Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine reserve design criteria and measures of success : Lessons learned from the Exuma Cays Land and Sea Park, Bahamas

Among the many potential benefits of no-take marine reserves, three important postulated effects are (1) to supply biomass of harvestable individuals to fished areas through emigration; (2) to increase spawning-stock biomass, which subsequently magnifies larval recruitment; and (3) to restore more natural size-frequency distributions of the protected populations, specifically to enhance the larger size classes, which may affect sex ratios and reproductive output. The Exuma Cays Land and Sea Park (ECLSP), covering 442 km 2 in the central Bahamas, was established in 1958 and closed to fishing in 1986, making it one of the first and largest marine reserves or 'no-take' zones in the western Atlantic. The ECLSP is ideally situated between small-scale developments in the northern and southern Exuma Cays and encompasses a diversity of contiguous shallow-water habitats from the Great Bahama Bank to the eastern platform margin in Exuma Sound. Scientific investigations during the past decade have compared queen conch, spiny lobster, and grouper resources in the ECLSP to those in adjacent fished areas and have demonstrated greater species diversity, density, biomass, potential reproductive output, and larval densities for these species. The lack of historical data limits determination of whether closure to fishing has resulted in increases in these attributes over time, but available data strongly support the contention that the ECLSP has significantly greater spawning-stock biomass of various organisms because of protection from fishing. Although evidence is strong that the ECLSP is an important source of larvae to adjacent areas in the Exuma Sound ecosystem, few data show adult emigration to fished areas. Some target species outside the reserve may have declined, and because the ECLSP probably depends on larval transport from upcurrent areas, awareness is growing that this reserve will not be successful in isolation. Experiences in the ECLSP suggest that marine reserves will be most successful if they contain contiguous habitats from bank to deeper shelf (>30 m) environments, minimize threats such as coastal development, and provide protection of unique features such as spawning aggregations.
Methods to analyze cell type-specific gene expression profiles from heterogeneous cell populations

ABSTRACT Recent technical progress in DNA and protein identification has made genome-wide survey of gene expression at tissue and animal levels a routine approach, such as microarray and RNA sequencing technologies to measure mRNA abundance and mass spectrometry to measure protein abundance. A key limitation in applying these genome-wide gene expression profiling methods at tissue and animal levels is that the contribution of a specific cell type to the total amount of measured gene expression cannot be determined. Here, we review currently available approaches to resolve this and discuss future directions of study to solve questions not addressable by state-of-the-art techniques.
Differentiation of leukocytes in bovine milk

The somatic cell count (SCC) in milk is used as an indicator of udder health status. Elevated SCC are generally considered as an indication of mastitis. In addition, the differential cell count of milk somatic cells can be a useful tool in research because each cell type has its own specific function in the immune response. The aim of this study was to develop and validate a staining method for milk somatic cells. Therefore the panoptic staining method according to Pappenheim was adapted for the differentiation of milk somatic cell populations. Quarter composite milk samples from 28 German Braunvieh x Brown Swiss cows were separated into 3 groups based on their SCC levels. Group 1 consisted of 12 samples with a mean of 4.57′0.10, group2 of 8 samples at a mean of 5.39′0.06 and group 3 of 8 samples at a mean of 6.15′0.07 log 1 0 cells/ml, respectively. Results showed a distribution of lymphocytes, macrophages and neutrophils of 20.9, 45.6 and 33.5% in group 1, of 11.4, 25.1 and 63.5% in group 2 and of 3.3, 9.5 and 87.2% in group 3, respectively. In conclusion, the ratio of lymphocytes and macrophages decreases whereas the ratio of neutrophils increases with rising SCC.
EFFECT OF STORAGE PERIODS, CULTIVARS, ENVIRONMENTS AND PACKAGE MATERIALS ON GERMINATION, VIABILITY AND SEEDLING VIGOR OF WHEAT GRAINS

An experiment was carried out at Sakha Agricultural Research Station during 2010 and 2011 seasons to study the effect of storage periods, cultivars, environments and package materials on germination, viability and seedling vigor of wheat grains. Three cultivars of wheat (Gemmiza7, Sakha 93 and Giza 168) were used during this study. Grains were packaged in three package materials (Jute, Jute coated plastic, Metal cans) after that grains stored in three types of environments (Dust, Sand and Ash). The stored grains were tested after two different periods for germination, viability (Electrical conductivity and Acidity %) and seedling vigor (radical length, plumule length and seedling dry weight). The obtained results recorded highly significant differences among the tested cultivars for all studied characters. Moreover, increasing storage period after harvest until 18 months decreased significantly all characters except electrical conductivity and acidity percentage which were increased with increasing storage period. Also, highly significant differences were observed among grains quality characters due to the different storage environments. Grains stored in ash had the worst characters as compared with other environments while grains stored in dust and sand gave the best characters. Moreover, grains stored in metal cans produced the best characters while, grains stored in jute bags gave the worst characters. It could be recommended that using metal cans to store wheat grains tell 18 months without using any chemicals is the best method for saving viability and seedling vigor.
Biological flora of the British Isles : Avenula (Dumort.) Dumort

In the British Isles A. pratensis is largely confined to shallow, dry soils over calcareous bedrock, with A. pubescens, although not so strictly confined to calcareous substrata, nevertheless being favoured by these, but usually found on soils which are deeper and more moist. In addition to calcareous grasslands A. pratensis is found on cliffs, screes and quarries, and here its deep (up to 50 cm) roots, growing straight down, provide a firm achorage and access to water in the oftne droughty conditions prevailing. In contrast A. pubescens is a shallow-rooting species (up to 20 cm), and its roots form a plate with horizontal rather than vertical growth, generally unsuitable for colonizing cliffs, screes, etc (.)
The monophyly of Protorosauria (Reptilia, Archosauromorpha); a preliminary analysis

This paper presents a preliminary analysis of protorosaur interrelationships based on the combination of the data published by Benton & Allen (1997), Jalil (1997), and Dilkes (1998). As was found in previous analyses by these authors, protorosaurs yield low resolution under parsimony analysis because of a high percentage of missing data in some taxa. Kadimakara, Malerisaurus langstoni, and Trachelosaurus are the most problematical taxa in that respect. Their deletion from the analysis dramatically improved resolution in a strict consensus tree. The analyses here presented confirm the result obtained by Dilkes (1998) that showed the protorosaurs as conventionally conceived to be paraphyletic. Prolacerta is more closely related to Proterosuchus and Euparkeria than to the other taxa conventionally included in protorosaurs (in one data combination, Protorosaurus joined Prolacerta, Proterosuchus and Euparkeria). Macrocnemus, Langobardisaurus, Tanystropheus and Tanytrachelos form a well-confirmed clade that may include the enigmatic Cosesaurus. In various data combinations Drepanosaurus and Megalancosaurus were found to be either related to (in a basal polytomy), or nested within protorosaurs. In either case, Drepanosaurus and Megalancosaurus were found to be more closely related to one another than to other protorosaurs, and as a group they were in some searches found to be more closely related to the Macrocnemus - Langobardisaurus - tanystropheid clade than to Protorosaurus or Prolacerta. The position of Jesairosaurus within the Protorosauria remains unresolved, although in one search the genus grouped with Drepanosaurus and Megalancosaurus in an unresolved trichotomy. Future analysis of protorosaur interrelationships based on the original material will not only have to address the problem of missing data, but also problems of character analysis and coding.
Plains lubber grasshopper (Brachystola magna) as a potential intermediate host for Oxyspirura petrowi in northern bobwhites (Colinus virginianus).

SUMMARY Oxyspirura petrowi is a heteroxenous parasitic nematode that has been reported in high prevalences from birds in the Order Galliformes experiencing population declines in the USA. There is a paucity of information regarding the natural history O. petrowi , including the life cycle and e ﬀ ects of infection on wild bird populations. In order to study the life cycle of this parasite, we collected plains lubber grasshoppers ( Brachystola magna ) from a ﬁ eld location in Mitchell County, Texas. We found third-stage larvae (L3) in 37.9% (66/174) B. magna . We determined that they were O. petrowi through morphological comparison of L3 from experimentally infected Acheta domesticus and by sequence analysis. Then, we showed that B. magna are a potential intermediate hosts for O. petrowi infections in northern bobwhites ( Colinus virginianus ) in a laboratory setting by experimental infection. We ﬁ rst detected shedding of eggs in feces using a fecal ﬂ oat technique 52 days post infection. In addition, we recovered 87 O. petrowi from experimentally infected northern bobwhites. Although we detected shedding in feces, recovery of eggs was low (>5 eggs/g). Future work is needed to understand shedding routes and shedding patterns of northern bobwhites infected with O. petrowi.
Molecular Phylogeny of Poa L. sensu lato (Poaceae) with a Focus on West Asian Species

Poa L. , is known as a highly diverse cosmopolitan genus with taxonomic difficulties that includes unknown species and species with uncertain affinities mainly in West Asia and North Africa. Poa also exhibits a close relationship with two West Asian genera, Eremopoa Roshev. and Oreopoa H. Scholz & Parolly. This study was conducted to: 1) fill the gap of information on the affinities between Poa species with an emphasis on West Asian Poa; 2) revise and evaluate the accuracy of traditional infrageneric classification of West Asian Poa; and 3) clarify the relationship between Poa and two allied genera of Poaceae Barnhart, Eremopoa and Oreopoa. DNA molecular evidence from present phylogenetic analyses of West Asian species of Poa, Eremopoa and Oreopoa, resulted in some great findings as follow: I) Poa caucasica Trin. , which is currently assigned to subsection Nivicolae of section Poa from subgenus Poa resolved as a unique new distinct lineage within Poa. II), New treatments are suggested for Poa densa Troitsky, Poa masenderana Freyn & Sint. , Poa cenisia All. , Poa psychrophila Boiss. & Heldr. and Poa lipskyi. III) Three unclassified species of Poa pseudobulbosa, Poa diversifolia and Poa aitchisonii are assigned here to subgenus Poa and supersection Poa. IV), The present molecular evidence supports inclusion of Eremopoa in Poa and confirms reduction of Eremopoa to a level of subgenus of Poa. V) Present phylogenetic analyses also indicate that monotypic genus Oreopoa H. Scholz & Parolly is part of Poa. These findings require an urgent modification in subgeneric and sectional classification of the genus Poa.
Molecular basis of membrane stability and dynamics

Dit proefschrift is onderverdeeld in vier verschillende delen, die overeenkomen met de vier verschillende onderwerpen die ik heb gewerkt . In hoofdstukken 2-4, bestudeerden we het werkingsmechanisme van antimicrobiele peptiden. We concentreerden ons op twee korte peptiden, de cyclische BPC194 en zijn lineaire analoge BPC193. Hoewel beide bezitten dezelfde aminozuursequentie, maar het cyclische peptide kan microbiele cellen te doden. Met behulp van een combinatie van fluorescentie-gebaseerde technieken met moleculaire dynamica simulaties, kwamen we erachter dat het cyclisch peptide plooien in de juiste conformatie op membraanbindende, inserts diep, vormt porien en fuseren de membranen . In hoofdstuk 5, wij ontwerpen en gesynthetiseerd een DNA - peptide hybride te moduleren de oligomerisatie van een membraan kanaal met behulp van complementaire DNA-strengen of een G-quadruplex motief. In beide gevallen heeft de daaruit zender heeft voorkeur voor een specifieke oligomere toestand van een vaste grootte . In hoofdstuk 6 hebben we de effecten van koolhydraten op het membraan organisatie. We combineerden fluorescentie microscopie met moleculaire dynamische simulaties en ontdekte dat alleen de niet-reducerende koolhydraten, sucrose en trehalose, hebben een effect op de lipid raft organisatie. Die twee disachariden worden meestal gesynthetiseerd door verschillende organismen, om te overleven in extreme uitdroging omstandigheden. In hoofdstuk 7 bestudeerden we de lokalisatie, oligomerisatie en dynamiek van verschillende plasmamembraan aminozuur transporters van S. cerevisiae. De verdeling van deze eiwitten in het membraan niet homogeen. We kwamen erachter dat de reden dat de extreem trage verspreiding die we gemeten voor die eiwitten samen met hun lage bedragen zou kunnen zijn.
Salmonella Incidence and Distribution of Serotypes throughout Processing in a Spanish Poultry Slaughterhouse.

A survey of contamination with Salmonella spp. was done at 11 sampling sites in a poultry slaughter establishment in Spain for a total of 192 samples. Samples included fecal material, utensils, water, and poultry carcasses and livers at several stages of processing. Salmonella incidence rates increased from 30% in fecal material collected from incoming birds to 60% in air-chilled carcasses and 80% in cold-stored livers, indicating that cross-contamination occurred. The rate of incidence of Salmonella organisms on carcasses averaged 56.7% through post-picking to post-air chilling and reached a maximum of 70% on carcasses at the post-spray wash site. Poultry livers were more heavily contaminated with salmonellae, as 55% and 80% samples after evisceration and cold storage, respectively, were positive for those pathogenic bacteria. From a total of 112 strains isolated, 87 (77.6%) were S. enteritidis , 7 (6.2%) Salmonella serotype 4,5,12:b:-(II), and 6 (5.4%) Salmonella serotype 4,12:b:-(II), and the remaining 12 strains were equally distributed among S. typhimurium . S. virchow , and S. blockley (3.6% each). Serotypes isolated from feces were later detected in matched carcasses and livers indicating a cross-contamination of carcasses by endogenous microflora in bird feces. The incidence of Salmonella serotype 4,5, 12:b:-(II) and that of S. typhimurium were significantly higher (P < 0.05) in samples obtained prior to evisceration than in those collected after that particular step. The situation with S. enteritidis was quite the reverse, since this serotype was more frequently detected in samples taken after the evisceration step (P < 0.01).
Long term effects of a food supplement HiveAlive™ on honey bee colony strength and Nosema ceranae spore counts

The long term effect of HiveAlive™, a commercial food supplement, was evaluated with respect to colony population size and Nosema ceranae spore loads. The supplement was administered in sugar syrup at a dose of 2.5 ml per liter of syrup to up to 20 colonies per group for a period of 2 years. Its use before and after winter increased a colony’s worker population size by 89% and reduced Nosema ceranae spores by 57% compared to control colonies. These results represent the first-known hive manipulation to have a lasting effect on nosema spore levels. The positive effect of HiveAlive™ may have been a result of its continued use over a two-year period.
Consortium of Phosphate-solubilizing Bacteria and Fungi for Promotion of Growth and Yield of Chickpea (Cicer arietinum)

The combined inoculation of two or more microbial species, such as phosphate-solubilizing bacteria (PSB) and arbuscular mycorrhizal fungus (AMF) and PSB and nitrogen fixers, has often been reported to exert positive effect on growth and yield of various crops; however, reports on dual inoculation of PSB and free-living phosphate-solubilizing fungi (PSF) are hardly available, which makes this study relevant. P-solubilization efficiency (SE) was highest for Bacillus sp. ; SE values for RM-2 were highest on the 2nd day of inoculation, whereas those for Aspergillus niger S-36 continuously increased up to the 5th day of incubation. We performed an experiment to evaluate the co-inoculation effect of two phosphate-solubilization-efficient strains of bacteria and fungi in a pot trial. RM-2 strain produced chitinase that might have conferred biocontrol properties on chickpea. The overall growth of plants via dual inoculation was significantly (P = 0.05) greater than that for control and single inoculations in a pot trial, indicating the positive synergistic effect of co-inoculation of PSB and PSF for crop improvement, which could be useful for farmers and sustainable agriculture.
Habitat Alteration Influences a Desert Steppe Lizard Community: Implications of Species-Specific Preferences and Performance

Abstract: Understanding community assembly is a fundamental goal of ecology and evolutionary biology, because it provides insight into how a given landscape changes in a synergistic fashion. With the current background of global environmental change, studies of how habitat alteration affects local communities often focus on species' responses to community-level changes instead of responses to specific ecological factors that elucidate the roles each factor plays in the final synergistic response. Here, we focus on the specific ecological mechanisms that drive changes in community structure. We investigated compositional patterns of lizard communities among natural and altered habitats (vegetatively sparse, natural, and dense) in the desert steppe ecosystem of Inner Mongolia, China. Habitat alteration induced significant changes in community composition of lizards and was associated with significant changes in both biotic and abiotic niches. Our preference (soil, thermal, and prey) and performance (locomotor, antipredator, and competitive) experiments identified many of the biotic and abiotic factors shaping lizard community responses to habitat change. In the natural habitat, where Phrynocephalus frontalis and Eremias multiocellata codominate, P. frontalis experienced low overlap (across lizard species) in preferred prey. Eremias multiocellata preferred the thermal environment of the natural habitat (and dense habitat), but this one factor did not fully explain its codominance. Phrynocephalus frontalis dominated in the sparse habitat, where this lizard species experienced its preferred tight soil and warm thermal environment and experienced low overlap of preferred prey. In the dense habitat, where E. argus dominates, P. frontalis and E. multiocellata exhibited impeded locomotor performance, whereas E. argus was not impeded by vegetation density. Eremias argus also preferred the thermal environment of the dense habitat (and natural habitat). Our results suggest, furthermore, that adult predation risk was not a major determinant of community divergence among habitats and that competition likely plays a more important role. Interspecific competition for microhabitat use may explain the low abundance of E. argus in the natural habitat and the low abundance of P. frontalis in the dense habitat. Overall, our assessment of lizard preferences and performances explained community composition across habitats. Our focus on ecological mechanisms associated with habitat alteration highlights the importance of vegetation conservation in lizard community management.
Hematological Studies on Salamanders in Relation to Their Ecology

from the general area of Neal Creek, North Carolina. The species from Indiana were: Ambystoma tigrinum tigrinmm (Green), A. maculatum (Shaw), Eurycea bislineata bislineata (Green), E. lucifuga (Rafinesque), Plethodon cinereus cinereus (Green), P. dorsalis (Cope), and P. glutinosus glutinosus (Green). Those from North Carolina were: Desmognathus ochrophaeus carolinensis (Dunn), D. phoca (Matthes), D. quadramaculatus qiadramaculatus (Holbrook), and Gyrinophilus danielsi danielsi (Blatchley). The Necturus used came from Wisconsin. The number of red blood cells was determined by standard techniques. In order to insure more nearly accurate results, five individual counts were made from each pipette and then the average was taken as the final count. Measurements of red blood cell size were made by means of a Spencer micrometer, using blood smears stained with Wright's stain. Widths and lengths of 500 cells were obtained from blood samples from five individuals. Blood sugar levels of six species of salamanders were determined by the Folin-Wu micro method. These animals were: Amnbystoma tigrinum, Ambystoma maculatum, Eurycea bislineata, Necturus maculosus, Plethodon cinereus, Plethodon glutinosus. Animals had been kept in a good state of nutrition at room temperature for approximately one week before being sacrificed.
Esterase isozymes in three species of sarcophagid flies (Sarcophagidae: Diptera)

Electrophoretic banding pattern of Esterase was analyzed by polyacrylamide gel electrophoresis in Sarcophaga ruficornis, S.argyrostoma and S.dux. Five regions of activity were observed. Of the five esterases detected only EST- 4 was consistently observed in all the species. The EST- 4 locus revealed polymorphism for these electrophoretic phenotypes governed by two electromorphs EST- 4 A and EST- 4 B . The EST banding pattern does not reveal any notable interspecific difference.
The Effect of Mechanically Induced Stress on the Growth of Cauliflower, Lettuce and Celery Seedlings

Brushing cauliflower, lettuce and celery seedlings with paper for 1.5 min each day for 11–13 d, 10–12 d or 21–28 d, respectively resulted in smaller, more compact, plants than the unbrushed controls. In all three species shoot fresh and dry weights and leaf area were reduced following brushing. In cauliflower and celery the largest growth reduction was in petiole length. In lettuce, which has no discernible petioles, the reduction in leaf length caused by brushing was proportionally greater than the reduction in leaf width. Brushing reduced hypocotyl length in cauliflowers and to a lesser extent in lettuce. Petiole and hypocotyl thickness was reduced in cauliflower, whereas hypocotyl thickness was increased in lettuce following brushing. Brushing increased leaf thickness in cauliflower, celery and to a lesser extent in lettuce and increased the percentage dry matter content of lettuce shoots. The weight of chlorophyll per fresh weight of leaf tissue increased following brushing in celery and lettuce and declined in cauliflowers. Root length and the number of branches per root system were reduced in all three species following brushing. Root dry weight was reduced and the root:shoot dry weight ratio was increased in lettuce, reduced in celery and unaffected in cauliflowers. There were different patterns of response to brushing, the reduction in leaf weight being greatest in the youngest leaf of cauliflower and least in the youngest leaf of lettuce and celery. Growth responses to brushing were seen several days after brushing had ceased, noticeably in leaves which were barely visible at the time of brushing. It is suggested that growth retardation of cauliflowers, lettuce and celery, induced by mechanical stress such as brushing may prove valuable as a means of ‘conditioning’ the seedlings to withstand both the physical and physiological stresses which occur at and during transplanting.