bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Shields stress to reconstruct and forecast changes in river metabolism
Authors: CRONIN GREG , MCCUTCHAN JAMES H. , PITLICK JOHN , LEWIS WILLIAM M. 
Published: May 2007

Summary1. Discharge patterns of streams and rivers may be substantially affected by changes in water management, land use, or climate. Such hydrological alterations are likely to influence biotic processes, including overall ecosystem metabolism (photosynthesis and respiration). One regulator of aquatic ecosystem metabolism directly tied to hydrology is movement of bed sediments.2. We propose that ecosystem metabolism can be reconstructed or predicted for any suite of hydrological conditions through the use of quantitative relationships between discharge, bed movement and metabolism. We tested this concept on a plains reach of the South Platte River in Colorado.3. Movement of bed sediments was predicted from river discharge and the Shields stress, a ratio of velocity‐induced stress to sediment grain size. Quantitative relationships were established empirically between metabolic response to bed movement and recovery from bed movement, thus linking metabolism to hydrology.4. The linkage of metabolism to hydrology allowed us to reconstruct daily photosynthesis and respiration over the 70‐year period for which discharge is known at our study site on the South Platte River. The reconstruction shows major ecological change caused by hydrological manipulation: the river has lost two‐thirds of its photosynthetic potential, and the ratio of photosynthesis to respiration is now much lower than it was prior to 1960.5. The same approach could be used to anticipate ecological responses to proposed hydrological manipulations, to quantify benefits of hydrological restoration, or to illustrate potential effects of change in climate or land use on flowing‐water ecosystems.
Wide‐angle linear forward modelling of synthetic seismograms
Authors: Dey A. , Gisolf A. 
Published: May 2007

ABSTRACTWe address the issue of linearity and scale dependence in forward modelling of seismic data from well logs, for large ray parameters, wide angles or large offsets. We present a forward model, within the context of seismic‐to‐well matching, that is linearized in the elastic properties of the earth. This model preserves linearity at large ray parameters and can handle fine‐layering effects such as induced anisotropy. Starting from a low‐contrast small‐ray‐parameter model, we extend it to a large‐ray‐parameter model by fully linearizing the elastic‐property contrasts. Overall linearity of the forward model is extended by partitioning the compressional‐wave and shear‐wave velocity fields into two fundamental scales: a kinematic scale that governs wavefield propagation effects and a dynamic scale that governs wavefield scattering effects. This analysis reveals that the standard practice in forward modelling of strongly filtering the ratio of compressional‐wave velocity to shear‐wave velocity is well founded in the underlying physics. The partitioning of the velocity fields also leads naturally to forward modelling that accounts fully for stretch effects, to resolution of the angle‐of‐incidence versus ray‐parameter dichotomy in seismic‐amplitude analysis, and to full accounting for induced anisotropy and dispersion effects due to fine‐layering of isotropic media. With the onset of routine long‐offset acquisition and the compelling need to optimize asset management in order to maximize reserve recovery, this forward model recognizes the physics of seismic wave propagation and enables a more complete exploitation of amplitude information in pre‐critical seismic data.
Genomic and evolutionary analyses of Tango transposons in Aedes aegypti, Anopheles gambiae and other mosquito species
Authors: Coy M. R. , Tu Z. 
Published: May 2007

Abstract Tango is a transposon of the Tc1 family and was originally discovered in the African malaria mosquito, Anopheles gambiae. Here we report a systematic analysis of the genome sequence of the yellow fever mosquito, Aedes aegypti, which uncovered three distinct Tango transposons. We name the only An. gambiae Tango transposon AgTango1 and the three Ae. aegypti Tango elements AeTango1–3. Like AgTango1, AeTango1 and AeTango2 elements both have members that retain characteristics of autonomous elements such as intact open reading frames and terminal inverted repeats (TIRs). AeTango3 is a degenerate transposon with no full‐length members. All full‐length Tango transposons contain subterminal direct repeats within their TIRs. AgTango1 and AeTango1–3 form a single clade among other Tc1 transposons. Within this clade, AgTango1 and AeTango1 are closely related and share approximately 80% identity at the amino acid level, which exceeds the level of similarity of the majority of host genes in the two species. A survey of Tango in other mosquito species was carried out using degenerate PCR. Tango was isolated and sequenced in all members of the An. gambiae species complex, Aedes albopictus and Ochlerotatus atropalpus. Oc. atropalpus contains a rich diversity of Tango elements, while Tango elements in Ae. albopictus and the An. gambiae species complex all belong to Tango1. No Tango was detected in Culex pipiens quinquefasciatus, Anopheles stephensi, Anopheles dirus, Anopheles farauti or Anopheles albimanus using degenerate PCR. Bioinformatic searches of the Cx. p. quinquefasciatus (~10 × coverage) and An. stephensi (0.33 × coverage) databases also failed to uncover any Tango elements. Although other evolutionary scenarios cannot be ruled out, there are indications that Tango1 underwent horizontal transfer among divergent mosquito species.
Empirical evaluation of non‐invasive capture–mark–recapture estimation of population size based on a single sampling session
Authors: PUECHMAILLE SEBASTIEN J , PETIT ERIC J 
Published: May 2007

SummaryNon‐invasive genetic data analysed with capture–mark–recapture (CMR) models can be used to estimate population size, particularly for elusive and endangered species. Data generated from non‐invasive genetic sampling are different, however, from conventional CMR data because individuals can be contacted several times within a single sampling session. Two methods have been proposed recently to accommodate this type of data, but no study has attempted to compare their estimates and evaluate their reliability compared with independent estimates of population size.We investigated the reliability and accuracy of estimating the abundance of lesser horseshoe batsRhinolophus hipposiderosby genotyping DNA from droppings collected non‐invasively at three colonies over 2 consecutive years. The number of times that each individual was ‘contacted’ (i.e. the number of droppings per individual) was used to estimate population size with two different published methods: a maximum likelihood and a Bayesian estimator.Among the 586 samples extracted, 534 provided a complete genotype at six to eight microsatellite loci, which enabled a reliable discrimination of 165 individuals. Statistical estimates of colony sizes often included independent estimates obtained from visual counts, validating the method. Discrepancies appeared when capture heterogeneity was not taken into account while it occurred.Synthesis and applications.We have taken a first step towards improving methods of estimating numbers of bats by demonstrating that genetic data produced from bat faecal DNA are of high quality and can provide accurate estimates of population size even when samples are taken during only one sampling session. Such protocols provide valuable management tools for elusive and rare species in general. The method is relatively easy and cost‐efficient because only one sampling session is required.
Repeatedly out of Beringia:Cassiope tetragonaembraces the Arctic
Authors: Eidesen Pernille Bronken , Carlsen Tor , Molau Ulf , Brochmann Christian 
Published: May 2007

AbstractAim Eric Hultén hypothesized that most arctic plants initially radiated from Beringia in the Late Tertiary and persisted in this unglaciated area during the Pleistocene glaciations, while their distribution ranges were repeatedly fragmented and reformed elsewhere. Whereas taxonomic and fossil evidence suggest thatCassiope tetragonaoriginated in Beringia and expanded into the circumarctic area before the onset of the glaciations, lack of chloroplast DNA (cpDNA) variation may suggest that colonization was more recent. We address these contradictory scenarios using high‐resolution nuclear markers.Location Circumpolar Arctic.Methods The main analysis was by amplified fragment‐length polymorphism (AFLP), while sequences of chloroplast DNA verified the use ofCassiope mertensianaas an outgroup forC. tetragona.Data were analysed using Bayesian clustering, principal coordinates analyses, parsimony and neighbour‐joining, and measures of diversity and differentiation were calculated.Results The circumpolarC. tetragonassp.tetragonawas well separated from the North AmericanC. tetragonassp.saximontana. The genetic structure in ssp.tetragonashowed a strong east–west trend, with the Beringian populations in an intermediate position. The highest level of diversity was in Beringia, while the strongest differentiation in the data set was found between the populations from the Siberian Arctic west of Beringia and the remainder.Main conclusions The results are consistent with a Beringian origin of the species, but the levels and geographical patterns of differentiation and gene diversity suggest that the latest expansion from Beringia into the circumarctic was recent, possibly during the current interglacial. The results are in accordance with a recent leading‐edge mode of colonization, particularly towards the east throughout Canada/Greenland and across the North Atlantic into Scandinavia and Svalbard. As fossils demonstrate the presence of the species in North Greenland 2.5–2.0 Ma, as well as in the previous interglacial, we conclude thatC. tetragonaexpanded eastwards from Beringia several times and that the earlier emigrants of this woody species became extinct. The last major westward expansion from Beringia seems older, and the data suggest a separate Siberian refugium during at least one glaciation.
Asynchronous forest–stream coupling in a fire‐prone boreal landscape: insights from woody debris
Authors: ARSENEAULT DOMINIQUE , BOUCHER ÉTIENNE , BOUCHON ÉLODIE 
Published: May 2007

Summary

We used dendrochronology to reconstruct the transfer of coarse woody debris across a forest–stream interface in a fire‐prone boreal landscape. A sequence of regulating factors was considered from source to sink of in‐stream woody debris (SWD), including fire history at the landscape scale, patterns of post‐fire recovery of riparian forest and inputs of SWD at the scale of a stream reach and its associated floodplain, and burial of SWD at an excavated site.
Fires occurred repeatedly in the studied landscape (at least in 1708, 1733, 1791, 1811, c. 1838, c. 1850, 1882, 1941 and 1998), and were generally patchy on the floodplain because of the firebreak effect of the riparian corridor. Unburned forest remnants were regularly generated at the stream margin, thus permitting temporally continuous but spatially localized transfer of woody material across the forest–stream interface. These remaining forest patches also increased forest resilience by dispersing seeds and promoting conifer re‐establishment in burned areas.
Because of higher severity compared with previous fires, the 1941 fire burned almost everywhere on the floodplain, creating only a few widely isolated unburned forest remnants. Consequently, following an abrupt post‐fire increase, SWD inputs almost completely ceased. In addition, post‐fire recovery of the riparian wood source is slow because of the spatially restricted seed source.
In this alluvial stream, wood burial is faster than decay and largely determines the residence time of SWD. Because the residence time is about 150 years, the current density of SWD is high and contrasts sharply with the very low tree density at the stream margin. Although this long residence time helps maintain stream integrity while the forest is recovering from the 1941 fire, it is unlikely that SWD inputs would resume extensively before burial of the current SWD pool.
Our research exemplifies the potentially complex impacts of disturbances on material transfer between a source and a sink ecosystem. We conclude that when certain components of ecosystems are coupled by unidirectional flow, those components will behave asynchronously if a disturbance impact at the source ecosystem does not propagate rapidly to the sink and the source and the sink recover at different rates.
Use of two different dietary energy and protein contents to define nutritive requirements of lactating buffalo cows
Authors: Bovera F. , Cutrignelli M. I. , Calabrò S. , Piccolo G. , Tudisco R. , D'Urso S. , Infascelli F. 
Published: May 2007

SummaryTwo total mixed rations, differing in energy and protein concentrations (diet A: 6.1 MJ/kg DM of NEl, 112.5 g/kg DM of metabolizable protein, MP, and 101.7 g of protein digestible at the intestinal level, PDI, vs. diet B: 6.4 MJ, 95.1 g of MP, 78.9 g of PDI) were administered ad libitum for 1 year to two groups of 12 buffaloes in which the partial monthly turnover of animals allowed the lactation stage to be maintained close to 160 days. The diets were formulated to obtain, with a daily intake of about 15.5 kg of DM, a balanced energy supply but an excess of protein (diet A); the opposite occurred with diet B. The average dry matter intake recorded during the trial was 14.5 kg for diet A and 15.0 kg for diet B. Milk production was similar for both groups (7.94 kg vs. 7.95 kg). The diet with a higher protein concentration brought about a significant increase in protein, casein and non‐protein nitrogen contents in the milk. A significant increase in milk fat percentage was observed when the animals were fed the diet with a higher energy concentration. The serum urea concentration (8.62 mm/l) of buffaloes fed diet A was outside the physiological range for lactating buffaloes. The energy and protein conversion efficiencies for milk production were more favourable when their supplies were balanced: 3.58 MJ of NEl/kg of FPCM for diet A; 2.50 g of MP or 2.07 g of PDI/g of protein milk for diet B. Moreover, when the requirements were satisfied, greater energy or protein supplies failed to induce significant changes in milk yield and quality. Finally, regarding the great differences between estimated MP requirements and those recorded during the trial, the authors suggest that the equations used in the CPM‐Dairy software, formulated for dairy cows, are not applicable in buffaloes.
Subacute rumen acidosis in lactating cows: an investigation in intensive Italian dairy herds
Authors: Morgante M. , Stelletta C. , Berzaghi P. , Gianesella M. , Andrighetto I. 
Published: May 2007

SummarySubacute rumen acidosis (SARA) represents one of the most important metabolic disorders in intensive dairy farms that affects rumen fermentations, animal welfare, productivity and farm profitability. The aim of the present study was to study the occurrence of SARA in intensive Italian dairy herds and to determine the relationship between diet composition, ruminal pH and short chain fatty acids (SCFA) concentration. Ten commercial dairy herds were investigated; twelve cows in each herd were selected randomly among animal without clinical signs of disease, with good body condition and between 5 and 60 day‐in‐milk (DIM), to perform rumenocentesis and obtain rumen fluid. Ruminal pH was determined immediately after sampling and concentration of SCFA in ruminal fluid was determined on samples after storage. An other objective of this research was to study in detail the effects of rumenocentesis on animal health: this study could confirm the extreme validity of this technique as ruminal sampling. Results were subject to anova and correlation analysis using sigma stat 2.03. The results indicated the presence of SARA in three herds (more than 33% cows with rumen pH < 5.5), a critical situation (more than 33% cows with rumen pH < 5.8) in five farms and a normal rumen pH condition in two herds. In particular, dairy herds show on average SCFA concentration of 150, 145, 123 mmol/l for low pH, critical pH and normal pH herds respectively. There were not significant differences among diet composition even if herds with SARA showed a light discordance between initially chemistry composition and residual feed. In the affected herds it was not possible to understand the exact causes of SARA. Animal management seems to be one of the most important factors in developing SARA including total mixed ration preparation.
Use of Silybum marianum fruit extract in broiler chicken nutrition: influence on performance and meat quality
Authors: Schiavone A. , Righi F. , Quarantelli A. , Bruni R. , Serventi P. , Fusari A. 
Published: May 2007

SummaryThe present study aimed at evaluating the effects of different doses of silymarin in diet on broiler performances and meat quality. For the trial, 180 male chicks (ROSS 508), were allocated in to three groups (S0, S40 and S80) of 60 animals each receiving a basal diet supplemented with 0 ppm, 40 ppm and 80 ppm of a sylimarin (provided by a dry extract of Silybum marianum fruits) respectively. During the trial feed consumption and live body weight were taken every 20 days. At the age of 40 and 60 days blood samples were taken in order to evaluate protein, aspartate aminotransferase, cholesterol, tryglicerides and uric acid. At the age of 60 days animals were slaughtered, dressing percentages were evaluated and samples of breast and meat were taken to evaluate chemical composition and susceptibility of lipid peroxidation by means of thiobarbituric acid reactive substances. Silymarin at the tested doses did not affect growth performances but slightly affected slaughtering yields negatively, no specific hepatoprotective effect was found. Treatments reduced lipid content of both breast and thigh and increased muscles resistance to oxidative stress.
Characterization of Reactions to Powdery Mildew (Podosphaera pannosa) in Resistant and Susceptible Rose Genotypes
Authors: Dewitte A. , Leus L. , Van Huylenbroeck J. , Van Bockstaele E. , Höfte M. 
Published: May 2007

AbstractFungal development of powdery mildew Podosphaera pannosa (Wallr.: Fr.) de Bary on rose leaves depends on constitutive or induced resistance mechanisms present in attacked rose genotypes. The relationship between fungal development and plant resistance was investigated microscopically on young greenhouse leaves of four rose genotypes with different levels of resistance: Rosa wichuraiana, R. laevigata anemoides and R. hybrida cultivars ‘Excelsa’ and ‘Gomery’. Induced plant reactions, hydrogen peroxide production and cross sections through infected leaves were examined. The variation in development of the fungus on these rose genotypes depended on the relative presence of normal haustoria, abnormal haustoria, induced cell reactions, papilla formation or physical barriers. Formation of papillae could arrest up to one third of the successful penetrations. Papillae formation was often succeeded by total cell reaction. Abnormal haustoria were detected as rudimentary haustoria, haustoria with abnormal shape or haustoria without extra haustorial matrix. Post‐haustorial cell reactions, with and without cell collapse, were detected. In non‐collapsed cells, appositions were directed to both cell wall and haustorium. This was followed by accumulation of non‐identified, probably antifungal compounds. Both single and multicell reactions occurred. Hydrogen peroxide was detected during papilla formation and induced cell reactions.
Pathogenicity Confirmation of Ganoderma Disease of Coconut Using Early Diagnosis Technique
Authors: Karthikeyan M. , Radhika K. , Bhaskaran R. , Mathiyazhagan S. , Samiyappan R. , Velazhahan R. 
Published: May 2007

AbstractThe pathogenicity and diagnostic methods were standardized for Ganoderma disease of coconut. The pathogenicity of Ganoderma lucidum isolated from coconut was tested using six types of inoculation techniques. Two diagnostic methods, viz. indirect enzyme‐linked immunosorbent assay (ELISA) and polymerase chain reactions (PCR) were applied for the confirmation of pathogenicity in coconut seedlings. Polyclonal antibodies (PAbs) were raised against mycelial, basidiocarp and specific proteins of Ganoderma and used for detection of Ganoderma in inoculated seedlings through indirect ELISA technique. All the three PAbs could detect Ganoderma in diseased coconut root tissues in early stage of the disease before symptom expression by indirect – ELISA at the antiserum dilution of 1 : 1000 for mycelial protein, 1 : 700 for Ganoderma specific protein and 1 : 3000 for basidiocarp protein. Low cross‐reactions were observed with saprophytic fungi occurring in coconut roots and also with other basidiomycetous fungi. In PCR, primers Gan1 and Gan2 generated from internal transcribed spacer region of rDNA were used the detection that produced a product of 167‐bp size in Ganoderma infected plants. In the present investigation, spawn inoculum responded earlier within 8 weeks compared with other methods of inoculation as expressed by OD value in ELISA test. This was also confirmed by PCR technique. The combination of these two diagnostic methods for detection of Ganoderma infection was highly reliable, rapid and sensitive.
Development and Validation of Conventional and Quantitative Polymerase Chain Reaction Assays for the Detection of Storage Rot Potato Pathogens, Phytophthora erythroseptica, Pythium ultimum and Phoma foveata
Authors: Cullen D. W. , Toth I. K. , Boonham N. , Walsh K. , Barker I. , Lees A. K. 
Published: May 2007

AbstractThe diseases pink rot, watery wound rot and gangrene are important storage rot diseases of potato associated predominantly with Phytophthora erythroseptica (P.), Pythium ultimum (Py.) and Phoma exigua (Phoma) var. foveata respectively. Reliable molecular‐based diagnostic tests are required that will not only allow unequivocal identification of symptoms but will further advance epidemiological studies of these potato diseases to increase our understanding and contribute to more effective management and control strategies to the potato industry. Primers and probes were designed in specific regions of the internal transcribed spacer (ITS) regions to develop conventional and real‐time quantitative polymerase chain reaction (PCR) assays able to detect all possible fungal and oomycete pathogens causing pink rot, watery wound rot and gangrene. The specificity of each diagnostic assay was rigorously tested with over 500 fungal/oomycete plant pathogen isolates from potato and reference culture collections, and both conventional and real‐time PCR methods produced similar results. In terms of sensitivity, the detection limits for real‐time PCR went below ag DNA levels compared with pg DNA levels with conventional PCR. The real‐time PCR assays developed to detect Phoma foveata and Py. ultimum on tubers were suitable for the comparative Ct method (ΔΔCt) of quantification using the cytochrome oxidase gene of potato as a normalizer assay; an advantage as the need for a standard curve is eliminated. Each assay detected Phoma species (var. foveata or exigua) from naturally infected tubers showing symptoms of gangrene, and P. erythroseptica or Py. ultimum were also detected following inoculation of Russet Burbank tubers. Each diagnostic assay developed could reliably detect and distinguish between the pink rot, watery wound rot and gangrene‐causing potato pathogens.