Miracle-dz/UniFAR-FTUs huggingface dataset:
An analysis of the meroplankton assemblages of Station L4 and the development and application of molecular techniques to aid taxonomic resolution.

Zooplankton data from 20 years of weekly sampling were used to determine inter-and intra-annual patterns of meroplankton community change at Station L4, off the coast of Plymouth, UK. From these data, abundances were calculated for ﬁve groups; Cirripedia, Decapoda, Polychaeta, Echinodermata and Lamellibranchiata. This taxonomic level of analysis was chosen to minimize the potential effects of variation in taxonomic expertise over the 20-year period. Analyses showed that while there is some annual variability, it is seasonal variation that accounts for the major changes in the meroplanktonic community composition throughout the time series. Cirripedia are the most abundant meroplankton in March and April, followed by Echinodermata in August, and Lamellibranchiata in September and October. Abundance is low during the winter period. The average monthly contribution of the meroplankton community as a percentage of the total zooplankton abundance is highest in spring, when meroplankton (predominantly Cirripedia) can account for up to 42.5% of the total zooplankton community following spawning events linked to phytoplankton blooms. Little evidence was found for any major trends of change in the meroplankton community (at the taxonomic level examined here) at Station L4 over the 20-year period.
Investigating Annual Variation in Fruit Quality Using Nutrient Assays and Multidimensional Fluorescence Spectroscopy

Migratory songbirds rely on high-quality sources of food during annual migrations. During fall migration in eastern North America, many birds switch to a diet of fruits at stopover sites. In order to sustain them during their journey, birds may select fruits rich in nutrients that provide high energy, such as fats. While studies have evaluated the nutritional value of a variety of fruits, a less studied phenomenon is the impact of changing weather conditions on the nutritional quality of fruits available for migratory birds to eat. In this study, fruits from 12 species of locally growing shrubs in Rochester, NY were collected in 2012 and 2013 and analyzed for their energy density, percent fat content, total soluble solids content, acid detergent fiber content, ash content, and water content. The goal of this study was to determine if there is a variation in the nutritional quality of fruits between the two years, and if the variation can be correlated with different weather and growing season conditions during the two years. Results indicate that Red Osier Dogwood, a drought intolerant native plant, produced fruit with lower energy density and fat content in 2012, which experienced higher temperatures than 2013 during every season. On the other hand, Gray Dogwood, a closely related native plant, showed less variation in nutritional quality between the two years. This was also the case for droughtresistant non-native plants, such as Autumn Olive and Multiflora Rose. Spicebush is a drought tolerant native plant that seemed to produce fruits with greater fat content and energy density during 2012. These results suggest that different fruits may respond differently to fluctuating weather conditions, which may be a result of variation in ripening time of the fruit, and the level of tolerance of the plant for different climatic conditions.
A Non-generative Framework and Convex Relaxations for Unsupervised Learning

We give a novel formal theoretical framework for unsupervised learning with two distinctive characteristics. First, it does not assume any generative model and based on a worst-case performance metric. Second, it is comparative, namely performance is measured with respect to a given hypothesis class. This allows to avoid known computational hardness results and improper algorithms based on convex relaxations. We show how several families of unsupervised learning models, which were previously only analyzed under probabilistic assumptions and are otherwise provably intractable, can be efficiently learned in our framework by convex optimization.
Taxonomy of the Leuconostocs

The leuconostocs are traditionally found in association with plant matter, fermented dairy products, and wines. More recently, new strains have been isolated from meats and clinical sources. Since 1983, six new strains have been added to the genus. The development of new taxonomic methodologies make likely the addition of more strains to this genus in the near future. A brief history, characteristics, isolation, and taxonomic tests for the genus Leuconostoc are presented.
What is Geosaurus? Redescription of Geosaurus giganteus (Thalattosuchia: Metriorhynchidae) from the Upper Jurassic of Bayern, Germany

The holotype and referred specimens of Geosaurus giganteus, a metriorhynchid crocodile from the Tithonian (Upper Jurassic) of Germany, is redescribed, along with a historical overview of the genus and species. This taxon is unique among metriorhynchids as its serrated, strongly lateromedially compressed dentition is arranged as opposing blades, suggesting it was adapted to efficiently slice through fleshy prey. A new phylogenetic analysis of Crocodylomorpha is presented, which finds G. giganteus to be nested within what is currently considered Dakosaurus, whereas the other species currently assigned to Geosaurus form a clade with Enaliosuchus and the holotype of Cricosaurus. The phyletic relationship of G. giganteus with other metriorhynchids indicates that the current definition of the genus Geosaurus is polyphyletic, and that the inclusion of subsequent longirostrine species to this genus is in error. The re-analysis presented herein demonstrates Geosaurus to be composed of three species sensu stricto. The appropriate taxonomic amendments to the Metriorhynchidae are also provided. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157, 551–585.
Búsqueda y selección de información en recursos digitales: Percepciones de alumnos de Física y Química de Educación Secundaria Obligatoria y Bachillerato sobre Wikipedia

This paper describes the information search and selection skills, as established by the digital competence, of a secondary education students group. It aims to answer what are the digital resources they use, their reasons for using them, and the use and reliability given to the information obtained from Wikipedia. In order to achieve these goals, the literature about digital competence, ICT and Wikipedia has been considered in order to design a questionnaire. According to the answers obtained and to the literature, the use of new technologies frequently doesn´t make a student competent in processing digital information. Moreover, the students don´t have a critical attitude about how they have to search and select information from Internet.
STRUCTURE-FUNCTION STUDIES OFTRANSLOCATED EFFECTORS FROMTHE LATE BLIGHT PATHOGEN

An almost universal feature of successful pathogens is the secretion of effector proteins, many of which translocate inside host cells. These effectors manipulate host processes for the pathogen’s benefit. However, in response to this manipulation, plants have evolved to monitor for effectors and trigger defence responses. Amongst plant pathogens, oomycetes of the genus Phytophthora have arguably caused almost unrivalled levels of human suffering and represent significant threats to global food security. The late blight pathogen, Phytophthora infestans, is the most devastating pathogen of potato – the fourth most important food crop worldwide. Effective and durable resistance against late blight is desperately needed; and will depend on an improved understanding of the mechanistic basis of disease. Determining the adaptive functions of effectors might reveal previously unexploited management strategies. This work details structure-function studies of two translocated effectors from the late blight pathogen; PexRD2, a representative RXLR effector, and CRN8, an effector with kinase activity. Efforts to heterologously express CRN8 were hampered by protein insolubility and low yields. However, the crystal structure of PexRD2 revealed that it homodimerises, and was crucial to the discovery of a conserved oomycete effector protein fold, the WY-domain fold. Yeast two-hybrid screening identified four PexRD2-interacting host proteins, including MAPKKKe, a known positive regulator of plant immunity. MAP-kinase cascades transduce the perception of invading pathogens into effective defence responses, and MAPKKKe is involved in resistance against P. infestans. PexRD2 specifically suppresses cell deaths that are either MAPKKKe-dependent or triggered by MAPKKKe overexpression. PexRD2 also inhibits MAPKKKe-triggered MAPK activation. Further, structure-led mutagenesis of PexRD2 suggests that this effector benefits the pathogen by interacting with MAPKKKe to inhibit the kinase’s signalling. Discovering the PexRD2-MAPKKKe interaction, and its implications for plant immunity, has suggested unexploited management strategies that could enhance crop resistance to this devastating pathogen.
Automatic Transcription of Polyphonic Vocal Music

This paper presents a method for automatic music transcription applied to audio recordings of a cappella performances with multiple singers. We propose a system for multi-pitch detection and voice assignment that integrates an acoustic and a music language model. The acoustic model performs spectrogram decomposition, extending probabilistic latent component analysis (PLCA) using a six-dimensional dictionary with pre-extracted log-spectral templates. The music language model performs voice separation and assignment using hidden Markov models that apply musicological assumptions. By integrating the two models, the system is able to detect multiple concurrent pitches in polyphonic vocal music and assign each detected pitch to a specific voice type such as soprano, alto, tenor or bass (SATB). We compare our system against multiple baselines, achieving state-of-the-art results for both multi-pitch detection and voice assignment on a dataset of Bach chorales and another of barbershop quartets. We also present an additional evaluation of our system using varied pitch tolerance levels to investigate its performance at 20-cent pitch resolution.
Comparative anatomy and phylogenetic systematics of the family Uranoscopidae (Actinopterygii:Perciformes)

The anatomy of the family Uranoscopidae including osteological and mycological features is examined and described in details based on eight genera and 32 uranoscopid species. As results of anatomy and phylogenetic analysis, the monophyly of the family is reconfirmed to be strongly supported by 59 synapomorphies (plus 11 according to ACCTRAN). The phylogenetic relationships of uranoscopids were inferred from the morphological characters in 113 transformation series. Pleuroscopus and Xenocephalus, having a sister relationship, are branched off initially from remaining members, and monophyletic Kathetostoma is branched off. Kathetostoma has a sister relationship with a monophyletic group comprising Uranoscopus, Genyagnus, Ichthyscopus and Astroscopus. Selenoscopus is inferred as nesting deeply phylogenetically within Uranoscopus. In addition, a sister relationship of the Uranoscopidae and Trachinidae is examined to be supported by 22 synapomorphies (plus two according to ACCTRAN). The newly defined family Uranoscopidae comprises seven genera: Pleuroscopus, Xenocephalus, Kathetostoma, Uranoscopus, Genyagnus, Ichthyscopus and Astroscopus. The monotypic genus Selenoscopus is synonymized with Uranoscopus. The benthic life style of Uranoscopidae is described and discussed.
A Family of Four LRR-RLKs Modulate Development and Defense Signaling in Arabidopsis thaliana through Interaction with the Co-receptor BAK1

8 Explanation of Dissertation Format . 9 Chapter 1: Introduction . 10 Receptor-like Kinases . 10 RLK-mediated Steroid Signaling . 11 BR Perception . 11 BR Signaling Pathway . 11 Defense Signaling through RLKs . 14 Pathogen Perception . 15 PTI Signaling Pathways . 17 BAK1 Alleles and Phosphorylation Differentially Affect BAK1 Function in PTI . 18 Cross-talk Between BR and PTI Signaling Pathways . 19 Cell-death Control by Receptor-like Kinases . 21 SERK roles in cell-death regulation . 21 RLP regulation of cell death . 24 Tracheary Element Differentiation . 25 LRR-RLK Function in Abscission . 26 Additional SERK-dependent Pathways . 28 Receptor-like Kinase Regulation of Root Development . 31 Root Apical Meristem Maintenance . 34 Root Epidermal Cell Fate . 38 Lateral Root Development . 40 Vascular Patterning . 44 Chapter 2: Material and Methods . 50 Plant Growth . 50 Mutant and Transgenic Lines . 50 Cloning . 51 Sequence Analysis . 53 Hormone and Peptide Treatment . 53 RNA Extraction and RT-PCR . 53 PCR . 54 Histology and Histochemical Analysis . 54 Microscopy, Image Acquisition and Measurements . 55
Patterning the Xenopus neurectoderm : the role of otx2 in the determination of cement gland and anterior neural fates

During gastrulation, the dorsal ectoderm of the embryo is induced and patterned to give rise to an anteroposterior array of structures. My thesis research has specifically addressed how anterior neurectodermal derivatives (midbrain and forebrain) and associated non-neural cement gland are appropriately positioned in the Xenopus embryo during this process. The cement gland is a mucus-secreting organ that forms from the anterior-most ectoderm at the dorsalventral border, which is equivalent to the ectoderm overlying the mammalian chin. The presumptive cement gland and anterior neurectoderm form an anterior domain defined by expression of the homeobox gene otx2, the vertebrate homologue of the Drosophila anterior gap gene orthodenticle. In mouse, otx2 is essential for development of the rostral head, however, since otx2 is expressed in both ectoderm and mesendoderm, the requirement and function of otx2 in the ectoderm are not known. I have analyzed the role of otx2 in anterior ectodermal development in Xenopus in the following manner. First, I used a hormone inducible otx2-glucocorticoid receptor fusion to demonstrate that otx2 is sufficient for cement gland formation, but that it can activate cement gland development only in ventrolateral ectoderm after mid-gastrula. Second, I have shown that coexpression of otx2 and BMP4 promotes cement gland formation and that this unique juxtaposition normally occurs only in the cement gland primordium. This allows cement gland development exclusively from the ventral aspect of the otx2 expression domain and not dorsally in the neurectoderm. Third, I have found that otx2 activates anterior and represses posterior neural gene expression in embryos and in isolated ectoderm. I have created a dominant negative otx2engrailed repressor fusion, which ablates cement gland and head formation, phenocopying the otx2 mouse mutant. Together these data have led to a model in which otx2 acts in the ectoderm to promote anterior neural and cement gland fates while repressing posterior neural gene expression, with otx2 activity spatially and temporally modulated by overlap with additional factors. Thesis advisor: Hazel Sive Title: Associate Professor
The Acute and Chronic Toxicity Effects of Triorganotins on the Growth of Microalgae, Skeletonema costatum

The use of triorganotins as insecticides, bacteriocides, and antifouling agents has increased dramatically over the past 30 years, In this paper, to evaluate the acute and chronic toxicity effects of various triorganotins (TBTO, TBTE, CTPT, TBTCI) on the growth of microalgae, Skeletonema costatum, we carried out the short term and long term experiments, respectively. In the short-term experiments, the growth of S. costatum was inhibited by the various triorganotins in the dose dependent manners, but recovered by the time laps. The growth inhibition of triorganotins were decreased in the groups with higher initial cell density. These data were resulted from the dilution effect and the biodegradation of triorganotins by the microalgae. In the long-term experiments, S. costatum died completely at the 1 g/L of TBTP and CTPT, but didn`t in short-term experiments. The facts suggest that the toxicity of the chronic exposure of triorganotins should be increased in the natural sea water with low phytoplankton density.
Execution and elimination of apoptotic cells

My special thanks go to my supervisor PD Dr. Marcel Leist for providing me with this interesting and stimulating thesis. I want to thank him for sharing his broad knowledge with me, always being helpful and enthusiastic, all the interesting discussions, and the proofreading of this thesis. I want to thank Prof. Dr. P. Nicotera for providing excellent working facilities and for stimulating discussions. I had the opportunity to join the " Graduiertenkolleg für Biochemische Pharmakologie " directed by Prof. Dr. A. Wendel. I am grateful for this privilege. He gave me the opportunity to take part in this program. The fascinating training courses and congresses gave me the possibility to broaden my scientific horizon much beyond my actual work. The work presented here benefited greatly from collaborations with many members of the chair of biochemical pharmacology. I am especially grateful to Dr. T. Meergans for the preparation of Hsp70, Markus Latta and Matthias Kresse for their help with in vivo experiments, Siegfried Morath for the LTA, and G. Pinski for carrying out LPS determinations. The technical assistance of and Claudia for stimulating discussions and the excellent atmosphere in the lab. I am particularly indebted to Melanie and Katharina for their support and encouragement. In vivo and in vitro evidence for extracellular caspase activity released from apoptotic cells. Abbreviations Abbreviations Act D actinomycin D ATP adenosine triphosphate BMDM bone marrow derived macrophages CHAPS
Genetic characterization of uncultured fungal endophytes from Bouteloua eriopoda and Atriplex canescens

Obligate fungal endophytes form cryptic communities in vascular plants that can defy detection and isolation by microscopic examination of reproductive structures. Molecular detection by PCR amplification of fungal DNA sequences alone is insufficient, since target endophyte sequences are unknown and difficult to distinguish from sequences already characterized as plant DNA. We have successfully separated fungal and plant ribosomal DNA sequences by amplifying plant-extracted DNA with polymerase chain reaction, and separating sequences with denaturing gradient gel electrophoresis (DGGE). The resulting electrophoregrams theoretically produce specific bands unique for each organism present in a plant-endophyte community. This method has successfully identified endophyte sequences in B. eriopoda and A. canescens, and has tracked these endophytes as they are transferred to novel hosts.
The discovery of SycO reveals a new function for type three secretion effector chaperones

The Type Three Secretion (T3S) system is a device used by many Gram-negative pathogens that allows bacteria to deliver effector proteins straight into the eukaryotic cell cytosol. These effectors interfere with various signaling pathways to subvert the host cell functions. The secretion machinery of the T3S system consist of a basal body spanning the bacterial inner and outer membrane followed by a stiff hollow needle outside the bacterium. The fully assembled secretion apparatus constitute a continuous hollow conduit that connects the bacteria to the eukaryotic target cell. After cell contact, virulence proteins -called effectors- are injected directly into the cytosol of the host cell via the T3S apparatus. Several effectors of the T3S system require the assistance of specific cytosolic chaperones to be efficiently exported. There are three classes of T3S chaperones. Effector proteins are assisted by Class I chaperones. Although Class I chaperones are well characterized, their main function is still a matter of controversy. In this thesis, we demonstrate that orf155 encodes a specific chaperone for the effector YopO that we called SycO. We showed that SycO enhances YopO secretion in vitro and is required for translocation of YopO into infected cells. By pulldown assay we demonstrated that residues 20 to 77 of YopO are required and sufficient for SycO binding. Using crosslinking experiments and size exclusion chromatography analysis, we determined the stoichiometry of purified SycO and YopO-SycO complexes. SycO alone forms dimers in solution and the YopO-SycO complex has a 1:2 stoichiometry. These results suggested that SycO is a typical chaperone of the Class I. YopO is a serine/theronine kinase that interacts with Rho and Rac and disrupts the cytoskeleton of the target cells. YopO has been shown to localize at the cell plasma-membrane. By transfection of YopO-EGFP hybrid proteins into HEK293T cells, we demonstrated that the chaperone-binding domain (CBD) coincides with the membrane localization domain of YopO. Nevertheless, the CBD was not needed for the kinase activity of YopO. By ultracentrifugation, we also showed that the CBD causes YopO aggregation in the bacteria, when SycO does not cover it. Further, we show that the CBD of YopE and YopT also caused aggregation in the bacteria in the absence of SycE and SycT respectively. YopE, YopT and T3S effectors in other systems also act at the membrane of the eukaryotic host cell. We propose a new hypothesis concerning the role of T3S chaperones. The sub-cellular localization domain of effectors is aggregation-prone and creates the need for a chaperone inside bacteria. We propose that masking such aggregation-prone localization domains may be a general function for type III effector chaperones.
Roles of CmFL, CmAFL1, and CmSOC1 in the transition from vegetative to reproductive growth in Chrysanthemum morifolium Ramat.

Summary The transition from vegetative to reproductive growth is marked by the termination of vegetative development and adoption of a floral identity by the shoot apical meristem. This process is called the floral transition. To elucidate the molecular determinants involved in this process in chrysanthemum (Chrysanthemum morifolium Ramat.), we isolated the following three floral identity and/or integrator genes from plants: CmFL, a homologue of FLORICAULA (FLO)/LEAFY (LFY); CmAFL1, a member of the APETALA1 (AP1)/FRUITFULL (FUL) sub-family; and CmSOC1, a member of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) sub-family. Up-regulated expression of CmFL in Arabidopsis resulted in an early-flowering phenotype. Our data show significant up-regulation of expression of all three of the above-mentioned genes and a strong correlation between the floral transition and gene expression under three different photoperiodic conditions. This study strongly suggests that CmFL, CmAFL1, and CmSOC1 are involved in the transition from vegetative to reproductive growth, and are activated co-ordinately after the floral transition in early-developing inflorescences in chrysanthemum.