Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Mechanism for Regulating Transforming Growth Factor β (TGF-β) Signaling

Transforming growth factor β (TGF-β) mediates its biological effects through three high-affinity cell surface receptors, the TGF-β type I, type II, and type III receptors, and the Smad family of transcription factors. Although the functions of the type II and type I receptors are well established, the precise role of the type III receptor in TGF-β signaling remains to be established. While expression cloning signaling molecules downstream of TGF-β, we cloned GIPC (GAIP-interactingprotein, C terminus), a PDZ domain-containing protein. GIPC binds a Class I PDZ binding motif in the cytoplasmic domain of the type III receptor resulting in regulation of expression of the type III receptor at the cell surface. Increased expression of the type III receptor mediated by GIPC enhanced cellular responsiveness to TGF-β both in terms of inhibition of proliferation and in plasminogen-activating inhibitor (PAI)-based promoter gene induction assays. In all cases, deletion of the Class I PDZ binding motif of the type III receptor prevented the type III receptor from binding to GIPC and abrogated the effects of GIPC on type III receptor expressing cells. These results establish, for the first time, a protein that interacts with the cytoplasmic domain of the type III receptor, determine that expression of the type III receptor is regulated at the protein level and that increased expression of the type III receptor is sufficient to enhance TGF-β signaling. These results further support an essential, non-redundant role for the type III receptor in TGF-β signaling.
Spatial modelling of biodiversity at the community level

Summary 1Statistical modelling is often used to relate sparse biological survey data to remotely derived environmental predictors, thereby providing a basis for predictively mapping biodiversity across an entire region of interest. The most popular strategy for such modelling has been to model distributions of individual species one at a time. Spatial modelling of biodiversity at the community level may, however, confer significant benefits for applications involving very large numbers of species, particularly if many of these species are recorded infrequently. 2Community-level modelling combines data from multiple species and produces information on spatial pattern in the distribution of biodiversity at a collective community level instead of, or in addition to, the level of individual species. Spatial outputs from community-level modelling include predictive mapping of community types (groups of locations with similar species composition), species groups (groups of species with similar distributions), axes or gradients of compositional variation, levels of compositional dissimilarity between pairs of locations, and various macro-ecological properties (e.g. species richness). 3Three broad modelling strategies can be used to generate these outputs: (i) ‘assemble first, predict later’, in which biological survey data are first classified, ordinated or aggregated to produce community-level entities or attributes that are then modelled in relation to environmental predictors; (ii) ‘predict first, assemble later’, in which individual species are modelled one at a time as a function of environmental variables, to produce a stack of species distribution maps that is then subjected to classification, ordination or aggregation; and (iii) ‘assemble and predict together’, in which all species are modelled simultaneously, within a single integrated modelling process. These strategies each have particular strengths and weaknesses, depending on the intended purpose of modelling and the type, quality and quantity of data involved. 4Synthesis and applications. The potential benefits of modelling large multispecies data sets using community-level, as opposed to species-level, approaches include faster processing, increased power to detect shared patterns of environmental response across rarely recorded species, and enhanced capacity to synthesize complex data into a form more readily interpretable by scientists and decision-makers. Community-level modelling therefore deserves to be considered more often, and more widely, as a potential alternative or supplement to modelling individual species.
Statistical Relationship between Parr-to-Smolt Survival of Snake River Spring–Summer Chinook Salmon and Indices of Land Use

Abstract We used simple regression models to demonstrate an association between land use and parr survival of chinook salmon Oncorhynchus tshawytscha from overwintering areas in the Snake River drainage of Idaho and Oregon to the first main-stem dam encountered during emigration to the Pacific Ocean. We used data on tagged (passive integrated transponder tags) releases of naturally produced Snake River spring–summer chinook parr and subsequent tag detections, as well as indices of land use, vegetation, and road density. We spot-checked the land-use and vegetation indices in a field survey of spawning and rearing areas in the summer of 1999, and we believe that they are reliable indicators of land-use patterns. The models also employed month of release, length of parr at release, and a drought index as independent variables. The models were developed and tested using parr tagged from 1992 through 1998. Age-0 parr that reared in wilderness areas (a land-use category; not necessarily federally designated Wil.
Promise and problems in applying quantitative complementary areas for representing the diversity of some Neotropical plants (families Dichapetalaceae, Lecythidaceae, Caryocaraceae, Chrysobalanaceae and Proteaceae)

Priority areas forin situconservation are an unavoidable consequence of competition with other land uses, although they are certainly not to be seen as the only areas of value for conservation. In 1990 an international workshop was convened in Manaus, Brazil, to identify priority areas within Amazonia by committee (Workshop-90). A substantial part of the data for this assessment came from five plant families recorded for theFlora Neotropica. We compare the success of the Workshop-90 method in representing these plant species with the results of using a simple quantitative method for seeking complementary areas. The promises of quantitative methods are twofold. First, they force people to make their values explicit, which is important because priorities are dependent on the values and goals of individuals and are not universal. Second, quantitative methods can achieve representation of more of what is valued. For example, within the 90 top-priority areas (an arbitrary but convenient figure taken from Workshop-90), species representation is shown to be increased when using the complementary areas method by 83%. Simple computer implementations of this method can provide the means for fast inter-active exploration of flexibility in the many alternative area choices. This permits monitoring and review with minimum effort as new data on species and threats are acquired. On the other hand, the problem for all methods is the need for very large numbers of data, whether based on species or on any other surrogates for biodiversity, if well-informed decisions are to be made. This is not a particular problem of quantitative methods, but their explicit nature does highlight the shortcomings of data. For example, patterns in theFlora Neotropicadata show effects from small samples even though these data are among the best available for any large tropical wet-forest region. Furthermore, in order to assess the longer-term consequences of area choices, quantitative methods will require many explicit local data on factors affecting viability, threat and cost.
Differential response of male and female emerald ash borers (Col., Buprestidae) to (Z)‐3‐hexenol and manuka oil

We conducted two trapping experiments in green ash plantations in Ontario, Canada to compare the response of the emerald ash borer (EAB), Agrilus planipennis, to (Z)‐3‐hexenol (Z3‐6:OH) and manuka oil. In the first experiment, Z3‐6:OH (7.6 mg/day) in purple prism traps hung 1.5 m above ground caught significantly more EAB than the unbaited controls, with male catches significantly greater than female catches at two locations. Manuka oil (50 mg/day) attracted equal numbers of males and females but they were significantly greater than the controls at only one location. Adding (Z)‐3‐hexenal or (Z)‐3‐hexenyl acetate in binary or ternary combinations with Z3‐6:OH did not enhance trap catch. In the second experiment, Z3‐6:OH released at two rates (7.6 or 80 mg/day) in light green prism traps placed in the ash canopy also caught significantly more males than females and more males than the unbaited controls or manuka oil‐baited traps. Manuka oil had no significant effect on catches relative to the controls. Combining Z3‐6:OH with manuka oil did not enhance catches of EAB. We conclude that there was a strong male‐biased EAB response to Z3‐6:OH lures, whereas manuka oil, when effective, attracted both sexes equally. Z3‐6:OH in light green prism traps in the canopy is an effective lure for EAB, particularly for males.
Phylogenetic reconstruction of carnivore social organizations

It is generally assumed that carnivore social organizations evolved directionally from a solitary ancestor into progressively more advanced forms of group living. Although alternative explanations exist, this evolutionary hypothesis has never been tested. Here, I used literature data and maximum likelihood reconstruction on a complete carnivore phylogeny to test this hypothesis against two others: one assuming directional evolution from a non-solitary ancestor, and one assuming parallel evolutions from a socially flexible ancestor, that is, an ancestor with abilities to live in a variety of social organizations. The phylogenetic reconstructions did not support any of the three hypotheses of social evolution at the root of Carnivora. At the family level, however, there was support for a non-solitary and socially flexible ancestor to Canidae, a socially flexible or solitary ancestor to Mustelidae, a solitary or socially flexible ancestor to Mephitidae, a solitary or group living ancestor to Phocidae, a group living ancestor to Otariidae and a solitary ancestor to Ursidae, Felidae, Herpestidae and Viverridae. There was equivocal support for the ancestral state of Procyonidae and Hyaenidae. It is unclear whether the common occurrence of a solitary ancestry at the family level was caused by a solitary ancestor at the root of Carnivora or by multiple transitions into a solitary state. The failure to support a solitary ancestor to Carnivora calls for caution when using this hypothesis in an evolutionary framework, and I suggest continued investigations of the pathways of the evolution of carnivore social organizations.
Muskellunge scale interpretation: The question of aging accuracy

Abstract Age and growth data extracted from scales are often used when managing fish populations. However, accurate interpretation of scale annuli in certain species, such as muskellunge Esox masquinongy, has been suspect. The accuracy of age determination was tested with three experienced esocid scale readers who interpreted positive photo images made from acetate slide impressions projected on a microfiche reader. Images were made from scales of 25 known-age muskellunge (3–10 years old) from five Wisconsin lakes. Each scale image was interpreted twice; once with fish length, sex, and date of capture given and once without any information. Of 149 scale interpretations, 32% were assessed with the correct age, 54% underaged, and 14% overaged. The average interpretation deviated from the known age by 1.0 years. Accuracy did not improve when additional fish information was available. General confidence in the interpreter's age assessments was low and possibly related to quality of the photo images. Interpret.
Inflatable soft jumper inspired by shell snapping

Isochoric snapping of elastomeric spherical caps enables fast actuation in fluidic soft robots. Fluidic soft actuators are enlarging the robotics toolbox by providing flexible elements that can display highly complex deformations. Although these actuators are adaptable and inherently safe, their actuation speed is typically slow because the influx of fluid is limited by viscous forces. To overcome this limitation and realize soft actuators capable of rapid movements, we focused on spherical caps that exhibit isochoric snapping when pressurized under volume-controlled conditions. First, we noted that this snap-through instability leads to both a sudden release of energy and a fast cap displacement. Inspired by these findings, we investigated the response of actuators that comprise such spherical caps as building blocks and observed the same isochoric snapping mechanism upon inflation. Last, we demonstrated that this instability can be exploited to make these actuators jump even when inflated at a slow rate. Our study provides the foundation for the design of an emerging class of fluidic soft devices that can convert a slow input signal into a fast output deformation.
Genetic Mapping of a Phytopathogenic Basidiomycete, Ustilago violacea

The phytopathogenic Heterobasidiomycete Ustilago violacea (Pers.) Roussel has 14 identified linkage groups and may have 15-20 groups. Assigning mutant genes to known or to new linkage groups and constructing linkage maps in a species with a relatively large number of groups present a formidable task. Efficient meiotic and mitotic mapping strategies have been devised and successfully used (1) to determine centromere-linked values for selected mutations and (2) to detect linked genes. The available data clearly indicate that the genetic organization of the chromosomes in this Heterobasidiomycete differs from that of the chromosomes of the saprophytic Ascomycete species with extensive linkage maps.
Plasticity of olfactory‐guided behaviour and its neurobiological basis: lessons from moths and locusts

The sense of smell plays an important role in guiding the behaviour of many animals including insects. The attractiveness of a volatile is not only dependent on the nature of the chemical, but might change with the physiological status (e.g., age/hormone or mating status) or environmental conditions (e.g., photoperiod or temperature) of the individual. Here we summarize our studies focused on the plasticity of olfactory‐guided behaviour and its neurobiological basis linked with the physiological status in Lepidoptera and migratory locusts. In moths and locusts, age and juvenile hormone changed the behavioural responses to pheromones. In moths, mating had an effect on pheromone responses in males and plant odour responses in females. In all cases of behavioural plasticity studied, we found changes in the sensitivity of olfactory interneurons in the antennal lobe, whereas the peripheral system does not seem to show any plasticity in that context. Changes in the central nervous system were slow under the influence of juvenile hormone (days) or fast after mating (minutes). The olfactory system seems thus to adapt to the physiological or environmental situation of an animal to avoid a waste of energy. We discuss possible mechanisms underlying the observed plasticity.
TESTS OF DENSITY-DEPENDENT HABITAT SELECTION IN A PATCHY ENVIRONMENT'

A simple regression analysis can be used to assess the response of animal density to differences in habitat quality. The same test can evaluate general predictions of habitat selection theory as well as search for differences in the shapes of habitat suitability- density functions, something previous tests have been unable to do. Combined with de- mographic or other estimates of fitness, regression tests can provide new insights into the evolution of habitat selection. Regression and fitness tests were used to explore the pattern of density-dependent habitat use in two temperate-zone rodents. The intensity of population regulation appeared to be inversely related to a habitat's carrying capacity. Variation in density-dependent habitat choice suggests new and unexpected dispersal strategies that vary with habitat heterogeneity. The predictions of the theory are complicated when habitat quality varies independently of population density. Sweepstake fitness rewards may be reaped by animals that would previously have been assumed to have made a suboptimal habitat choice. At the level of microhabitat, habitat selection models appeared to be much less capable of predicting variation in population density. Such a relation could be due to complex and inverse relationships between microhabitat quality and carrying capacity, or it could simply reflect scaling patterns in habitat selection.
Deconvolution analysis to quantify autotrophic and heterotrophic respiration and their temperature sensitivities

Bååth E, Wallander H. 2003. Soil and rhizosphere organisms have the same Q10 for respiration in a model system. Global Change Biology 9: 1788–1791. Bhupinderpal-Singh, Nordgren A, Ottosson-Löfvenius M, Högberg MN, Mellander P-E, Högberg P. 2003. Tree root and soil heterotrophic respiration as revealed by girdling of boreal Scots pine forest: extending observations beyond the first year. Plant, Cell & Environment 26: 1287– 1296. Boone RD, Nadelhoffer KJ, Canary JD, Kaye JP. 1998. Roots exert a strong influence on the temperature sensitivity of soil respiration. Nature 396: 570–572. Hansen J, Türk R, Vogg G, Heim R, Beck E. 1997. Conifer carbohydrate physiology: updating classical views. In: Rennenberg H, Eschrich W, Ziegler H, eds. Trees – contributions to modern tree physiology. Leiden, the Netherlands: Backhuys, 97–108. Hanson PJ, Edwards NT, Garten CT, Andrews JA. 2000. Separating root and microbial contributions to soil respiration: a review of methods and observations. Biogeochemistry 48: 115–146. Heinemeyer A, Hartley IP, Evans SP, Carreira de la Fuentes JA, Ineson P. 2007. Forest soil CO2 flux: uncovering the contribution and environmental responses of ectomycorrhizas. Global Change Biology 13: 1786–1797. Högberg MN, Briones MJI, Keel SG, Metcalfe DB, Campbell C, Midwood AJ, Thornton B, Hurry V, Linder S, Näsholm T et al. 2010. Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest. New Phytologist 187: 485–493. Högberg P, Nordgren A, Buchmann N, Taylor AFS, Ekblad A, Högberg MN, Nyberg G, Ottosson-Löfvenius M, Read DJ. 2001. Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 411: 789–792. Raich JW, Schlesinger WH. 1992. The global carbon-dioxide flux in soil respiration and its relationship to vegetation and climate. Tellus Series B 44: 81–99. Yuste JC, Janssens IA, Carrara A, Ceulemans R. 2004. Annual Q10 of soil respiration reflects plant phenological patterns as well as temperature sensitivity. Global Change Biology 10: 161–169. Zhou X, Luo Y, Gao C, Verburg PSJ, Arnone JA III, Darrouzet-Nardi A, Schimel DS. 2010. Concurrent and lagged impacts of an anomalously warm year on autotrophic and heterotrophic components of soil respiration: a deconvolution analysis. New Phytologist 187: 184–198.
Effect of diet on survival, in the laboratory and the field, of sterile male Mediterranean fruit flies

To improve the effectiveness of the sterile insect technique against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), our objectives in this study were two‐fold. First, to evaluate the ability of sterile males of the Vienna‐8 strain to survive starvation, we compared them to wild males under laboratory conditions. The second objective was to determine the effect of protein‐rich nutrition on sterile male fly survival, under starvation conditions in the laboratory, under semi‐natural conditions in a field enclosure, and under natural conditions in the open field. Therefore, we released marked sterile flies of the two diet regimes, protein‐fed or protein‐deprived, and monitored their survival by recapturing them after 4, 6, and 7 days. In the laboratory, wild males endured starvation significantly better than sterile ones and protein addition to sterile fly diet resulted in even greater reduced capability to endure starvation. On the other hand, the addition of protein to sterile‐male diet did not affect their ability to survive in a field enclosure or in the open field. We conclude that under natural conditions, where food is available, sterile male fly survival is unaffected by protein‐rich pre‐release diet.
Callus induction, plant regeneration and chromosomal variations in barley

SUMMARY Callus cultures were induced on mature embryo mesocotyl explants in Hordeum vulgare cv. Zafer-160. The callus induction ratio was 54% in Murashige–Skoog (MS) medium supplemented with 1 mg 1−1 2,4-dichlorophenoxyacetic acid (2,4-D). After transfer at 22, 45, 360, 540 days of culture to MS medium containing lower concentrations of 2,4-D (0·5, 0·1, 001 mg 1−1) or MS medium lacking 2,4-D, 45-day-old callus cultures showed somatic embryogenesis. The optimum 2,4-D concentration for somatic embryogenesis was 0·01 mg 1−1. Callus cultures of 360 days showed regeneration via both somatic embryogenesis and organogenesis under the same conditions. Abnormalities in both number and structure of chromosomes increased with the age of calli. This phenomenon might be related to the loss of regeneration ability in 540-day-old calli. In-vitro regenerated plantlets gave rise to normal-looking plants after their transfer to soil. Regenerated plants had the normal diploid chromosome number (2n = 14) in their root tips.
An Index of Biotic Integrity: A Test with Limnological and Fish Data from Sixty Florida Lakes

Abstract An index of biotic integrity (IBI) that used eight fish assemblage metrics was examined for effectiveness in estimating anthropogenic impacts to 60 Florida lakes ranging in size from 2 ha to more than 12,400 ha. The lakes ranged in trophic status from oligotrophic to hypereutrophic and had aquatic macrophyte abundances (percent lake volume infested) ranging from less than 1% to 100%. Fish species were classified by trophic feeding guild and tolerance to increases in turbidity or warming and decreases in dissolved oxygen concentration. Fish assemblage metrics tested were as follows: Number of fish species, number of native fish species, number of Lepomis species, number of piscivorous species, number of generalist species, number of invertivore species, number of species intolerant of increased turbidity or warming and decreased dissolved oxygen concentration, and number of species tolerant of increased turbidity or warming and decreased dissolved oxygen concentration. The total IBI scores and the.
Internal cation concentrations of the halotolerant bacterium Brevibacterium sp. in response to the concentrations and species of external salts

Internal cation concentrations of the halotolerant bacterium Brevibacterium sp. were investigated, with the cells grown in a complex media supplemented with nine kinds of salts. With increases in the external NaCl concentration, the amount of Na+ ion in the cells increased, while the intracellular concentration of the K+ ion remained almost constant (about 300mM). The same tendency was observed when NaCl was replaced with KCl, although the Na+ ion was very low (about 15mM). On the contrary, intracellular concentrations of Mg2+ and Ca2+ decreased slightly with the increase in NaCl or KCl concentrations in the medium. When the RbCl concentration in the medium was increased to more than 100mM, Rb+ ions in the cells increased about one hundred times, 550-600 mM, while K+ ions decreased to one-tenth. The same experiment was resumed using the chemically defined medium. We observed two different phenomena. First, the intracellular Na+ content (about 200mM) was more than ten-fold higher than that of the cells grown in the complex medium. Second, the release of K+ ions from the cells at alkaline pH was not as remarkable as that in the complex medium. The release of K+ ions observed in the complex medium was correlated with the addition of 50 mM diethanolamine-hydrochloride for adjusting medium pH at 9.0.