Miracle-dz/UniFAR-FTUs huggingface dataset:
Bifurcation analysis and dynamic behavior to a predator-prey model with Beddington-DeAngelis functional response and protection zone

In this paper we study the protection zone problem to a predator-prey model subject to Beddington-DeAngelis functional responses and small prey growth rate. This is a successive work to a previous paper of the authors [X. He, S. N. Zheng, Protection zone in a diffusive predator-prey model with Beddington-DeAngelis functional response, J. Math. Biol. 75 (2017) 239-257], where the model with large prey growth rate was considered. At first we establish the existence and multiplicity of positive steady state solutions, and then give the dynamic behavior of the evolution problem. It is proved that there may be no positive steady state, or may have at leat one, two, or even three positive steady states, depending on the parameters involved such as the growth rate, the predation rate, and the food handling time of the predators, the growth rate and the refuge ability of the preys, and the sizes of the habitat with protection zone. In addition, it is shown that the dynamics of the solutions rely on the initial state as well, e.g., though there could be multiple positive steady states, the prey will go to extinction as time tends to infinity if its initial value is small.
Environmental controls on the distribution of archaeal lipids in Tibetan hot springs: insight into the application of organic proxies for biogeochemical processes

Summary Glycerol dialkyl glycerol tetraether (GDGT) membrane lipids of Archaea respond to gradients in temperature and pH; however, it is unclear how these lipids respond to gradients of other environmental variables. Here, we analysed water chemistry, archaeal lipids and amoA- and nirS genes from 37 Tibetan hot springs. Strong correlations between intact polar lipids and their degradation product core lipids indicate that these two pools of lipids are closely related and may be formed in situ in the hot springs. Cluster analysis resulted in three major groups, within each of which the individual samples showed better correlations between ring index or TEX86 (TetraEther Index of tetraethers with 86 carbons) and temperature, pH or geochemical variables (e.g. nitrite, phosphate) in the polar fraction than in the corresponding core fraction. Most of these relationships did not exist when all of the samples were considered as a whole. Abundances of amoA- and nirS genes were strongly correlated with some of the intact polar- or core lipids. Our results suggest link between specific microbial functions (e.g. ammonia oxidation or nitrite reduction) and the production of individual GDGT lipids and highlights the potential utility of GDGT lipids as proxies for biogeochemical processes.
Life history data of lizards of the world

Life is defined by a capacity for reproduction, yet the ways in which animals reproduce vary tremendously among species. Reproductive life histories are complex phenomena influenced by a variety of factors, such as physical condition of individuals, food supply, bauplan, and phylogenetic history, which are often correlated. Understanding life histories is crucial in evolutionary ecology because they represent different strategies that evolved to maximize individual fitness. Variation in life history can be attributed to both historical (=phylogenetic) and non-historical (=environmental) causes. We compiled a large data set on lizard life history variables. Our data set consists of life history data for 737 lizard populations, representing 337 species in 33 families from 280 study sites globally. About 64% of these data were collected directly by the authors. Regarding data collected by authors, we sexed lizards by dissection and direct examination of gonads. Females were considered reproductive if vitellogenic follicles or oviductal eggs were present. We regarded the simultaneous presence of enlarged vitellogenic follicles and either oviductal eggs or corpora lutea as evidence for the sequential production of more than one clutch of eggs per year. We considered clutch size as the number of vitellogenic follicles or oviductal eggs in mature females. For each population, we recorded the following variables, if available: adult female mass (g), adult female SVL (mm), female SVL at maturity (based on SVL of smallest reproductive female), offspring SVL (based on hatchling size or smallest individual in population), clutch or litter size (number of offspring per clutch or litter for all reproductive females in the population), total number of clutches or litters per year, clutch frequency (single- or multiple-brooded), relative clutch or litter mass [total volume of eggs or embryos (cc) divided by adult female mass (g)], reproductive mode (oviparous or viviparous), foraging mode (sit-and-wait or active), distribution (tropical or temperate), and preferred habitat type (aquatic, arboreal, bromelicolous, fossorial, psammophilous, saxicolous, semi-arboreal, or terrestrial). These data are valuable to test various life history hypotheses, including phylogenetic design constraints and effects of ecology and climate on reproductive tactics.
Alternatives to the Isomerase-dependent Pathway for the β-Oxidation of Oleic Acid Are Dispensable inSaccharomyces cerevisiae

Fatty acids with double bonds at odd-numbered positions such as oleic acid can enter β-oxidation via a pathway relying solely on the auxiliary enzyme Δ3-Δ2-enoyl-CoA isomerase, termed the isomerase-dependent pathway. Two novel alternative pathways have recently been postulated to exist in mammals, and these additionally depend on Δ3,5-Δ2,4-dienoyl-CoA isomerase (di-isomerase-dependent) or on Δ3,5-Δ2,4-dienoyl-CoA isomerase and 2,4-dienoyl-CoA reductase (reductase-dependent). We report the identification of the Saccharomyces cerevisiae oleic acid-inducible DCI1 (YOR180c) gene encoding peroxisomal di-isomerase. Enzyme assays conducted on soluble extracts derived from yeast cells overproducing Dci1p using 3,5,8,11,14-eicosapentenoyl-CoA as substrate demonstrated a specific di-isomerase activity of 6 nmol × min−1 per mg of protein. Similarly enriched extracts from eci1Δ cells lacking peroxisomal 3,2-isomerase additionally contained an intrinsic 3,2-isomerase activity that could generate 3,5,8,11,14-eicosapentenoyl-CoA from 2,5,8,11,14-eicosapentenoyl-CoA but not metabolize trans-3-hexenoyl-CoA. Amplification of this intrinsic activity replaced Eci1p since it restored growth of theeci1Δ strain on petroselinic acid for which di-isomerase is not required whereas Eci1p is. Heterologous expression in yeast of rat di-isomerase resulted in a peroxisomal protein that was enzymatically active but did not re-establish growth of theeci1Δ mutant on oleic acid. A strain devoid of Dci1p grew on oleic acid to wild-type levels, whereas one lacking both Eci1p and Dci1p grew as poorly as the eci1Δ mutant. Hence, we reasoned that yeast di-isomerase does not additionally represent a physiological 3,2-isomerase and that Dci1p and the postulated alternative pathways in which it is entrained are dispensable for degrading oleic acid.
The effects of the Rwandan civil war on poaching of ungulates in the Parc National des Volcans

One of the greatest threats that the mountain gorilla Gorilla gorilla beringei faces is the repeated setting of snares for ungulates by people living adjacent to the Parc National des Volcans in Rwanda. Two vets (one expatriate and one Rwandan) are permanently employed to monitor the health of habituated groups of mountain gorillas and to remove snares if an animal becomes caught in one. This study examined how snaring has changed as a result of the Rwandan civil war and how ungulates in the park have been affected. In the region around the Karisoke Research Station ungulate numbers have remained stable and in the case of the black-fronted duiker Cephalophus nigrifrons they have increased at higher altitudes. However, a questionnaire survey among local people showed that there has been a perceived decrease in crop raiding by all ungulates in the west of the park, suggesting a decline in numbers. In the east of the park there appears to have been a decrease in the numbers of black-fronted duikers but an increase in the number of buffaloes Syncerus caffer. The price of bushmeat in real terms has decreased since the war, despite the increase in the price of domestic meat, and poachers interviewed were selling bushmeat more frequently than they did before the war. The level of poaching, therefore, appears to have increased since the war.
Hello, Startup: A Programmer's Guide to Building Products, Technologies, and Teams

This book is the "Hello, World" tutorial for building products, technologies, and teams in a startup environment. It's based on the experiences of the author, Yevgeniy (Jim) Brikman, as well as interviews with programmers from some of the most successful startups of the last decade, including Google, Facebook, LinkedIn, Twitter, GitHub, Stripe, Instagram, AdMob, Pinterest, and many others. Hello, Startup is a practical, how-to guide that consists of three parts: Products, Technologies, and Teams. Although at its core, this is a book for programmers, by programmers, only Part II (Technologies) is significantly technical, while the rest should be accessible to technical and non-technical audiences alike. If you're at all interested in startups-whether you're a programmer at the beginning of your career, a seasoned developer bored with large company politics, or a manager looking to motivate your engineers-this book is for you.
Preliminary genetic analysis of koaro (Galaxias brevipinnis) in New Zealand lakes: Evidence for allopatric differentiation among lakes but little population subdivision within lakes

Abstract Lake systems are often notable for the diversification of freshwater fish species. This has yet to be documented in New Zealand, although a possible case has been described in Galaxias brevipinnis from Lake Okareka, where lake‐ and stream‐resident fish show morphological and ecological differences. Samples of G. brevipinnis collected from three New Zealand lakes (Wakatipu, Wanaka, and Okareka) were examined using microsatellite DNA analysis to look for evidence of genetic structuring among samples within lakes (possibly indicative of incipient sympatric speciation or natal stream loyalty). Comparison among lakes was made to provide a context for genetic structuring within lakes. There was evidence of genetic differentiation among lake populations, reflecting original founder effect and subsequent genetic drift. However, there was little evidence of restricted gene flow among samples from different parts of lakes and their tributaries. Namely, there is no genetic evidence of incipient speciation in Lake Okareka, and little or no evidence of stream loyalty in Lake Wakatipu. However, the situation in Lake Okareka warrants further analysis using more microsatellite loci and wider sampling.
Predicting territory density of Dusky Orange-crowned Warblers Oreothlypis celata sordida breeding on Santa Catalina Island, California

Capsule Territory density of the Dusky Orange-crowned Warbler Oreothlypis celata sordida, endemic to the California Channel Islands, USA, varied with vegetation greenness and oak coverage on Santa Catalina Island. Aims To model factors affecting territory density of warblers on Santa Catalina Island. Methods Breeding warblers were monitored in a dry and a more mesic habitat on the island in 2006–2008 and modelled using a GIS tool to predict territory density. Data of three-year territory boundaries with ecological covariates were used to develop a regression tree and project the distribution of territory density on an island-wide scale. The fitted model was indirectly evaluated using the island-wide point counts. Results The territory density of warblers differed between mesic and xeric habitats in response to oak coverage and food abundance in oaks. In the model, Normalized Difference Vegetation Index and oak coverage were the best predictors. Individual density estimates from distance sampling were comparable with the model prediction. Conclusion Plot-based surveying and statistical modelling provided an insight on how breeding warblers responded to resource abundance. This approach may facilitate the management of these insular birds that are highly dependent on oak habitats on the island where habitat loss has been occurring due to anthropogenic fire.
Original Synthetic Report: The peopling of the Americas: a complex issue for Amerindian, Na-Dene, Aleut and Eskimo first inhabitants

Aim: To compare the Amerindians HLA allele frequencies with those of other First American Natives and also those of other worldwide populations in order to clarify the still unclear peopling of the Americas and the origins of Amerindians. Subjects and methods: All possible HLA data already obtained about early Native American populations are used. Genetic distances and N-J dendrogram method are applied. Results and conclusions: Results and discussion have given to the following conclusions: 1) Pacific Ocean boat trips may have contributed to the HLA genetic American profile (or vice versa); 2) North West Canadian Athabaskans have had gene flow with close neighboring populations, Amerindians, Pacific Islanders including East Australians, and Siberians; 3) Amerindians entrance to America may have been different to that of Athabaskans, Aleuts and Eskimos; Amerindians may have been in their lands long before Athabaskans and Eskimos because they present and altogether different set of HLA-DRB1 allele frequencies; 4) Amerindians show very few ―particular‖ single-locus alleles, but have unique extended haplotypes; 5) Our results do not support the three-wave model of American peopling, but another model where the Pacific Coast is also an entrance point. Reverse migration (America to Asia) is not discarded and different movements of people in either direction in different times are supported by the Athabaskan population admixture with Asian-Pacific population and with Amerindians. Key words: Aleuts, Amerindians, Athabaskans, Eskimo, HLA, peopling of America.
A Highly Sensitive Sandwich Enzyme Immunoassay of Human Growth Hormone in Serum Using Affinity-Purified Anti-Human Growth Hormone Fab′-Horseradish Peroxidase Conjugate

Abstract A highly sensitive sandwich enzyme immunoassay (EIA) for human growth hormone (hGH) was developed. hGH to be assayed was incubated with an anti-hGH IgG-coated polystyrene ball, and then the polystyrene ball after washing was incubated with anti-hGH Fab1 -peroxidase conjugate. Peroxidase activity bound to the polystyrene ball was correlated to the amount of hGH to be assayed. Polystyrene balls were coated by physical adsorption with rabbit anti-hGH IgG which was not affinity-purified. Rabbit anti-hGH Fab1 which had been affinity-purified was coajugated with horseradish peroxidase using N-succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate. The sensitivity was 0.06 pg of hGH per tube or 6 pg/ml of serum when 0.01 ml of serum samples was used. No significant interference was observed in the presence of 8 ng/tube of human prolactin, 8 μU/tube of human thyroid-stimulating hormone, 50 mU/tube of human luteinizing hormone, 10 mU/tube of human follicle-stimulating hormone, or 5 U/tube of human c.
EVIDENCE THAT OPIATERGIC AND α-ADRENERGIC MECHANISMS STIMULATE RAT GROWTH HORMONE-RELEASE VIA GROWTH RELEASING FACTOR (GRF)

An antiserum raised against human pancreatic growth hormone-releasing factor-(1–40) (hpGRF-40) was found to recognize the rat hypothalamic growth hormone-releasing factor (rhGRF): This antiserum, when given iv to adult male rats, completely abolished GH release induced by a synthetic rhGRF (0.2, 1 μg/kg BW), and inhibited the physiological GH secretion over 2 days. After passive immunization with anti-hpGRF-40 serum, iv injection of either FK 33–824 (100 μg/kg BW), an enkephalin analogue, or clonidine (125 μg/kg BW), an α-adrenergic agent, failed to stimulate GH release in the unanesthetized rat. These results indicate that the GHreleasing actions of opiatergic and a-adrenergic mechanisms are mediated through stimulation of endogenous rhGRF release in the rat.
Prevalence and species identification of Pratylenchus spp. in Manitoba potato fields and host suitability of ‘Russet Burbank’

Abstract The objectives of this study were to determine the occurence and identity of Pratylenchus species in Manitoba potato (Solanum tuberosum) fields with a history of Potato Early Dying disease using both morphometric and molecular techniques. In addition, suitability of the most widely used potato cultivar in Manitoba, ‘Russet Burbank’, as a host for Pratylenchus spp. was determined. During the summer of 2004 and 2005, 283 soil samples were collected from 31 potato fields with a history of occurrence of Potato Early Dying encompassing the major potato growing areas in Manitoba. Pratylenchus spp. were detected in 39% of the fields and densities in soil samples ranged from 45 to 631 nematodes kg−1 fresh soil with a median density of 125 nematodes kg−1 fresh soil. Morphometrics of female nematodes and molecular analysis (polymerase chain reaction followed by sequencing and comparison of sequence data to the GenBank BLAST database) showed that the species of Pratylenchus in potato fields was P. neglectus. Further, the near absence of male Pratylenchus in the soil samples is consistent with the parthenogenic nature of P. neglectus. Potato 'Russet Burbank' was a poor host to populations of Pratylenchus sp. present in two fields. We suggest that the presence of suitable host plants, cereals and canola, in rotation with potato in Manitoba and soil texture have favoured P. neglectus rather than P. penetrans, the most widespread Pratylenchus species found in soil regularly cropped to potato in the Eastern United States and Canada. More studies are warranted to determine whether Pratylenchus spp. such as P. neglectus in Manitoba are causing damage to crops in rotation with potato and if they play a role in the Potato Early Dying disease complex.
Principal component analysis with drop rank covariance matrix

This paper considers the principal component analysis when the covariance matrix of the input vectors drops rank. This case sometimes happens when the total number of the input vectors is very limited. First, it is found that the eigen decomposition of the covariance matrix is not uniquely defined. This implies that different transform matrices could be obtained for performing the principal component analysis. Hence, the generalized form of the eigen decomposition of the covariance matrix is given. Also, it is found that the matrix with its columns being the eigenvectors of the covariance matrix is not necessary to be unitary. This implies that the transform for performing the principal component analysis may not be energy preserved. To address this issue, the necessary and sufficient condition for the matrix with its columns being the eigenvectors of the covariance matrix to be unitary is derived. Moreover, since the design of the unitary transform matrix for performing the principal component analysis is usually formulated as an optimization problem, the necessary and sufficient condition for the first order derivative of the Lagrange function to be equal to the zero vector is derived. In fact, the unitary matrix with its columns being the eigenvectors of the covariance matrix is only a particular case of the condition. Furthermore, the necessary and sufficient condition for the second order derivative of the Lagrange function to be a positive definite function is derived. It is found that the unitary matrix with its columns being the eigenvectors of the covariance matrix does not satisfy this condition. Computer numerical simulation results are given to valid the results.
Low light availability affects leaf gas exchange, growth and survival of Euterpe edulis seedlings transplanted into the understory of an anthropic tropical rainforest

Euterpe edulis Mart. (Arecaceae) is a threatened palm tree of the Brazilian Atlantic Rainforest understory with fundamental importance for the restoration of degraded forest environments. We assessed the leaf gas exchange, growth and survival of E. edulis seedlings transplanted at three different forest sites (S1, S2 and S3) in the same area in which cocoa trees had been cultivated in a rustic agroforestry system. Measurement was carried out during the first year after seedling transplantation. The sites were characterised according to canopy openness (CO) and total daily photosynthetic photon flux density (PPFD). Average CO and PPFD values were 13.3%, 8.0% and 6.7%, and 3.34, 2.79 and 0.62 mol m−2 d−1 for S1, S2 and S3, respectively. A progressive decline in seedling survival was observed in all sites throughout the experiment. At 387 d after planting, survival at S1, S2 and S3 was 57%, 44% and 37%, respectively. The gross light-saturated photosynthetic rate (Amax), leaf area and plant biomass were significantly higher (P < 0.05) in S1 and S2 when compared with S3. The values of dark respiration rate (R d) and photosynthetic compensation irradiance (I c) were sufficiently low for a positive carbon balance. Notwithstanding, the interpretation of results of microclimate variables together with leaf gas exchange and growth variables indicated that seedlings at all sites were in a suboptimal condition to achieve Amax, which is probably the main cause of the dramatic decline in the seedlings’ survival throughout the first year after transplantation. From a practical point of view, if the values of CO and PFD are lower than 10% and 3 mol m−2 d−1, respectively, it is suggested that the transplanting of E. edulis seedlings to the understory of abandoned agroforestry systems be accompanied by cultural practices, such as the thinning and pruning of tree tops.
Ecology of Freshwater Ostracoda (Crustacea) from Lakes and Reservoirs in Bolu, Turkey

ABSTRACT Freshwater ostracods are important for interpreting the water quality of aquatic habitats. However, using ostracods in this way requires knowledge of their ecology and habitat preferences, particularly because species may show different responses to different ecological conditions. I documented ecological requirements of five ostracod species and their distribution in ten similar-sized lakes and reservoirs in Bolu, Turkey. Five species (Darwinula stevensoni, Cypria ophthalmica, Cypridopsis vidua, Cyclocypris ovum, Fabaeformiscandona fabaeformis) were found from natural lakes, while no ostracods were encountered from reservoirs. A canonical correspondence analysis suggested that salinity, temperature, redox potential, and pH were the four most influential factors on the species habitat preference in these lakes. These results were also supported with unweighted pair group mean averages (UPGMA) that also showed ostracod preference for certain ecological conditions in these lakes was mostly species-specific, depending on the changes in the levels of variables. UPGMA analysis for clustering of species and environmental data revealed three main species assemblages. The first group was represented by a single species, F. fabaeformis, whose occurrence was closely related to water hardness. The second group included two species, D. stevensoni and C. ophthalmica, that were found in relatively alkaline waters with moderate temperature. The third group was represented by two species, C. vidua and C. ovum.
Observations on behavior and ecology in an Australian turtle, Chelodina expansa (Testudines: Chelidae)

Observations of natural populations and captives over a period of 6 years provide preliminary information on the ecology of a poorly known and secretive species. Included are observations on habitat partitioning in small pools where two other chelid species occur and notes on the carnivorous diet and manner of feeding. Head bobbing and self-grooming behavior are described.