Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a growth-transition matrix for the stock assessment of the green sea urchin (Strongylocentrotus droebachiensis) off Maine

The green sea urchin (Strongylocentrotus droebachiensis) is important to the economy of Maine. It is the state’s fourth largest fishery by value. The fishery has experienced a continuous decline in landings since 1992 because of decreasing stock abundance. Because determining the age of sea urchins is often difficult, a formal stock assessment demands the development of a size-structured population dynamic model. One of the most important components in a size-structured model is a growth-transition matrix. We developed an approach for estimating the growth-transition matrix using von Bertalanffy growth parameters estimated in previous studies of the green sea urchin off Maine. This approach explicitly considers size-specific variations associated with yearly growth increments for these urchins. The proposed growth-transition matrix can be updated readily with new information on growth, which is important because changes in stock abundance and the ecosystem will likely result in changes in sea urchin key life history parameters including growth. This growth-transition matrix can be readily incorporated into the size-structured stock assessment model that has been developed for assessing the green sea urchin stock off Maine.
The impact of land use on species composition and habitat structure in Sudanian savannas — A modelling study in protected areas and agricultural lands of southeastern Burkina Faso

Abstract Schmidt, M. , E. Mbayngone, Y. Bachmann, K. Hahn, G. Zizka & A. Thiombiano (2016). The impact of land use on species composition and habitat structure in Sudanian savannas — A modelling study in protected areas and agricultural lands of southeastern Burkina Faso. Candollea 71: 265–274. In English, English abstract. Sudanian Savannas are under high agricultural pressure and are therefore changing rapidly. Due to high population densities and an increasing need for food and cash crops, the mosaic of traditional agroforestry systems, fallows and savanna is being transformed into intensively used croplands and savannas only remain in protected areas. The focus of this study is to characterize the differences in plant diversity and composition between protected areas and surrounding agricultural lands and to identify areas most important for plant conservation. Building on observation and collection records, we modelled distributions of individual plant species and summarized these. We mapped the species richness of vascular plants in general, of woody plants, graminoids and forbs, the share of weeds and the average size of grasses and trees and calculated means for the reserves and outside areas. Distinct differences between protected areas and agricultural lands have been found in the richness of herbs (both forbs and graminoids) and weeds as well as in the size of grasses: Woody species seem to be less affected by human impact in the agricultural lands concerning both species richness and plant size. Weeds are playing an important role in the higher species richness of the agricultural lands. Received: May 24, 2016; Accepted: July 20, 2016; First published online: August 2, 2016
Differential accumulation of manganese in three mature tree species (Holoptelia, Cassia, Neem) growing on a mine dump

Three trees, including Cassia siamea (Cassia), Azadirachta indica (Neem), Holoptelia integrifolia (Holoptelia) belonging to three different families were identified from a manganese mine tailing dump. Manganese content in dump soil and in the stem, green leaves and dry, fallen leaves of the plants was determined. Values were compared with similar samples collected from normal vegetation. Under control condition, manganese content was highest in Cassia. Distribution of metal in samples collected from the dump site revealed that Holoptelia has a special ability to accumulate high amounts of manganese under stress condition followed by Cassia and Neem. There is no literature on metal accumulation in Holoptelia. Mechanism of manganese sequestration in Holoptelia is different from the other two trees growing in the same soil.
The Future of Publishing Herpetological Research: Peer Review, “Pre-Publications”, and Openness and Transparency of Data

Abstract The availability of new technologies, combined with changing perceptions of traditional journal publications, has created a wave of “new models” for reviewing and publishing scientific research. As the Journal of Herpetology (JH) celebrates its 50th anniversary, this is an appropriate time for the membership of SSAR to consider what kinds of changes in JH are needed to meet the needs of those who publish research in herpetology. In this review, I focus on three issues with traditional models of journal publications: criticisms of the peer-review process (especially bias and elitism); issues with rapid communication of research findings; and increasing calls for better transparency and openness of data. For issues such as gender or age bias, I provide support for calls for changes such as double-blind reviews to reduce the prevalence of such bias and also review new methods for making peer reviews more open and efficient. Conversely, I find serious problems with mechanisms such as citable “pre prints” that have been suggested as a means to increase the speed at which research findings are made available and review alternate models that can accomplish the same goal without sacrificing the integrity of journal publications. Ultimately, how JH and other herpetological journals respond to these challenges will be an ongoing process in which the membership needs to be strongly engaged.
Immunohistochemical detection of Brucella mellitensis and Coxiella burnetii antigens in formalin-fixed tissues of West African Dwarf goats

Title: Immunohistochemical detection of Brucella mellitensis and Coxiella burnetii antigens in formalin-fixed tissues of West African Dwarf goats Background: The information on the evidence of Brucella mellitensi and Coxiella burnetti infections or co-infection in goats had been scanty, This investigation reports the immuno-histochemical evidence of Brucella mellitensi and Coxiella burnetti infections in West African dwarf goats. Methods and Findings: Goats presented for post mortem in the Department of Veterinary Pathology, University of Ibadan were used for this investigation. By simple randomisation, lung, kidney, liver and spleen of fifteen goats were used for this immunohistochemical evaluation using stardard technique. 60% of the goats examined were positive for Brucella mellitensis, 33% were positive for Coxiella burnetti while 7% were positive for both infection. The spleen liver, kidney and lungs were positive for Brucella mellitensis while only the spleen and lungs were positive for Coxiella burnetti. Coxiella burnetti antigens were located in the cytoplasm of macrophages of alveoli of the lung and in the red splenic pulp while Brucella melitensis antigens were located in the cytoplasm of macrophages in the lung, in the red splenic pulp, Kupffer cells of the liver, macrophages in the glomeruli and epithelial cells of cortical tubules. Conclusions: This appears to be the first report of immunohistochemical detection of Brucella and Coxiella antigens in tissues of West African dwarf goats. The presence of these antigens in apparently healthy and pneumonic goats showed the level of risk posed by goatsâ€™ meat and meat products in the spread of these zoonotic diseases hence the need for facilities for rapid detection of these diseases.
Merits of a weed-sensing sprayer to control weeds in conservation fallow and cropping systems

Field studies were conducted from 1993 through 1995 to determine potential reductions in herbicide use and associated cost savings by utilizing a weed-sensing sprayer, named Detectspray, to control weeds throughout the fallow season and to control perennial weeds after crop harvest. The Detectspray system gave comparable weed control to conventional broadcast spraying on 80% of the application dates and reduced glyphosate/dicamba use over the fallow season by 19 to 60%. This reduced herbicide use resulted in cost savings of $6 to $32 ha−1. A fallow treatment that combined two herbicide applications with the Detectsprayer plus one to two wide-blade tillage operations was less costly than conventional tillage at two of 11 sites and at all sites retained more surface crop residues to reduce the risk of erosion. Postharvest glyphosate use on quackgrass with the Detectsprayer was reduced 50 to 78% compared to broadcast applications and resulted in cost savings of $16 to $25 ha−1. Clopyralid use on Canada thistle with the Detectsprayer was reduced 71 to 80%, with cost savings of $44 to $50 ha−1. The Detectspray system is a useful tool to effectively manage weeds in conservation fallow and reduced tillage cropping systems.
Long-term changes in the herb layer of a southern Swedish broadleaf forest

The forest herb layer is reacting fast to the changes in the environment due to its sensitivity and short life cycle. The forest overstory has a strong influence over the availability of the environmental factors and also represents a powerful competitor for the available resources. The species of the herbaceous ground flora have different requirements and sensitivities in regard to the environment, therefore each of them has to be treated separately in order to detect the factors that influence and direct the changes in their abundance. Measurements from 30 permanent sample plots extending during the period 1988-2015 in a hornbeam forest in Stenshuvud National park, southern Sweden, were used to quantify the inter-annual variation and long-term trends of the herb layer and its interactions with the environmental factors. Mean Ellenberg indicator values were used to assess the responses of the herb layer community to the variations in environmental factors.Results of paired t-tests show that the species richness is decreasing, while the evenness remained quite stable, probably partly due to the closing up of the canopy which is also reflected by the Ellenberg mean indicator values for light. Ellenberg mean indicator values also indicate that the temperatures have been increasing, while the climate became more oceanic. However, mean indicator values also suggest a decreasing soil moisture, soil reaction and available nitrogen. Overall, the total cover has increased, while some species like Hedera helix and Hepatica nobilis have manifested declining covers through time. Fifteen of the ground flora species present in 1988 were absent in 2015, while only two species colonised the area. Roe deer has probably played an important role in shaping the abundance of several species, due to its rapid increase in population density until early 1990s. The regression analyses revealed that precipitation amounts during spring have quite strong relationships with both total cover and covers of some species.
Habitat structure influences the song characteristics within a population of Great Tits Parus major

ABSTRACT Capsule: The structure of Great Tit Parus major songs is shaped by the acoustic properties of the habitat within the breeding territory of individuals. Aim: To test whether the structure of the habitat influences song structure within a population of Great Tits P. major. Methods: We recorded Great Tit songs from 42 territories on two different days and measured the habitat structure in each territory. We also trapped the males and estimated the breeding density around each territory, so were able to control the analysis by date, breeding density and male characteristics. Results: Song pause length was positively affected by the ground cover, while the song rate and the minimum frequency were negatively affected by the shrub cover. Male size negatively affected the peak frequency of the songs, whereas the age of the males affected the frequency range; older males sang with a broader bandwidth. Conclusion: This study suggests that Great Tits are capable of adjusting their vocalizations in each territory, presumably to enhance transmission owing to vocal plasticity.
An exploration of NK landscapes with neutrality

Recent research into the evolution of RNA molecules has raised awareness of the neutral theory of evolution. Several fitness landscape models based upon the NK model have been proposed to investigate the behaviour of populations evolving on neutral landscapes. In this study, Kauffman's results pertaining to the NK fitness landscape model are replicated and a new visualisation technique is developed to illustrate the presence of ruggedness and neutrality across a landscape. These results are extended to the neutral NKp and NKq variants of the NK model. It is shown that these two models of neutrality result in landscapes with significant structural differences. An important goal in evolutionary computation is a greater understanding of the relationship between landscape structure and the optimal choice of evolutionary algorithms. A series of simulations is run comparing the performance of a variety of individual and population-based algorithms on a range of neutral and non-neutral landscapes. It is found that hill-climbing algorithms are generally capable of finding better individual solutions, but population-based algorithms tend to find higher average solutions. Finally, it is shown that crossover allows a population on a neutral landscape to maintain a much higher level of genetic diversity on a neutral layer than a population using mutation alone. Furthermore, populations using crossover suffer a less dramatic loss of diversity when a new fitness level is discovered, and recover diversity more rapidly.
Trophic response of estuarine fishes to long-term changes of river runoff

A long-term (13 year) study was carried out to analyze the response of estuarine fishes (numbers, biomass and trophic organization) to seasonal and interannual variations of Apalachicola River flow and associated habitat changes of the receiving estuary (East Bay, Apalachicola Bay system, Florida). Periodic peak floods and prolonged droughts were important events that led to altered patterns of individual fish distribution in terms of numerical abundance and biomass. There was considerable interannual variation in the temporal distribution of the dominant fish species over the study period. Individual estuarine fish species use the estuary as a nursery ground with species-specific ontogenetic feeding patterns that are defined by the complex productivity patterns of the system. In East Bay, there was a dichotomous response of the estuarine trophic organization with herbivores and omnivores (dominated by infaunal and epifaunal macroinvertebrates) directly responsive to river-associated physicochemical factors whereas the carnivores (dominated by the fishes) responded to biological factors such as predation and competition. Estuarine fish organization was indirectly responsive to changes of river flow through prey responses to state habitat and productivity variables associated with river flows. This suggests that the fish associations were strongly dependent on interannual patterns of Apalachicola River flow but that such relationships were primarily caused by biological interactions as defined by specific predator/prey relationships. A prolonged drought led to reduced fish species richness and trophic diversity; such habitat stress was related to enhanced instability of the biological components of the estuary as a function of changes in nutrient cycling. The food web was simplified while overall fish biomass and individual species populations were numerically reduced. The trophic response times of fish assemblages were measured in years from the point of the initiation of the drought. Changes in flow rates that exceeded specific natural levels of variance could be followed by identification of the subtle yet important changes in estuarine productivity and related changes of fish representation within the food web. The use of individual fish species as indicators of such responses is not consistent with the processes that define the long-term behavior of estuarine populations.
INFLUENCE OF GIBBERELLIC ACID AND PLANT GEOMETRY ON GROWTH, FLOWERING AND CORM PRODUCTION IN GLADIOLUS (GLADIOLUS GRANDIFLORUS) UNDER JAMMU AGROCLIMATE

The present investigation was conducted to study the effect of gibberellic acid and plant geometry on growth, flowering and corm production in gladiolus cv. ‘Novalux’ under Jammu conditions. Four concentrations of GA3 (0, 100, 200 and 300 ppm) and three levels of spacing (20x40cm, 30x40cm and 40x40 cm) were tested in Factorial RBD with three replications. The analyzed data indicated that maximum plant height, number of leaves, leaf width, spike length, rachis length, corm diameter, corm weight and early flowering was recorded at 300 ppm GA3. Corms planted at a spacing of 40x40cm exhibited highest plant height, rachis length, number of florets per spike, floret diameter, number of corms per plant, corm diameter, corm and cormel weight. Among interactions, treatment of corms with 300ppm GA3 and spacing at 40x40 cm was found more effective in the enhancement of vegetative and floral attributes.
Can regular replace irregular migration across the Mediterranean? Project Report. CEPS MEDAM Mercator Dialogue on Asylum and Migration, June 2019

Irregular migration from Africa across the Mediterranean to the EU has become a central policy issue. While the establishment of a Libyan SAR zone and of a Libyan coast guard has lowered the numbers crossing the Mediterranean since mid-2017, there are strong concerns about the sustainability of the current approach and its reliability given the severe political instability in Libya. Due to this state of affairs, increasing legal access to the EU – for study and work purposes – has re-appeared on the European agenda as one potential way to reduce irregular crossing in the future. This comes at a time where legal access to the EU labour markets for African citizens has been steadily reduced. Moreover, actions aimed at streamlining access to existing pathways for legal migration, or opening new ones, can be used as lever in improving cooperation in migration management with countries of origin when it comes to returns and readmissions. We review the evidence bearing on to what extent increasing legal access via labour migration is effective in reducing irregular migration. While our focus is on irregular crossings of the Mediterranean, we draw on evidence from different world regions. We conclude that increasing legal pathways for migration from Africa to Europe, in itself, will have only a limited effect on the number of people trying to cross irregularly. Substitution can take place only if expansion of legal pathways – tailored to labour market needs and migrant profiles – is envisaged in a comprehensive policy mix including strong enforcement of migration legislation (i.e. control of employers at destination together with border control) and streamlining of recruitment procedures.
Biology of the ectomycorrhizal genus, Rhizopogon: III. Influence of co-cultured conifer species on mycorrhizal specificity with the arbutoid hosts Arctostaphylos uva-ursi and Arbutus menziesii.

Seedlings of Pseudotsuga menziesii (Mirb.) Franco, Pinus ponderosa Dougl. ex Laws, Arbutus menziesii Pursh. , and cuttings of Arclast apliylos uva-ursi (L.) Spreng were grown in monoculture and in conifer-hardwood dual-culture combinations in the glasshouse and inoculated with spore slurries of six Rhizopogon species. The primary objectives were to assess and compare the pattern of host specificity between symbionts and to study the influence of co-cultured plants on ecromycorrhiza development. The Rhizopogon spp. ranged from genus-specific to multiple-host compatible. In monoculture, four Rhisopogon sp, (R. ellenae Smith, R. occidentalis Zeller & Dodge, R. smithii Hosfnrd and R. subcaerulescens Smith) formed ectomycorrhizas with Pinus ponderosa, and two Rhizopogon sp. (R. parksii Smith and R. vinicolor Smith) formed ectomycorrhizas with Pseudotsuga menziesii. None of the fungi tested developed ectomycorrhizas on Arbutus menziesii or Arctostaphylos uvaursi in monoculture. In dual culture, three of the four Rhizopogon species (R. ellenae, R. occidentalis and R. subcaerulescens) that formed ectomycorrhizas on Pinus ponderosa, formed some ectomycorrhizas on Arbutus menziesii and Arrtastaphvlos uva-ursi. Rhizopogon parksii and R. tinicoior only formed ectomycorrhizas on Pseudotsuga mensiesti.
Cultural uses of plants among Basikhel tribe of District Tor Ghar, Khyber Pakhtunkhwa, Pakistan.

Relation between plants and cultures is indispensable. The link between culture and plant resources was explored first time for the Basikhel tribe of Tor Ghar District. This tribe is one of the largest tribe of District Tor Ghar. It has long established tribal culture. The study was conducted during the years 2012 and 2013. The information was gathered from 200 informants from 15 randomly selected villages. Data was obtained through semi structured interviews, group discussions and EPA. The local people use 250 species of the vascular plants belonging to 90 families for 23 different cultural uses such as food, fodder, timber, fuel wood, medicine, furniture and agricultural implements. The inhabitants of the area are highly dependent on local flora for their different cultural needs. Total of 150 species belonging to 50 families were documented for the medicinal uses. Informant consensus showed that wound healing and gastrointestinal treatment were ranked highest among all medicinal uses. For each plant its botanical name, family name, local names and conservation status was also recorded. Three species were found most threatened. This study is a part of an ongoing research project in which we will explore plant resources utilized by five different tribes of the District Tor Ghar in the near future.
Polyploidy: a missing link in the conversation about seed transfer of a commonly seeded native grass in western North America

The use of local, native plant materials is now common in restoration but testing for polyploidy in seed sources is not. Diversity in cytotypes across a landscape can pose special seed transfer challenges, because the methods used to determine genetically appropriate materials for seed transfer do not account for cytotypic variation. This lack of consideration may result in mixing cytotypes through revegetation, which could reduce long‐term population viability. We surveyed nine populations of a native bunchgrass, Pseudoroegneria spicata, in three EPA Level III Ecoregions in the western United States to determine the frequency of polyploidy, whether there are differences in traits (phenotype, fecundity, and mortality) among plants of different cytotypes, and whether cytotype frequency varies among ecoregions. We assessed trait variation over 2 years in a common garden and determined ploidy using flow cytometry. Polyploidy and mixed cytotype populations were common, and polyploids occurred in all ecoregions. Four of the nine populations were diploid. The other five had tetraploids present: three had only tetraploid individuals whereas two had mixed diploid/tetraploid cytotypes. There was significant variation in traits among cytotypes: plants from tetraploid populations were larger than diploid or mixed populations. The frequency and distribution of cytotypes make it likely that seed transfer in the study area will inadvertently mix diploid and polyploid cytotypes in this species. The increasing availability of flow cytometry may allow ploidy to be incorporated into native plant materials sourcing and seed transfer.