Miracle-dz/UniFAR-FTUs huggingface dataset:
New members of the Coenzyme Q series from the Legionellaceae

Since the discovery of Legionella pneumophila, the causative agent of Legionnaires disease, two other groups of fastidious bacteria have been isolated which share many phenotypic characteristics with L. pneumophila [1-7] which have been referred to as "Atypical Legionella-Like Organisms" (ALLO) [2]. One group contains strains known as the Pittsburgh pneumonia agent (PPA) [6] and the Tatlock strain [8], for which the name Tatlockia micdadei has been proposed [4]. Members of the second group are serologically and genetically more diverse [2,3,7]. The name Fluoribacter [4] has been proposed for the latter group, and presently three species F. bozemanae, F. dumoffii and F. gormanii are recognised [4,7]. The taxonomic interrelationships of Legionella, Tatlockia and Fluoribacter are, however, equivocal, and additional criteria are required to tighten the generic and species descriptions. Ubiquinones (Coenzyme Q) are constituents of bacterial plasma membranes, and play an important role in electron transport and oxidative phosphorylation. Furthermore, recent studies have indicated that the structural variations exhibited by these compounds are of value in bacterial classification (see [9] for review). Ubiquinones, 2,3-dimethoxy-5-methyl-6-polyprenyl1,4-benzoquinones form a relatively large homologous series in which the length of the C-6 isoprenyl side-chain may vary from 1 to up to 12 isoprene units (Fig. 1). The major constituents of bacterial ubiquinones have been shown however to possess between 7 and 10 isoprene units (i.e. n = 7 to 10, Fig. 1) [9]. Recently, Finnerty et al. [10] reported Legionella pneumophila possessed ubiquinones as its sole respiratory quinones. Although the detailed structure of the ubiquinones of L. pneumophila was not determined, the authors noted that it possessed a side-chain containing more than 10 isoprene units [10]. This report is of considerable interest, as ubiquinone isoprenologues with more than 10 isoprene units have been found previously only in small amounts in a Pseudomonas sp. [11] and trace amounts in certain photosynthetic bacteria [ 12,13]. In this paper we report the structure of the ubiquinones of L. pneumophila. The opportunity was taken to also determine the ubiquinone content of other Legionella species, and representatives of the genera Fluoribacter and Tatlockia.
Does immunity regulate ejaculate quality and fertility in humans

The production of high-quality ejaculates may represent significant costs during male reproduction. Spermatozoa are perceived as nonself by the immune system and are exposed to immunological attacks in the male reproductive tract. Autoimmunity to spermatozoa results in the production of antisperm antibodies that reduce sperm quality and hence fertility. Thus, males are dependent on the testis being an immunoprivileged site to reduce immunological reactions against their own sperm, and immunoprivilege is obtained by the blood-testis barrier and by hormonal immunosuppression. A meta-analysis on the effects of immunosuppressive corticosteroid treatment of male infertility revealed that treatment reduced the level of antisperm antibodies, improved sperm motility and sperm count, and increased conception rate. These results emphasize the importance of immunosuppression and the associated pathogenicity from infectious organisms as important costs for the production of highquality ejaculates. Key words: antisperm antibodies, corticosteroid treatment, ejaculate quality, immunosuppression, male infertility, meta-analysis, parasite resistance, sperm. [Behav Ecol]
Helpers liberate female fairy-wrens from constraints on extra-pair mate choice

In cooperatively breeding superb fairy-wrens (Malurus cyaneus), all males contribute to the feeding and defence of young. Despite the expectation that such paternal care should be directed only to relatives, DNA fingerprinting revealed that most offspring (76%, 138 out of 181) were sired by extra-group males that contributed no care, and that almost all broods (95%, 38 out of 40) contained young sired by extra-group fathers. This is the highest known incidence of cuckoldry. This remarkable mating system is produced by female control of fertilization and consistent preference for certain extra-group male genotypes. This choice leads to the production of sons that also gain extra-group fertilizations. One constraint on the extra-pair mate choice of females is the level of parental assistance received from males. Males living in pairs contribute relatively more parental care and are more likely to gain paternity in one of their broods (85%, 11 out of 13) than dominant males in multi-male cooperative groups (30%, 8 out of 27). In groups helpers compensate for the lower parental assistance of dominant males, so the total feeding rate is similar between pairs and groups. This suggests that females allow males in pairs more paternity to ensure their assistance with parental care. Helpers provide an alternative source of paternal investment, and allow females to express unrestricted mate choice. Mating options for females in other species with female control of fertilization may also reflect a trade-off between acquiring the genes of high-quality males for their offspring and parental care of those offspring.
Lobula Plate Tangential Cells in Drosophila melanogaster; Response Properties, Synaptic Organization & Input Channels

40 Introduction . 41 Materials and methods . 45 Results . 48 The Gal4-3A expression pattern . 48 Protocerebral projections of VSand HS-cells express markers for output synapses . 50 MARCM analysis identifies protocerebral projections as sole expression sites of presynaptic markers in VS-cells . 50 Dendritic tips and central projections of all VS-cells show evidence for inhibitory input synapses . 52 Dendritic tips and central projections of the HSE-cell show evidence for inhibitory input synapses 55 Indications for GABAergic input onto LPTCs . 56 Discussion . 58 Connectivity of VSand HS-cells in the fly visual system . 58 Genetic methods for the analysis of synaptic connectivity . 59 Evidence for exclusively postsynaptic VSand HS-cell dendrites in the lobula plate . 60 Evidence for inhibitory input to VSand HS-cell axon terminals in the protocerebrum . 62 Supplementary Material . 64 Acknowledgements . 65
Isolation of a heterocyts - forming Cyanobacterium and quantification of its biotechnological potential with respect to redox properties at single cell level

This paper describes the isolation of an oxygenic heterocyst- forming cyanobacterium (IS-H) from meso-thermal samples (Obanul Mare - Mangalia), and quantitative results concerning its biotechnological potential, namely the ability of individual cell within the filament to reduce extracellular added artificial electron acceptor. Special emphasis is focused on quantitative determinations by automated image analysis of the ability of each individual cell to reduce MTT, an artificial electron acceptor. Our results show a strong decrease (almost 4 times in 24 hours) in the blue signal during MTT reductions by each individual analyzed cell, as a consequence of orange light absorption by reduced MTT. Up to our best knowledge this is the first report on the use of automated image analysis for the measurement of reduction of artificial electron acceptors at single cell level in cyanobacteria. This paper argues for the importance of mathematical methods of signal and image processing, a methodology capable of precise, detailed, tireless, and objective analysis of color intensity measurement of each individual cell.
Positive biodiversity–productivity relationship due to increased plant density

1 Positive effects of biodiversity on plant productivity may result from diversity‐induced changes in the size or density of individual plants, yet these two possibilities have never been tested at the same time in a biodiversity experiment with a large species pool. Here, we distinguish between size effects and density effects on plant productivity, using data from 198 experimental grassland communities that contained 1–16 species. Plant modules such as tillers or rosettes were defined as relevant units, being equivalent to plant individuals in the majority of species. 2 In agreement with previous studies, we found positive effects of species richness on above‐ground productivity. We show that this positive biodiversity effect resulted from diversity‐induced increases in module density rather than from increases in module size. In contrast, variation in productivity within diversity levels was related to module size rather than module density. 3 The size–density relationships varied among plant functional groups and among species but their average response to increasing species richness paralleled the pattern observed at the level of the entire plant communities: species richness had a positive effect on above‐ground species biomass and species module density but not on species module size. Twenty‐four out of 26 overyielding species had denser populations and 25 out of 28 underyielding species had smaller modules in mixtures than in monocultures. 4 Synthesis. In grasslands, an increase in community productivity must involve an increase in plant size or density. We found that diversity‐induced increases in productivity were related to diversity‐induced increases in density, whereas diversity‐independent increases in productivity were related to increases in plant size. Our results suggest that increased density of overyielding species in mixtures was the main driver of the positive biodiversity–productivity relationship in our experiment. We conclude that the mechanisms leading to enhanced productivity of species‐rich as compared with species‐poor communities cannot be derived from mechanisms explaining high productivity within communities that contain a particular number of species.
Analysis of microsatellite loci in yak

Summary The genetic diversity of nine microsatellite loci in five yak populations, including Maiwa yak (Hongyuan and Ruoergai populations), Jiulong yak, Datong yak, Tianzhu white yak, were studied by means of PCR, polyacrylamide gel electrophoresis and silver staining. The number of alleles was counted, and allele frequencies, polymorphism information content (PIC), heterozygosity (H) and effective number of alleles (Ne) were calculated for each population. According to allele frequencies of nine microsatellite loci, genetic distance was calculated, and clustering dendrogram map was drawn up of five yak populations. The results showed that every microsatellite locus analyzed was polymorphic in these yak populations and all of them were highly polymorphic loci. The average numbers of alleles and polymorphism information content (PIC) in each locus were 6.8(from 5 to 9) and 0.6534 (from 0.5037 to 0.7351) respectively, and the difference of average PIC among these populations was not significant. The average heterozygosity in all populations was 0.6625, which varied from 0.6883 which was the highest in Ruoergai population of Maiwa yak to 0.6317 which was the lowest in Jiulong yak. Accordingly, the average effective number of alleles was 3.2680 (varied from 3.189 to 3.4478), in which the lowest is for Jiulong yak. The result of genetic distance indicated that the distance between Jiulong yak and Hongyuan population of Maiwa yak was the most significant and the least between the two populations of Maiwa yak, the values were 1.506 and 1.062 respectively. The five yak populations were classified as two groups by clustering analysis, Jiulong yak was a separate group, the other populations were in another.
Global warming and positive fitness response in mountain populations of common lizards Lacerta vivipara

Recent global warming threatens many species and has already caused population‐ and species‐level extinctions. In particular, high risks of extinction are expected for isolated populations of species with low dispersal abilities. These predictions rely on widely used ‘climatic envelope’ models, while individual responses, the ultimate driver of a species response to climate change, have been most often neglected. Here, we report on some changes in life‐history traits of a dispersal‐limited reptile species (a poorly studied taxa) living in isolated populations. Using long‐term data on common lizards collected in southern France, we show that individual body size dramatically increased in all the four populations studied over the past 18 years. This increase in body size in all age classes appeared related to a concomitant increase in temperature experienced during the first month of life (August). Daily maximum temperature in August increased by 2.2°C and yearling snout‐vent‐length increased by about 28%. As a result, adult female body size increased markedly, and, as fecundity is strongly dependent on female body size, clutch size and total reproductive output also increased. For one population where capture–recapture data were available, adult survival was positively related to May temperature. All fitness components investigated therefore responded positively to the increase in temperature, such that it might be concluded that the common lizard has been advantaged by the shift in temperature. We contrast these short‐term results with the long‐term habitat‐based prediction that these populations located close to mountain tops on the southern margin of the species range should be unable to cope with the alteration of their habitat. To achieve a better prediction of a species persistence, one will probably need to combine both habitat and individual‐based approaches.
Barbados deep-water sponges

Deep-water sponges dredged up in two locations off the west coast of Barbados are systematically described. A total of 69 species is recorded, among which 16 are new to science, viz. Pachymatisma geodiformis, Asteropus syringiferus, Cinachyra arenosa, Theonella atlantica. Corallistes paratypus, Corallistes tubulatus, Scleritoderma cyanea, Spongosorites silquariae, ? Halichondria ruetzleri, Leucophloeus lewisi, Acanthella vaceleti, Bubaris flagelliformis, Biemna oxeata, Phlyctaenopora halichondrioides, Echinochalina melana, Strongylophora stoneae. Of each species illustrations of the habit and/or the skeletal architecture and spiculation are provided. A review of West Indian deep water sponges is given in the form of tables of records of deep water sponges arranged according to the major higher taxa. A special report is given of the distribution of the quantitatively important sponges in a transect perpendicular to the coast off Paynes Bay from 110 to 325 m. Along this depth gradient it was possible to distinguish three distinct zones: an upper (110-137 m) zone poor in specimens, with Spongosorites siliquaria n.sp. and Topsentia porrecta as characteristic species, a zone from 137-172 m rich in species and numbers, and a third zone below 208 m in which Vetulina stalactites is the dominant sponge. These three zones may be related to the morphology of the sea bottom and the grain size of the sediment.
Matching Distributions via Optimal Transport for Semi-Supervised Learning

Semi-Supervised Learning (SSL) approaches have been an influential framework for the usage of unlabeled data when there is not a sufficient amount of labeled data available over the course of training. SSL methods based on Convolutional Neural Networks (CNNs) have recently provided successful results on standard benchmark tasks such as image classification. In this work, we consider the general setting of SSL problem where the labeled and unlabeled data come from the same underlying probability distribution. We propose a new approach that adopts an Optimal Transport (OT) technique serving as a metric of similarity between discrete empirical probability measures to provide pseudo-labels for the unlabeled data, which can then be used in conjunction with the initial labeled data to train the CNN model in an SSL manner. We have evaluated and compared our proposed method with state-of-the-art SSL algorithms on standard datasets to demonstrate the superiority and effectiveness of our SSL algorithm.
Morphological variation and cannibalism in a larval salamander (Ambystoma macrodactylum columbianum)

We document morphological variation and its association with larval cannibalism in a population of long-toed salamanders, Ambystoma macrodactylum columbianum. Larvae observed in a natural pond engaged in cannibalism. Additionally, these larvae possessed significantly longer and wider heads, as well as larger vomerine teeth, than did conspecifics of the same size reared in the laboratory for 1 month after capture. This variation in trophic structures is consistent with the characteristics of "cannibal" morphs that have been documented for larvae of another salamander species. We extend current knowledge of the development of this morphology by using multivariate statistical analysis to examine, further, a possible basis for this variation in head shape. Principal component analysis indicated that after the removal of the effects of body size, variation in the distance between the eyes (interocular width) accounted for most of the remaining total overall variation in head shape. Multivariate ontogenetic tra.
CHANGES IN THE DIATOM MICROFLORA OF A EUTROPHIC LAKE SINCE 1900 FROM A COMPARISON OF OLD ALGAL SAMPLES AND THE SEDIMENTARY RECORD

Diatoms in a series of old plankton samples collected from Vaxjosjon, southern Sweden, between 1912 and 1971 were compared to the planktonic diatom record of the sediment accumulated during the same period. Contemporary descriptions of the floristic composition of the various samples were found to be unreliable. Clear taxonomic discrepancies between the written records and the sediment record necessitated the re-examination of all old samples and the adoption of a standardised taxonomy. When compared on this basis changes through time in the composition of the diatoms in the old samples were found to be in close agreement with changes recorded in the sediment. The re-emergence of Melosira italica subsp. subarctica in the mid 1940's, probably as a result of the partial improvement in the lake following sewage diversion, is seen clearly in both sets of data. The importance of storing algal samples for use in future palaeoecological research is stressed.
Effects of 5-HT (serotonin) on reproductive behaviour in Heterodera schachtii (Nematoda)

The effects of serotonin (5-hydroxytryptamine or 5-HT) on the reproductive behaviour of Heterodera schachtii was examined. Male and juvenile H. schachtii were incubated in 5-HT for 15 min. Stylet thrusting was stimulated by 10 mM 5-HT, whereas 0.1 mM 5-HT was without effect. Prolonged treatment of males with 10 mM 5-HT induced eversion of the spicules and extrusion of materials from the reproductive tract. Treatment with 60 mM triethanolamine and Wright's stain indicated that extrusions did not contain spermatids or spermatozoa. We confirm the effects of 5-HT on reproductive behaviour and suggest that the stylet and pharynx may subserve a reproductive function during later life stages in H. schachtii.
Enzymes of carbohydrate and amino acid metabolism in developing and mature nodules of white clover

The enzymic potential for the metabolism of carbohydrate (photosynthetic products) and amino acids (the assimilation of NH 4 + ) was determined by enzyme assay and by immunodetection in developing and mature nodules of white clover. White nodules appeared within 6 d of placing stolon tip cuttings in wet sand. The protein content and enzyme activities of these young nodules increased by 10-fold within 9 d. The expression of leghaemoglobin and nitrogenase components 1 and 2 were just detectable in nodules at 7 d. All other enzymes measured were found in young roots and white nodules as well as in mature red nodules. However, the expression of sucrose synthase and glutamine synthetase (the key enzymes of sucrose metabolism and NH 4 + assimilation, respectively) were greatly enhanced in nodules compared with roots. Nodule protein content, leghaemoglobin levels and enzyme activities peaked at approximately 50 d after taking stolon cuttings, and then declined by about 50% by 80 d. The results are discussed in the context of carbon and nitrogen fluxes in legume nodules.
Modifications in Microstructure of Cultured and Wild Scallop Shells (Pecten maximus)

Abstract The aim of the present work was to compare microstructure in strong and weak scallop Pecten maximus shells of cultured and wild origin using observations from scanning electron microscopy (SEM) and atomic force microscopy (AFM). The scallops representing the strongest and the weakest shells from each origin and age were selected for the microstructure observations. SEM observations showed various abnormalities of the microstructure, whereas AFM observations did not reveal any abnormalities of the nanostructure. The observed abnormalities were separated into two categories: irregularities and modifications. Irregularities were not directly linked to the microstructure and included bubbly sheets, bacteria, sponge, and hexagonal shapes on the inner layer. Modifications were directly linked to the microstructure and included irregular laths, crystal fragments, and severely modified granule layer covering the myostracal layer. Although irregularities were observed in samples of both cultured and wild P. maximus shells, modifications of the microstructure were observed only in those of cultured origin. Abnormalities were observed more frequently in four- and five-year-old scallop shells, whereas no abnormalities were observed in any of the shell samples from one-year-old scallops. These results suggest that abnormalities in scallop shells develop over time and that cultured scallops seem to be more at risk to develop modifications in microstructure compared with wild scallops. To be able to optimize conditions in aquaculture procedures, more investigation is needed on how the culture environment influence the biomineralization process in hard shelled molluscs.
A procedure for calculating the thermal constants associated with the flight period of Cerambyx welensii Küster and Prinobius myardi Mulsant from field observations

Field observations conducted in a dehesa in the southwest of the Iberian Peninsula over a period of 8 years (2002–2009) allowed the development and validation of two degree‐day phenology models for predicting the flight period of Cerambyx welensii Küster (1846) and Prinobius myardi Mulsant (1892). The start dates and functional development temperatures for the two species were estimated using an iterative method. The start dates were found to be 1 April for C. welensii and 15 April for P. myardi. The minimum development temperature for both species was 12 °C. The thermal constants associated with each flight percentage studied (1–99% at 10% intervals) were calculated from Gompertz curves fitting the equation CPE = exp[−exp(3.97 + 0.009DD)] (r2 = 0.955) for C. welensii and CPE = exp[−exp(6.50–0.008DD)] (r2 = 0.817) for P. myardi, where CPE is the cumulative percentage of emergence and DD is degree‐days. The validation procedure revealed that the proposed models predict cumulative flight percentages with errors of 2.5–4.3 days for C. welensii and 3.2–18.2 days for P. myardi The simplicity of the proposed method for calculating thermal constants and the small errors with which they can be estimated allow the widespread use of the models for efficiently managing populations of the two xylophagous cerambycids under study. This can be incorporated into a useful and novel element in the fight against the deterioration of a valuable ecosystem within the European Union.