Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of simulation modeling to evaluate management strategies for reintroduced riparian brush rabbits in California

© 2016, U.S. Fish and Wildlife Service. All rights reserved. The riparian brush rabbit Sylvilagus bachmani riparius is restricted to areas of dense cover along rivers and tributaries in the Central Valley of California, USA, and is considered endangered under the U.S. Endangered Species Act. An approved recovery plan for this subspecies recommended establishment of three additional self-sustaining populations within its historical range. Concurrent with habitat restoration efforts that included revegetation of levees and provision of flood refugia, we reintroduced 325 captive-bred individuals to the San Joaquin River National Wildlife Refuge between July 2002 and July 2005, and monitored their survival with radiotelemetry. Using available survival estimates and estimated reproductive parameters, we developed a population viability analysis model to determine the risk of extinction of the reintroduced population under a series of alternate scenarios including different release strategies. All model scenarios resulted in high probabilities of extinction over 20 y in the absence of either ongoing supplementations or significant improvements to vital rates. Extinction risks over 20 y appeared independent of initial release strategies. The risk of extinction remained high (>99%) even when the initial founder population was supplemented with captive-bred brush rabbits for up to 10 y. Supplementing the population annually for the entire 20-y period would be required for the population to persist given current estimates of vital rates. These results suggest that the reintroduced population is not self-sustaining and continued releases will not provide the anticipated longterm benefits. Additionally, our understanding of the integral components of habitat and potential limiting factors should be refined to address their influence on demographics and the cause of brush rabbit declines at the release site in a comprehensive way. These results underscore the importance of viability analyses and developing testable hypotheses about potential limiting factors early in reintroduction efforts to more efficiently guide data-gathering and monitoring criteria, identify data deficiencies, and refine reintroduction techniques in the early stages of management.
Growth and Yield of Sweet Corn with Legume Living Mulches(Agronomy)

To evaluate the effect of living mulch, we examined the weed biomass and the growth and yield of sweet corn (Zea mays L.) cultivated with three legume living mulches without the application of herbicide and without tillage. The living mulch plants alfalfa (Medicago sativa L.), red clover (Trifolium pratense L.) and white clover (Trifolium repens L.) were seeded in autumn. During the corn growth period in the following year, weed growth was effectively suppressed by all three living mulch plants. Both growth rate and yield of sweet corn with white clover living mulch were comparable to the conventional cultivation, but alfalfa and red clover living mulches caused the yield reduction in sweet corn. The percentage of stand was thought to have been reduced due to the competition for light and nutrients. The nitrogen absorption rate of sweet corn increased with its growth. On the other hand, the nitrogen absorption rate of living mulch plants decreased with the growth of sweet corn. These results suggest that competition between sweet corn and living mulch plants for nitrogen would be small. We concluded that white clover is the best of the three legume living mulch plants for weed control without significantly affecting sweet corn production.
Carbon Stock of Prevailing Land Use Systems under East Siang District, Arunachal Pradesh, India

Carbon sequestration through sink enhancement by way of integration of trees into landscapes is one of the cost-effective mitigation strategies in the terrestrial ecosystem may be categorized into vegetative carbon and soil carbon components. The capacity of terrestrial ecosystems to sequester carbon varies based on its land use patterns. Land use, land use change and forestry (LULUCF), an approach that became popular in the context of the Kyoto protocol, allows afforestation and reforestation as greenhouse gas offset activities (Nair et al., 2011).
Staining of elastic and muscle fibers to morphometric studies in Chelonia mydas

Introduction: The present study aimed to establish the staining protocol for quantification of elastic fibers and muscle fibers in arterial vessels through the Verhoeff method adapted with eosin in Chelonia mydas. Materials and Methods: Aorta and pulmonary arteries of 11 individuals of the species Chelonia mydas were used. The fragments were fixed in formaldehyde solution buffered 10% for 24 hours, subjected to routine histological processing and staining technique to be adapted Verhoeff, take the photografies and analyzed by Image Pro Plus Software. Results: The combination of ferric hematoxylin Verhoeff use blushed black elastic arteries blades, already eosin stained muscle fibers and collagen, allowing the tissue quantification through distinction staining by software. Conclusion: The protocol is a low-cost alternative that facilitate the acquisition of morphometric data for research with turtles.
Agrobacterium tumefaciens-mediated transformation of brahmi [Bacopa monniera (L.) wettst.], a popular medicinal herb of India

Agrobacterium-mediated genetic transformation of Brahmi [Bacopa monniera (L.) Wettst. ] was standardized using the Agrobacterium tumefaciens strain EHA105 that harboured the binary vector pBE2113 containing genes for β-glucuronidase (GUS) and neomycin phosphotransferase. Putative transformants were selected by the ability of the leaf explants to produce kanamycin-resistant calluses that regenerated into kanamycin-resistant plantlets. Successful transformation was confirmed by histochemical assay for GUS activity, PCR analysis and RT-PCR. The frequency of transformation from the leaf explants was more than 60% and a period of nearly two months was required for the regeneration of transgenic plantlets from the explants. The morphology of the transformed plants resembled that of the parent. The development of an efficient transformation protocol for Brahmi can lead to the genetic improvement of the plant for secondary metabolite content in future.
‘Freshmarket 9’ Tomato

‘Freshmarket 9’ tomato (Lycopersicon esculentum Mill.) sets over a wide range of temperatures (16° to 36°C) and humidities (above 80%), a characteristic that extends its production periods in spring and fall. ‘Freshmarket 9’ is a firm, deep-round tomato with superior crack resistance and is suited to vine ripe harvest. It is resistant to race 1 of Fusarium oxysporum Schl. f. sp. lycopersici (Sacc.) Synder and Hansen (fusarium wilt) and Stemphylium solani Weber (gray leaf spot). ‘Freshmarket 9’ was released in 1982 by the Texas Agricultural Experiment Station.
Antibacterial Activity Of Allium cepa (Onions) And Zingiber officinale (Ginger) On Staphylococcus aureus And Pseudomonas aeruginosa Isolated From High Vaginal Swab

The antibacterial activity of raw and aqueous extracts of Allium cepa (onions) and Zingiber officinale (ginger) against Staphylococcus aureus and Pseudomonas aeruginosa, (from high vaginal swab) that are common cause of nosocomial (hospital-acquired) and urinary tract infections was investigated using the cup-plate diffusion method. The result showed that ethanolic extract of ginger gave the widest zone of inhibition against the two test organisms at the concentration of 0.8gml-1. However, Pseudomonas aeruginosa was more sensitive to the extract of onion bulbs compared to Staphylococcus aureus. It was also observed that the solvent of extraction and its varying concentrations affected the sensitivity of the two organisms to the plant materials. The minimum inhibitory concentration (MIC) of ginger extracts on the test organisms ranged from 0.1gml-1 0.2gml-1, showing that ginger was more effective and produced marked inhibitory effect on the two test organisms compared to the onion extracts. This investigation indicates that, though both plants had antibacterial activity on the two test organisms, ginger had more inhibitory effect thus confirming their use in folk medicine.
The concept of the integrated innovation process

Building on the idea of innovation platforms, the traditional innovation process can be seen from a different perspective as consisting of a product innovation process and a technology innovation process. This paper describes how firms can explore these innovation platforms to deploy their competencies to different markets. An example drawn from the field of bionics illustrates the application of the model.
Phylogeography and population structure in highly mobile marine taxa in the western Indian Ocean : bottlenose dolphins (Tursiops spp.) and common dolphins (Delphinus sp.)

In the marine environment, where barriers to dispersal are limited, taxa normally exhibit genetic homogeneity across large spatial scales. Extraordinarily, marine mammals regularly exhibit genetic differentiation within their cruising range. Furthermore, recent radiation in Delphininae has resulted in several closely related species that remain taxonomically unresolved, particularly bottlenose dolphins (BND) Tursiops spp. and common dolphins (CD) Delphinus spp. , making these taxa interesting for studying evolutionary processes. Using mitogenomes and a multi-locus dataset, BNDs from the northwest Indian Ocean (IO) were compared with other recognized species/ecotypes around the world. A new (third) lineage of Indo-Pacific BND, T. aduncus, was identified from the region. Reconstructions of ancestral biogeography and divergence date estimates, suggest a divergence mechanism within T. aduncus that coincides with climate change over the Pleistocene. Reconstructions of ancestral morphology suggest a coastal ancestry for BNDs. Significant population structure was exhibited between T. aduncus populations in the western IO based on mtDNA control region sequences and 14 microsatellite loci. Genetic subdivision appears to correlate with habitat heterogeneity across the study area, which may be driving differentiation through local adaption. Traditional and geometric morphometric techniques were used to investigate congruency between genetic and phenotypic differentiation of three BND lineages in the northwest IO. Strong differences were exhibited in morphology between common BNDs, T. truncatus, and T. aduncus. The T. aduncus lineages were similar, however significant differences in morphology were evident. Significant genetic structure was evident between CD populations off Portugal, South Africa and Oman, based on mtDNA sequences and 14 microsatellites. Further analyses support the taxonomic designation of D. capensis tropicalis in the northwest IO. Both genera exhibit significant population structure over spatial scales outdistanced by their dispersal abilities. Contemporary and historic environmental heterogeneity are suggested as drivers for this structure. Further evidence is provided for the northwest/northern IO as a region of evolutionary endemism, which will inform regional conservation initiatives.
Sexual reproduction in Favella ehrenbergii (Ciliophora, Tintinnina) taxonomical implications

Des conjugaisons se sont produites dans les cultures en masse de F.e. , destinees a l'etude de la construction de la lorica. Il existerait de nombreux phenotypes de lorica chez F.e. et il a necessite de reviser la classification des tintinnides basee seulement sur cet element beaucoup trop variable. Ici la reproduction sexuee permet une definition satisfaisante de l'espece F.e. selon le concept biologique de l'espece de Mayr
Storage cells – oil and protein bodies

Molecular Cell Biology of the Growth and Differentiation of Plant Cells encompasses cell division, cell enlargement and differentiation; which is the cellular basis of plant growth and development. Understanding these developmental processes is fundamental for improving plant growth and the production of special plant products, as well as contributing to biological understanding. The dynamics of cells and cellular organelles are considered in the context of growth and differentiation, made possible particularly by advances in molecular genetics and the visualization of organelles using molecular probes. There is now a much clearer understanding of these basic plant processes of cell division, cell enlargement and differentiation. Each chapter provides a current and conceptual view in the context of the cell cycle (6 chapters), cell enlargement (5 chapters) or cell differentiation (9 chapters). The book provides state of the art knowledge (and open questions) set out in a framework that provides a long term reference point. The book is targeted at plant cell biologists, molecular biologists, plant physiologists and biochemists, developmental biologists and those interested in plant growth and development. The book is suitable for those already in the field, plant scientists entering the field and graduate students.
Sharing the top : how do spotted hyaenas cope with lions ? : apex predator coexistence in a wooded savana

Being at the top of the food chain, apex predators have the potential to influence the whole community structure through food webs, even within their own guild. In Africa, lions (Panthera leo) and spotted hyaenas (Crocuta crocuta, hyaenas hereafter) are the largest and most numerous predators, with hyaenas often thought to be subordinate to the larger lion Never the less, our understanding of their interactions is limited, even more in wooded ecosystems. This work focuses on identifying the mechanisms allowing for hyaenas and lions to coexist, such as resource and habitat partitioning. The main hypothesis is that hyaenas should avoid lions both spatially and temporally. A literature review shows that despite the high potential for exploitative and interference competition (high range and diet overlaps), hyaenas are present at nearly all sites occupied by lions and their densities are positively correlated. I collected data on hyaena and lion ecology, through direct observations and GPS collars, during 2.5 years of fieldwork in Hwange National Park (HNP), Zimbabwe. HNP is characteristic of a semi-arid dystrophic wooded savanna dominated by elephants (Loxodonta africana). In HNP, hyaena ecology is largely influenced by the location of artificial waterholes, elephant carcasses and lions. Hyaenas select for habitats where prey are abundant and locations close to artificial waterholes, as do lions. Hyaenas only spatially avoid lions in extreme conditions of vulnerability and risk. Elephant carcasses are a major source of food for hyaenas and their used increased during a period of increased intraguild competition with lions, which lead to switch in hyaena foraging strategy from active hunting to scavenging. The presence of large carcasses is probably promoting coexistence between the two large carnivores. Encounters with lions at carcasses are common and can occur during several consecutives nights with the two predators staying in the vicinity of each other. However, when not related to food, encounters are very short with both predators often moving away after being in contact. In stark contrast with the classical hypothesis, hyaenas in HNP do not show a general pattern of lion avoidance. Interactions between these two species are complex and hyaenas appear to respond to lion presence is reactive rather than predictive and very dynamic. Even though lions are their main competitors, in some circumstances hyaenas stay in their vicinity, as they can also be a source of food through scavenging and kleptoparatism. These results bring some light on the mechanisms of interaction and coexistence between large carnivores as well as the impact on management decisions on their ecology that could prove useful for planning their conservation
Residency and Movement of Juvenile Chinook Salmon at Multiple Spatial Scales in a Tidal Marsh of the Columbia River Estuary

AbstractUse of the Columbia River estuary by juvenile Pacific salmon Oncorhynchus spp. is garnering more attention as managers look to improve salmon survival through estuary restoration. Studies have shown that juvenile salmon are abundant in shallow-water habitats within the Columbia River estuary, but information on how juveniles exploit specific estuarine habitats is lacking. We used a combination of physical marks and PIT tag technology to record residence time, movement, and growth of juvenile Chinook Salmon O. tshawytscha, particularly subyearlings, within an emergent marsh of the Columbia River estuary during 2005, 2006, and 2008. We documented marsh-scale residency and movement within the marsh complex and channel-scale residency and movement within two small secondary channels. Many juvenile Chinook Salmon remained in the marsh for 2–4 weeks and increased in FL by 10–20 mm, with an average growth rate of 0.53 mm/d. Chinook Salmon entered secondary channels most frequently in late afternoon and o.
A Differential-selective Medium and Dry Ice-generated Atmosphere for Recovery of Campylobacter jejuni.

A selective-differential medium for isolation of Campylobacter jejuni from chicken carcasses was developed. The medium, Campy-Cefex, consisted of Brucella agar, 5% lysed horse blood, 0.05% ferrous sulfate (FeSO4.7H2O), 0.05% sodium pyruvate, 0.02% sodium bisulfite, and antibiotic supplements of 33 mg/L sodium cefoperazone and 200 mg/L cycloheximide. A total of 41 chicken carcass samples were plated onto Campy-Cefex, Campylobacter cefoperazone desoxycholate agar, and Campylobacter brucella agar plate media. Campy-Cefex proved as productive and selective as the other media. Campy-Cefex allowed for easier differentiation of C. jejuni from other flora compared to differentiation on Campylobacter cefoperazone desoxycholate agar medium. Differentiation of the non- Campylobacter spp. flora from Campylobacter spp. was the same on both Campy-Cefex and Campy-BAP. The selectivity for the organism on Campy-Cefex was better than on Campy-BAP. Growth of seven isolates of C. jejuni in microaerobic-(5% O2, 10% CO2, 85% N2) and dry ice-generated atmospheres was also assessed. After 24 h of incubation, the mean log10 CFU generated, using the same culture suspensions and medium, was 2.07 and 1.81 for the microaerobic and dry ice atmospheres, respectively. These two developments allow for simplification of materials and methods required to isolate C. jejuni from foods.
DNA methylation in lung fibroblasts and its role in pulmonary fibrosis

Altered methylation and subsequent changes in gene expression have been implicated in several fibroses including lung however, the full extent and role of altered DNA methylation in fibrotic lung fibroblasts is unknown. Emerging evidence also suggests gender-specific methylation differences are common in disease and could elucidate why diseases characterised by pulmonary fibrosis including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc) have a sex-biased prevalence. Using a genome-wide array-based approach, this thesis investigates differentially methylated and expressed genes in fibrotic compared to control lung fibroblasts, gender-specific methylation and expression differences and the effects of modulating DNA methylation using a DNA methyltransferase (DNMT) inhibitor, 5-Aza-2’deoxycytidine (5-Aza). Data show primary human IPF and SSc lung fibroblasts have multiple genes with altered DNA methylation and expression compared to control lung fibroblasts. Multiple biological processes were enriched in these genes, many of which are relevant to fibrosis including, transcriptional regulation, extracellular matrix (ECM) organisation, Wnt signalling and apoptosis. Using siRNA knockdown and collagen gel contraction assays, novel genes including Tenascin-XB (TNXB), which encodes the ECM glycoprotein Tenasicn-X (TNX), were identified as having potential functional significance in the pathogenesis of pulmonary fibrosis. Furthermore, multiple genes including TNXB had altered methylation and expression in IPF compared to SSc lung fibroblasts and may distinguish IPF from other diseases associated with pulmonary fibrosis. Multiple genes were identified with gender-specific differences in methylation and expression in lung fibroblasts. Interestingly, multiple genes with altered methylation in IPF males compared to control males were not the same genes with altered methylation in IPF females compared to control females, which may in part explain why IPF predominates in males. The final chapter of my thesis shows 5-Aza treatment alters the methylation and expression of multiple genes in primary human lung fibroblasts. Strong correlation between changes in methylation and changes in expression were identified suggesting DNA methylation can directly regulate the expression of multiple genes in lung fibroblasts.
A test of BIOME-BGC with dendrochronology for forests along the altitudinal gradient of Mt. Changbai in northeast China

Aims Process-based models are basic tools for predicting the response of forest carbon to future climate change. The models have commonly been tested for their predictions of spatial variation in forest productivity, but much less for their ability to predict temporal variation. Here, we explored methods to test the models with tree rings, using BIOME-BGC as an example. Methods We used net primary productivity (NPP) data and tree rings collected from five major forest types along the altitudinal gradient of Mt. Changbai, northeast China, to test local-parameterized BIOMEBGC model. We first test the model’s predictions of both spatial (Test 1) and temporal changes (Test 2) in productivity. Then we test if the model can detect the climatic factors limiting forest productivity during historical climate change, as revealed by dendroclimatic analyses (Test 3). Important Findings Our results showed that BIOME-BGC could well simulate NPP of five forest types on Mt. Changbai, with an r2 of 0.69 between modeled and observed NPP for 17 plots along the altitudinal gradient (Test 1). Meanwhile, modeled NPP and ring-width indices were correlated and showed similar temporal trends for each forest type (Test 2). While these tests suggest that the model’s predictions on spatial and temporal variation of NPP were acceptable, a further test that relate the correlations of modeled NPP with climate variables to the correlations of ring widths with climate (Test 3) showed that the model did not well identify the climatic factors limiting historical productivity dynamics for some forest types, and thus cannot reliably predict their future. Both dendrochronology and BIOME-BGC showed that forest types differed markedly in the climate factors limiting productivity because of differences in tree species and climate condition, and thus differed in responses to climate change. Our results showed that a successful prediction of spatial NPP patterns cannot assure that BIOME-BGC can well simulate historical NPP dynamics. Further, a correlation between modeled NPP and tree-ring series cannot assure that the limiting climatic factors for productivity have been correctly identified by the model. Our results suggest the necessity to test the temporal predictions of process-based models in a more robust way, and further integration of dendrochronology and biogeochemistry modeling may be helpful for this purpose.
Noccaea nepalensis, a new species from Nepal, and four new combinations in Noccaea (Brassicaceae)

L'espece nouvelle Noccaea nepalensis est decrite et illustree. Ses affinites avec deux autres especes d'Himalaya, N. andersonii et N. yunnanensis, sont discutees. Une evaluation critique des limites de Thlaspi et Noccaea autorise la reconnaissance de ces deux genres. Les combinaisons nouvelles N. andersonii, N. cochlearioides, N. flagellifera, et N. yunnanensis sont proposees.