Miracle-dz/UniFAR-FTUs huggingface dataset:
MONOPHYLY AND COMPARISONS BETWEEN TREES

Abstract— The Farris method for assessing the empirical status of groups, as either monophyletic, paraphyletic or polyphyletic, is discussed. The reasons for presenting the method in terms of the behaviour of abstract, rather than real, characters are upheld. The method (i) reflects the insight that monophyly and related terms are used in comparisons between trees, (ii) avoids the problems associated with definitions based on the exclusion of subgroups, (iii) avoids the contentious issue of inclusion vs. exclusion of a group's most recent common ancestor. The Farris method is shown to be equivalent to the cluster distortion method for comparing the shapes of a pair of trees. Descriptor variables for each cluster in a reference tree are mapped on to a comparison tree. If a cluster's descriptor requires homoplasy then the cluster is a nonmonophyletic group. If the cluster descriptors behave according to Wagner parsimony, the kind of nonmonophyletic group is determined by the kind of homoplasy exhibited by the descriptor variable. The single cluster distortion coefficient is shown to be equal to (1‐ri), where ri is the retention index of the descriptor variable on the comparison tree. The overall distortion coefficient acts as a tree comparison metric and is defined as (1‐RI) where RI is the ensemble retention index.
Variation in the train morphology of peacocks (Pavo cristatus)

A sample of full-trained adult male peacocks was collected and measured to determine whether or not there were any morphological correlates of train elaboration. Peacocks with longer or heavier trains are those with relatively large fat reserves for their overall body mass. The proportion of feathers in the train which have eyespots is also greater in peacocks with a relatively large muscle. These relationships indicate that train elaboration may be condition-dependent. Females that prefer males with larger trains may therefore gain good condition males, which may reflect overall genetic quality. There is also a significant tendency for larger-trained peacocks to have high louse loads, after controlling for body mass. It may be that larger-trained males are older, and have accrued more lice than younger ones. Alternatively, long-trained males may have acquired more lice through direct contact with more females than shorter-trained birds.
Thermal time – concepts and utility

This paper (i) reviews temperature/development rate relationships in plants and poikilothermic invertebrates, (ii) argues that the relationship is often linear over much of the range up to the thermal optimum (T o ) and provides a possible mechanism, (iii) provides evidence of a trade-off between the base temperature (T b ) and the thermal constant (DD) that enables each species to adapt to its thermal environment, and (iv) indicates some of the practical and ecological implications. Where a linear relationship has been characterised it is possible to estimate the base temperature for development (T b , expressed in °C) and the thermal constant for development (DD, the reciprocal of the temperature coefficient (a), expressed in degree [°C] days accumulated above T b ). A possible basis for the linear relationship between rate and temperature is proposed based on the Arrhenius and Sharpe-Schoolfield equations involving activation enthalpy and progressive inactivation of the reactant molecules at both low and high temperatures. Knowledge of T b and DD enables rates of development of organisms/ processes to be calculated and compared at any given temperature between T b and T o . An analysis of published results for differentiation processes (differentiation = a change of state) in species of insects, Collembola, spiders, nematodes and plants showed that T b tended to vary with the temperature of the niche to which the organism is adapted, and that there was a trade-off between T b and DD. Tropical species had higher values of T b than temperate and DD decreased as T b increased (and vice versa). This conferred a competitive advantage on each species in the thermal environment to which it was adapted. The decrease in DD tended to be relatively greater than the increase in T b further favouring a high T b in tropical species. A mechanism for the trade-off is suggested whereby DD and T b were shown to be correlated (P < 0.01) with the activation enthalpy (H A ) of an assumed, rate-limiting enzyme. Thermal time can also be applied to processes involving growth (= an increase in dry weight) when the DD requirement for development to maturity is the sum of the requirements for differentiation and growth. Rates of both differentiation and growth can vary greatly between species, depending upon the niche they inhabit, and the implications of such differences for resource requirements are considered. In insects and nematodes, but not in annual plants, development is usually coupled to growth. Consequently, when resources are inadequate, mature size in these animals varies less than in plants. Thermal time is shown to provide insight into the life strategies of species within their communities and to have practical implications.
Association of Verticicladiellaprocera and Leptographiumterrebrantis with insects in the Lake States

Verticicladiellaprocera Kendrick was isolated from damage associated with Dendroctonusvalens Lec, Hylobiusradicis Buch. , Hylobiusrhizophagus M.B. W. , Hylobiuspales (Herbst), and Pachylobiuspicivorus (Germ.) on pines in Minnesota, Wisconsin, and Michigan. The fungus was also isolated from surface-sterilized adult D. valens, H. radicis, H. pales, and P. picivorus. Leptographiumterrebrantis Barras and Perry was isolated from the galleries of D. valens on trees stressed by fire, flooding, windthrow, and tissue attacked by H. radicis or H. rhizophagus. Verticicladiellaprocera was not pathogenic on white pine seedlings whereas L. terrebrantis killed 70% of seedlings inoculated. Verticicladiellaprocera appears to be weakly pathogenic and is associated with primary (H. radicis and H. rhizophagus) and secondary (P. picivorus, D. valens, H. pales) forest insects in the north central United States. Leptographiumterrebrantis was more virulent than V. procera and was associated with a secondary bark beetle which common.
CA2+ CURRENT FROM OOCYTE TO NURSE CELLS AND SUPPRESSION OF URIDINE INCORPORATION IN THE GERMINAL VESICLE OF HYALOPHORA CECROPIA

Summary In ovarian follicles of Hyalophora cecropia, [3H]uridine incorporation by germinal vesicles is normally arrested at the start of vitellogenesis when a Ca2+ current arises through the intercellular bridges connecting the oocyte to its nurse cells. We show here that the germinal vesicle resumes uridine incorporation following inhibition or reversal of this current. Inhibition/reversal was achieved by treating follicle with any one of three inhibitors that block the Ca2+ current by very different mechanisms. Vanadate was used to block Ca2+ extrusion by the nurse cells, which drives the current. BAPTA was used to buffer Ca2+ activities in the nurse cero, and A23187 was used to increase the membrane conductance of Ca2+. Measurements with ion selective microelectrodes indicated that in all these cases [Ca2+]i in nurse cells equaled or exceeded that in the oocyte; and in all these cases uridine incorporation resumed in the germinal vesicle. Resumption correlated not with the level of [Ca2+] i in the oocy.
Enhanced ozone-tolerance in wheat grown at an elevated CO2 concentration: ozone exclusion and detoxification.

Elevated [CO2 ] has been shown to protect photosynthesis and growth of wheat against moderately elevated [O3 ]. To investigate the role of ozone exclusion and detoxification in this protection, spring wheat (Triticum aestivum L. ev. Wembley) was grown from seed, in controlled-environment chambers, under reciprocal combinations of [CO2 ] at 350 or 700 μmol mol-1 and [O3 ] peaking at < 5 or 60 nmol mol-1 , respectively. Cumulative ozone dose to the mesophyll and antioxidant status were determined throughout flag leaf development. Catalase activity correlated with rates of photorespiration and declined in response to elevated [CO2 ] and/or [O3 ]. Superoxide dismutase activity was not significantly affected by either condition. Neither ascorbate nor glutathione content was enhanced by elevated [CO2 ]. In wheat, at moderately elevated [O3 ], our results show that stomatal exclusion plays a major role in the protective effect of elevated [CO2 ] against O3 damage.
Release of mitochondrial aspartate aminotransferase (mAST) following transient focal cerebral ischemia suggests the opening of a mitochondrial permeability transition pore

The present experiments were undertaken to study if ischemia and reperfusion in the brain are accompanied by a mitochondrial permeability transition (MPT), leading to the release of mitochondrial proteins into the cytosol. The protein studied was the mitochondrial isoform of aspartate aminotransferase (mAST). In vitro experiments showed that isolated brain mitochondria exposed to calcium (50 μM) and phosphate (0.5 mM) displayed rapidly developing swelling, as evidenced by a change in light scattering at 540 nm. The swelling which could be reversal by chelation of external calcium, was associated with release of mAST. Focal ischemia of 2 h duration was induced by occlusion of one middle cerebral artery (MCA) by an intraluminal filament technique. The ischemia gave rise to a marked decrease in respiratory control ratio (RCR) of mitochondria in the homogenate. The RCR recovered partly after 1 h of recirculation, but decrease again after 4 h. The mAST in the cytosolic fraction did not change at the end of the ischemia, but increased significantly after 1 h of recirculation in the focus of the lesion, but not in the penumbra. Little further change occurred thereafter (4 h). It is concluded that in densely ischemic areas, recirculation yields rapidly developing dysfunction of the inner mitochondrial membrane, with release of mitochondrial proteins. © 1997 John Wiley & Sons, Ltd.
Segments, Lineage Boundaries and the Domains of Expression of Homeotic Genes

It is now possible to monitor directly the pattern of activity of homeotic and segmentation genes in the Drosophila embryo. Precisely bounded domains of expression are established in the blastoderm, at the time when cells became committed to specific segment identities. Some patterns of expression appear in their final form; others evolve rapidly during formation of the blastoderm. Transcripts of the homeotic gene Ultrabithorax accumulate at high levels in a single parasegment of the blastoderm, and in a block of seven parasegments of the extended germ band. The boundaries of these Ubx domains appear to lie precisely at presumptive A -P compartment boundaries. During formation of the germ band, the abundance of Ultrabithorax transcripts shows a transient segment ‘pair-rule’ modulation. I suggest that this reflects an interaction between the Ultrabithorax gene and a segment pair-rule function, which may serve to establish the precise correlation between lineage boundaries and the domains of Ultrabithorax expression.
Rapid response reactions of roots to boron deprivation

Upon B removal from the nutrient solution, several response reactions of root cells can be measured within minutes. These include: reduction of cell wall elasticity modulus e, increase of hydraulic conductivity, reduced activity of plasmalemma-bound inducible (NADH) reductase, (smaller) changes of the membrane potential, and liberation of Ca2+ (apoplastic and membrane-bound). The B most demanding (root) tissues are epidermal and outer cortical cells of the extension zone, xylem vessels, and root hair tips. Deprivation of B leads to morphological changes which can be noticed within hours to days, including browning of tissues, growth inhibition, death of apical meristems, and lack of root hairs. How the primary response reaction(s) lead to the expression of visible symptoms, however, is not yet clear. The present review summarizes rapid responses to B deprivation and shows several possibilities how primary might be linked to secondary reactions, including cytoskeleton-mediated responses. Schnelle Reaktionen von Wurzeln auf Bor-Mangel Nach Umsetzen auf ein B-Mangelmedium konnen verschiedene Reaktionen von Wurzelzellen innerhalb von Minuten beobachtet werden, wie z.B. Verringerung des Zellwandelastizitatsmoduls e, Zunahme der hydraulischen Leitfahigkeit, verringerte Plasmalemma-gebundene induzierbare (NADH) Reduktaseaktivitat, (kleinere) Anderungen des Membranpotenzials und eine Freisetzung von apoplastischem und membrangebundenem Ca2+. Die Wurzelgewebe mit dem hochsten B-Bedarf scheinen die epidermalen und auseren Rindenzellen der Streckungszone, Xylem und Wurzelhaarspitzen zu sein. B-Entzug fuhrt zu morphologischen Anderungen, die innerhalb von Stunden und Tagen sichtbar werden, wie Gewebeverbraunung, Wachstumshemmung und Absterben apikaler Meristeme, sowie Fehlen von Wurzelhaaren. Wie die raschen Reaktionen zur (sekundaren) Auspragung von Mangelsymptomen fuhren, ist jedoch noch nicht klar. In dieser Ubersicht werden rasche Reaktionen auf B-Entzug zusammengefasst und Moglichkeiten zur Verknupfung primarer und sekundarer Reaktionen diskutiert.
Genetic improvement of feed efficiency of beef cattle: what lessons can be learnt from other species?

About half of the feed in beef production systems is used to maintain the breeding herd. Of the remaining 50%, about 20% is used by the breeding cow for pregnancy and lactation and 30% is used by the growing calf. There seems little opportunity to improve efficiency of production (lactation and growth) but reasonable opportunity to increase maintenance efficiency. The mean heritability of net feed efficiency from 35 estimates across 7 species/types was 0.25 ± 0.02. Unfortunately, the genetic correlation between net feed efficiency in young bulls and mature cows is likely to be significantly less than 1, thus responding slowly to selection. While it seems clear that improvements in maintenance efficiency can be made, they may come at a cost. In poultry and mice, increased net feed efficiency has been associated with increased fatness but in pigs and beef cattle there is some evidence of the reverse. While a number of studies have predicted that selection for efficiency may result in lower proportions of crucial, metabolically active visceral organ tissues, there are few studies to support this. Poultry and mouse studies both clearly show that increased net feed efficiency is associated with decreased heat production. This decrease is due to both decreased cost of digestion (heat loss) and decreased activity. In poultry, this decreased heat loss resulted in the more efficient line being more affected by high temperatures. Also, it is possible that at low temperatures, the differences in efficiency may not exist. At this stage it is not clear if the decreased activity is an adaptive advantage or disadvantage. In mice and possibly also pigs and poultry, increased net feed efficiency has been associated with a decreased reproductive rate measured as litter size or egg number. This should definitely be of concern when embarking on selection for improved net feed efficiency in the beef industry. It is recommended that since feed intake is both difficult and expensive to measure, a gene or marker test should be developed, and correlated effects on a range of production traits be carefully evaluated.
Description of a New Species of Microcerberus From the South China Sea and a Proposal for a Revised Classification of the Microcerberoidea (Isopoda)

Viene descritto Microcerberus redangensis n. sp. del sistema interstiziale della costa di Pulau Redang, un'isola della costa nord-orientale della Malesia. Vengono riesaminate tutte le specie note di Microcerberus e, sulla base dei caratteri morfologici del pleopode II O, si propone l'istituzione di 4 gruppi di specie: remanei, anfindicus, mirabilis e stygius. Restano da inquadrare per le loro peculiari caratteristiche M. delamarei e M. machadoi mentre M. predatoris, M. monodi e M. littoralis dovranno essere riesaminate essendo state descritte su immaturi. Viene inoltre istituito un nuovo genere, Bulgarocerberus n. gen., per la specie phreaticus. Specie tipo: Bulgarocerberus phreaticus (Cvetkov 1963). Viene riportata infine la distribuzione generale di tutte le specie di Microcerberoidea e vengono discussi i problemi biogeografici dei vari generi e gruppi di specie.
EFFECT OF N SUPPLY ON SHOOT AND ROOT MINERAL COMPOSITION IN RETAMA RAETAM

In deserts, biological processes decrease at the end of the vegetation period by lack of soil moisture and increasing heat. Important processes for plant nutrient uptake are negatively affected like N fixation, litter decomposition and denitrification. Desert plants must therefore adapt their mineral household towards best use of available nutrients and storage of minerals in perennial organs. Here we studied this pattern by experiments of the effect of nitrogen nutrition on mineral concentration and plant growth of Retama raetam (Forssk.) Webb. Berth for two years in sand culture. In summary, the mineral household of R raetam seems to be well adapted to unfavourable desert habitat independent from the N source and N level.
Generation of expressed sequence tags, development of microsatellite and single nucleotide polymorphism markers in Primula sieboldii E. Morren (Primulaceae) for analysis of genetic diversity in natural and horticultural populations

Primula sieboldii is a self-incompatible ornamental plant that has been cultivated for more than 300 years in Japan. In order to increase the available genomic resources for this species, 5651 expressed sequence tags (ESTs) were generated from seedling and winter bud cDNA libraries. After clustering and assembling ESTs, 2960 unigene elements that contain an homologous sequence to an S locus-linked gene of P. vulgaris were identified. In total, 127 simple sequence repeats (SSRs) were found. The most frequent di- and tri-SSR motifs were GA (78.6%) and ATT (12.9%), respectively. Twenty SSR and 40 single nucleotide polymorphism (SNP) markers were developed. These markers were evaluated for polymorphisms using 24 individuals (Y) from a population in Yatsugatake and 14 individuals (PS) from across the distributional range of P. sieboldii in Japan. The average level of expected heterozygosity within Y and PS was 0.39 and 0.48, respectively for EST-SSR markers and 0.26 and 0.29, respectively for SNP markers. The level of polymorphism for EST-SSR markers was lower than that for genomic SSR markers developed in a previous study. We also surveyed the genetic diversity of 56 cultivars, which had lower allelic richness than the Y and PS populations.
GENETIC ANALYSIS OF THE SPECIES OF SIGARA S. STR. (HETEROPTERA, CORIXIDAE)IN THE ITALIAN PENINSULA

Abstract The genetic differences in three populations of Sigara s. str. belonging to S. striata, S. dorsalis, and S. basalis, distributed in northern (Veneto, South Tyrol) and central (Umbria, Molise) Italy, were assayed by horizontal starch electrophoresis. Adult specimens were examined. Twelve enzymes were assayed, eight of which gave satisfactory results. Five of the eight alloenzymes were further investigated to differentiate the three species: phos‐phoglucomutase (Pgm‐1, Pgm‐2), esterase (Est‐1, Est‐2, Est‐3), su‐peroxide dismutase (Sod‐1, Sod‐2), phosphoglucose isomerase (Pgi‐1, Pgi‐2), isocitrate dehydrogenase (Idh) coding for 10 studied loci. A total of 208 adults of the three taxa (142 for S. basalis, 49 for 5. dorsalis, and 17 for 5. striata) were analysed. Nei's unbiased genetic distances were calculated and values between congeneric species ranged from 0.009 to 0.25, as illustrated in a phenogramme constructed by the unweighted pair‐group cluster analysis method. Sigara basalis presented the h.
Evaluation of Cell Culture Methods for Detection of Largemouth Bass Virus

Abstract Largemouth bass virus (LMBV), a recently discovered iridovirus found in the eastern United States, is usually detected by isolation in cell culture. Although LMBV will replicate in several cell lines, optimal cell culture methods for the detection of this virus have not been determined. We tested inoculation method, adsorption time, incubation temperature, and various cell lines to determine the conditions that would provide the most sensitive cell culture assay for LMBV. The optimal inoculation procedure tested was to remove the culture medium from the culture well before the addition of the inoculum, and the optimal adsorption procedure tested was to allow the virus to adsorb for 40 min while the plates were on an orbital shaker. Following inoculation, incubation at 30°C resulted in a higher number of viral plaques than incubation at 25°C or 32°C. Four cell lines (bluegill fry (BF-2), fathead minnow (FHM), epithelioma papulosum cyprini, and channel catfish ovary cells) inoculated with LMBV had .
Roles of Kallikrein-Related Peptidase in Epidermal Barrier Function and Related Skin Diseases

The skin barrier usually refers to the physical barrier formed by the cuticle and sebum membrane of the skin. This barrier not only protects against the onslaught of microorganisms and percutaneous penetration of chemicals and allergens but also prevents the loss of nutrients and moisture from the body. Corneodesmosomes play an important role in maintaining the function of the keraphyllous skin barrier. Desmogleins, desmocollin, and corneodesmosin are examples of corneodesmosomes. The breakdown of these proteins causes the degradation of corneodesmosomes, leading to keratinocyte exfoliation. Kallikrein-related peptidases (KLKs) are serine proteases secreted from granular keratinocytes to the upper granular layer and cuticular space, and they play important roles in the process of keratinocyte exfoliation. By degrading corneodesmosomes, KLK5, KLK7, and KLK14 can cause keratinocyte exfoliation. KLK8 may also participate in de-keratinization by cooperating with other kallikreins. Furthermore, the expression of KLKs is regulated by protease inhibitors, including serine protease inhibitors, lymphoepithelial Kazal-type inhibitor (LEKTI), serine protease inhibitor Kazal-type 6 (SPINK6), and SPINK9. Moreover, abnormal expression of KLKs may destroy the skin barrier homeostasis, causing a range of skin diseases such as Netherton syndrome (NS), atopic dermatitis (AD), rosacea, and psoriasis.