Miracle-dz/UniFAR-FTUs huggingface dataset:
Fish Species Richness in Relation to Lake Area, pH, and Other Abiotic Factors in Ontario Lakes

Survey data from 2931 Ontario lakes were analyzed to determine how fish species richness was empirically related to a set of 19 physical and chemical limnological variables. Lake area was the dominant factor, explaining 18% of the variation in species number. Total aluminum, latitude, dissolved organic carbon, and elevation together explained an additional 16%. The strong relationship between species number and lake area was quantified using lakes with pH and then applied to ail the surveyed lakes to estimate species number. Deviations from the expected values indicated that species number decreased with decreasing pH below 6.0, resulting in significantly fewer species in lakes with pH < 6.0. In the subset of lakes with pH < 6.0, pH alone explained 21% of the variation in species number; elevation, lake area, and dissolved organic carbon together explained an additional 20%. Interactions between pH and lake area were identified; lake size decreased significantly both at low pH (<6.8) and at high pH . An u.
Extensification of grassland use in the Welsh uplands: sheep performance in years 1–6

Fothergill, M. , Davies, D. A. , Morgan, C. T. (2001). Extensification of grassland use in the Welsh uplands: sheep performance in years 1-6. Grass and Forage Science, 56, (2), 105-117. Sponsorship: UK Ministry of Agriculture Fisheries and Food.
Ecological correlates of roe deer fawn survival in a sub-Mediterranean population

We investigated the effect of body mass, spring and summer total rainfall, birth period, and local population density on the survival of 130 roe deer (Capreolus capreolus (L., 1758)) fawns captured over seven fawning seasons (1997–2003) and radio-monitored daily. We modelled survival using the program MARK, incorporating biological questions into different models, following a priori hypotheses. The best model was selected using Akaike’s information criterion. The population was surveyed by counts and estimates were obtained using mark–resight methods. Weekly survival of roe deer fawns exhibits a pseudo-threshold time trend. Probability of survival is low (0.33 ± 0.0046) in summer, increases (0.79 ± 0.0021) in fall, and approaches the highest value typical of adult survival (0.90 ± 0.00091 and 0.96 ± 0.00021 by the end of March and May, respectively) during early spring following birth. The final model predicts that survival of roe deer fawns is positively affected by total precipitation in spring and body.
ORGANIZATIONS

The Society is a corporation organized in 18d3 for the purpose of enlightening the public concerning the cruelty, futility and immorality involved in vivisectional experiments on animals, and striving for the total abolition of vivisection, It encourages the passage of laws mandating methods of research and testing alternate to those using animals, combats pound seizure legislation and cooperates with other organizations in underwriting research not using animals,
Efeito da estocagem em baixa temperatura na capacidade reprodutiva e longevidade de Trissolcus basalis (Wollaston) e Telenomus podisi Ashmead (Hymenoptera: Scelionidae)

Female longevity and fecundity of Trissolcus basalis (Wollaston) and Telenomus podisi Ashmead were evaluated at 25oC after storage periods ranging from one to 140 days at 15oC, in intervals of 10 days. The oviposition capacity of both parasitoids was also evaluated at 15oC, following pre-ovipositional periods ranging from one to 60 days, also at 10-day intervals. Females of both species survived for more than five months when stored at 15oC, however fecundity was significantly reduced by the exposure to the low temperature. Despite the reduction in fecundity, both species were able to parasitize host eggs at 25oC after spending 140 days at 15oC. Although parasitism was observed at 15oC, only 3.1% and 0.2% of the exposed eggs were parasitized by T. basalis and T. podisi, respectively. The proportion of males was significantly increased in the progeny of T. basalis females, maintained at 15oC, for any of the storage periods investigated. Similar results were obtained for T. podisi stored at 15oC up to 50 days; however the females of this species, maintained at the lower temperature for longer periods, either laid no eggs or produced progenies with sex-ratio similar to the control insects, kept at 25oC. The presence of females in the offspring of both parasitoid species indicate that mating occurred at the lower temperature. The increased longevity and reduced fecundity of T. basalis and T. podisi obtained when the adults were stored at 15oC, show that both species hibernate, and this arrestment can be useful as a tool for mass production and storage of T. basalis and T. podisi during autumn and winter.
Response of Small Mammal Populations to Fuel Treatment and Precipitation in a Ponderosa Pine Forest, New Mexico

Mechanical and fire treatments are commonly used to reduce fuels where land use practices have encouraged accumulation of woody debris and high densities of trees. Treatments focus on restoration of vegetation structure, but will also affect wildlife populations. Small mammal populations were monitored before and after dense tree stands were thinned on 2,800 ha in NM, U.S.A. Mammals were live‐trapped in upland and riparian habitats from 2002 to 2006 in thinned and unthinned forests. Populations of deer mice (Peromyscus maniculatus) and voles (Microtus spp.) were estimated using mark–recapture data. An index of abundance was used for chipmunks (Tamias spp.) and woodrats (Neotoma spp.). Deer mice responded positively to thinning in 2005 in upland and riparian habitats. Voles responded positively to thinning in 2005 and 2006 in riparian habitats. There was no change related to thinning in relative abundance of chipmunks and woodrats or in total small mammal biomass. Because abiotic processes affect wildlife populations, we also examined response of deer mouse populations to precipitation. After removing treatment effects, populations were modeled with winter and summer precipitation. In both upland and riparian habitats, deer mouse populations had a curvilinear response to precipitation from the preceding winter, while responding negatively to summer rainfall only in riparian habitats. Increases in deer mice populations occurred on thinned sites during a year of high winter precipitation, generally associated with depressed populations, indicating that forest thinning moderated this relationship. Results suggest that precipitation plays a role in determining timing and presence of response to restoration treatments.
Taxonomy of the Narcissus Flycatcher Ficedula narcissina complex: an integrative approach using morphological, bioacoustic and multilocus DNA data

The taxonomy of the Narcissus Flycatcher Ficedula narcissina-Yellow-rumped Flycatcher Ficedula zanthopygia complex from East Asia has long been debated. Most authors recognize two species: F. narcissina, with the subspecies narcissina (most of Japan and Sakhalin Island), owstoni (south Japanese islands) and elisae (northeast China) and F. zanthopygia (monotypic), although species status has been proposed for elisae and sometimes for owstoni. Here, we revise the taxonomy of this complex based on an integrative approach utilizing morphology, songs and mitochondrial and nuclear DNA for all taxa. All taxa were diagnosably different in plumage, and there were also structural differences among them, although the northernmost populations of owstoni (sometimes recognized as jakuschima and shonis) were somewhat intermediate in plumage, structure and male plumage maturation between southern populations of owstoni and narcissina. All taxa had different songs, and a discriminant function analysis of four song variables correctly classified 100% of all songs. A strongly supported phylogeny was recovered based on three mitochondrial genes and three nuclear introns (total of 3543 bp), revealing a sister relationship between F. zanthopygia and the other taxa, between F. n. narcissina and F. n. owstoni, and between F. n. elisae and F. n. narcissina + F. n. owstoni. The corrected COI distances among the three F. narcissina subspecies ranged from 2.8% (narcissina-owstoni) to 8.2% (narcissina-elisae). We suggest that the congruent differences in multiple independent traits and the deep genetic divergences among the four taxa in the F. narcissina-F. zanthopygia complex support treatment of all of these taxa as separate species. However, we acknowledge the paucity of data for F. owstoni and recommend further studies of this taxon. We suggest listing both F. elisae and F. owstoni, which have small and fragmented populations, as globally threatened.
Spatio-temporal distributions of zoobenthos in soft substratum of Izmir Bay (Aegean Sea, eastern Mediterranean), with special emphasis on alien species and ecological quality status

The soft-bottom zoobenthic community structure of Izmir Bay was examined seasonally at eight stations (depth-range: 19–67 m) in 2009. A total of 427 species were found. Polychaeta had the highest number of species (50% of total species) and individuals (75%), whereas Echinodermata possessed the highest biomass (47%). The number of species varied from 3 to 79 (0.1 m−2), the density from 60 to 5360 ind.m−2, and the biomass from 1 to 530 g.m−2. The most numerically dominant species were the polychaetes Aricidea claudiae, Streblospio gynobranchiata, Levinsenia demiri and Sternaspis scutata. The distribution of zoobenthos was strongly related to spatial differences in total organic carbon, sediment texture and depth among different regions of the bay rather than temporal differences among seasons. However, significant seasonal variability in community structure (mainly differences in the relative abundance of species) was present. The inner region of the bay can be classified as ‘poor’ or ‘bad’ based on the results of biotic indices (H′, AMBI, m-AMBI and BENTIX). Among biotic indices, only H′ and m-AMBI appeared to be capable of explaining the bay's benthic quality status. Thirteen alien species were also found. Streblospio gynobranchiata, Prionospio pulchra, Pseudopolydora paucibranchiata and Polydora cornuta formed dense populations in the inner most polluted part of the bay and are considered to be new pollution indicator species in the eastern Mediterranean Sea.
Freshwater snails of the genus Gyraulus (Planorbidae) in Australia: the taxa of Tasmania

Abstract The classification of freshwater snails belonging to the genus Gyraulus (Basommatophora: Planorbidae) from Tasmania is revised according to morphological observations on type materials, other shells collected in the 19thC, and about 920 alcohol-preserved specimens from 17 localities and mostly collected during the last 30 years. Four species-group taxa (atkinsoni, meridionalis, scottianus, tasmanicus) have previously been named from shells collected in Tasmania; two of these are type species for genera named by Iredale (1943) (meridionalis for Plananisus, scottianus for Pygmanisus). The present observations on the shell and body (pigmentation, kidney, intestinal loop and genital organs) suggest that there are two widely distributed species, G. meridionalis (including tasmanicus as a synonym) and G. scottianus. Lectotype material for G. meridionalis is designated here, from Circular Head, Tasmania. Although G. atkinsoni may be a conspecific form of meridionalis, it is maintained here as a distinct.
Mitochondrial DNA Mixed‐Stock Analysis of American Shad: Coastal Harvests Are Dynamic and Variable

Abstract Populations of American shad Alosa sapidissima are generally declining in size along the U.S. East Coast. Coastal harvest of migrating mixed-stock assemblages has been proposed as a possible cause of the decline, but the extent of fishing pressure on any particular stock has not been evaluated. To assess origin of shad harvested in the coastal fishery, we applied genetic mixed-stock analysis by using mitochondrial DNA (mtDNA) variation. We examined American shad from the coastal mixed fisheries off both Virginia and Maryland in 1992 and off Virginia alone in 1993 (N = 250 and 270, respectively), comparing mtDNA restriction fragment patterns for the coastal individuals with an archival database containing mtDNA genotypes of 1,734 individuals from 16 North American river stocks distributed from Florida to Canada. We used two different maximum-likelihood approaches to estimate the contributing-stock composition of oceanic mixtures, one yielding conditional estimates of stock composition, given obser.
Temporal patterns in the surface abundance of Calanus finmarchicus and C. helgolandicus in the northern North Sea (1958-1996) inferred from Continuous Plankton Recorder data

Patterns in the temporal abundance of Calanus finmarchicus and C. helgolandicus in 3 sub-regions of the northern North Sea are described from Continuous Plankton Recorder data, updating earlier studies with information from 3 more years (1994, 1995 and 1996). Abundances are considered using time-series techniques that allow the annual seasonal cycles observed within each sub-region to change over the long term. It is demonstrated that, as long-term trends of C. finmarchicus and C. helgolandicus fluctuated in the northern North Sea between 1958 and 1996, simultaneous changes also occurred in the annual seasonal cycles of both species. The results are discussed in relation to local sea-surface temperatures and the North Atlantic Oscillation index.
Re-establishment rate of reindeer lichen species following conventional disc trenching and HuMinMix soil preparation in Pinus-lichen clear-cut stands: a survey study in northern Sweden

Abstract The re-establishment rates of reindeer lichen following conventional soil preparation by disc trenching and gentle soil preparation using HuMinMix apparatus were calculated from data acquired in surveys of 17 Pinus–lichen clear-cut stands in northern Sweden conducted 1–15 years after the treatments. The maximum lichen cover and biomass recorded in areas scarified by disc trenching were 29% and 24% of the lichen cover and biomass measured in adjacent intact lichen mats in the surveyed stands after 15 years. By contrast, 9 years after scarification, the corresponding percentages measured in areas disturbed by the HuMinMix treatment were 91% and 100%, respectively. According to calculated linear regressions, the reindeer lichen cover could be completely re-established just one decade after HuMinMix treatment. Ground lichen diversity in the scarified areas was also inventoried. The significant increase in lichen diversity for HuMinMix, especially of early-successional species, could explain the more rapid re-establishment of late-successional lichens (e.g. Cladonia stellaris spp.), compared with disc trenching. Thus, the study demonstrates that both the degree of initial disturbance and the re-establishment rate of reindeer lichen must be considered when estimating the effects of scarification on lichen loss for reindeer grazing over time.
Larval growth rates and sexual differences of resource allocation in the cetoniine scarab Mecynorhina polyphemus Fabricius 1781 (Coleoptera: Scarabaeidae: Goliathini)

Larval ontogeny of the scarab Mecynorhina polyphemus was monitored throughout all instars, and larvae were weighed at 7-day intervals. Durations of the prepupal, pupal and postpupal stages were recorded. Larvae increase their body masses over 300 times during ontogeny. Male imagines are larger than females, and this is primarily a function of faster growth rates during instar III, resulting in significantly heavier larvae at the end of this instar. The durations of the three instars are not significantly different in males and females, but the duration of the prepupal and postpupal phases is significantly longer in males. There is a strong correlation in both sexes between maximal larval mass and the mass of the imago, but larval mass–imago mass scales with significantly different slopes in males and females. Male larvae must allocate increasingly more resources into production of cephalic horns with increments in larval mass, requiring differently proportioned pupal chambers.
Damage Detection

A break in both strands of the DNA double helix is potentially very dangerous for organisms because the free ends can recombine inappropriately with other parts of the genome and cause substantial damage. Eukaryotic cells sense and attempt to repair such breaks very rapidly, through the recruitment of DNA repair proteins to the sites of damage, forming nuclear repair foci. Soutoglou and Misteli have tethered various repair factors individually to unbroken DNA in human tissue culture cells and find that, surprisingly, even in the absence of DNA damage, repair foci form at the tether site. The DNA damage response may thus involve amplification of the damage signaling cascade, and the damage-sensing proteins may detect alterations in the higher-order structure of chromatin around the break. E. Soutoglou, T. Misteli, Activation of the cellular DNA damage response in the absence of DNA lesions. Science 320, 1507-1510 (2008). [Abstract] [Full Text]
Vegetational Diversity, Ants (Hymenoptera: Formicidae), and Herbivorous Pests in a Neotropical Agroecosystem

The effect of vegetational diversity on ants and herbivores was studied in a maize-bean (Zea mays-Phaseolus vulgaris) biculture and a maize monoculture in Nicaragua. Three basic hypotheses were examined: (1) the abundance of herbivores on maize would be less in the biculture than in the monoculture, (2) ant foraging activity would be higher in the biculture, and (3)the effect of ants as natural enemies of maize pests would account for differences in the abundance of those pests in the bicultures. The effects of plant diversity on the abundance of Spodoptera frugiperda (J. E. Smith), the fall armyworm, and Dalbulus maidis (De Long & Wolcott), the corn leafhopper, were examined. Ant-foraging activity was estimated as the proportion of tunafish baits occupied by ants in monocultures and bicultures. The effect of ants on the maize herbivores was investigated by excluding ants through selective poisoning. Cropping patterns significantly influenced the numbers of fall armyworm and corn leafhopper, but in different ways. The corn leafhopper was more abundant in bicultures, and the fall armyworm was more abundant in monocultures. No significant difference was found in the proportion of baits occupied by ants in maize monocultures and maize- bean bicultures. Ants had a significant effect on the two main maize pests, S. frugiperda and D. maidis . There were significantly higher numbers of both pests in plots where ant foraging activity was reduced with insecticide. These results suggest the possibility of using ants as agents of biological control in the maize agroecosystem in Nicaragua.
Presenilins mediate a dual intramembranous γ‐secretase cleavage of Notch‐1

Following ectodomain shedding, Notch‐1 undergoes presenilin (PS)‐dependent constitutive intramembranous endoproteolysis at site‐3. This cleavage is similar to the PS‐dependent γ‐secretase cleavage of the β‐amyloid precursor protein (βAPP). However, topological differences in cleavage resulting in amyloid β‐peptide (Aβ) or the Notch‐1 intracellular domain (NICD) indicated independent mechanisms of proteolytic cleavage. We now demonstrate the secretion of an N‐terminal Notch‐1 Aβ‐like fragment (Nβ). Analysis of Nβ by MALDI‐TOF MS revealed that Nβ is cleaved at a novel site (site‐4, S4) near the middle of the transmembrane domain. Like the corresponding cleavage of βAPP at position 40 and 42 of the Aβ domain, S4 cleavage is PS dependent. The precision of this cleavage is affected by familial Alzheimer's disease‐associated PS1 mutations similar to the pathological endoproteolysis of βAPP. Considering these similarities between intramembranous processing of Notch and βAPP, we conclude that these proteins are cleaved by a common mechanism utilizing the same protease, i.e. PS/γ‐secretase.
CONTROL OF PEST SPECIES

The authors evaluated cultural methods used for reintroducing Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) to mined sites in the Rocky Mountains and Northern Plains. Fresh topsoil, surface-applied mulch and removal of plant competition proved useful during the first two years following germination. Cool, wet conditions during the second growth-year also promoted successful establishment of this once widelydistributed species.
Comparing the effects of offset and non‐offset circle hooks on catch rates of fish and sea turtles in a shallow longline fishery

1.This study compared the catch rates of targeted dolphinfish or mahimahi (Coryphaena hippurus), and sea turtles and other fish bycatch in a shallow-set Costa Rican longline fishery using 14/0 circle hooks with and without a 10° offset. The effect of hook offset on hooking location and injury in captured sea turtles, specifically if the hooking was external, in the mouth, or in the esophagus was also evaluated. 2.Results were compared from six trips totalling 33 876 hooks with squid (Dosidicus gigas) used as bait. In total, mahimahi catch-per-unit-effort (CPUE, expressed as number caught per 1000 hooks) was similar between hook types (CPUE∼52). 3.Olive ridley sea turtles (Lepidochelys olivacea) were caught on all 42 sets. In total, 640 olive ridley turtles were caught and released alive. There were no significant differences in the number of sea turtles caught between hooks with and without an offset (CPUE∼19) nor between hook type and anatomical hooking location, suggesting similar levels of injury for turtles caught on each hook type. 4.These data suggest that a 10° offset on 14/0 circle hooks does not confer any selective advantages over hooks with no offset with respect to capture rates of mahimahi, sea turtles, sharks, or pelagic stingrays in a shallow set pelagic longline fishery. Copyright © 2010 John Wiley & Sons, Ltd.
Molecular Identity of Species and Isolates of Internal Pore Fungi Antrodia spp. and Oligoporus placenta

Summary Antrodia vaillantii (DC.: Fr.) Ryv. , A. serialis (Fr.) Donk, A. sinuosa (Fr.) P. Karsten, A. xantha (Fr.: Fr.) Ryv. and Oligoporus placenta (Fr.) Gilb. & Ryv. form a group of internal brown-rot fungi (‘Porenschwämme’), which are associated with decay of coniferous woodwork in buildings and timber in ground contact. The fungi have similar occurrence, biology, fruit bodies and mycelia. Their nomenclature has a confusing history and is still not uniform. For a better understanding of the domestic pore fungi and for a reliable species differentiation and identification of isolates, the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) was amplified by polymerase chain reaction and sequenced. Isolates from decayed wood and from culture collections were used. The ITS sequences characteristic of A. vaillantii, A. serialis,A. sinuosa, A. xantha and O. placenta were obtained and deposited in the international databases. The ITS size ranges from 636 to 668 bp. Intraspecific variation was low. A dendrogram was performed for the phylogenetic relationship. Some isolates obtained mislabelled were named correctly according to the ITS sequence. The sequences contribute to our collection of ITS data from internal wood decay fungi made to characterize fungi in culture.
A Correction to the Review Titled: "Oncogenic EGFR Signaling Networks in Glioma" by P. H. Huang, A. M. Xu, F. M. White

The corrected sentence reads, “The point mutations R84K, A265V/D/T, P545L, and G574V are located at the interfaces of domains I, II, and IV, which prevents the formation of the closed inactive form and shifts the equilibrium to favor the open form of the receptor. ” The online full text view of the article has been corrected. A corrected PDF (http://stke.sciencemag.org/cgi/reprint/2/87/ re6.pdf) is available starting 22 September 2009.