Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of predation, trout density and discharge on habitat use by brown trout, Salmo trutta, in artificial streams

SUMMARY 1. The effects of predation risk, fish density and discharge on habitat use by juvenile brown trout, Salmo trutta, in four artificial streams were studied. Each stream contained three habitats, riffles, runs and pools, the latter two each being further divided into shallow margins and deeper mid-regions. 2. The presence of northern pike, Esox Indus, caused trout to decrease use of pool midregions, where pike also occurred, and to increase use of other habitats. Increasing the number of trout caused trout to increase use of pools and the shallow margins of runs. Decreasing discharge reduced the area of the run and pool margins covered by water, thereby reducing use of these areas by trout. 3. Habitat selection indices for the different treatments were calculated. The data indicated that riffles and the mid-regions of runs were preferred habitats, whereas run margins and pools were inferior habitats used when intraspecific fish densities were high. 4. Despite density- and discharge-dependent habitat use by trout, the number of trout consumed by pike was independent of trout density and discharge. 5. The results reveal the flexibility of habitat use by trout and illustrate the potential danger of applying data on habitat use in one stream to others where habitat availability and bioric interactions may differ.
Meta-analysis of interspecies microarray sets of cardiac diseases revealed common and disease-specific signatures

Cardiac diseases are the most common life-threatening diseases in the world. The present study aimed to identify the common and disease-specific signatures for various cardiac diseases by using interspecies microarray sets. By meta-analysis of the datasets, we found 106 common differentially expressed genes (DEGs) between humans and mice. The common DEGs were further examined using various methods such as functional enrichment analysis, randomized network analysis, and cluster-network analysis. By analysis of 11 functional clusters, we obtained 12 highly sensitive common cardiac disease-associated genes that had never been identified before. To examine the sensitivity of the genes to the cardiac pathology, junctate-transgenic (TG) mice with cardiac hypertrophy and arrhythmias symptoms were used. The study led to the identification of eight positive genes (i.e., Synpo2l, Pros1, Crlf1, Col3a1, Frzb, Tm9sf3, Prdx4, and Ltbp2), highly upregulated in the TG mice. Cluster and network analysis showed that the cell survival and death network (cluster 7), extracellular network (cluster 9), and inflammation network (cluster 11) are cardiac disease-specific clusters. We also found that transforming growth factor-β signaling was closely related to the common signatures and that necrosis factor-κB signaling was a core pathway for inflammatory dilated cardiomyopathy. Taken together, our data provide a comprehensive analysis method to identify common and disease-specific signatures.
Evidence of panmixia between sympatric life history forms of coastal cutthroat trout in two lower Columbia River tributaries

Abstract Coastal cutthroat trout Oncorhynchus clarkii clarkii exhibit resident and migratory life history strategies that often occur sympatrically, but the relationship between these forms within a population is poorly characterized. Through use of passive integrated transponder technology, migratory and resident coastal cutthroat trout were identified in two lower Columbia River tributaries (Abernathy Creek and the Chinook River) separated by more than 80 km. Genetic data from 17 highly variable microsatellite loci were used to ascertain the genetic population structure of these life history forms within and between streams. No distinct genetic separation was observed between the life history forms within a stream, as assessed by four different statistical approaches: permutation tests based on the genetic differentiation index F ST, principal components analysis of individuals, analysis of molecular variance, and contingency tests of allele frequency heterogeneity. Genetic differences were an order of .
Rôle des cellules mésectodermiques issues des crêtes neurales céphaliques dans la formation des arcs branchiaux et du squelette viscéral

The participation of neural crest cells in the formation of the branchial arches and especially of the hypobranchial skeleton has been studied with heterospecific grafts of quail neural tube into the chick embryo. According to the labelling technique devised by Le Douarin, the differences between quail and chick interphase nuclei make it possible to use quail cells as cellular markers in this system. The excision of the mesencephalo-rhombencephalic primordium of 4- to 12-somite chick embryos results in the atrophy of the branchial arches, and in important deficiencies of the hypobranchial skeleton. Nevertheless, the nearly complete absence of the branchial mesenchyme does not prevent the visceral pouches and clefts from forming. The isotopic and isochronic graft of quail neural primordium into the chick shows that the mesenchymal component of the branchial arches is of neurectodermal origin, except for the muscle plates and the endothelium of the aortic arches, which derive from the mesoderm. The mesencephalic neural crests give rise to the totality of the mesenchyme of the first branchial arch and partially to that of the second one, while the rhombencephalon contributes to the formation of the second, third and fourth arches. The stability of the marker system produced by quail cells implanted into the chick makes it possible to follow the migrating cells until they have reached their definitive localization in the various structures of the hypobranchial skeleton, which thus appears to be entirely of neurectodermal origin. The cells arising from the mesencephalic neural primordium constitute the lower jaw skeleton (Meckel9s cartilage and bones) and are all still in the process of migration at the 6-somite stage. Cells originating from the rhombencephalon have left the neural axis at the 9- to 10-somite stage for the anterior part (in front of the first somite) and at the 11- to 12-somite stage for the posterior rhombencephalon. Differentiation of mesectodermal cells into chondrocytes and osteocytes has been observed during the morphogenesis of the visceral skeleton.
Fertilization and early embryology: Autocrine/paracrine function of transforming growth factor-β1 in porcine granulosa cells

The present study was undertaken to investigate the effects of transforming growth factor (TGF)-beta 1 on ovarian steroidogenesis in immature or moderately mature porcine granulosa cells in vitro. TGF-beta 1 (0.01-10 ng/ml) significantly attenuated progesterone release from the basal and follicle stimulating hormone-stimulated porcine granulosa cells, and significantly increased DNA synthesis. TGF-beta 1 also significantly increased the extracellular accumulation of cyclic AMP, but did not change the production of inositol phosphate or the intracellular calcium concentration in these cells. Thus, TGF-beta 1 appears to have a direct effect on porcine granulosa cell function, regulating the differential synthesis of progesterone mainly via the intracellular signal transduction of the cyclic AMP-protein kinase A pathway. This growth factor may play a physiologically significant role in controlling differentiation of immature and moderately mature porcine granulosa cells via an autocrine/paracrine mechanism.
Corn Tolerance to Weed Interference Varies with Preceding Crop

Abstract Crop diversity may improve tolerance to weed interference and reduce the need for herbicides. This experiment measured weed interference in corn as affected by the preceding crop in two studies. The first study, based on interference of the resident weed community, compared dry pea, soybean, canola, and spring wheat for effect on corn tolerance to weeds. Prominent weeds were green and yellow foxtail. The second study examined corn tolerance to a uniform infestation of foxtail millet as affected by dry pea, soybean, spring wheat, and corn as preceding crops. Each plot was split into weed-free and weed-infested subplots in both studies. Corn was most tolerant to weed interference following dry pea; compared with soybean, dry pea improved corn tolerance more than twofold. Corn also yielded the highest in weed-free conditions following dry pea; compared across 4 yr, corn yielded 7 to 23% more following dry pea than following either soybean or spring wheat. Crop diversity has helped producers reduce herbicide inputs in the Great Plains and may provide an additional benefit of reducing weed impact on crop yield. Nomenclature: Green foxtail, Setaria viridis (L.) Beauv. ; yellow foxtail, Setaria pumila (Poir.) Roemer & J.A. Schultes; canola, Brassica napus L. ; corn, Zea mays L. ; dry pea, Pisum sativum L. ; foxtail millet, Setaria italica (L.) Beauv. ; soybean, Glycine max (L.) Merr. ; spring wheat, Triticum aestivum L.
Momentum and energy in the wake of a pigeon (Columba livia) in slow flight

A technique is described whereby the vortex wake of birds in slow forward flight may be investigated with a view towards testing some of the assumptions and predictions of existing theoretical models of bird flight. Multiflash stereophotogrammetry was used to analyse the wake as a pigeon passed through a cloud of neutrally-buoyant helium bubbles. All photographs obtained support the hypothesis that the wake is composed of a chain of discrete, small-cored vortex rings. This being the case, velocity profiles taken from sections through the wake allow us to estimate the momentum in the wake as represented by vortex rings. The momentum in the wake appears to be approximately half that required for weight support in unaccelerated, level flight. The possible causes and consequences of this paradoxical result are discussed.
Human finger types

In the present investigation measurements were made of 620 hands, of which 402 were males and 218 females. All of the subjects were white adults, mostly medical students in the University of Toronto, supplemented by other students, members of the staff, militia recruits, and friends of the writer. No one was measured who had a history of fracture or dislocation of either the index, ring, or middle fingers. In the human hand the middle finger is the longest, the thumb is the shortest, and the little finger is the next shortest. The relative lengths of the index and ring fingers make a disputable point, and to elucidate it the present investigation was undertaken. Authorities differ as to the relative lengths of the index and ring fingers. Wood Jones (’20) and Schultz (’24) state that the index finger is usually longer than the ring finger and Wood Jones describes the long index finger as a ‘characteristic human specialisation. ’ Baker ( ’88), on the contrary, found the ring finger to be the longer, though he adds that “the index finger sometimes equals the ring finger and rarely exceeds it. ” Ecker (’74), working with negroes, found the ring finger to be longer in males and the index finger to be longer in females. hlantegazza (’77) found “over 500 with a longer ring fhger, men predominating, and under 100 with a longer index finger, women predominating. ’’ A similar observation was made by Pfitzner, as quoted by Schwalbe ( ’90).
Transcriptome profiling of the shoot and root tips of S562L, a soybean GmCLAVATA1A mutant

Plant shoot apical meristems (SAM) and root apical meristems (RAM) contain stem cells that form overall-plant architecture. Mechanisms acting in these regions keep a balance between the stem cell population and differentiation. These mechanisms are well-studied in Arabidopsis, but little is known in the legume soybean (Glycine max (L.) Merr. ). In Arabidopsis, the Leucine-rich repeat (LRR) Receptor kinase CLAVATA1 (CLV1) is a crucial regulator of this process in the SAM. In soybean, the receptor most similar to ATCLV1 is GmNARK, which is involved in nodulation control. In contrast, the homeologous partner of GmNARK in soybean, called GmCLV1A, appears to have no function in ‘Autoregulation of nodulation’ (AON) a role in regulating shoot architecture in the SAM. Here, the transcriptome of the shoot and root tip areas of a chemically induced and TILLING-selected GmCLV1A missense mutant, S562L, and its wild type, cultivar Forrest, were analysed to identify genes which are affected by impaired function of GmCLV1A. Among the differentially expressed genes identified, many were categorised as having a role in receptor kinase activity, transcription or defense/stress-response. Molecular categories over-represented in the shoot tip of the mutant include those involved in hormone biosynthesis/activity and secondary metabolism, signalling, photosynthesis, and transport. Functional categories including those involved in polyamine metabolism, nucleotide metabolism, RNA regulation, protein targeting and protein degradation were under-represented in the shoot tip of the mutant. In the root tip, categories associated with signal ling, transport, protein synthesis and metabolism were over-represented in the mutant, while categories associated with cell wall degradation, stress, RNA regulation, protein degradation and targeting were under-represented in the mutant. Factors similar to Arabidopsis regulatory components are most likely functioning in specialised shoot structures in legumes. Furthermore, GmCLV1A may have an unexpected role in the regulation of flavonoid biosynthesis in soybean.
LRRK-2 as a Key Molecule Bridging Inflammation to Parkinson's Disease

The pathogenetic mechanisms leading to typical Parkinson’s Disease (PD), the second most common human neurodegenerative disorder remains unknown. Genetic variants of Leucine-Rich Repeat Kinase 2 (LRRK-2) are associated with a significantly enhanced risk for PD. The discovery that late-onset PD could be caused by the inheritance of a mutation in the LRRK-2 gene leading to familial as well as sporadic forms of PD has provided researchers an opportunity to explore the pathophysiological events underlying this complex disease. Despite extensive research our understanding of LRRK-2 biological function and regulation remains rudimentary. In this review, we give an insight into the role of LRRK-2 in modulating inflammation in the central nervous system and we hypothesize that LRRK-2 dysfunction may favor the neurodegenerative process
Long-term biomass yield and species composition in native perennial bioenergy cropping systems.

Biomass yield is an important factor when recommending native perennial plants and mixtures for bioenergy production. Our objective was to determine long-term biomass yields in fertilized and unfertilized native plant monocultures and mixtures that show promise for bioenergy across diverse environments in the Upper Midwest. We measured biomass yields, species composition, and diversity annually in monocultures and mixtures ranging from 4 to 24 planted species including grasses, legumes, and other forbs; each managed with and without 67 kg N ha–1 fertilizer applied annually at nine locations for 7 yr. Without N fertilization, switchgrass (Panicum virgatum L.) monocultures and an eight-species mixture of grasses and legumes produced the most biomass over locations and years (5.1 Mg ha–1). With N fertilizer, switchgrass monocultures and a four-species mixture of grasses produced the highest yields (6.8 and 6.4 Mg ha–1). Over time, biomass yields increased for switchgrass, decreased for Canada wild rye (Elymus canadensis L.), and remained stable for the high diversity mixtures. Other mixtures had nonlinear changes in yield, likely related to changes in species composition. Although the relative abundance of individual species changed over time, Shannon diversity was constant except for the four-species legume mixture where it decreased. Contrary to other studies, N fertilization did not decrease species diversity through time. Diversity was positively related to biomass yield following establishment, but the strength of the relationship diminished with stand age. Native plant mixtures managed with and without N fertilizer can yield similar biomass compared with highly productive monocultures in the Upper Midwest.
Mortality of Landlocked Atlantic Salmon (Salmo salar) Hooked on Flies and Worms in a River Nursery Area

Abstract To evaluate mortality of landlocked Atlantic salmon (Salmo salar) caught on flies and worms in a typical river nursery area, a study was carried out at the East Outlet of Moosehead Lake, Maine, in June 1975-1977. Of 177 fish caught in the 3 yr, 22% died after hooking. All of the 74 control fish caught in a fishway trap survived. Mortality of worm-hooked fish (35%) was significantly greater than that of fish hooked on flies (4%). Higher mortality of worm-hooked fish was attributed largely to anatomical site of hooking. Nearly 37% of worm-caught fish were hooked in the esophagus, but most fly-caught fish were hooked either in the jaws or mouth. Mortality of fish that bled after hooking (86%) was significantly greater than that of nonbleeding fish (15%). No significant differences were found between hooking mortality of fish of ages II and III nor between legal size (≳356 mm) and sublegal fish. We concluded that closure of heavily fished landlocked Atlantic salmon nursery areas to worm fishing may b.
Genetic panmixia in New Zealand's Grey-faced Petrel: implications for conservation and restoration

Abstract Seabirds are highly vagile yet many have restricted gene flow owing to physical barriers (e.g. land or ice) or non-physical barriers (e.g. philopatry), which often results in population divergence. Identification of distinct units is important for defining conservation status, guiding restoration of populations and coastal ecosystems, and managing the effect of anthropogenic activities (e.g. fisheries by-catch, customary harvesting). We collected DNA samples from 390 Grey-faced Petrels (Pterodroma macroptera gouldi) at 13 colonies across their New Zealand breeding range to examine population genetic structure. We sequenced part of the mitochondrial control region and genotyped 12 microsatellite DNA loci. We found high diversity in mitochondrial DNA in all colonies. Analyses showed a lack of genetic structure in Grey-faced Petrels that we propose is a result of high levels of gene flow. Although, we found no genetically distinct populations we suggest that any translocations for conservation should be done with caution and with some consideration of the proximity of a restoration site to a natal Grey-faced Petrel colony. Also, the high levels of gene flow we found suggest that the method of using acoustic attraction and natural behaviour to establish new colonies offers a useful addition, or alternative, to translocations of chicks. These results provide a genetic basis for conservation and restoration efforts for the Grey-faced Petrel.
Aspects of the breeding biology of the Tinkling Cisticola Cisticola rufilatus

The Tinkling Cisticola Cisticola rufilatus is a shy, elusive species that is easily overlooked unless its distinctive call is heard. Consequently, the habits and general biology of the species are poorly known and most of our knowledge of the species is based on observations made by Vincent (1948). Here we report on aspects of the breeding biology of the Tinkling Cisticola as observed over two breeding seasons (2005/06 and 2006/07) in the Polokwane Nature Reserve (23°58′ S, 29°28′ E, 1 350 m above sea level), South Africa. Tinkling Cisticolas were captured with mist-nets, individually banded with numbered metal bands and some individuals were fitted with a combination of coloured plastic leg bands to aid in future identification. Banded birds were observed with binoculars (10 × 50) either from a hide or by walking slowly through the study area to obtain information about site fidelity, roles of the sexes in breeding and to get crude estimates of their territory sizes. Nests were located by walking through different territories and inspecting potentially suitable nest sites and using parental behaviour. When a nest was found during the nest construction or the laying period, it was visited daily to determine when incubation commenced. Once incubation commenced, nests were monitored every second day until day 10, when nests were once more visited daily in order to accurately determine the incubation period. All other nests found during the incubation or nestling period were visited on alternate days. The fresh egg mass (g) and dimensions, i.e. the maximum length (L; mm) and maximum width (W; mm) were recorded at two nests. The fresh egg mass (FEM) was taken as the mass of the eggs at clutch completion. Nestling growth and development were recorded with regard to: (1) plumage development, (2) increase in mass (g) measured with a portable digital electronic balance and (3) increase in tarsus length (mm) and head length (mm) measured with a vernier calliper and as described by de Beer et al. (2001). The growth rate of two nestlings was determined by fitting the growth curve by a logistic equation, having the form:
The Ecology of Avian Vocal Learning

Repertoire sizes and song development among birds must be understood as facets of life history strategies. In some groups repertoires appear related to population densities, with more frequent interactions in dense populations leading to an escalation of signal diversity. The extent and timing of vocal learning also differs among taxonomic groups and depends to some extent on habitat stability, site fidelity, and dispersal strategies of young. (Accepted for publication 1 October 1982)
Cloning, Expression and Characterization of PnLOX2 Gene Related to Aspergillus flavus-resistance from Peanut (Arachis hypogaea L.) Seed Coat

Aspergillus flavus is one of the major diseases of peanut. The objective of the study was to clone PnLOX2 gene from peanut seed coat and analyze its expression. Real-time RT-PCR analysis indicated that the gene was overexpressed in the challenge of Aspergillus flavus and the greatest expression occurred 10 days after inoculation. The full length of PnLOX2 gene was 2592bp and encoded a 97.5kDa protein containing 863 amino acids. The fusion protein (apparent 121.5kDa) only existed in the precipitation and the maximum was obtained by inducing at 37oC for 3.5h. As a result of response to the challenge of Aspergillus flavus, PnLOX2 gene was more greatly expressed in the resistant genotype than in the susceptible genotype. It indicated that PnLOX2 gene was closely related to Aspergillus flavus-resistance of peanut. Further investigations were needed to bacteriostatically identify the gene in vitro.