dbh) with canopy closures of 40% and greater. Owls used forests composed of medium trees (28-52 cm dbh) and habitats with less than 40% canopy closure, which is less frequently than expected. Fewer than 2% of telemetry locations occurred in clearcut/shrub/plantation habitat which represented 30% of available habitat. Foraging owls used microhabitats that were characterized by multiple vegetative strata, large tree size classes, high tree basal areas and woody debris. The median 100% minimum convex polygon home-range was 1,439 ha (n = 5, June to December, 1987). Telemetry locations were statistically independent when separated by five days. Estimates of minimum convex polygon and modified minimum convex polygon size based on statistically independent telemetry data were significantly smaller than estimates based on continuous and single-observation monitoring.
Individual Recognition of Amphibians: Effects of Toe Clipping and Fluorescent Tagging on the Salamander Plethodon vehiculum

-Recognition of individual animals is essential for a wide variety of research and monitoring studies involving amphibians, but little information exists on the effects that marking methods have on survivorship, life history, and behavior. We evaluated toe clipping and subcutaneous injections of a fluorescent-elastomer for individual identification of the western red-backed salamander, Plethodon vehiculum, on Vancouver Island, British Columbia. In the laboratory, no confirmed mortality of marked or unmarked (control) salamanders occurred over 64 weeks. The number of toe clips lost as the result of regeneration increased steadily after 35 weeks postmarking, but few fluorescent marks were lost or misidentified. In the field, we recaptured more fluorescent-marked (60%) than toe-clipped (40%) salamanders from September 1997 to May 1998 but detected no differences in growth or spatial movements. In a second field experiment (27 April to 31 May 1999), toe-clipped salamanders gained less weight in relation to their initial body size than did fluorescent-marked and control salamanders. These data suggest that toe clipping affects the ability of individuals to take full advantage of optimal foraging conditions that prevail in May, which, in turn, might affect the quantity of stored energy reserves required for survival over adverse, dry periods in sum-
A fossil Osmunda from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae

The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.
Cloning, biochemical identification, and expression analysis of a gene encoding S-adenosylmethionine decarboxylase in navel orange (Citrus sinensis Osbeck)

Summary Polyamines have been shown to be involved in a variety of plant physiological processes such as growth, development, and stress responses. As S-adenosylmethionine decarboxylase (SAMDC) is the rate-limiting enzyme for polyamine biosynthesis, efforts were made to isolate the gene encoding SAMDC from ‘Newhall’ navel orange (Citrus sinensis Osbeck). RT-PCR, in combination with a bioinformatics approach, produced a cDNA (CsSAMDC) containing an intact open reading frame (ORF) of 1,095 bp. The deduced amino acid sequence shared high homology (>75%) with four selected plant SAMDCs and possessed several highly-conserved amino acid residues or motifs. Expression of CsSAMDC in Escherichia coli gave rise to a protein of the expected size, which was shown to have biochemical activity via a SAMDC assay. The expression pattern of the CsSAMDC gene in ‘Newhall’ callus tissue broadly matched the growth of callus cells and the fluctuation in endogenous polyamine levels. Levels of transcription of CsSAMDC in ‘Newhall’ shoots were enhanced by treatment with 10% (w/v) polyethylene glycol. In addition, the steady state level of CsSAMDC mRNA varied in genotypes with varying levels of tolerance to salinity or to low temperature stress, as revealed by the earlier induction of CsSAMDC mRNA at the initial stages of either stress treatment in tolerant genotypes. These results suggest that CsSAMDC is a stress-responsive gene and that temporal changes in its expression profile may be part of the mechanism responsible for genotypic variations in stress tolerance.
ENTEROHAEMORRHAGIC E. COLI (EHEC) - A NATION-WIDE SWEDISH SURVEY OF BOVINE FAECES

A l'automne 1995, le premier foyer de maladie due a E. coil ent6roh6morragique touchant 102 personnes a ete signals en Suede. D'apres les foyers d'autres pays, on salt que du bate infects de fagon sub-clinique est souvent la source infectieuse. Par suite, une etude de prevalence a ete commenc6e en avril 1996 et sera terminee en ao0t 1997. Son but est de preciser la frequence d'E. coil ent6roh6morragique ou producteurs de verotoxines dans la population bovine suedoise. Des feces doivent etre prelevees chez 3.000 bovins dans les 16 principaux abattoirs. Le nombre d'echantillons dans chaque abattoir est proportionnel au nombre de bovins abattus. Les resultats seront utilises pour Mink si des mesures specifiques doivent etre prises pour ! utter contre ces colibacilles chez les bovins. En avril 1995, 2.195 6chantillons individuels ont 6t6 analyses et les resultats preliminaires montrent que 25 (1,1 p. cent) contenaient E. coil serotype 0,57 produisant des verotoxines (VT, et/ou VT2), positifs pour le gene eaeA. Deux cent cinquante autres echantillons (11,4 p. cent), non 0,57, ont ete identifies comme contenant des souches de coliformes produisant une v6rotoxine. Parmi elles, environ 13 p. cent poss6daient 6galement le gene eaeA. Les s6rotypes de ces souches seront determines. Les resultats montrent que E. coil ent6roh6morragique existe dans la population bovine suedoise et que la distribution des bovins hebergeant des souches d'E. coli ent6roh6morragiques est correlee a cells de la distribution generale des bovins en Suede.
Identification of sources of resistance against virulences of Colletotrichum capsici causing fruit rot of chilli (Capsicum annuum L.)

*Corresponding Author: e-mail: pns@hillagric.ernet. in Anthracnose/ die-back or ripe fruit rot, caused by Colletotrichum capsici (Sydow) Butler and Bisby, is the major constraint in chilli (Capsicum annuum L.) production in tropical and sub tropical areas, especially under humid conditions. Chilli being one of the most remunerative spice and vegetable cash crops in Himachal Pradesh is affected severely by this disease during humid weather and the pathogen has been reported to possess a high degree of pathogenic variability (1). Yield losses in bell pepper by C. capsici during the years 1985-1987 were estimated to the tune of 27.17% in H.P. (2). Identification of resistance sources and nature of resistance in a given host is a pre-requisite before development and deployment of resistant varieties. Studies conducted on resistance aspect of this disease shows very little resistance in chilli germplasm which indicate the presence of diverse population within the fruit rot/ dieback or anthracnose fungus (3, 4, 5). The present studies were conducted to find out effective sources of resistance against different races of the pathogen and the results obtained are presented herein.
Farmers Markets and Seafood: Where Is It Feasible?

National-level empirical research can inform how policy can effectively support direct seafood markets. The US Department of Agriculture maintains a directory of farmers markets that has not been extensively used in direct seafood marketing research. I use this directory data to estimate the probability that farmers markets near commercial fishing ports in the United States offer seafood. The results provide insight into two policy-relevant constraints on direct marketing: (1) geographic limits to seafood sales at farmers markets and (2) accessibility challenges for low-income populations. I find that seafood sales at farmers markets are concentrated within 50 miles of commercial fishing ports and that lower-income people are less likely to have access to seafood at farmers markets. I discuss advances made in collecting data from direct marketing farmers and the potential value in collecting analogous data from direct marketing fishers.
Improving Multilingual Models with Language-Clustered Vocabularies

State-of-the-art multilingual models depend on vocabularies that cover all of the languages the model will expect to see at inference time, but the standard methods for generating those vocabularies are not ideal for massively multilingual applications. In this work, we introduce a novel procedure for multilingual vocabulary generation that combines the separately trained vocabularies of several automatically derived language clusters, thus balancing the trade-off between cross-lingual subword sharing and language-specific vocabularies. Our experiments show improvements across languages on key multilingual benchmark tasks TyDi QA (+2.9 F1), XNLI (+2.1\%), and WikiAnn NER (+2.8 F1) and factor of 8 reduction in out-of-vocabulary rate, all without increasing the size of the model or data.
Using molecular analysis to investigate phylogenetic relationships in two tropical pathosystems: Witches' broom of cacao, caused by Moniliophthora perniciosa, and mango anthracnose, caused by Colletotrichum spp

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy USING MOLECULAR ANALYSIS TO INVESTIGATE PHYLOGENETIC RELATIONSHIPS IN TWO TROPICAL PATHOSYSTEMS: WITCHES’ BROOM OF CACAO, CAUSED BY MONILIOPHTHORA PERNICIOSA, AND MANGO ANTHRACNOSE, CAUSED BY COLLETOTRICHUM SPP. By Tara Luana Barrett Tarnowski December 2009 Chair: Randy C. Ploetz Cochair: Jeffrey R. Rollins Major: Plant Pathology The increasing availability of DNA sequence data has enabled rapid advances in molecular systematics. This is especially true for the Fungi, where systematics and taxonomy relied previously on largely artificial, morphologically based systems. Many of the advances in fungal systematics have been made with phytopathogens. Characterizing the relationships of lineages among phytopathogenic genera provides insight into not only basic systematic information, but can also address applied questions on host specificity, life strategy and pathogenicity. With DNA sequence-based phylogenetic analyses, two broad topics were investigated: 1) relationships among biotypes of Moniliophthora perniciosa, causal agent of witches’ broom of cacao, and 2) host and tissue specificity of Colletotrichum gloeosporioides sensu lato on mango. Sequences from the ITS1-5.8S-ITS2 ribosomal DNA region (ITS), intergenic spacer (IGS) region, and RNA polymerase large subunit (RPB1) regions were analyzed for 36 accessions of M. perniciosa from all reported biotypes of the pathogen. Maximum parsimony and maximum likelihood analyses resolved three major clades within the species: a clade that contained all isolates from Theobroma spp. and most isolates from Solanum spp. ; a clade that contained most
Effects of Different Colored Light-quality Selective Plastic Films on Growth, Photosynthetic Abilities, and Fruit Qualities of Strawberry

Light quality regulates plant growth and photosynthesis, the drivers of fruit quality, and light quality can be controlled by colored light-quality selective plastic films in field production. To identify the optimal color of plastic film for high-quality strawberry (Fragaria × ananassa) fruit production, plant growth, photosynthetic abilities, and fruit qualities were investigated under transparent (T), red (R), yellow (Y), green (G), blue (B), and purple (P) films. The R film showed the maximum promoting effects on leaf area, petiole length, leaf biomass, and shoot biomass. The R film improved photosynthetic abilities by increasing photosynthetic pigment content, quantum yield (φPo), electron transfer (Ψo and φEo), the density of reaction centers (RC/CSm), and the photosynthetic performance index (PIabs), and by decreasing the dissipation of absorbed solar energy as heat (φDo), while varied reverse effects were detected under other films. For fruit qualities, the R film also improved fruit weight and the content of total sugar, anthocyanin, and soluble protein. Therefore, the R light-quality selective plastic film should be suitable for strawberry production due to the promoting effects on plant growth, photosynthetic abilities, and fruit weight and quality. Additional key words: facility cultivation, horticulture, light quality, physiology, strawberry production
Cooperation in Knowledge‐Intensive Firms

The extent to which a knowledge‐intensive firm should induce cooperation between its employees is analyzed in a relational contracting model. We extend the existing literature on agent cooperation by analyzing the implications of incomplete contracts and agent holdup. A main result is that if the agents’ holdup power is sufficiently high, it is suboptimal to implement cooperation, even if helping effort is productive. This implies, contrary to many property rights models, that surplus may suffer if the investing parties (the agents) are residual claimants. We also show that long‐term relationships facilitate cooperation even if agents cannot monitor or punish each other.
Banks’ Interventions and Firms’ Innovation: Evidence from Debt Covenant Violations

We examine the effect of banks’ interventions on corporate innovation and firms’ value via the lens of debt covenant violations. Banks’ interventions have a significantly negative effect on the quantity of innovations but no significant effect on their quality. The reduction in quantity is concentrated in innovations that are unrelated to the violating firm’s core business, which leads to a more-focused scope of investment in innovation and ultimately an increase in the firm’s value. Human capital redeployment appears to be a plausible underlying mechanism through which banks’ interventions refocus the scope of innovation and enhance a firm’s value. Our paper sheds new light on the real effect of bank financing.
Estimating survival rates of snowshoe hares

Survival rates were estimated by 4 methods (minimum survival, Jolly-Seber, and 2 radio-telemetry techniques) for snowshoe hares (Lepus americanus) near Kluane Lake in the southern Yukon from 1978 to 1982. Jolly-Seber and minimum survival estimates from live trapping underestimated survival rates by 13 and 30%, respectively, when compared to telemetry estimates, which produced higher and nearly identical estimates of survival. Telemetry methods are recommended for estimating survival of hares. J. WILDL. MANAGE. 50(4):592-594 Survival is an important demographic parameter, and changes in juvenile and adult survival rates are known to drive the 10-year snowshoe hare cycle (Keith and Windberg 1978). Two detailed analyses of this cycle (Keith and Windberg 1978, Krebs et al. 1986) found that survival rates tended to be underestimated (assuming census data and reproductive rates were accurate). In this paper we compare 4 methods of estimating survival rates for snowshoe hares to determine the source of this bias. We thank B. S. Gilbert, R. A. Moses, and C. J. Krebs for their help in collecting these data and the Arct. Inst. North Am. for providing facilities at Kluane Lake. This research was supported by the Nat. Sci. and Eng. Res. Counc. Can.
Cutaneous Lesions Associated with Reo-like Virus in a Gren Lizard (Lacerta viridis LAURENTI 1768)

In this case, a green lizard (Lacerta viridis LAURENTI 1768) caught in Uludag, Bursa, north-western Turkey, was diagnosed as reovirus by electron microscopy. In the macroscopical examination, wart-like growths were seen on the dorsum of the animal on the skin between the forearms and on the back close to the pelvic region. In the microscopical examination of hematoxylin and eosin stained sections, hyperkeratosis, ballooning degeneration and eosinophilic inclusions in the cytoplasm were observed. There was no positive reaction for papillomavirus in immunohistochemistry. Electron microscopic study of these growths revealed the presence of viral particles belonging, from the morphological aspect, to the family Reoviridae.
Microsoft Word-IGC_2016_paper_32.docx

In railway transportation, reducing the effects of the train-induced vibrations on the nearby structures is a challenging task. Trenches are one of the simplest among the various mitigation measures for the attenuation of groundborne vibrations. This paper deals with the study of the effectiveness of open and filled trenches in vibration screening. In the present study, the far-field is modelled using the scaled boundary finite element method (SBFEM). The trainload is simulated using two simultaneously applied concentrated line loads which cover a wide frequency range that normally arises in case of a heavy axle train passage. The developed code is first verified by solving the problem available in the literature. Various parameters such as geometric features of the open trench like width and depth of the trench and distance of the trench from the rail (active and passive isolation) as well as the backfill material in filled trench are considered and their effect in screening the ground-borne vibrations is investigated. Results show that among the geometric parameters the role of the depth of the trench is very significant. Open trench was found to be more effective than the filled trenches.