bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luminous pulses during triggered lightning
Authors: Winn W. P. , Eastvedt E. M. , Trueblood J. J. , Eack K. B. , Edens H. E. , Aulich G. D. , Hunyady S. J. , Murray W. C. 
Published: April 2012

A triggered lightning flash that transferred negative charge to ground in central New Mexico produced more than three levels of branching above the main channel to ground in a 1 km vertical field of view. A high‐speed video recording shows that the main channel had about 50 brief luminous pulses, many of which were superimposed on a slowly changing persistent luminosity. In contrast, superposition was rare in the uppermost visible branches because luminous pulses first appeared on preexisting dark channels before merging into a luminous channel. This observation suggests that luminous pulses in triggered and natural lightning originate only on dark branches and that the complexity of the main channel to ground is the result of multiple mergers of dark branches with pulses into luminous branches without pulses. This suggestion is contrary to an earlier conclusion that there are two kinds of luminous pulses. We also observe behavior characteristic of electromagnetic waves on transmission lines: when a downward propagating luminous pulse reaches a junction with another initially dark branch, it travels both upward and downward along that branch. Upon reaching the ground the downward propagating wave produces a bright reflection which also splits at the junctions, producing luminosity for a short distance upward in one direction while propagating much farther upward along the path charged by the downward propagating wave. However, when a downward moving luminous pulse reaches a junction with an initially luminous branch, splitting is not evident, probably due to the greater conductivity of the luminous channel.
Influences of Hatchery Supplementation, Spawner Distribution, and Habitat on Genetic Structure of Chinook Salmon in the South Fork Salmon River, Idaho
Authors: Matala Andrew P. , Narum Shawn R. , Young William , Vogel Jason L. 
Published: April 2012

Abstract
We evaluated the genetic influence of hatchery supplementation on distinct naturally spawning populations of Chinook salmon Oncorhynchus tshawytscha in the South Fork Salmon River (SFSR), Idaho. Genetic tissue samples were collected from unmarked natural-origin and McCall Fish Hatchery (MFH)-reared Chinook salmon carcasses, and fish were identified by an adipose fin clip at five main-stem sites located both upstream and downstream of a seasonal exclusionary weir in the upper SFSR. We evaluated allele frequency data across 95 single-nucleotide polymorphism loci to determine the extent of genetic differentiation among collections. Genetic distance analyses and homogeneity tests indicated little subpopulation distinction in the upper SFSR. The weak overall genetic structure (global F ST = 0.010) is likely reflective of a population diversity similar to the historical structure with introgression by MFH stock in the naturally spawning population of the upper SFSR. Further analyses were conducted to evaluate the genetic structure among the upper SFSR and spawning aggregates in two adjacent SFSR tributaries: the Secesh River, which is devoid of any hatchery stocking, and Johnson Creek, where a discrete supplementation program has been implemented using only Johnson Creek fish. Our results indicated variable abundances of SFSR hatchery spawners distributed spatially among the three main watersheds. Gene flow appears to be restricted and genetic differentiation to be relatively large despite substantial hatchery releases in the upper SFSR. Three historical aggregates of Chinook salmon appear to persist in the SFSR metapopulation, where variable hatchery influences are coincident with the distribution of suitable spawning habitat and watershed-specific management objectives.
Received January 5, 2011; accepted December 12, 2011
Effects of Shading on the Reproductive Output and Embryo Viability of Gulf Killifish
Authors: Gothreaux C T , Green C C 
Published: April 2012

Abstract
Gulf killifish Fundulus grandis broodstock (7.3 ± 0.2 g [mean ± SE]) were held in static outdoor tanks at a 4:1 (female : male) sex ratio and a density of 20 fish/m3. Shade cloth was used to cover 0, 40, or 80% of the surface area of 12 randomly selected outdoor tanks. Eggs were collected from all tanks twice per week by using spawning mats suspended 15 cm below the water surface. Collected eggs were measured volumetrically and assessed for total number and embryo viability. The use of shade cloth had a significant effect on water temperature, the number of eggs collected, and embryo viability. Specifically, shading affected mean weekly water temperature, and the 80% treatment had significantly lower temperatures than both the 0% and 40% treatments during the months of June through August and than the 0% treatment in September. There was a clear cyclical reproductive pattern across all treatments, in which peaks in egg production occurred between the full and new moon phases for the majority of collection dates. Significant differences in the mean number of eggs collected among shade cloth treatments were present only for the month of September, when the 80% treatment produced significantly fewer eggs. The proportion of viable embryos was significantly higher for the 80% treatment than for the other treatments for the months of June, July, and August. The use of shade cloth during the summer months can increase the number of viable embryos produced during the summer depression of the protracted, bimodal spawning season of cultured Gulf killifish.
Primary and Secondary Responses of Juveniles of a Teleostean, Pikeperch Sander lucioperca, and a Chondrostean, Persian Sturgeon Acipenser persicus, to Handling during Transport
Authors: Falahatkar Bahram , Akhavan Sobhan R , Efatpanah Iraj , Meknatkhah Bahman 
Published: April 2012

Abstract
The dynamics of stress responses in small, juvenile pikeperch Sander lucioperca (as a representative teleostean) and small, juvenile Persian sturgeon Acipenser persicus (as a chondrostean) were determined during capture and transportation for release into rivers. Blood samples were obtained from juveniles from a pond, channel, and loading basin and at 1.5 and 24 h after loading. Samples were analyzed for cortisol, glucose, and lactate concentrations, and mortality was recorded. Plasma cortisol concentrations increased, reaching a maximum in Persian sturgeon from the channel and pikeperch from the loading basin. Significant increases in plasma glucose concentrations were observed in samples from the channel and at 1.5 h after loading for Persian sturgeon and pikeperch, respectively. Similarly, significant decreases in lactate concentrations were observed 1.5 h after loading in both species. The results of this study show the sensitivity of these species to stress during transportation. They suggest a higher resistance to transportation stress by the sturgeon than the pikeperch, but it is highly recommended that transportation procedures and capture techniques be modified so that they are appropriate for the species.
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
Authors: Tan Joshua , Kuchibhatla Durga , Sirota Fernanda L. , Sherman Westley A. , Gattermayer Tobias , Kwoh Chia Yee , Eisenhaber Frank , Schneider Georg , Maurer-Stroh Sebastian 
Published: April 2012

Abstract
Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic.
Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.
Contact: sebastianms@bii.a-star.edu.sg
Supplementary information: Supplementary data are available at the Bioinformatics online.
Meta‐analysis: probiotics in antibiotic‐associated diarrhoea
Authors: Videlock E. J. , Cremonini F. 
Published: April 2012

SummaryBackgroundDiarrhoea is a common occurrence in association with antibiotic administration. Earlier studies and meta‐analyses have suggested that probiotic administration reduces the incidence of antibiotic‐associated diarrhoea (AAD).AimTo estimate the reduction in risk of AAD with administration of probiotics in randomised placebo‐controlled trials and to identify factors associated with such reduction.MethodsMeta‐analysis of randomised, double‐blinded, placebo‐controlled trials including patients treated with antibiotics and administered a probiotic for at least the duration of the antibiotic treatment. The outcome was incidence of diarrhoea irrespective of the presence of
C

lostridium difficile or the development of pseudomembranous colitis. Meta‐analysis and meta‐regression methods were used to synthesise data and to assess influence of: mean age, duration of antibiotics, risk of bias and incidence of diarrhoea in the placebo group on outcomes. Subgroup analyses explored effects of different probiotic species, patient populations and treatment indications.ResultsA total of 34 studies were included with 4138 patients. The pooled relative risk (RR) for AAD in the probiotic group vs. placebo was 0.53 (95% CI 0.44–0.63), corresponding to a number needed to treat (NNT) of 8 (95% CI 7–11). The preventive effect of probiotics remained significant when grouped by probiotic species, population age group, relative duration of antibiotics and probiotics, study risk of bias and probiotic administered. The pooled RR for AAD during treatment for
H

elicobacter pylori (H. pylori) was 0.37 (95% CI 0.20–0.69), corresponding to a NNT of 5 (95% CI 4–10).ConclusionsThis updated meta‐analysis confirms earlier results supporting the preventive effects of probiotics in AAD.
Long‐term, open‐label trial: safety and efficacy of continuous maintenance treatment with pantoprazole for up to 15 years in severe acid‐peptic disease
Authors: Brunner G. , Athmann C. , Schneider A. 
Published: April 2012

SummaryBackgroundTo date, the safety and tolerability of proton pump inhibitors (PPIs) have been demonstrated in studies of up to 10 years.AimTo report on the tolerability, safety and efficacy of up to 15 years' continuous treatment with pantoprazole in patients with severe acid‐peptic disease.MethodsFollowing healing of endoscopically confirmed peptic ulcer or reflux oesophagitis during 4–12 weeks' treatment with pantoprazole (40–80 mg/day), adult patients received open‐label maintenance treatment with pantoprazole (40–160 mg/day) for up to 15 years in a single centre combined study (10‐year initial study; 5‐year extension study). Safety assessments were carried out using endoscopy, clinical examination, clinical laboratory investigations, serum gastrin determination, gastric mucosal histology and mucosal endocrine cell quantification.ResultsThe safety set comprised 142 patients. At 12 weeks, healing rates were 95.8%. During long‐term treatment, mean fasting gastrin levels rose from baseline to moderate levels throughout the study. Mean enterochromaffin‐like cell density showed a moderate initial increase during the first 3 years, remaining stable thereafter. These changes were not associated with any clinically relevant changes of the gastric mucosa. Patients with successful Helicobacter pylori eradication showed long‐term regression of antral and corpus gastritis during continued pantoprazole treatment.ConclusionsDaily pantoprazole maintenance therapy for up to 15 years for severe acid‐peptic disease is effective and well tolerated, with no identified safety concerns. The longest study to date, these data provide reassuring evidence for the long‐term safety of pantoprazole.
Implications of PNPLA3 polymorphism in chronic hepatitis C patients receiving peginterferon plus ribavirin
Authors: Valenti L. , Aghemo A. , Stättermayer A. F. , Maggioni P. , De Nicola S. , Motta B. M. , Rumi M. G. , Dongiovanni P. , Ferenci P. , Colombo M. , Fargion S. 
Published: April 2012

SummaryBackgroundHomozygosity for the PNPLA3 p.I148M polymorphism influences steatosis and fibrogenesis in chronic hepatitis C (CHC).AimTo evaluate the effect of p.148M/M on sustained virological response (SVR) and viral kinetics in patients who underwent antiviral therapy with peg‐interferon and ribavirin, stratified according to viral genotype and fibrosis severity, and secondarily, the interaction with interleukin‐28B
(
IL28B
) genotype on liver damage.MethodsIn this observational study, we considered 602 treatment‐naïve consecutive patients from tertiary referral centres in Milan and Vienna [61% genotype 1 (G1), 30% advanced fibrosis, 33%
IL28B
rs12979860 CC].ResultsThe p.148M/M genotype, detected in 8% of patients, did not influence SVR in the overall series (P = 0.29), but it was associated with SVR (3/17, 17% vs. 56/121, 46%; P = 0.034) and complete early viral response (4/17, 23% vs. 68/121, 56%; P = 0.018) in G1/4 patients with advanced fibrosis. After adjustment for age, viral load,
IL28B
CC genotype, treatment dose, and steatosis, p.148M/M remained a predictor of SVR in G1/4 patients with advanced fibrosis (OR 0.23, 95% CI 0.04–0.87). The p.148M/M genotype was associated with more advanced fibrosis in the overall series (P = 0.049), whereas the rs12979860
IL28B
CC genotype only in patients negative for p.148M/M (P = 0.017), independently of age, BMI and alanine transaminase levels (OR 1.51, 95% CI 1.01–2.27).Conclusions

PNPLA3
p.148M/M genotype was negatively associated with SVR and early viral kinetics independently of steatosis, albeit only in difficult‐to‐cure G1/4 patients with advanced fibrosis, whereas stratification for the p.148M/M

PNPLA3
genotype unmasked an association between
IL28B
CC genotype and more severe liver fibrosis.
Comparison of the effectiveness of two protocols for vaccination (standard and double dosage) against hepatitis B virus in patients with inflammatory bowel disease
Authors: Gisbert J. P. , Menchén L. , García‐Sánchez V. , Marín I. , Villagrasa J. R. , Chaparro M. 
Published: April 2012

SummaryBackgroundThe response rate to hepatitis B virus (HBV) vaccination in patients with inflammatory bowel disease (IBD) is low.AimTo compare two vaccination protocols—the standard dose and the double dose—in IBD patients.MethodsPatients diagnosed with IBD from three tertiary hospitals were vaccinated against HBV with two different protocols: the standard protocol (Engerix‐B single dose at 0, 1 and 6 months) and the new faster protocol based on a double dose (Engerix B double dose at 0, 1 and 2 months). Anti‐HBs titres were measured 1–3 months after the last dose. A multivariate analysis was performed to identify factors that were predictive of response to the vaccine.ResultsThe study sample comprised 148 patients (mean age 40 years, 69% Crohn's disease), 70% of whom were receiving immunosuppressive therapy (22% thiopurines, 23% anti‐TNF and 25% both). The standard protocol was followed in 46% of patients and the double dose protocol in 54%. Considering anti‐HBs >10 IU/L as a successful response to vaccination, the seroconversion rate was higher among patients vaccinated with the double dose than with the standard dose: 75% (95% CI, 65–85%) vs. 41% (95% CI, 29–54%) (P < 0.001). In the multivariate analysis, vaccination with the double dose was the only factor associated with a better response to the vaccine (OR, 4; 95% CI, 2–8; P < 0.001).ConclusionsThe response rate to the HBV vaccination in IBD patients is low. Administration of a double dose was associated with a higher response rate. Therefore, the double dose protocol could be a suitable option in patients with IBD.
Elevated factor VIII levels and risk of venous thrombosis
Authors: Jenkins P. Vince , Rawley Orla , Smith Owen P. , O'Donnell James S. 
Published: April 2012

SummaryModern thrombophilia testing fails to identify any underlying prothrombotic tendency in a significant number of patients presenting with objectively confirmed venous thromboemboembolism (VTE). This observation has led to a search for other novel inherited or acquired human thrombophilias. Although a number of putative mechanisms have been described, the evidence behind many of these candidates remains weak. In contrast, an increasing body of work supports the hypothesis that increased plasma factor VIII (FVIII) levels may be important in this context. An association between elevated plasma FVIII levels and VTE was first described in the Leiden Thrombophilia Study (LETS). Subsequently, these conclusions have been supported by an increasing number of independent case–control studies. Cumulatively, these studies have clearly demonstrated that high FVIII levels constitute a prevalent, dose‐dependent risk factor for VTE. Furthermore, more recent studies have shown that the risk of recurrent venous thrombosis is also significantly increased in patients with high FVIII levels. In this review, we present the evidence supporting the hypothesis that elevated FVIII levels constitute a clinically important thrombophilia. In addition, we examine the biological mechanisms that may underlie persistently elevated FVIII levels, and the pathways through which high FVIII may serve to increase thrombotic risk.
Lymph node dissection – understanding the immunological function of lymph nodes
Authors: Buettner M , Bode U 
Published: April 2012

SummaryLymph nodes (LN) are one of the important sites in the body where immune responses to pathogenic antigens are initiated. This immunological function induced by cells within the LN is an extensive area of research. To clarify the general function of LN, to identify cell populations within the lymphatic system and to describe the regeneration of the lymph vessels, the experimental surgical technique of LN dissection has been established in various animal models. In this review different research areas in which LN dissection is used as an experimental tool will be highlighted. These include regeneration studies, immunological analysis and studies with clinical questions. LN were dissected in order to analyse the different cell subsets of the incoming lymph in detail. Furthermore, LN were identified as the place where the induction of an antigen-specific response occurs and, more significantly, where this immune response is regulated. During bacterial infection LN, as a filter of the lymph system, play a life-saving role. In addition, LN are essential for the induction of tolerance against harmless antigens, because tolerance could not be induced in LN-resected animals. Thus, the technique of LN dissection is an excellent and simple method to identify the important role of LN in immune responses, tolerance and infection.
Inferring habitat suitability and spread patterns from large‐scale distributions of an exotic invasive pasture grass in north Australia
Authors: Petty Aaron M. , Setterfield Samantha A. , Ferdinands Keith B. , Barrow Piers 
Published: April 2012

Summary1. The understanding of large‐scale patterns in expanding populations of alien invasive plants can be used to infer the environmental limiting factors, habitat heterogeneity and, ultimately, the range expansion potential of invasive plants.2. We used multivariate analysis and a novel quantile regression technique accounting for spatial autocorrelation to compare and contrast factors influencing the abundance and distribution of the African grass Andropogon gayanus (gamba grass) at two large‐scale invasion sites in the tropical savanna region of Australia. We collected data using aerial and ground surveys and tested for limiting factors using three landscape‐scale indices related to soil quality, soil moisture and invasion history.3. In one site, gamba grass was principally colonising drainage lines and riparian areas. Occupation of these areas was limited in proportion to the distance from the original gamba grass source. In the second site, gamba grass abundance was independent of distance from the original source and was well established in all vegetation communities, although abundance was also limited in higher elevation sites away from drainage lines.4. Comparisons between these sites with different patterns of invasion enabled the estimation of both the invasion pathways and range expansion potential of gamba grass. Our results indicated that gamba grass spreads from riparian communities to invade upland sites and has the potential to invade 70% of north Australia’s upland savanna communities.5. Aerial surveys comprehensively assessed patterns over a larger area than ground surveys and were much more economical.6. Synthesis and applications. Large‐scale surveys across multiple sites are critical to understanding the dynamics of recent alien species invasions where little is known about the pattern and potential range of spread. The application of quantile regression and aerial surveys shows promise as aerial surveys are efficient at capturing a large amount of data. The novel quantile regression technique we demonstrate here can account for both spatial autocorrelation and noisy ecological data from aerial surveys while returning robust results. We were thus able to demonstrate widespread colonisation of creek lines by gamba grass and recommend that management focuses on detection and eradication along drainage lines in addition to the present focus on transport corridors.
Reduced pesticide toxicity and increased woody vegetation cover account for enhanced native bird densities in organic orchards
Authors: MacLeod Catriona J. , Blackwell Grant , Benge Jayson 
Published: April 2012

Summary1. Organic farming is often promoted as a solution for counteracting the adverse impacts of agricultural intensification on biodiversity. However, it is unclear whether the biodiversity benefits derived from organic farming require an adoption of organic farming in its entirety (i.e. a systems‐level approach) or whether the benefits derived are because of just a small subset of the associated management practices.2. Using bird survey data collected from kiwifruit orchards in New Zealand, we assessed whether orchards managed under an organic system support higher bird densities than those under integrated management systems. To determine whether biodiversity gains might also be achieved on non‐organic orchards, we tested whether variation among kiwifruit orchards in the amount of (non‐crop) woody vegetation cover, density of shelterbelts and toxicity of pesticide applications are better predictors of bird densities than management systems.3. Composite measures of breeding season densities of all native species and the subset of native insectivores were higher on organic orchards than integrated management orchards. Densities of introduced bird species were comparable among management systems.4. Pesticide use and habitat composition variables were better predictors of native bird densities than management system, with native bird densities negatively associated with pesticide toxicity ranking and/or positively associated with woody vegetation cover.5. Synthesis and applications.A complete conversion to an organic system may not be required to improve biodiversity in agroecosystems. Instead, the transfer of specific land management practices known to benefit biodiversity in organic systems has the potential to enhance biodiversity in other more intensively managed systems (e.g. integrated management). This may be a path towards attaining biodiversity benefits at a larger scale, because such changes may be more straightforward than conversion to an organic system.