Miracle-dz/UniFAR-FTUs huggingface dataset:
The phylogenetic position and phenotypic changes of a Chlorella-like alga during 5-year microcosm culture

Recent phylogenetic studies of Chlorella-like algae revealed that this group has diversified into free-living and endosymbiotic niches, the latter within protists and invertebrate organisms. Our previous studies using a long-term culture composed of an alga (Chlorella vulgaris, rDNA sequence unknown), a bacterium (Escherichia coli) and a ciliate (Tetrahymena thermophila), suggested that some clones in the algal population developed an endosymbiotic ability with T. thermophila while others developed an ectosymbiotic ability with E. coli from a non-associated stage. In this paper, an rDNA (18S, ITS1, 5.8S, ITS2)-based phylogeny of the ancestral strain and derived clones isolated from 5-year microcosm cultures was constructed and revealed that the alga belongs to the genus Micractinium. This result was supported by analysis of the secondary structure of the rRNA gene. No difference was observed in the sequence between the ancestral and derived clones. On the other hand, some morphological and physiological traits of the ancestral strain and the derived clones were analysed and revealed that several phenotypic changes had occurred among the algal clones. In particular, the derived clones obtained from long-term cultures had increased in cell size, changed in their ability to grow at pH 4.0, and developed a tendency for cell-aggregation or sedimentation.
Effects of Trap Fishing on Fish Populations Inhabiting a Fringing Coral Reef

Abstract Fish populations of two separate but structurally similar fringing coral reefs at La Gonave, Haiti, empirically determined to differ with respect to level of exploitation, were assessed by experimental trapping and visual censusing. The fish species composition, total fish abundance, and numerical catch per unit of effort did not differ significantly between sites. Scarids and chaetodontids, which collectively made up over 50% of the catch, were significantly smaller at the site of higher exploitation. The relatively small sizes of resident fishes on both reefs (no fish were over 30 cm in fork length) suggested there was overexploitation. The proportion of fish recruited to traps before reaching sexual maturity ranged from 23 to 78% among six exploited families. Because an enforcement infrastructure for fishery regulation currently does not exist in Haiti, we suggest a system of passive management employing fishermen cooperatives whereby new and modified gear could be introduced for exploitation .
On the prevalence of small-scale twist in the solar chromosphere and transition region

The solar chromosphere and transition region (TR) form an interface between the Sun’s surface and its hot outer atmosphere. There, most of the nonthermal energy that powers the solar atmosphere is transformed into heat, although the detailed mechanism remains elusive. High-resolution (0.33–arc second) observations with NASA’s Interface Region Imaging Spectrograph (IRIS) reveal a chromosphere and TR that are replete with twist or torsional motions on sub–arc second scales, occurring in active regions, quiet Sun regions, and coronal holes alike. We coordinated observations with the Swedish 1-meter Solar Telescope (SST) to quantify these twisting motions and their association with rapid heating to at least TR temperatures. This view of the interface region provides insight into what heats the low solar atmosphere.
Measurement of the shear and tensile fracture properties of leaves of pasture grasses

The shear fracture properties of leaves of pasture grasses were measured using a shearing device consisting of 2 blades at fixed angles. The mechanics of the shearing process were examined with both paper and leaves of Festuca arundinacea. The investigations indicated that the intrinsic strength of the material being cut is best represented as force exerted during the cut divided by the length of the cutting blade in contact with the material. Tensile fracture properties of leaves of 5 pasture grasses were also measured, and the relationship between tensile and shear properties was examined. Intrinsic shear strength was weakly negatively correlated with tensile strength.
Responses of moist non-acidic arctic tundra to altered environment: productivity, biomass, and species richness

In arctic Alaska, researchers have manipulated air temperature, light availability, and soil nutrient availability in several tundra communities over the past two decades. These communities responded quite differently to the same manipulations, and species responded individualistically within communities and among sites. For example, moist acidic tundra is primarily nitrogen (N)-limited, whereas wet sedge tundra is primarily phosphorus (P)-limited, and the magnitude of growth responses varies across sites within communities. Here we report results of four years of manipulated nutrients (N and/or P) and/or air temperature in an understudied, diverse plant community, moist non-acidic tussock tundra, in northern Alaska. Our goals were to determine which factors limit above-ground net primary productivity (ANPP) and biomass, how community composition changes may affect ecosystem attributes, and to compare these results with those from other communities to determine their generality. Although relative abundance of functional groups shifted in several treatments, the only significant change in community-level ANPP and biomass occurred in plots that received both N and P, driven by an increase in graminoid biomass and production resulting from a positive effect of adding N. There was no difference in community biomass among any other treatments; however, some growth forms and individual species did respond. After four years no one species has come to dominate the treatment plots and species richness has not changed. These results are similar to studies in dry heath, wet sedge, and moist acidic tundra where community biomass had the greatest response to both N and P and warming results were more subtle. Unlike in moist acidic tundra where shrub biomass increased markedly with fertilization, our results suggest that in non-acidic tundra carbon sequestration in plant biomass will not increase substantially under increased soil nutrient conditions because of the lack of overstory shrub species.
Can population surveys show if the Mediterranean monk seal colony at Cap Blanc is declining in abundance

Summary 1. The Mediterranean monk seal is an endangered marine mammal with only a few populations thought to be viable. The largest aggregation of this species is found at the Peninsula of Cap Blanc, on the western Sahara, where a colonial structure is maintained. The size of this colony is estimated by annual capture–recapture surveys, but it is unclear if the attained level of precision is enough to detect changes in numbers in the short term. 2. In this study, simulated capture–recapture experiments were used to investigate the relationship between population estimates and abundance. The statistical power necessary to detect a population decline with ongoing surveys was estimated, and the requirements for an improvement in precision were evaluated. Additionally, changes in abundance over consecutive surveys were examined for comparison with an alternative method of Bayesian inference. 3. Results indicated that the power to detect trends from the actual surveys was lower than should be required for the conservation of a small population, such as the colony at Cap Blanc. A 5% annual rate of decline in abundance would only be detected with high power after 12 years, with a population of 317 seals being reduced to 172. If the annual rate of decline was 10%, 8 years would be required to detect a reduction of 317 to 136 seals. 4. Capture–recapture surveys can produce reliable data but do not identify moderate or low population declines. The increase in precision of surveys is costly and time consuming, and other monitoring methods are needed to detect early signs of a decline. Bayesian methods cannot provide a better result because they are not robust to small sample size and heterogeneity in capture probabilities. Despite the need for alternative methods for earlier detection, capture–recapture surveys are still required to estimate the size of the colony, and precision in population estimates can be evaluated in relation to cost effectiveness.
Molecular cloning of metallothionein cDNA and analysis of metallothionein gene expression in winter flounder tissues

Investigations into the precise role played by metallothionein (MT) in heavy-metal metabolism have been hampered by difficulties in positively identifying and quantifying MT in fish tissues. This study describes the development of an antisense MT RNA (cRNA) probe that will enable MT mRNA levels to be measured with a high degree of specificity and precision. Cadmium chloride administration induces the producton of MT mRNA in the liver and kidney of winter flounder (Pseudopleuronectes americanus). Poly(A)+ RNA purified from liver samples of winter flounder after cadmium chloride injections was used to construct a cDNA library. Several recombinant clones made complementary to MT mRNA were selected from this cDNA library by an oligonucleotide derived from the N-terminal amino acid sequence of winter flounder metallothionein. Sequence analysis of two of the cDNA inserts gave the structure of the entire 3′ untranslated region, a coding region corresponding to winter flounder MT and 49 nucleotides of the 5′ untr.
Host feeding experience affects host plant odour preference of the polyphagous leafminer Liriomyza bryoniae

Herbivorous insects use highly specific volatiles or blends of volatiles characteristic to particular plant species to locate their host plants. Thus, data on olfactory preferences can be valuable in developing integrated pest management tools that deal with manipulation of pest insect behaviour. We examined host plant odour preferences of the tomato leafminer, Liriomyza bryoniae (Kaltenbach) (Diptera: Agromyzidae), which is an economically important agricultural pest widespread throughout Europe. The odour preferences of leafminers were tested in dependence of feeding experiences. We ranked host plant odours by their appeal to L. bryoniae based on two‐choice tests using a Y‐tube olfactometer with five host plants: tomato, Solanum lycopersicum Mill. ; bittersweet, Solanum dulcamara L. ; downy ground‐cherry, Physalis pubescens L. (all Solanaceae); white goosefoot, Chenopodium album L. (Chenopodiaceae); and dead nettle, Lamium album L. (Lamiaceae). The results imply that ranking of host plant odours by their attractiveness to L. bryoniae is complicated due to the influence of larval and adult feeding experiences. Without any feeding experience as an adult, L. bryoniae males showed a preference for the airflow with host plant odour vs. pure air, whereas females did not display a preference. Further tests revealed that adult feeding experience can alter the odour choice of L. bryoniae females. After feeding experience, females showed a preference for host plant odour vs. pure air. Feeding experience in the larval stage influenced the choice by adults of both sexes: for males as well as females reared on bittersweet the odour of that plant was the most attractive. Thus, host feeding experience both in larval and/or adult stage of polyphagous tomato leafminer L. bryoniae influences host plant odour preference by adults.
Evaluation of morphological parameters of bone formation in Sprague–Dawley rats of different ages by in vivo fluorochrome labeling

Abstract Our study focuses on the morphological parameters of bone growth and bone formation in Sprague–Dawley (SD) rats of different ages, using fluorochrome labeling in vivo. We concluded that bone longitudinal growth rate (LGR) and bone mineral apposition rate (MAR) were significantly increased in both the 1- and 3-month-old rats compared with the 6- and 14-month-old rats, and that of the parameters were significantly decreased in both the 6- and 14-month-old rats. Meanwhile, bone formation rate (BFR) and percent labeled perimeter (%L.Pm) peaked in 3-month-old rats, and were followed by remarkable decrease with aging. In the present study, static parameters including percent trabecular area (%Tb.Ar), trabecular thickness (Tb.Th) and trabecular number (Tb.N), contrary to previous reports, progressively increased, whereas trabecular separation (Tb.Sp) reduced with increasing age. Furthermore, bone mass increased for 14-month-old rats due to the significantly decreased bone turnover rate.
Shut up and play: A musical approach to engagement and social presence in Human Robot Interaction

With a view to studying the development of social relationships between humans and robots, it is our contention that music can help provide extended engagement and open ended interaction. In this paper we explore the effectiveness of music as a mode of engagement using Mortimer, a robot able to play a drum kit and employing a composition algorithm to respond to a human pianist. We used this system to conduct a comparative study into the effects of presenting the robot as a social actor or as an instrument. Using automated behavioural metrics, including face tracking, we found that participants in the social actor condition played for longer uninterrupted and stopped the robot mid-performance less. They also spent more time looking at the robot when not playing and less time looking at the piano when playing. We suggest these results indicate greater fluency of playing and engagement and more feelings of social presence towards the robot when presented as a social actor.
Chlorophyll Fluorescence Characteristics, Growth and Solute Accumulation During Summer in Seedlings of Native Plant Species Grown in Abandoned Agricultural and Degraded Lands

Abstract Chlorophyll fluorescence characteristics, proline, amino acids, total soluble carbohydrates and pigment contents were examined during the summer period in seedlings of seven multipurpose tree species, specifically Alnus nepalensis, Boehmeria rugulosa, Celtis austra-lis, Dalbergia sissoo, Ficus glomerata, Grewia optiva and Sapium se-biferum, grown in abandoned agricultural and degraded lands. All species invariably showed lower photochemical efficiency of photosys-tem II measured as Fv/Fm ratio in degraded land as compared to abandoned agricultural land except S. sebiferum, which exhibited identical efficiency at both sites. However, differences in percent reduction were observed among the species, with B. rugulosa exhibiting maximum reduction in Fv/Fm ratio in degraded land, whereas minimum reduction was observed in G. optiva and D. sissoo. Plants grown in degraded land also showed significant reduction in leaf area and total leaf number per
A finite‐difference treatment of interface condition for the parabolic wave equation

An elegant finite‐difference approach is introduced to handle the interface conditions between two layered media with different sound speeds and densities for the parabolic wave equation. Continuity of pressure as well as continuity of vertical particle velocity are preserved. The method is designed to be implicit and is unconditionally stable. The resulting mathematical expression is short. Since the entire procedure is systematic, it becomes easy to implement into computer programs. At every interface, it requires only a few scalar operations, thus, no additional memory capacity is required. Details of the mathematical treatment of the fiat boundary will be described. Test results are shown to compare with FFP results. A generalization to handle irregular interfaces will be outlined.
Seedling growth in conifers and angiosperms: impacts of contrasting xylem structure

Competitive interaction between conifers and angiosperms has moulded the structure of global vegetation since the Cretaceous. Angiosperms appear to enjoy their greatest advantage in the lowland tropics, an advantage often attributed to the presence of vessels in their xylem tissue. By monitoring the seedling growth of three members of the pan-tropical conifer family Podocarpaceae and three tropical angiosperm tree species, our aim was to determine whether these conifer and angiosperm seedlings showed distinct patterns of growth and light adaptation that might be attributed to the presence/absence of vessels. Angiosperm seedlings were consistently more efficient in terms of leaf area carried per unit stem investment, as well as more responsive to light climate than the conifer seedlings. Apparently linked to this were larger growth rate, stem hydraulic conductivity and stomatal conductance in the angiosperm sample. Stem hydraulic conductivity and maximum stomatal conductance were highly correlated among species and light treatments explaining the association between highly conductive vessel-bearing wood and high rates of gas exchange. We conclude that xylem vessels contribute to higher rates of gas exchange and more efficient production of leaf area in our sample angiosperms than in conifers. However, this advantage is limited by shade.
Pollen distribution at high elevation in Switzerland: Evidence for medium range transport

Since Switzerland has a complex topography with high mountains it was very uncertain how much and what kind of pollen can be found at high elevations. In order to study the content of air masses at high elevation a Burkard Seven Day Recording Volumetric Spore Trap was installed at the meteorological station at Gutsch (alt. 2300 m) in the Swiss Alps. Although there are no trees at all at this elevation it is amazing how much tree pollen is found. With the exception of Alnus viridis most of this pollen is transported across the Alps. Special attention is given to the pollen of Castanea which can serve as a real tracer, since this pollen originates exclusively from the southern part of Switzerland (Tessin). Grass pollen, on the other hand, has local sources, even at this elevation, once the snowy season has ended. Grass pollen and pollen of weeds, therefore, need not have been transported. The surprisingly high amount of pollen observed may also have a relevance for people with pollen sensitization because g.
Stimulus control of predatory attack in the brown tree snake (Boiga irregularis)

Three experiments studied predation upon neonatal rodents by brown tree snakes (Boiga irregularis). Experiment 1 showed that chemical cues arising from prey were used in foraging tests that could not be completed on the basis of vision alone. Experiment 2 provided only airborne chemical cues, and snakes performed at chance levels in selecting among odoriferous (baited) and non-odoriferous (unbaited) nests. Snakes performed above chance, however, when a chemical trail led to the baited nest (Experiment 3), suggesting that non-volatile chemicals are most important in guiding choice behaviour.
Colonization of non‐cassava plant species by cassava whiteflies (Bemisia tabaci) in Uganda

Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae) is the vector of cassava mosaic geminiviruses (CMGs), which are the main production constraint to cassava [Manihot esculenta Crantz (Euphorbiaceae)], both in Uganda and elsewhere in Africa. Two B. tabaci genotype clusters, Ug1 and Ug2, differentiated at 8% nucleotide (nt) divergence within the mitochondrial cytochrome oxidase I (mtCOI) gene, have been shown to occur on cassava in Uganda. However, the role of alternative hosts in the ecology of cassava B. tabaci genotypes and their possible involvement in the epidemiology of cassava mosaic disease (CMD) in Uganda remain unknown. In this study, we investigated the restriction of cassava B. tabaci genotypes to cassava and the colonization of alternative host species in select cassava‐growing areas of the country in 2003 and 2004. Bemisia tabaci adults and 4th instar nymphs were collected from cassava and 11 other cultivated and uncultivated species occurring adjacent to the sampled cassava fields. Phylogenetic analysis of mtCOI sequences revealed that only a single genotype cluster, Ug1, was present on both cassava and non‐cassava plant species sampled in this study. The Ug1 genotypes (n = 49) shared 97–99% nt identity with the previously described cassava‐associated B. tabaci populations in southern Africa, and were ∼8% and ∼13% divergent from Ug2 and the ‘Ivory Coast cassava’ genotypes in Uganda and Ivory Coast, respectively. The Ug1 genotypes occurred (as adults) on all 12 source‐plant species sampled. However, based on the presence of B. tabaci 4th instar nymphs, the Ug1 genotypes (n = 13) colonized cassava and five other non‐cassava plant species: Manihot glaziovii, Jatropha gossypifolia, Euphorbia heterophylla, Aspilia africana, and Abelmoschus esculentus, suggesting that cassava B. tabaci (Ug1 genotypes) are not restricted to cassava in Uganda. No Ug2‐like genotypes were detected on any of the plant species sampled, including cassava, in this study. The identification of additional hosts for at least one genotype cluster, Ug1, known also to colonize cassava, and which was hitherto thought to be ‘cassava‐restricted’ may have important epidemiological significance for the spread of CMGs in Uganda.
The effect of non-target species in presence-absence distribution surveys: A case study with hair-tubes

Abstract Detection of non-target species during distribution surveys may influence the detection of the focal species, due to bait being consumed, or trapping devices inactivated. The aim of this work was to evaluate the effect of non-target species (field mice, Apodemus sp.) on the detection and occupancy estimates of a target species (the red squirrel, Sciurus vulgaris) during hair-tubes surveys. Following a modelling approach that accounted for imperfect detection of both target and non-target species, we tested the hypothesis that detection probability of the red squirrel is affected by detection of field mice. We also investigated the level of bias that occurred in estimation of key-parameters such as probability of presence and detection probability. Our results show that detection of red squirrels and field mice using hair-tubes surveys is not independent. Detection probability of the red squirrel was higher when field mice did not visit the hair-tubes. Nevertheless, there was no bias in parameter estimates, therefore relatively accurate estimates would have been obtained despite this interference.
Patchiness in resource distribution mitigates habitat loss: insights from high‐shore grazers

Theory predicts that coarse-grained heterogeneity in the spatial distribution of resources benefits the abundances of exploiter populations that are vulnerable to habitat loss, in contrast to fine-grained habitat fragmentation. This generic principle has never been tested empirically, despite its potential application across scales of exploitation from foraging ranges to metapopulations. We designed a field experiment to measure population responses to the distributional pattern of limiting resources independently of resource richness. Populations of the rocky-shore snail Melarhaphe neritoides were monitored for responses in density to controlled manipulations of the pattern and abundance of refuges. On two shores, one with naturally high snail density and one with naturally low density, snail refuges were made by drilling holes into each of three 0.5-m2 plots in each of two categories of distribution pattern: patchy or even, at each of four richness levels: 4, 16, 36, or 64 holes per plot. We found that snail densities over the subsequent 2 yrs remained higher in patchy than even plots at the low-density shore, and higher in even than patchy plots at the high-density shore. Grazed areas were larger in patchy than even plots at low refuge richness, switching to larger in even than in patchy at high refuge richness. Both scales of pattern-by-richness interaction were explained by density-dependent overlap of foraging ranges around refuges. The novel implication for wildlife management is that vulnerable populations (often species of conservation concern) may benefit from clumping their resources, whereas robust populations (often pest species) may benefit from even distributions