Miracle-dz/UniFAR-FTUs huggingface dataset:
Macrofaunal community structure and sulfide flux at gas hydrate deposits from the Cascadia convergent margin, NE Pacific

Gas hydrates occur at the sediment surface on the southern summit of Hydrate Ridge, Cascadia convergent margin. The hydrates are found in mounds several meters in diameter and up to 2 m high, and are covered by sediment and mats of the filamentous sulfur-oxidizing bacteria Beggiatoa. The mounds are surrounded by vesicomyid clams (Calyptogena pacifica, C. kilmeri), which in turn are encircled by solemyid bivalves (Acharax sp.). The zonation pattern of 3 species (Calyptogena spp. and Acharax sp., which harbor chemoautotrophic bacteria in their gills, and the chemoautotrophic Beggiatoa), is also reflected in a change in the entire community structure. Beggiatoa, Calyptogena spp. and Acharax sp. are shown to be characteristic species for the different communities. The Beggiatoa community directly overlaying the gas hydrates consists of seep endemic species in high densities: gastropods (Provanna laevis, P. lomana, Pyropelta corymba, Hyalogyrina sp. nov.), bivalves (Nuculana sp. nov.) and polychaetes (Ampharetidae, Polynoidae, Dorvilleidae). Based on pooled samples, the rarefaction curves show a decrease in species diversity in the Beggiatoa and Calyptogena communities. The hydrogen sulfide gradients in the porewater of sediments below the different communities dominated by either Beggiatoa, Calyptogena spp. or Acharax sp. vary by 3 orders of magnitude. The diffusive sulfide flux based on the measured sulfide concentration gradients is highest in Beggiatoa sp. communities (23 ± 13 mol m-2 yr-1), slightly less in Calyptogena communities (6.6 ± 2.4 mol m-2 yr-1), and low in Acharax communities (0.05 ± 0.05 mol m-2 yr-1). The difference in the sulfide environment is a factor influencing the distribution patterns of the chemoautotrophy-dependant and heterotrophic species at the deep-sea sediments containing gas hydrate.
Water relations of white spruce (Piceaglauca (Moench) Voss) at tree line in north central Alaska

Factors affecting xylem pressure potential and stomatal behavior during the growing season were studied on white spruce (Piceaglauca (Moench) Voss) at tree line in the central Brooks Range of northern Alaska. Leaf conductance and xylem pressure potentials were low during days of moderate and high evaporative demand, even though soil moisture was near field capacity. Boundary line diagrams, regression analysis, and laboratory experiments indicate that stomata are sensitive to changes in vapor pressure deficit and xylem pressure potential. A correlation between resistance to water flow through the tree and soil temperature suggests that soil temperatures less than 9 °C are associated with increased resistance to water flow and may partially explain the position of white spruce tree line in northern Alaska.
The Role of Cell Wall Adjustments in Plant Resistance to Water Deficits

Reductions in rates of cell and tissue growth are a commonly observed response to water deficits resulting from drought or soil salinity. These can lead to reductions in plant size and yields. More severe stress can lead to accelerated death and complete loss of yields. This review deals with the final biophysical links in the chain of events underlying inhibition of growth in crop plants exposed to water deficits. It first examines and rejects the notion that a stress-induced reduction in cellular turgor pressure is necessarily a primary cause of growth inhibition. Data supporting the involvement of an additional and often overlooked biophysical response to water deficits are then reviewed: This response involves changes in tissue extension capacity, as a result of hardening (or softening) of expanding cell walls, and is termed cell wall adjustment. Wall hardening should increase the capacity of expanding cells to maintain turgor pressure but also acts to inhibit rates of cell expansion growth. The inhibition of cell expansion can lead to reductions in leaf area that limit rates of transpirational loss of soil water reserves; in nonirrigated crops exposed to terminal drought environments, this adaptation may prolong survival and allow time for completion of reproductive development. Conversely, wall hardening responses to intermittent water deficit episodes, e.g., in irrigated crops, could be undesirable. The survival of irrigated crops is largely assured and induction of wall hardening in the intervals between irrigation could unnecessarily reduce growth and yields. Appropriate manipulation of cell wall adjustments, via selection, breeding, or genetic engineering, could prove useful for the development of more stress-resistant crop plants suited to irrigated or nonirrigated environments.
Modeling and Control of Acute Infection of Toxoplasma Gondii

Toxoplasma gondii is a protozoan capable of replicating sexually in cats and asexually in other warm-blooded animals. When the parasites first enter a host, the replication process begins very quickly as the free parasites invade healthy host cells, until a host-mediated immune response suppresses replication of the rapidly replicating parasites. To study the effects of this process, a data-driven model is developed where the number of parasites and the IFN-γ level are selected as state variables. The reproduction number, R0 is calculated to determine the criteria for sustaining infection within the host. Stability analyses are carried out for the endemic equilibriums. Parameter fitting is performed using maximum likelihood to match existing data to the model. Finally, an optimal control problem is formulated to investigate the optimal immune strategy when minimizing the negative host reaction to increased IFN-γ levels. The results shed light into the role the immune response plays in suppressing acute infection of Toxoplasma gondii. © 2012 ASME
Outcomes of biotic interactions are dependent on multiple environmental variables

Question: Can variation in the outcome of biotic interactions in relation to environmental severity be more accurately predicted when considering multiple stress and/or disturbance variables? Location: Arctic-alpine tundra in Kilpisj€ North Finland. Methods: To test the impact of including multiple environmental variables in analyses of the outcomes of biotic interactions, we modelled reproductive effort and cover of 17 arctic-alpine species as a function of Empetrum nigrum subsp. hermaphroditum cover, geomorphological disturbance and soil moisture with statistical interactions of the explanatory variables included. We implemented a best-subset approach using generalized linear models (GLM) and selected the best model for each species based on Akaike’s information criterion (AIC). Results: For the majority of species, models including multiple environmental variables were selected as best. Reproductive effort depended on one or both environmental variables for all species, and 14 species were additionally influenced by Empetrum, with the impact of Empetrum varying with abiotic conditions in all but one of those species. Moreover, the three-way interaction of three explanatory variables was included in the best-fit models for six species. The impact of Empetrum on species cover showed a similar pattern, with 11 species affected by Empetrum and its statistical interactions with one or both abiotic variables. Conclusions: Biotic interactions have an important role in arctic-alpine vegetation, but to fully understand variation in their effects multiple environmental factors should be explicitly considered. In this study, the outcome of biotic interactions was frequently dependent on two abiotic variables (and occasionally additionally on their statistical interaction). Therefore, we demonstrate that studies based on only one environmental factor may cause misleading interpretations of the nature of biotic interactions in plant communities where there are multiple independent variables underlying the habitat severity gradient.
Finding the needle in the haystack: comparing sampling methods for detecting an endangered freshwater fish

Accurately detecting the presence or absence of threatened species is vital for threatened species management, and the detection power of individual sampling methods can vary significantly between species and life stages. The present study compares the detection power of six sampling methods in sampling the endangered Macquarie perch in riverine habitats in south-eastern Australia. In an initial survey in 1998 and 1999, fyke nets captured Macquarie perch at 100% of sites where the species was detected; gill-nets captured the species at 86%; with no other method having >50% detection efficiency. Most Macquarie perch were captured by fyke nets (90% in 1998 and 94% in 1999), followed by gill-nets (7 and 2%). A monitoring program at one of the survey sites over 7 years returned similar results with fyke nets detecting the species in all years. Fyke nets captured primarily young-of-year (YOY) individuals, whereas gill-nets captured adults and subadults. Boat electrofishing returned a high level of false negatives for Macquarie perch. Future sampling for this species should employ fyke and gill-nets to adequately characterise population structure (adults, juveniles, YOY), minimise false negatives and detect the occurrence of successful breeding the previous year.
Effect of food or water deprivation on circulating levels of pituitary, thyroid and adrenal hormones and on glucose and electrolyte concentrations in domestic ducks (Anas platyrhynchos)

In the natural environment, birds may frequently experience periods of starvation or dehydration, as a result of restrictions in food or water availability, temperature extremes, ecological competition and some migratory, sexual and nesting behaviour. In this paper the involvement of pituitary (growth hormone and luteinizing hormone), thyroid (thyroxine and triiodothyronine) and adrenal (corticosterone) hormones in the birds homeostatic response to these stresses has been investigated in ducks (Anas platyrhynchos) deprived of food or water for up to 36 h and in ducks additionally stressed by prior adaptation to hyper-osmotic drinking water and/or acutely orally loaded with crude North Sea oil. Variations in the peripheral plasma concentration of these hormones during food or water deprivation have also been correlated with stress induced alterations in body and organ weights and with accompanying changes in circulating sodium, potassium and glucose levels; their physiological roles during stress are discussed.
On Mongolian ornithopods (Dinosauria: Ornithischia). 1. Iguanodon orientalis Rozhdestvensky 1952

Abstract The type material of the Cretaceous ornithopod Iguanodon orientalis Rozhdestvensky, 1952 is redescribed. The characters which were originally used to establish a new species are shown to be either incorrect or indistinguishable from Iguanodon bernissartensis Boulenger, 1881. Additional material, previously unrecognized, further confirms the similarity of I. orientalis to I. bernissartensis . It is proposed that I. orientalis should be relegated in synonymy as a junior subjective synonym of I. bernissartensis Boulenger, 1881. The identification of the Barremian species I. bernissartensis in Asia indicates an unusually wide geographic spread for this species, and provides a potential biostratigraphic indicator for beds in Mongolia which had been previously dated variously between the Cenomanian and Maastrichtian stages.
Refugia within refugia – patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula

In Europe, southern peninsulas served as major refugia during Pleistocene cold periods. However, growing evidence has revealed complex patterns of glacial survival within these southern regions, with multiple glacial refugia within each larger refugial area. We investigated the extent to which patterns of endemism and phylogeographic are concordant across animal species in the Iberian Peninsula, one of the most important unglaciated areas in Europe during the Pleistocene, can be explained in terms of climatic stability. We found that historical climatic stability (notably climate velocity measures integrating macroclimatic shifts with local spatial topoclimate gradients) was often among the most important predictors of endemic species richness for different taxonomic groups using models that also incorporated measures of modern climate. Furthermore, for some taxonomic groups, climatic stability was also correlated with patterns of spatial concordance in interpopulation genetic divergence across multiple taxa, and private haplotypes were more frequently found in relatively stable areas. Overall, our results suggest that both endemism patterns and cross-taxa concordant phylogeographic patterns across the Iberian Peninsula to some extent are linked to spatial variation in Late Quaternary climate stability, in agreement with the proposed ‘refugia-within-refugia’ scenario. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 13–28.
A spider mating plug: origin and constraints of production

Males can increase their reproductive success by mechanically hindering females to mate with subsequent males. Research on mating plugs so far has focused on the fitness consequences and demonstrated that plug size can strongly determine its efficacy. Here, we explore: (1) the site of plug production in the erigonine spider Oedothorax retusus; and (2) whether males are limited in the production of plug material when mating with three females in succession. Micro-computed tomography, histological and ultrastructural sections demonstrate that the plug material is produced in a massive gland inside the sperm transfer organs of the male, the pedipalps. The glandular lumen is connected with the tube-like spermophore almost at its blind end. Probably, a reservoir of plug material is built up at the end of the spermophore and released after sperm transfer onto the female genital opening. Since not all males applied a large plug during their first mating, there was no significant decline in plug size over the course of the three successive matings. However, the size of the first plug significantly affected the size of the following plug. We discuss these findings in the light of plug limitation and mate choice. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 345–354.
Can translocations be used to mitigate human-wildlife conflicts?

Growing public concerns about lethal methods to mitigate human–wildlife conflicts place increasing constraints on wildlife management options. Translocations, perceived as humane and non-lethal solutions, are increasingly advocated to resolve these conflicts. The present study summarises the literature on translocations of wild mammals, with particular emphasis on ‘problem’ animals, reviews the impact of translocations on survival, behaviour, animal welfare and potential spread of diseases, and evaluates the feasibility and effectiveness of translocations to mitigate human–wildlife conflicts. Translocations may have a detrimental impact on survival rates and lead to extreme dispersal movements. In some species, stress-related capture results in substantial mortality. In other species, homing causes animals to leave the release area. In addition, some animals resume the nuisance behaviour at the release site. Individuals that survive a translocation may suffer from malnutrition, dehydration, decreased immunocompetence and predation. Supportive measures such as acclimatisation pens and provision of food and shelter can drastically reduce post-release dispersal movements and mortality, although the adoption of these measures increases the cost of translocation. Translocations have the potential to spread diseases to conspecifics, humans, domestic animals and livestock. Health surveillance, seldom implemented, is likely to add significantly to the cost of translocation. Very few studies have reported the costs of translocations or addressed which stakeholders are expected to pay for translocating problem animals. Alternative management options are rarely mentioned. Despite the perceived humaneness of translocations to mitigate human–wildlife conflicts, the fate of translocated animals has been rarely monitored. In addition, very few studies have mentioned whether and for how long the conflict was resolved. We suggest that determining whether the translocation leads to the resolution of the problem should be the main criterion to evaluate the success of the translocation of problem animals. We propose a list of criteria to assist decisions regarding the suitability, effectiveness and humaneness of translocations to manage problems posed by wild mammals.
Pancreatic stellate cells induce angiogenesis

膵星細胞は慢性膵炎や膵癌の際の線維化形成に中心的役割を果たす．最近，膵星細胞の多彩な細胞機能が明らかとなっている．今回，膵星細胞の血管新生誘導能について検討した．膵癌切除膵組織よりヒト膵星細胞を分離した．膵星細胞培養上清（CM）を作成し，ヒト臍静脈血管内皮細胞の増殖，遊走，細胞内シグナル伝達系に与える影響を検討した．更に，3次元管腔構造形成（in vitro血管新生能）ならびにヌードマウスの皮下でのin vivo血管新生誘導能についても検討した．CMは血管内皮細胞の増殖と遊走を刺激した．CMはERK系ならびにAkt系を活性化し，CMによる増殖ならびに遊走誘導は，これらのシグナル伝達系の抑制剤であるU0126およびwortmanninにより抑制された．CMは，in vitroおよびin vivoにおいて血管新生を誘導した．本研究により膵星細胞が血管新生能を有することが示された．
In-silico studies of Riparin B in the design of drugs: Physicochemical, pharmacokinetic and pharmacodynamic parameters

The process involved in the research, discovery and development of drugs is characterized by high extensive and complex cost linked to scientific and technological innovations, and it is necessary to study and verify the progress of research carried out in the field that results in patent applications. Aniba riparia (Nees) Mez is a plant species often used for therapeutic purposes, where its pharmacological properties are associated to the presence of alkaloids called riparins. 5 synthetic analog compounds (riparins A, B, C, D, E and F) were developed from natural riparins. These molecules, natural and synthetic, showed several pharmacological activities in tests performed in vitro and in vivo, highlighting the Central Nervous System (CNS). The objective of this work was to evaluate the physical-chemical, pharmacokinetic parameters (absorption, distribution, metabolism, excretion and toxicity) and pharmacodynamic parameters (bioactivity and adverse reactions) of Riparin B by means of in silico computational prediction. Online software such as Pre-ADMET, SwissADME, Molinspiration and PASS on line were used for the analysis. Riparin B fits the characteristics of druglikeness, pharmacokinetic properties appropriate to the predicted patterns and activities within the scope for the treatment of AD, demonstrating a possible potential in the inhibition of AChE. Therefore, in silico results allow us to conclude that riparin B is predicted to be a potential future drug candidate, especially via oral administration, due to its relevant Drug-likeness profile, bioavailability, excellent liposolubility and adequate pharmacokinetics, including at the level of CNS, penetrating the blood-brain barrier.
The use of specific linguistic features within the context of a casual conversation in a speech community

There seems to be nothing remarkable about the interaction between two interlocutors who have never been in contact with each other. These persons are able to understand themselves in contact situations because most times, a common language of communication is known that can sustain the exchange for the time necessary. However, when such exchange is between individuals with some level of contact or familiarity, the concept of speech community comes into play. The concept is useful but may be problematic at times and one cannot avoid applying this idea when trying to make sense of the process that takes place in the conversation, specifically a causal conversation. The aim of this sociolinguistic study is to explain how individuals are able to build social history, construct interactional talk, maintain relations with each other and reinforce solidarity from a two hour audio recorded conversation (ARC) between an ethnic Indian and a Nigerian in Marylebone, London using interactional socio-linguistic and conversation analytic. By doing so, the concept of a speech community as well as how a group can be identified as being members of a community is understood. A particular focus is paid to such linguistic features as the register of conversation, turn taking, discourse variation, phonological variation and grammatical variation characteristic of London, Nigerian and Indian English observed in the speech of the participants and how these features function to build and maintain relations. Keywords: Speech community, Casual conversation, Linguistic features, Sociolinguistics, ARC
Banks’ Endogenous Systemic Risk Taking∗

We develop a dynamic general equilibrium model that features endogenous systemic risk taking by banks. We use it to study the macro-prudential role of capital requirements. Bankers decide on the (unobservable) exposure of their banks to systemic shocks by balancing risk-shifting gains with the value of preserving their capital after such shocks. Capital requirements reduce systemic risk taking but at the cost of reducing credit and output in calm times, generating non-trivial welfare trade-offs. Interestingly, systemic risk taking is maximal after long periods of calm and may worsen if capital requirements are countercyclically adjusted.
Nitrogen fertilization of grass/clover swards under cutting or grazing by dairy cows.

Abstract Intensively managed perennial ryegrass/white clover (Lolium perenne L. and Trifolium repens L.) swards receive relatively high levels of fertilizer N, and high N surpluses can subsequently be found. The N-fertilization effects on growth, yield, and herbage quality were therefore examined on three farms over a period of three years. Nitrogen was applied at four rates (0, 75, 150, and 225 kg N year−1) with cutting or grazing regime in Year 1 and Year 2, after establishment. A spring-only application of 150 kg N was compared with four applications during the season, which was the fertilization management in the rest of the experiment. N-response was greatly affected by management. Under cutting it was higher in Year 1 [16 kg dry matter (DM) kg−1 N] than in Year 2 (9 and 13 kg DM kg−1 N with and without residual effects of fertilization in Year 1). Under grazing with one or two rest periods for cuts the N-response was only approximately half that under cutting. Under grazing there was only a response.
Evolutionary Ecology of Seed-Bank Annuals in Temporally Varying Environments

The production of long-lived seeds by annual plants introduces a unique form of age structure. In a temporally varying environment the dormant seed may experience many years with different weather, whereas the germinating individual experiences only the weather conditions of a single growing season. Natural selection operates on both the between-year dormancy and on non-seed-bank traits that affect the degree of specialization to conditions pertaining in different year types. We have used an integrated model that permits these two aspects of the life history to evolve simultaneously. This leads to predictions that are not attainable by considering the evolution of each in isolation. Changes in the survival probability of the between-year seed bank select for reinforcing changes in between-year dormancy and specialization. Changes in the probability of occurrence of different year types select for damping changes in between-year dormancy and specialization. Across a gradient in environmental quality, we predict that most change will occur in between-year dormancy, with little change in specialization. If between-year dormancy is fixed, however, a greater change in specialization should occur. The predictions of the model are discussed in terms of environmental gradients, seed-bank versus non-seed-bank annuals, and a variety of plant traits modeled elsewhere that may be involved in specialization to different types of years.