Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic structure among remnant populations of a migratory passerine, the Northern Wheatear Oenanthe oenanthe

Continuous animal populations often become fragmented due to anthropogenic habitat alterations. These small, fragmented populations are fragile due to demographic and genetic factors, whereas immigration can enhance their long-term viability. Previously, we showed that high philopatry affected the local dynamics of three small and remnant subpopulations of Northern Wheatears in The Netherlands. Here, we show that these three populations together with an additional larger population in the European lowlands are highly genetically differentiated based on 22 microsatellite markers. In contrast, we found no evidence for differentiation using two mitochondrial DNA markers. An IMa2 analysis indicates that gene flow has occurred regularly among our sampled populations. As immigration of colour-ringed birds among our sampled populations is rare at best, our results suggest that the populations have recently become isolated from one another. Low dispersal rates in highly mobile birds may occur when suitable habitat becomes highly fragmented, and will accentuate stochastic demographic processes and inbreeding, both reducing population viability. As dispersal rates are low among populations of Northern Wheatears in The Netherlands, there is only a small probability of recolonization of habitat patches where populations have become locally extinct.
Sexual dimorphism in gene expression and regulatory networks across human tissues

Sexual dimorphism manifests in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sexual dimorphism, we conducted a comprehensive assessment of gene expression and regulatory network modeling in 31 tissues using 8716 human transcriptomes from GTEx. We observed sexually dimorphic patterns of gene expression involving as many as 60% of autosomal genes, depending on the tissue. Interestingly, sex hormone receptors do not exhibit sexually dimorphic expression in most tissues; however, differential network targeting by hormone receptors and other transcription factors (TFs) captures their downstream sexually dimorphic gene expression. Furthermore, differential network wiring was found extensively in several tissues, particularly in brain, in which not all regions exhibit strong differential expression. This systems-based analysis provides a new perspective on the drivers of sexual dimorphism, one in which a repertoire of TFs plays important roles in sex-specific rewiring of gene regulatory networks. Highlights Sexual dimorphism manifests in both gene expression and gene regulatory networks Substantial sexual dimorphism in regulatory networks was found in several tissues Many differentially regulated genes are not differentially expressed Sex hormone receptors do not exhibit sexually dimorphic expression in most tissues
Foot and Skeletal Disorders in Laying Hens: Effects of Perch Design, Hybrid, Housing System and Stocking Density

Abstract In four experiments a total of 3660 SCWL laying hens kept in conventional cages at low and high stocking densities with and without a perch, Get-away (GA) cages and aviaries with litter (AL), were used for studies on the presence of bumble foot (BF), distal toe pad hyperkeratosis (TPH), keel bone lesions (KBL) and of the breaking strength of tibia and humerus. Commercial hybrids were used: LSL (Expts. 1, 2 and 4); LSL and Shaver (Expt. 3). Only clearly observed in systems with perches, the incidence of BF and KBL was mostly affected by perch design, while BF was also strongly affected by strain and housing system. LSL showed significantly higher incidence of BF, especially in GA and AL. TPH, only found in conventional cages, was affected both by strain and stocking density, LSL hens and lower stocking density showing significantly lower incidence. Apart from welded wire net platforms, a European beech hardwood circular prototype perch with a flattened upper and lower surface seemed to combine in .
Comparison of extractable soil phosphorus with dry matter production and phosphorus uptake by perennial ryegrass in a pot experiment

Three procedures for extraction of soil P [Morgan (Na acetate + acetic acid, pH 4.8), Olsen (NaHCO 3 , pH 8.5) and 0.01 M CaCl 2 solutions] were correlated with perennial ryegrass dry matter (DM) yields and P uptake in the grass DM. The effect of P uptake in grass DM on the decrease in soil-P concentrations was also examined. The comparisons are based on soil samples taken in County Cavan. Fifty-six soils were selected on the basis of their Morgan-P test results to give a range of soil-P levels (2.5 to 33.8 mg/l). Two hundred grams of each soil (dry weight) were weighed into plastic pots (9 cm surface diameter). Ten perennial ryegrass seeds were sown per pot in May. Grass was harvested six times over the growing season at approximately 3-week intervals. Grass DM yields were significantly (P < 0.001) correlated with the three soil tests: Morgan, r 2 0.79; Olsen, r 2 0.65; CaCl 2 , r 2 0.57. Total P uptake in the grass DM during the experiment was also significantly (P < 0.001) correlated with the results of the three soil tests: Morgan, r 2 0.90; Olsen, r 2 0.82; CaCl 2 , r 2 0.81. Total P uptake in the grass DM was significantly (P < 0.001) correlated with the decrease in soil-P concentrations during the experiment for each of the three soil tests: Morgan, r 2 0.84; Olsen, r 2 0.21; CaCl 2 , r 2 0.60. Of the three soil-P tests examined, the Morgan test best estimated the availability of soil P to perennial ryegrass and accounted for changes in soil-P concentrations in line with uptake in the grass DM over time.
Plant Performance and Nutrient Losses during Containerized Landscape Shrub Production using Composted Dairy Manure Solids as a Peat Substitute in Substrate

ADDITIONAL INDEX WORDS. nursery crops, potting media, walter’s viburnum, sandankwa viburnum, japanese privet SUMMARY. Concerns over the environmental impact and economics of harvesting sphagnum and reed-sedge peat have increased the desire to identify acceptable peat substitutes for use in container substrates. This preliminary study evaluated the use of composted dairy manure solids as a substitute for sphagnum or reed-sedge peat in container substrates for production of woody ornamental shrubs and assessed potential leaching of nutrients. Walter’s viburnum (Viburnum obovatum), sandankwa viburnum (Viburnum suspensum), and japanese privet (Ligustrum japonicum) were grown in 3-gal plastic containers with seven substrates containing (by vol.) 60% pine bark, 10% sand, and 30% sphagnum peat (S), reed-sedge peat (R), and/or composted dairy manure solids (C). Substrate composition had no effect on plant quality ratings for any species, growth index (GI) of walter’s viburnum, or shoot and root dry weight of walter’s viburnum and japanese privet. However, the GI of japanese privet and sandankwa viburnum was the lowest when grown in substrates containing a high percentage of reed-sedge peat (0S:3R:0C). Substrate effects on average nitrate + nitrite nitrogen leachate losses were minimal over the 88-day leachate collection period. However, the substrate containing the highest proportions of composted dairy manure solids (0S:0R:3C) generally had the highest average ammonium nitrogen and dissolved reactive phosphorus losses compared with other substrates. All substrates tested as part of this study appeared to be commercially acceptable for production of container-grown woody ornamental shrub species based on growth and quality. However, average nutrient losses from containers differed depending on the peat or peat substitute used to formulate the substrates.
Ontogeny of the Digestive Enzymes of Tadpoles of Lithobates catesbeianus

The transition from aquatic to terrestrial phase in amphibians, called metamorphosis, is accompanied by ecological, morphological, physiological, and biochemical changes. These enable the digestive system of the animal to take up nutrients when the feeding habit changes from omnivorous/herbivorous in tadpoles to carnivorous in adults. To better understand this process, this study investigated the activity of four hydrolases in the digestive system of bullfrog (Lithobates catesbeianus) at all stages of larval development in which the animals feed from exogenous sources. Digestive enzyme activity increased from the beginning of the feeding phase until pre-metamorphosis, which is related to the maturation of the digestive system. The increase was more significant in the period of pro-metamorphosis, coinciding with the accumulation of energy reserves necessary for metamorphosis and the increased growth of the animal. During the climax of metamorphosis, the activities of digestive enzymes decreased, because the animal does not eat during this period. At the end of metamorphosis, in stage 45, the activity of proteolytic enzymes, acid proteases and trypsin, increased 35% and 400%, respectively, when compared to stage 44. Conversely, maltase activity remained constant whilst amylase activity decreased by 70%, which is consistent with the carnivorous feeding habit of the adult. These results enhance understanding of the development of digestive enzymes in the larval phase and in the change from omnivorous/herbivorous to carnivorous feeding habits. In addition, these findings provide insights for the formulation of appropriate diets for each developmental phase of tadpoles.
POPULATION DYNAMICS OF SCELOPORUS GRAMMICUS (SAURIA : PHRYNOSOMATIDAE) AT DURANGO, MEXICO

kbs~n~c~-Population dynamics of Scelopmus grammicus were studied at La Michilía Biosphere Reserve, Durango, Mexico, from 1979 to 1982 using mark-recapture methods. Estimated population density waq 166 individuals (adults and subadults) per hectare, with adults averaging 42 individuals per hectare. Sex ratio wai approximately 1:1, with females slightly dominating at older ages. Six differerit age classes were established: a) juveniles from O to 3 months of age, b) s u b adults from 3 to 5 months of age, c) adults 1, individuals in their first reproductive season from 5 to 12 months of age, d) adults 11, individuals in their second reproductive season and older than 1 year, e) adults 111, individuals in their third reproductive season and older than 2 years, and f ) adults IV, individuals in their fourth reproductive season and older than 3 years. Average litter size for females was 6.17 neonates I 1.65 SE and varied widely (three to nine neonates) as a function of female body size. Estimated number of neonates in 10 hectares was 1,482 and embryo mortality was 7.2%. Mter hatching, he average mortality was higher than 55% from one age-class to the next. The mortality rate was lowest for the male adult 1 class (53.8%), and highest for the male adult 111 class (89.0%), below only the 100% mortality exhibited by adult IV individuals (the final age class). The population life table indicates a Slobodkiri Type IV survivorship curve, with high mortality occurring at younger ages and a population replacement rate (net reproductive rate) close to 1.00. Average generation time for this population was 1.09 years. This is the first study of the population dynamics of this species.
Effect of Fire on a Mixed Grass-Shrub Range in Southern Arizona.

There have been indications that control methods on certain southwestern shrubs are most effective at the driest seasons of the year. Parker (1939) noted that with most southwestern plants burning can be accomplished most effectively during April, May and June. Thornber (1907) reported that burning an area of burroweed in June not only killed the burroweed but such other shrubs as catclaw (Acacia Greggii), creosote bush (Larrea divaricata), Mormon tea (Ephedra trifurca) and graythorn (Zizyphus lycioides). Streets and Stanley (1938) concluded that the only practicable time to burn burroweed was in late spring (May and June) before the summer rains and in late fall (October and November) before the winter rains. Others have made similar observations.
Assessment of genetic diversity in natural European hophornbeam (Ostrya carpinifolia Scop.) populations in Turkey

ABSTRACT Genetic diversity is a crucial component for plant survivability and fitness in terms of adaptation, genetic stability and variability. In this study, a total of 160 genotypes were investigated using 12 random amplified polymorphic DNA (RAPD) primers to understand the genetic structure and diversity of nine naturally distributed Ostrya carpinifolia populations in Turkey. Twelve RAPD primers yielded 111 clearly identifiable DNA bands, of which 71 bands were found to be polymorphic (64%). Observed number of alleles (Na), effective number of alleles (Ne) and Nei's gene diversity (h) were found as 2, 1.53 and 0.32, respectively. Total genetic variation (HT), within-population genetic variation (HS) and Nei's genetic differentiation coefficient (GST) were found as 0.32, 0.09 and 0.70, respectively. Genetic diversity analysis (AMOVA) revealed highly significant (P < 0.001) genetic variations among and within populations. 69.94% of total variation was observed among populations while 26.69% was within populations. Gene flow value was calculated as 0.21 (Nm < 0.5), which could homogenize the genetic structure of a population. Two geographically isolated populations demonstrated high gene diversity and polymorphic loci ratio, indicating a relationship between geographic distribution of populations and eco-geographic factors. The findings of this study will pave the way for understanding the genetic diversity between inter- and intra-populations of O. carpinifolia species, as well as they would provide valuable information for management, conservation and utilization of in situ and ex situ Ostrya germplasms.
Correct Queen Maintenance before and after Instrumental Insemination, Tested in Egypt

SummaryA common Egyptian method of storing several queens in one bee colony, and caging them after instrumental insemination, was compared with a method recommended by the author. When queen cells were introduced into nuclei instead of virgin queens, the acceptance increased from 40–60% to 100%. Storage of virgins in a queen bank resulted in injuries to the queens, especially to their legs. When the storage period was shortened from 10 to 4 days after emergence, the percentage of non-injured queens increased from 46 to 100%. Legs of accepted, freely moving virgin queens were not injured. When queens were caged after instrumental insemination, only 1·8 million spermatozoa entered the spermatheca, but when newly inseminated queens were released, 5·1–5·2 million sperms entered. Thus a 2·8- to 2·9-fold increase was achieved.
Black Swans Cygnus atratus adopt related cygnets

In many species of bird with precocial young, breeding pairs occasionally adopt conspecific young into their broods or are the subject of 'egg-dumping'. Here I test the hypothesis that kin selection may play a role in such alloparental behaviour in a wild population of Black Swan Cygnus atratus in which closely related individuals of both sexes occur in the breeding population. A set of eight polymorphic microsatellite loci was used to determine the genetic relatedness between 11 alien cygnets and their foster parents. The mean relatedness between alien cygnets and their foster parents was significantly higher than expected by chance. Alien cygnets were also more likely to be cared for by high-quality pairs than by low-quality pairs. I therefore suggest that cygnets move from low-quality to related, high-quality pairs. In principle, all parties can derive fitness benefits from alloparental care in this system: the cygnet and its true parents from its higher survival and the foster family from kin selection.
Prevalence of Lactobacillus bulgaricus and Streptococcus thermophilus stability in commercially available yogurts in Sri lanka

Aims and Objectives: Common starter cultures found in fermented milk products are Lactobacillus bulgaricus and Streptococcus thermophilus. The viability of these bacteria is important in order to gain health benefits. It is important to investigate the stability of commercially available yogurts with respect to starter cultures and the quality. Materials and Methods: Yogurt samples were collected from highly marketed different brands designated as A, B, C, D, E, F, G and H from different areas from Sri Lanka. MRS and M17 agar were used to enumerate L. bulgaricus and S. thermophilus respectively and a pH change was measured. Results: The pH values decreased significantly and only two of these products maintained 106 cfuml-1 viable count of L. bulgaricus till the end of the shelf life. All products showed the highest number of S. thermophilus. Conclusion: The pH of the yoghurts significantly change with the storage. For optimum benefits, the yogurt products should be consumed within seventh to fourteenth day from its manufacturing date. Only two of the yoghurt products maintained 106 cfuml-1 viable count of L. bulgaricus till the end of the expiry. Asian Journal of Medical Sciences Vol.7(5) 2016 97-101
Separation of Motile Bovine Spermatozoa for In Vitro Fertilization by ElectricalCharge

Objective: Sperm selection is essential to Assisted Reproductive Technology (ART), influencing treatment outcomes and the health of the resulting offspring. Several techniques have been developed to recover a homogeneous population of highly motile sperm cells, including centrifugation gradients, swim up and filtration procedures. It is known that the head of spermatozoa has a negative electric charge, and several studies have tried to use this physiological characteristic for the selection of high quality motile sperm from frozen-thawed semen. The study aim was to design a device that would be able to separate viable, high quality sperm for IVF after thawing, using electrical characteristics of sperm. Methods: Samples of the semen solution were taken at different times from both the anode and cathode areas. The electric charges used were 0, 1, 5 and 10 volts (V), at times of 0, 5, 10 and 20 minutes. In the second phase of the experiment, to evaluate the ability of the selected sperm to fertilize oocytes, we fertilized oocytes with semen processed with either the EC (10 volts per 10 minutes) and the discontinuous gradients. Results: Concentration and motility were affected by the voltage: V0 was different from V1, V5 and V10 (P<0.0001). There were no differences when we compared the electric channel (EC) to the Percoll discontinuous gradient on cleavage rate and embryo development rate. To verify the effect of magnetic field on the ratio of sex we evaluated the embryo sex distribution: we did not find any effect on embryo sex ratio. Conclusion: In conclusion all these observations may allow for the streamlining of many IVF protocols. Further, the decreased time gametes are outside of the optimal environment of the incubator may potentially reduce the stress on the gametes during the IVF procedures. Future, work will focus on pregnancy rates of embryos produced with EC separated sperm after IVF.
The Phyllode Theory of the Monocotyledonous Leaf, with Special Reference to Anatomical Evidence

I. De Candolle's 'Phyllode Theory" 466 3. The relation of the ' Phyllode Theory ' to the theory of the origin of Monocotyledons through adaptation to the geophilous habit 468 3. The relation of the ' Phyllode Theory ' to the theory of the aquatic origin of Monocotyledons . 469 4. The ' L a m i n a ' in certain Monocotyledonous leaves . 470 6. An extension of the ' Phyllode Theory ' to the leaves of certain Gymnosperms . 473
Positive species diversity and above‐ground biomass relationships are ubiquitous across forest strata despite interference from overstorey trees

Summary There is growing concern over rates of global species diversity loss and its implications on healthy ecosystem functioning. While positive relationships between tree species diversity and forest biomass production have been observed, forests are structurally complex, consisting of understorey vegetation layers that also contribute to ecosystem functioning as they often account for the majority of species richness. However, relationships between understorey vegetation diversity and function are largely unexplored. Further, few studies have simultaneously assessed how both overstorey and understory vegetation interact and contribute to overall ecosystem function. By analysing Canada's National Forest Inventory data base using structural equation modelling, we explored the relationships between species richness and above-ground biomass production across forest vegetation strata while accounting for potentially confounding factors, including climate, physical site characteristics and forest ageing. We found positive relationships between species richness and biomass production across all forest vegetation layers, but the relationship was strongest for the overstorey layer. Species richness of the understorey tree, shrub and herb layers was positively related to overstorey species richness. However, overstorey biomass had a negative effect on the biomass production of all understorey layers. Our results suggest that resource filtering by overstorey trees might have reduced the strength of the positive diversity–productivity relationships in the forest understorey, supporting previous hypotheses that the magnitude and direction of diversity–productivity relationships is context specific and dependent on the conditions of the surrounding environment. Further, heterogeneity in understory resources, as affected by the overstorey, may promote niche complementarity as the main mechanism driving diversity–productivity relationships in understorey vegetation.
Optimum air-dry storage conditions for sweet orange (Citrus sinensis (L.) Osbeck) and lemon (Citrus limon (L.) Burm. f.) seeds

Storage behaviour and longevity of seeds of lemon (Citrus limon) and sweet orange (C. sinensis) were tested following desiccation to between 14% and 4% moisture content (fresh weight basis, w.b.) and subsequent hermetic air-dry storage for up to 914 d at temperatures between 15°C and -20°C, and up to 6 d in liquid nitrogen (-192°C). The results confirmed that both species showed intermediate seed storage behaviour. Air-dry storage environments therefore require careful optimisation to obtain maximum seed longevity. Seeds of sweet orange were less tolerant of desiccation and less than 20% of seeds survived more than 210 days at 5°C and 8.7% moisture content (63% equilibrium relative humidity at 20°C). The optimum air-dry environment for the medium term storage of the longer-lived lemon seeds was 5°C and 7.5% moisture content (48.3% equilibrium relative humidity at 20°C).
Toxicity of three pesticides to several rice-field cyanobacteria

Ten species of heterocystous cyanobacteria belonging to five genera, viz. Anabaena, Nostoc, Calothrix, Scytonema, and Westiellopsis, were isolated from coastal rice fields, Orissa State, India, and their relative tolerance to Sevin (carbaryl 50% WP) Rogor (dimethoate 30% EC), and Hildan (endosulfan 35% EC) was determined. The 10 species differed widely with respect to their tolerance to the pesticides; variation in the tolerance level to a specific pesticide existed among species of the same genus and also between genera. Though some of the species belonging to the genera Calothrix and Scytonema, which possess a sheath layer around their trichome, were comparatively more tolerant to the pesticides, the presence of additional cell envelope layers was not always found to be the only factor responsible for their tolerance to higher levels of the pesticides. Although the application of the recommended rates of these pesticides may not significantly reduce the growth of the cyanobacteria, higher levels, e.g., double the levels of Sevin and Hildan, in particular, can exceed the EC 50 level of most of the cyanobacteria studied.