bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting predictors of virologic response to PEGIFN + RBV therapy in HIV‐/HCV‐coinfected patients: the role of metabolic factors and elevated GGT levels
Authors: Mandorfer M. , Reiberger T. , Payer B. A. , Breitenecker F. , Aichelburg M. C. , Obermayer‐Pietsch B. , Rieger A. , Puoti M. , Zangerle R. , Trauner M. , Peck‐Radosavljevic M. 
Published: August 2013

SummaryEvaluation of metabolic factors and elevated γ‐glutamyltransferase (GGT) levels as independent predictors of treatment failure in a thoroughly documented cohort of HIV‐/HCV‐coinfected patients (HIV/HCV). Sixty‐four HIV/HCV patients treated with pegylated interferon‐α‐2a plus ribavirin (PEGIFN + RBV) at the Medical University of Vienna within a prospective trial were included in this study. In addition, 124 patients with HIV/HCV from the AIFA‐HIV and AHIVCOS cohorts were included as a validation cohort. Advanced liver fibrosis, GGT elevation, insulin resistance (IR) and low CD4+ nadir were defined as METAVIR F3/F4, GGT levels >1.5× sex‐specific upper limit of normal, homoeostasis model assessment of insulin resistance >2 and CD4+ nadir <350 cells/μL, respectively. HCV‐genotype 1/4 (OR26.3; P = 0.006), advanced liver fibrosis (OR20.2; P = 0.009), interleukin 28B rs12979860 non‐C/C SNP (OR8.27; P = 0.02) and GGT elevation (OR7.97; P = 0.012) were independent predictors of treatment failure, while both IR (OR3.51; P = 0.106) and low CD4 + nadir (OR2.64; P = 0.263) were not independently associated with treatment failure. A statistically significant correlation between GGT elevation and prior alcohol abuse (r = 0.259; P = 0.039), liver steatosis (r = 0.301; P = 0.034) and low‐density lipoprotein‐cholesterol (r = −0.256; P = 0.041) was observed. The importance of GGT elevation as an independent predictor of treatment failure was confirmed in a validation cohort (OR2.76; P = 0.026). While GGT elevation emerged as an independent predictor of treatment failure in both the derivation and the validation cohort, no independent associations between metabolic factors and treatment failure were observed. Thus, our findings suggest that GGT elevation is an independent predictor of treatment failure in HIV/HCV that can easily be incorporated into predictive algorithms.
Which trait dissimilarity for functional diversity: trait means or trait overlap?
Authors: de Bello Francesco , Carmona Carlos P. , Mason Norman W. H. , Sebastià Maria‐Teresa , Lepš Jan 
Published: August 2013

AbstractQuestionMany functional diversity indices require the calculation of functional trait dissimilarities between species. However, very little is known about how the dissimilarity measure used might affect conclusions about ecological processes drawn from functional diversity.MethodsWe simulated real applications of functional diversity, to illustrate the key properties of the two most common families of dissimilarity measures: (1) ‘Gower’ distance, using only ‘mean trait’ value per species and then standardizing each trait, e.g. relative to its range; (2) ‘trait overlap’ between species, which takes into account within‐species trait variability. We then examine how these approaches could affect conclusions about ecological processes commonly assessed with functional diversity. We also propose a new R function (‘trova’, i.e. TRait OVerlAp) which performs computations to estimate species trait dissimilarity with different types of data.ResultsThe trait overlap approach generally produces a less context‐dependent measure of functional dissimilarity. For example, the results are less dependent on the transformation of trait data (often required in empirical datasets) and on the particular pool of species considered (i.e. trait range, regularity and presence of outliers). The results therefore could be more easily compared across studies and biomes. Further, trait overlap more reliably reproduces patterns expected when niche differentiation structures communities. The Gower approach, on the contrary, more reliably detects environmental filtering effects.ConclusionThe two approaches imply different conceptions of how species dissimilarities relate to niche differentiation. Trait overlap is suitable for testing the effect of species interactions on functional diversity within local communities, especially when relatively small differences in species traits are linked to different resource acquisition. Gower is better suited to detecting changes in functional diversity along environmental gradients, as greater differences in trait values reflect increased niche differentiation. Combining trait overlap and Gower approaches may provide a novel way to assess the joint effects of environmental filtering and niche complementarity on community assembly. We suggest that attention should be given not only to the index of functional diversity considered but also whether the dissimilarity used is appropriate for the study context.
A family of null models to distinguish between environmental filtering and biotic interactions in functional diversity patterns
Authors: Chalmandrier L. , Münkemüller T. , Gallien L. , de Bello F. , Mazel F. , Lavergne S. , Thuiller W. 
Published: August 2013

AbstractQuestionsTraditional null models used to reveal assembly processes from functional diversity patterns are not tailored for comparing different spatial and evolutionary scales. In this study, we present and explore a family of null models that can help disentangling assembly processes at their appropriate scales and thereby elucidate the ecological drivers of community assembly.LocationFrench Alps.MethodsOur approach gradually constrains null models by: (1) filtering out species not able to survive in the regional conditions in order to reduce the spatial scale, and (2) shuffling species only within lineages of different ages to reduce the evolutionary scale of the analysis. We first tested and validated this approach using simulated communities. We then applied it to study the functional diversity patterns of the leaf–height–seed strategy of plant communities in the French Alps.ResultsUsing simulations, we found that reducing the spatial scale correctly detected a signature of competition (functional divergence) even when environmental filtering produced an overlaying signal of functional convergence. However, constraining the evolutionary scale did not change the identified functional diversity patterns. In the case study of alpine plant communities, investigating scale effects revealed that environmental filtering had a strong influence at larger spatial and evolutionary scales and that neutral processes were more important at smaller scales. In contrast to the simulation study results, decreasing the evolutionary scale tended to increase patterns of functional divergence.ConclusionWe argue that the traditional null model approach can only identify a single main process at a time and suggest to rather use a family of null models to disentangle intertwined assembly processes acting across spatial and evolutionary scales.
Functional and phylogenetic community assembly linked to changes in species diversity in a long‐term resource manipulation experiment
Authors: Gerhold Pille , Price Jodi N. , Püssa Kersti , Kalamees Rein , Aher Kaia , Kaasik Ants , Pärtel Meelis 
Published: August 2013

AbstractQuestionThere are contrasting opinions about how communities assemble along a productivity gradient, particularly in relation to competitive interactions. One view is that functionally similar, and closely related species, are less likely to co‐exist (limiting similarity). Alternatively, competitive exclusion may act on dissimilar species because species bearing traits associated with low competitive ability are excluded (weaker competitor exclusion). We ask if patterns of functional and phylogenetic diversity are related to changes in species diversity in response to fertility manipulations.LocationSpecies‐rich mesophytic grassland in Estonia.MethodsThe grassland has been manipulated from 2002 to 2011 to increase (fertilizer addition) and decrease productivity (sucrose addition) in small‐scale (50 cm × 50 cm) plots. We linked annual increases and decreases in species diversity to changes in functional and phylogenetic diversity. We used abundance‐weighted mean pair‐wise functional or phylogenetic distance of all possible species pairs.ResultsWe found convergence in four traits (plant height, leaf distribution, lateral spread, type of reproduction) and a decrease in mean functional and phylogenetic diversity, in support of weaker competitor exclusion or habitat filtering. There was less support for limiting similarity, with divergence found for two traits associated with decreasing species diversity (leaf distribution in the sucrose treatment and lateral spread in the fertilizer treatment).ConclusionsOur results support the view that competition can lead to the exclusion of weaker competitors, rather than increasing functional and phylogenetic diversity, as expected from the principle of limiting similarity. However, multiple assembly processes, which are generally seen as mutually exclusive, are operating simultaneously, albeit on different traits and at different stages of community assembly.
In Vitro Screening of Fungicidal Chemicals for Antifungal Activity against Saprolegnia
Authors: Hu Xue‐Gang , Liu Lei , Hu Kun , Yang Xian‐Le , Wang Gao‐Xue 
Published: August 2013

AbstractSaprolegnia is an important fish fungal pathogen that often results in significant economic losses to freshwater aquaculture. To find effective drugs to control saprolegniasis, 30 fungicidal chemicals used in agriculture were screened, in which kresoxim‐methyl and azoxystrobin, with minimum inhibitory concentration (MIC) values of 1.0 and 0.5 mg/L, respectively, showed good in vitro antifungal activities against Saprolegnia. Azoxystrobin has the most promising anti‐Saprolegnia activity with 50% effective concentration (EC50) value of 0.212 mg/L against mycelial growth and minimum fungicidal concentration (MFC) value of 0.13 mg/L against spores, while EC50 and MFC values to kresoxim‐methyl are 0.240 and 0.25 mg/L, respectively. Through the acute toxicity assay using goldfish, Carassius auratus, azoxystrobin exhibited wider margin of safety with a safe concentration (SC) value of 0.553 mg/L than kresoxim‐methyl with an SC value of 0.131 mg/L. These findings demonstrated that azoxystrobin has the potential for the development of therapy for the control of Saprolegnia in aquaculture. Both kresoxim‐methyl and azoxystrobin were tested with a post‐antifungal effects (PAFE) assay and the results revealed that the two chemicals had no significant effect on fungal growth inhibition after a 1‐hour exposure, indicating that the treatment needs to be carried out over an extended period.
Genetic Diversity and Differentiation in Broodstocks of the Endangered Chinese Sucker, Myxocyprinus asiaticus, Using Microsatellite Markers
Authors: Xu Nian , Yang Zhong , Que Yanfu , Shi Fang , Zhu Bin , Xiong Meihua 
Published: August 2013

AbstractChinese Sucker, Myxocyprinus asiaticus, is a valuable and endangered freshwater species in China. We investigated genetic diversity and differentiation of four M. asiaticus broodstock populations using 10 microsatellite loci. Three populations showed weak genetic differentiation among them. The other and the most distant population exhibited the lowest genetic diversity. It was inferred that wild M. asiaticus ancestry in the Yangtze River had sufficient gene flow among localities, while under the situation of population decline and fragmentation, restocking programs without genetic management might aggravate loss of genetic diversity and increase genetic differentiation. Maintenance of population connectivity among localities requires real attention in future restocking efforts.
Feasibility of Offshore Co‐culture of Abalone, Haliotis discus hannai Ino, and Sea Cucumber, Apostichopus japonicus, in a Temperate Zone
Authors: Qi Zhanhui , Wang Jun , Mao Yuze , Liu Hongmei , Fang Jianguang 
Published: August 2013

AbstractFeasibility of offshore co‐culture of abalone and sea cucumber was investigated in Northern China. Survival and growth of abalone, Haliotis discus hannai Ino, and sea cucumber, Apostichopus japonicus, co‐cultured in abalone cages from suspended longlines, in the offshore area, were examined. Abalone and sea cucumbers were co‐cultured at density ratios of both 3:1 and 6:1 for 1 yr. Abalone were fed with fresh kelp and no additional feed was given to sea cucumbers. Survival of abalone and sea cucumber was 100% for all treatments. Abalone and sea cucumber grew well; the body weight (BW) of abalone and sea cucumber was nearly doubled and had reached a commercial size. There were no significant differences in the growth rates for both abalone and sea cucumber between the two density treatments. The specific growth rate of BW of abalone (SGRbw) was highest in June, with a value of 0.536%/d. Growth rate of sea cucumber (SGRsc) was highest in December, reached 1.84%/d, with an annual average SGRsc of 0.182%/d. Results suggested that the offshore co‐culture of abalone and sea cucumber was feasible offshore. The co‐culture of abalone with sea cucumbers may provide an additional valuable crop without additional financial input.
Effects of Inorganic and Organic Fertilization on Physicochemical Parameters, Bacterial Concentrations, and Shrimp Growth in Litopenaeus vannamei Cultures with Zero Water Exchange
Authors: Lara‐Anguiano Guillermo F. , Esparza‐Leal Héctor M. , Sainz‐Hernández Juan C. , Ponce‐Palafox Jesús T. , Valenzuela‐Quiñónez Wenceslao , Apun‐Molina Juan P. , Klanian Mariel Gullian 
Published: August 2013

AbstractTo identify ways to improve water quality and shrimp production in closed systems, two parallel experiments (one in tanks and one in ponds) were conducted using Pacific white shrimp, Litopenaeus vannamei, cultures. In both experiments, the effects of inorganic (Nutrilake®) and organic (molasses) fertilization on physicochemical parameters, bacterial concentrations, and shrimp performance under zero water exchange were evaluated. Fertilization with both molasses and Nutrilake enhanced the feed conversion rate, as well as shrimp survival and production. In tanks, the shrimp survival and production rates were highest in the molasses treatment, but this effect was not observed in ponds. In ponds, fertilization with Nutrilake increased nitrogen and phosphorus concentrations more than did the controls and molasses treatments toward the end of the experiment. In tanks, fertilization with molasses reduced ammonia concentrations toward the end of the experiment, but the same effect was not observed in ponds. In ponds, fertilization reduced the proportion of Vibrio spp. bacteria, which most likely reduced the incidence of disease from these potentially pathogenic organisms. In both culture systems, fertilization increased the proportion of Bacillus spp., which most likely enhanced food availability.
Assessment of Aquatic Aeromonas spp. Isolates' Susceptibility to Cinnamaldehyde, Vanillin, and Crude Kigelia africana Fruit Extracts
Authors: Okolie Chinenye , Chenia Hafizah Y. 
Published: August 2013

AbstractAeromonas spp. are primary and opportunistic fish pathogens that are responsible for severe economic losses in aquaculture, and are exacerbated by their increasing incidence of antimicrobial resistance. Phytochemicals are being explored as alternatives to conventional antimicrobial agents since they have destressing, growth‐promoting, immune‐stimulating, and antimicrobial properties. The susceptibility of 93 aquatic Aeromonas spp. and six Plesiomonas shigelloides isolates (from cultured catfish, koi carp, tilapia, and seawater) to three phytochemicals, viz.: cinnamaldehyde (10–1250 µg/mL), vanillin (5–250 µg/mL), and crude Kigelia africana fruit extracts (4–10 mg/mL ethyl acetate, dichloromethane, methanol, and hexane) were assessed using the disk diffusion assay and compared to ampicillin and tetracycline, using activity indices. No zones of inhibition were obtained with 10 µg/mL of cinnamaldehyde, or with 5–250 µg/mL of vanillin. However, varying degrees of inhibition were observed with higher concentrations of cinnamaldehyde, as well as with the K. africana methanol extract. Cinnamaldehyde (≥500 µg/mL) and the K. africana methanol extract displayed better antimicrobial activity against study isolates in comparison to vanillin and ampicillin. They appear to be promising and sustainable phytochemicals that might be useful as alternatives to the antimicrobial agents currently in use in aquaculture.
Impacts of Bolbophorus damnificus (Digenea: Bolbophoridae) on Production Characteristics of Channel Catfish, Ictalurus punctatus, Raised in Experimental Ponds
Authors: Wise David J. , Li Menghe H. , Griffin Matt J. , Robinson Edwin H. , Khoo Lester H. , Greenway Terrence E. , Byars Todd S. , Walker Josh R. , Mischke Charles C. 
Published: August 2013

AbstractBolbophorus damnificus was recognized as a threat to channel catfish, Ictalurus punctatus, production in Louisiana and Mississippi in 1997 and 1999, respectively. Severe to moderate outbreaks (≥34% prevalence) are correlated to heavy losses, but impact of mild outbreaks with low prevalence (<33%) was unknown. Laboratory and field studies were conducted to evaluate sublethal acute (early stage) and chronic (late stage) trematode infection impacts on catfish production. Fish raised in ponds seeded with ram's horn snails from ponds harboring active B. damnificus outbreaks resulted in infection prevalence ranging from 1.6 to 20.4%. Compared to fish raised in ponds not seeded with infected snails (0% prevalence), fish biomass, number harvested, and total feed fed were significantly lower. These data agree with previous studies where mild infections reduced feed consumption, fish production, and economic returns. Infected fish were collected from ponds and used in a laboratory growth study. Once removed from the infection source, weight gain, growth rate, feed consumption, and feed efficiency were equal to or greater than trematode‐free fish. This suggests that although early B. damnificus infection (premetacercarial development) can severely impact production, infection has little impact on performance once metacercarial cysts are fully developed, and the infection source is removed.
A pill for HCV – myth or foreseeable future?
Authors: Jaroszewicz Jerzy , Flisiak Robert , Dusheiko Geoffrey 
Published: August 2013

AbstractWeekly injections with pegylated‐IFNa (PegIFN) combined with daily ribavirin (RBV) are still the standard of care for chronic hepatitis C in most of the world. Sustained virological response (SVR) of 40–50% for patients infected with HCV genotypes (GT) 1 or 4 and 70–90% for genotypes 2–3 are achieved with this regimen. Triple therapy, registered in both the EU and USA, utilizing the first‐generation direct protease inhibitors is able to increase the SVR rates to 75%, but its use is restricted to patients infected with HCV GT1. Additional limitations include challenging dosing schedules, complex treatment algorithms, limited efficacy in patients with previous null response to PegIFN/RBV therapy and additional side effects. There is also an important need for more effective antiviral therapy for difficult‐to‐treat populations with PEG‐IFN intolerance, particularly those with cirrhosis and non‐responders to previous therapies. All‐oral, IFN‐free therapies are an evolutionary step for future anti‐HCV therapies. Initial results of clinical studies conducted during the last year give hope for ‘a pill for HCV’ at least in selected CHC populations. In 2013 several clinical trials of all‐oral anti‐HCV therapies had been completed, first all‐oral combination submitted for registration and some conclusions could be drawn. However, there is not yet a clear direction for IFN‐free therapies in treatment naïve patients or more complex non‐responders.
Influenza A(H1N1)pdm09 vaccine effectiveness and other characteristics associated with hospitalization in chronic liver disease patients
Authors: Ohfuji Satoko , Fukushima Wakaba , Sasaki Yachiyo , Tamori Akihiro , Kurai Osamu , Kioka Kiyohide , Maeda Kazuhiro , Maeda Akiko , Hirota Yoshio 
Published: August 2013

AbstractBackground & AimsTo date, few studies have investigated the clinical effectiveness of influenza vaccine in chronic liver disease patients. The aim of this study was to examine the effectiveness of monovalent inactivated influenza A(H1N1)pdm09 vaccine and other characteristics associated with hospitalization in patients with chronic hepatitis C.MethodsWe conducted a hospital‐based cohort study during influenza A(H1N1)pdm09 pandemic. A total of 408 patients (132 vaccinated, 276 unvaccinated) with detectable HCV‐RNA were followed up with respect to any hospitalization using a weekly postal questionnaire. Reported hospitalizations were verified by medical records.ResultsDuring the epidemic period, 28 hospitalizations (6 vaccinated, 22 unvaccinated) were observed. After adjustment for potential confounders, vaccination decreased the odds ratio (OR) for hospitalization with marginal significance (OR = 0.43, 95%CI = 0.16–1.17). Besides, positive association with hospitalization was observed in patients with albumin levels <3.5 g/dl (OR = 8.40, 3.66–19.3) and steroid users (OR = 5.58, 0.98–31.7).ConclusionsAmong patients with chronic hepatitis C, A(H1N1)pdm09 vaccine appeared to have a protective effect against hospitalization. Those patients with a higher risk for hospitalization should be carefully followed during the influenza season, even when vaccinated.
Systemic and local expression levels of TNF‐like ligand 1A and its decoy receptor 3 are increased in primary biliary cirrhosis
Authors: Aiba Yoshihiro , Harada Kenichi , Komori Atsumasa , Ito Masahiro , Shimoda Shinji , Nakamura Hitomi , Nagaoka Shinya , Abiru Seigo , Migita Kiyoshi , Ishibashi Hiromi , Nakanuma Yasuni , Nishida Nao , Kawashima Minae , Tokunaga Katsushi , Yatsuhashi Hiroshi , Nakamura Minoru 
Published: August 2013

AbstractBackground & AimsThrough a genome‐wide association study of a Japanese population, we recently identified TNFSF15, a gene encoding TNF‐like ligand 1A (TL1A), as a susceptibility gene for primary biliary cirrhosis (PBC). We investigated the clinical significance of TL1A and one of its receptors, decoy receptor 3 (DcR3), in PBC.MethodsWe analysed the systemic and local expression of TL1A and DcR3 in 110 PBC patients and 46 healthy controls using enzyme‐linked immunosorbent assay, quantitative polymerase chain reaction and immunohistochemical staining.ResultsSerum TL1A levels were significantly increased in PBC patients at both early and late stages as compared with healthy controls, and its levels were significantly decreased in early‐stage PBC patients after ursodeoxycholic acid (UDCA) treatment. TL1A was immunohistochemically localized to biliary epithelial cells, Kupffer cells, blood vessels and infiltrating mononuclear cells in the PBC liver. In addition, TL1A messenger RNA expression was increased in the PBC liver as compared with the non‐diseased liver. Serum DcR3 levels were also significantly increased in PBC patients, and were significantly decreased after UDCA treatment in early‐stage PBC patients.ConclusionsThese results indicate that TL1A and DcR3 may play an important role in the pathogenesis of PBC.