Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of epicormic sprouts on Sitka spruce stems in response to windthrown gap formation

Summary Sprouting as a response to injury or changed environmental conditions is uncommon in conifers, but it is a feature of Sitka spruce (Picea sitchensis (Bong.) Carr. ). This study provides observations from two surveys of epicormic sprouts on standing and fallen trees in windthrown gaps within planted Sitka spruce forests of upland Britain. In a survey in Kielder Forest, epicormic sprouts were found on standing trees in closed stands and on trees at the edge of small gaps (area 4‐96 m 2 ). However, the branches were smaller, younger and had lower annual increment than those from trees on the edge of large gaps (area 215‐1494 m 2 ) and along a roadline within the same stand. In a survey at five sites in upland Britain, fallen trees were found to be alive in half of the 109 windthrown gaps, and there were epicormic branches showing excurrent vertical growth in a quarter of the gaps. The presence of epicormic branches on fallen trees, and their size was related to gap size as expressed by mean skyview. Sprouting on standing trees may affect timber quality by increasing the number and size of knots, and this has implications for the trend in management towards increased thinning and group felling. Sprouting on fallen trees may assist the perpetuation of the former canopy species in gap filling and this has implications for stand dynamics in retentions and natural reserves of spruce.
The effects of nutrient supply on flowering and seed production in Poa annua

The effect of nutrient concentration on the reproductive development and seed yield of Poa annua was examined in a sand culture experiment. The nutrient concentration during the initial vegetative stage did not affect the time taken for double ridge formation by the main shoot but did influence the subsequent development of the inflorescence as did the post-initiation level of nutrients. At low nutrient levels flowering was inhibited in some individuals but at the higher concentrations inflorescence emergence was hastened, inflorescence size was increased and, in particular, the number of spikelets and hence the number of seeds per inflorescence was greatly increased. The mean weight of 100 seeds was unaffected by the nutrient concentration. The number of reproductive tillers per plant was increased by high nutrient supply but the proportion of dry weight allocated to root development was reduced.
e effect of palmitic acid fortified maize wet milling by-product on the performance of weaner rabbits

A 6-week experiment was carried out to determine the effect of palmitic acid fortified maize wet mill - ing by-product on the performance of weaner rabbits. Forty-eight weaner rabbits (New Zealand White and Dutch breeds) were assigned to four dietary treatments of 0%, 25%, 30% and 50% levels of the palmitic acid fortified maize wet milling by-product. e four treatments were replicated three times with 4 weaner rabbits per replica- tion. e maize by-product was dried to a moisture content of 8% and added 2 litres of ungraded palmitic acid bought on the market to 100 kg of the maize by-product and dried again to a moisture content of 6% and used to formulate experimental diets: 0% diet (control) contains no maize wet milling by-product, 25% diet contains 25% of the by-product replacing maize, 30% and 50% diets contain 30% and 50% of the by-product replacing maize, respectively. Each of the experimental diets was randomly assigned to a group of 12 weaner rabbits with 4 rabbits per replication and fed for 6 weeks (42 days). Data were collected on feed intake, growth rate, feed conversion ratio. e analysis of the data indicated that there were no significant differences ( P > 0.05) in growth rate, feed intake and feed conversion ratio between the control receiving 0% palmitic acid fortified maize wet milling by-product and the 25%, 30% and 50% treatment levels. However, the optimal performance of rabbits at 30% and 25% levels of the by-product was higher (P 0.05) in the lumbar region, breast weight, however, there were differences P < 0.05 in the viscera weight in rabbits receiving the 30% and 25% levels of the by-product. Costs of production were highly reduced by the replacement.
Environmental impact of capture‐based bluefin tuna aquaculture on benthic communities in the western Mediterranean

Tuna farming is based on fishing bluefin tuna in their natural habit of the western Mediterranean and fattening them in floating cages. Although this type of aquaculture is expanding rapidly in the Mediterranean Sea, very little information is available for an environmental impact assessment and environmental monitoring of tuna ranching. Spatial and temporal scales of impact need to be established before the norms and regulations affecting this new branch of aquaculture can be properly implemented. The biotic indices measured pointed to detectable impact only under the cages, although multivariate techniques defined an environmental gradient of stressed macrofaunal assemblages. The benthic surveys carried out indicated that high impact was restricted to a radius of roughly 5 m from the cages with a transitional radius at 35 m. This zone was characterized by high densities of opportunistic species. There was a further zone of moderately stressed benthic environment extending to about 180–220 m from the cages. This moderately stressed zone exhibited slight changes in community structure, because the densities of some species were stimulated. At distances greater than 220 m from the tuna farm, the system apparently returned to normal conditions. The fallow period produced partial remediation of the area affected, except in the sediment underneath the cages where even a 6-month fallow period was not sufficient for the community to totally recover.
Phylogeographical analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deeply divergent mitochondrial lineages

Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the northern European coastline. The aim of this study was to assess the genetic structure of this species using mitochondrial and nuclear sequence data. We analysed partial mitochondrial cytochrome c oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens collected from ten sites ranging from Spain to Norway. For selected specimens, we also sequenced the hypervariable V7 expansion segment of the nuclear 18S rRNA gene as a supplementary marker. Furthermore, we studied the infection rate of all analysed specimens by the alphaproteobacterium Wolbachia. Our analyses revealed two deeply divergent mitochondrial lineages for Ligia oceanica that probably diverged in the late Pliocene to mid Pleistocene. One lineage comprised specimens from northern populations (‘lineage N’) and one primarily those from France and Spain (‘lineage S’). Distribution patterns of the haplotypes and the genetic distances between both lineages revealed two populations that diverged before the Last Glacial Maximum. Given that we found no homogenization of mitochondrial haplotypes, our present results also reject any influence of Wolbachia on the observed mtDNA variability. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 16–30.
FINE STRUCTURAL STUDIES ON THE INTERPHASE AND DIVIDING APICAL CELLS OF SPHACELARIA TRIBULOIDES (PHAEOPHYTA) 1

The apical cells of Sphacelaria tribuloides Menegh. are larger than other thallus cells, contain more organelles and appear polarized. Their tip portion, where they grow, contains a well developed Golgi apparatus, abundant endoplasmic reticulum (ER) membranes, mitochondria, chloroplasts and a large number of small vacuoles. It seems likely that a continuous flow of membranous material from the ER membranes to the dictyosomes and from the latter to the plasmalemma of the extending tip portion takes place. In contrast, the basal pole possesses fewer organelles and is occupied mainly by large‐sized, sometimes central vacuoles. The apical cells undergo two distinct types of highly asymmetrical differential divisions giving rise to cells of the thallus and hair initials. During the early stages of mitosis the nuclear envelope remains intact, except for fenestrated poles. Microtubules pass through the fenestrae into the nucleoplasm. During meta‐phase, a typical chromosome plate is organized. The sites of attachment of spindle microtubules to the chromosomes are structurally different from the rest of the chromosomes. At late anaphase, the nuclear envelope breaks down completely. During telophase, a new membrane encloses the chromosomes which are decondensed and the nucleoli are reorganized. Cytokinesis proceeds long after mitosis at a stage in which the nuclei have increased in size and have moved farther apart. A membranous furrow develops centripetally, without the participation of microtubules. However, microtubules traverse the thin cytoplasmic strands which, in both interphase and cytokinetic cells, meander among the vacuoles of the basal pole of the cell and the internuclear space. Dictyosomes appear to be involved in the subsequent wall deposition.
Licmosphenia revisited: transfer to Licmophora, redescription of L. clevei Mereschkowsky and descriptions of three new species

Licmosphenia Mereschkowsky (Licmophorales: Licmophoraceae) is distinguished from Licmophora C. Agardh almost entirely by the presence of an apical window in the septum of the valvocopula. Recently, SEM images of three new species, all with coarse striae, showed that the valve morphology was indistinguishable from a group of Licmophora species including L. ehrenbergii, and gene sequence data showed Licmosphenia sister to the few available Licmophora spp. Two questions remain: (1) what is the structure of Licmosphenia spp. with fine striae? and (2) what would further molecular evidence contribute to understanding whether these genera are distinct or not? New LM and SEM observations on Licmosphenia species and sequence data from additional Licmophora species now answer these questions. Valve ultrastructure of a new, finely striated species with a small apical aperture, from Mallorca, Spain, is similar to finely striated Licmophora species, and the position of Licmosphenia in the phylogenetic tree is now within the Licmophora clade. The presence of apical apertures in two morphological groups of Licmophora suggests that the apical window has arisen at least twice. Licmophora is the older genus name and we therefore formally transfer all Licmosphenia species to it. In addition to Licmophora garyi from Mallorca, we describe a curved species from the Adriatic, Licmophora arcuata, similar to L. grunowii but with much coarser striae, and a species from Guam with a very large apical aperture, L. pisciformis. We also designate an epitype for Licmosphenia clevei Mereschkowsky, the type species of that genus.
How phylogenetic inference can shape our view of heterochrony: examples from thecideide brachiopods

Abstract Heterochrony is considered to be an important and ubiquitous mechanism of evolutionary change. Three components are necessary to describe heterochrony: phylogenetic relationships, size and shape change, and timing of developmental events. Patterns and processes of heterochrony are all too often invoked before all three components have been investigated. Phylogenetic hypotheses affect the interpretation of heterochrony in three ways: rooting of a clade, topology of a clade, and character polarity. To study these effects we examined the distribution of shell microstructure, lophophore support structures, and body size in four different phylogenetic hypotheses of thecideide brachiopods (Triassic to Recent), a group of minute, cryptic, benthic marine invertebrates. Thecideides are consistently monophyletic in experiments using terebratulide, strophomenate, and spire-bearing outgroups together and separately, varying ingroup membership, and experimentally withholding certain character complexes. Thecideide monophyly is also supported by bootstrap analysis. Hypotheses of heterochrony in thecideide origins and evolution are therefore not merely artifacts of classification and can be pursued further. Using either strophomenate or spire-bearing outgroups, Triassic Thecospira is the most primitive thecideide. Trees constructed using terebratulide outgroups are rooted instead at Eudesella, a taxon derived in every other phylogenetic reconstruction, and the Triassic thecideides occupy derived rather than primitive positions. Our phylogenetic results support the traditional interpretation of the reduction or loss of the secondary fibrous shell layer as a paedomorphic pattern, whereas the evolution of lophophore support structures suggests a peramorphic pattern. Reduction in thecideide adult body size is gradual, phylogenetically, and results in an overall paedomorphic pattern. Heterochrony in these three character suites may play a role in the subsequent evolution of the clade, but apparently not in the origin of the clade, as is commonly thought. Heterotopy, rather than—or in addition to—heterochrony, may account for both the origin and evolution of the lophophore support structures and in the reduction and loss of the secondary shell layer. These phylogenetic hypotheses suggest that heterochrony can result from a complex mosaic of processes and provide specific, testable predictions about the processes responsible for producing the patterns, whether heterochronic or not. Categorizing an entire clade (such as thecideides), rather than individual characters, as globally paedomorphic may allow interesting peramorphic patterns in individual characters to be overlooked.
Organizational Systematics: Taxonomic Lessons from Biology

This paper argues that important lessons about the theory and method of organizational classification may be learned from biological systematics, defined as the "science of differences. " Three main components of systematics studies are discussed: (1) taxonomy, the development of a concept of organizational differences; (2) evolution, the tracing of the lineages of organizational form; and (3) classification, the development of procedures for identifying and placing organizational forms into classes. Furthermore, two kinds of classification are identified and several theories of classification are discussed. Systematics is seen as a necessary prerequisite to studies aiming to identify generalizable principles of organizational function and process. Finally, some implications for defining populations and drawing samples of organizations are noted, along with other implications for organization design and development and managerial practice.
Impacts of Interannual Environmental Forcing and Climate Change on the Distribution of Atlantic Mackerel on the U.S. Northeast Continental Shelf

Abstract The Northwest Atlantic stock of Atlantic mackerel Scomber scombrus is distributed from Cape Hatteras to Newfoundland and migrates great distances on a seasonal basis. Atlantic mackerel are sensitive to changes in temperature, preferring water greater than 5° C. Annual changes in the winter and early-spring distributions of Atlantic mackerel were investigated using satellite imagery, research trawl surveys, geographical information systems, and spatial and standard statistical analyses. During the past 40-plus years (1968–2008), the distribution of the stock has shifted about 250 km to the north and east. Also, a change has occurred in the depth distribution of the stock, from deeper off-shelf locations to shallower on-shelf ones. Areal and bathymetric changes in distribution are correlated with interannual temperature variability and gradual warming. These results have implications for U.S. commercial and recreational mackerel fisheries because, despite the current high abundance of the stock, the changes in distribution will probably make it more difficult to find and catch Atlantic mackerel in certain areas in the future.
Genetic aspects of common health disorders and measures of fertility in Holstein Friesian dairy cattle

The purpose of this study was to estimate genetic parameters for measures of fertility and several health disorders in dairy cows. Data consisted of 33732 records, of which 9163 were on heifers, on 305-day milk yield, health disorders and inseminations. Measures of fertility were calculated from calving and insemination dates and included calving interval, days to first service and conception to first service. Health disorders included milk fever, mastitis and lameness. Genetic and phenotypic (co)variances were estimated using restricted maximum likelihood. Heritability estimates for both health disorders and fertility traits were low, ranging from 0·003 to 0·080. All genetic correlations between 305-day milk yield and health and fertility traits, in cows and heifers together, were antagonistic implying that selection for milk yield may have caused a deterioration in health and fertility. The unfavourable correlation between milk yield and health and fertility traits, plus the economic importance of the latter, suggests that future breeding goals should be expanded to include some health disorders and fertility.
Extensively-Drug Resistant Klebsiella pneumoniae Recovered From Neonatal Sepsis Cases From a Major NICU in Egypt

Background Neonatal sepsis is a nuisance to clinicians and medical microbiologists, particularly those cases caused by Klebsiella pneumoniae. Thus, we aimed at investigating the profile and mechanisms of antibiotic resistance and the clonal relationships between K. pneumoniae isolated from neonates at the largest tertiary care hospital’s neonatal intensive care units (NICUs) in Minia, Egypt. Methods This study comprised 156 neonates diagnosed with culture-proven sepsis from February 2019 to September 2019, at a major NICU of Minia City. All K. pneumoniae isolates were collected and characterized by antimicrobial profile, resistance genotype, and pulsed-field gel electrophoresis typing. Results Twenty-four K. pneumoniae isolates (15.3%) were collected out of the 156 sepsis diagnosed neonates. These samples showed extensive drug resistance (XDR) to most of the tested antimicrobials, except fluoroquinolones. All the K. pneumoniae isolates possessed blaVIM and blaNDM carbapenemase genes, while blaKPC gene was detected in 95.8%. Considering extended-spectrum β-lactamases genes, blaCTX–M was found in all the isolates and blaOXA–1 gene in 75% of them. The plasmid-mediated quinolone resistance gene qnrS, was predominantly found among our isolates in comparison to qnrB or qnrA. A moderate degree of clonal relatedness was observed between the isolates. Conclusion To the best of our knowledge, this the first report of an alarming occurrence of XDR among K. penumoniae isolates recovered from neonatal sepsis in Egypt. Our data necessitate proper antimicrobial stewardship as the choices will be very limited.
Anatomy, histochemistry and biochemistry of glucovanillin, oleoresin and mucilage accumulation sites in green mature vanilla pod (Vanilla planifolia; Orchidaceae): a comprehensive and critical reexamination

Introduction. Mature green vanilla pods accumulate 4-O-(3-methoxy-benzalde- hyde)-β-D-glucoside (glucovanillin), which, upon hydrolysis by an endogenous β-glucosidase, liberates vanillin, the major aroma component of vanilla. Sites of storage of glucovanillin in the pod have been controversially reported for decades; we aim, using precise and widely accepted technical terminology, to clarify this controversy by providing an anatomical, histochemical and biochemical evidence-based picture of glucovanillin accumulation sites. The pod also synthe- sizes an oleoresin and a mucilage of unknown constitutions; we report here their localization and structures. Materials and methods. The pod anatomy was examined by light and epi- fluorescence microscopy. A protocol was established allowing fine hand-dissection of diverse anatomical parts of the pod (mesocarp, placentae, trichomes, intralocular interstitial cell-free region and seeds). Glucovanillin and γ-pyranones were extracted and analyzed by HPLC, while the structures of the mucilaginous polysaccharides were determined after permethylation. Results and discussion. Glucovanillin is essentially stored in the placentae (92%) and margi- nally in trichomes (7%); traces were measured in the mesocarp and intralocular interstitial cell- free medium. Trichomes store massive amounts of a fluorescing oleoresin (44%) rich in alke- nylmethyldihydro-γ-pyranones and synthesize a mucilage made of a glucomannan and a pectic polysaccharide carrying monomeric arabinose and galactose side-chains. Conclusion. To date, the physiological roles of glucovanillin, long-chain pyranones, and mucilage remain unknown. France / Vanilla planifolia / Orchidaceae / vanilla / trichomes / vanillin / oleoresins / fluorescence / mucilages / polysaccharides
A Bayesian hierarchical analysis of stock-recruit data: quantifying structural and parameter uncertainties

Stock-recruit functions are important in fisheries stock assessment, but there is often uncertainty surrounding the appropriate stock-recruit model and its parameter values. Combining different stock-recruit data sets of related species through Bayesian hierarchical analysis can decrease these uncertainties and help to characterize appropriate stock-recruit forms and ranges of plausible parameter values. Two different stock-recruit functions (Beverton-Holt and Ricker) have been parameterized in terms of the steepness, which is a parameter that is comparable between popula- tions. In the hierarchical analysis, the prior probability distribution of parameters for the cross-population variation in steepness is determined through a concise model structure. By calculating the Bayes' posteriors for alternative model forms, model uncertainty is accounted for. This methodology has been applied to Atlantic salmon (Salmo salar) stock- recruit data to provide predictions for the steepness of the stock-recruit function for Baltic salmon for which no stock- recruit data exist. Resume : Les fonctions stock-recrutement sont de grande importance pour l'evaluation des stocks des peches commer- ciales, mais il y a souvent de l'incertitude au sujet du choix d'un modele approprie et des valeurs de ses parametres. La combinaison de plusieurs series de donnees de stock-recrutement d'especes apparentees dans une analyse hierar- chique bayesienne peut reduire ces incertitudes, aider a identifier les relations stock-recrutement appropriees et deter- miner les etendues plausibles des valeurs des parametres. Nous avons caracterise les parametres de deux fonctions stock-recrutement (Beverton-Holt et Ricker) en ce qui concerne l'inclinaison de la pente, qui est un parametre compa- rable entre les populations. Dans l'analyse hierarchique, la distribution de probabilite a priori des parametres en ce qui a trait a la variation de l'inclinaison d'une population a une autre est determinee par une structure de modele concis. Le calcul des distributions bayesiennes a posteriori pour les differentes formes de modeles permet de tenir compte de l'incertitude. Nous avons applique cette methodologie a des donnees de stock-recrutement du saumon de l'Atlantique (Salmo salar) afin de pouvoir predire l'inclinaison de la fonction stock-recrutement du saumon de la Baltique pour lequel il n'existe pas de donnees sur la relation stock-recrutement. (Traduit par la Redaction) Michielsens and McAllister 1047