bluuebunny/crossref_metadata_2025 huggingface dataset:
A game of hide and seek between avirulence genes AvrLm4‐7 and AvrLm3 in Leptosphaeria maculans
Authors: Plissonneau Clémence , Daverdin Guillaume , Ollivier Bénédicte , Blaise Françoise , Degrave Alexandre , Fudal Isabelle , Rouxel Thierry , Balesdent Marie‐Hélène
Published: November 2015

Extending the durability of plant resistance genes towards fungal pathogens is a major challenge. We identified and investigated the relationship between two avirulence genes of Leptosphaeria maculans, AvrLm3 and AvrLm4‐7. When an isolate possesses both genes, the Rlm3‐mediated resistance of oilseed rape (Brassica napus) is not expressed due to the presence of AvrLm4‐7 but virulent isolates toward Rlm7 recover the AvrLm3 phenotype.

Combining genetic and genomic approaches (genetic mapping, RNA‐seq, BAC (bacterial artificial chromosome) clone sequencing and de novo assembly) we cloned AvrLm3, a telomeric avirulence gene of L. maculans. AvrLm3 is located in a gap of the L. maculans reference genome assembly, is surrounded by repeated elements, encodes for a small secreted cysteine‐rich protein and is highly expressed at early infection stages.

Complementation and silencing assays validated the masking effect of AvrLm4‐7 on AvrLm3 recognition by Rlm3 and we showed that the presence of AvrLm4‐7 does not impede AvrLm3 expression in planta. Y2H assays suggest the absence of physical interaction between the two avirulence proteins.

This unusual interaction is the basis for field experiments aiming to evaluate strategies that increase Rlm7 durability.
Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality inLiliaceae
Authors: Carta Angelino , Peruzzi Lorenzo
Published: November 2015

The factors driving genome size evolution in Liliaceae were examined. In particular, we investigated whether species with larger genomes are confined to less stressful environments with a longer vegetative season.

We tested our hypotheses by correlating the genome size with other plant traits and environmental variables. To determine the adaptive nature of the genome size, we also compared the performances of Brownian motion (BM) processes with those inferred by Ornstein–Uhlenbeck (OU) models of trait evolution.

A positive correlation of genome size with plant size, mean temperature and habitat moisture and a negative correlation with altitude and precipitation seasonality were found. Models of trait evolution revealed a deviation from a drift process orBM. Instead, changes in genome size were significantly associated with precipitation regimes according to anOUprocess. Specifically, the evolutionary optima towards which the genome size evolves were higher for humid climates and lower for drier ones.

Taken together, our results indicate that the genome size increase in Liliaceae is constrained by climate seasonality.
Improving the safety of oral immunotherapy for food allergy
Authors: Vazquez‐Ortiz Marta , Turner Paul J.
Published: November 2015

Food allergy is a major public health problem in children, impacting upon the affected individual, their families and others charged with their care, for example educational establishments, and the food industry. In contrast to most other paediatric diseases, there is no established cure: current management is based upon dietary avoidance and the provision of rescue medication in the event of accidental reactions, which are common. This strategy has significant limitations and impacts adversely on health‐related quality of life. In the last decade, research into disease‐modifying treatments for food allergy has emerged, predominantly for peanut, egg and cow's milk. Most studies have used the oral route (oral immunotherapy, OIT), in which increasing amounts of allergen are given over weeks–months. OIT has proven effective to induce immune modulation and ‘desensitization’ – that is, an increase in the amount of food allergen that can be consumed, so long as regular (typically daily) doses are continued. However, its ability to induce permanent tolerance once ongoing exposure has stopped seems limited. Additionally, the short‐ and long‐term safety of OIT is often poorly reported, raising concerns about its implementation in routine practice. Most patients experience allergic reactions and, although generally mild, severe reactions have occurred. Long‐term adherence is unclear, which rises concerns given the low rates of long‐term tolerance induction. Current research focuses on improving current limitations, especially safety. Strategies include alternative routes (sublingual, epicutaneous), modified hypoallergenic products and adjuvants (anti‐IgE, pre‐/probiotics). Biomarkers of safe/successful OIT are also under investigation.
Towards plant pangenomics
Authors: Golicz Agnieszka A. , Batley Jacqueline , Edwards David
Published: November 2015

As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.
The Metaphysical Consequences of Counterfactual Skepticism
Authors: Emery Nina
Published: November 2015

A series of recent arguments purport to show that most counterfactuals of the formif A had happened then C would have happenedare not true. These arguments pose a challenge to those of us who think that counterfactual discourse is a useful part of ordinary conversation, of philosophical reasoning, and of scientific inquiry. Either we find a way to revise the semantics for counterfactuals in order to avoid these arguments, or we find a way to ensure that the relevant counterfactuals, while not true, are still assertible. I argue that regardless of which of these two strategies we choose, the natural ways of implementing these strategies all share a surprising consequence: they commit us to a particular metaphysical view about chance.
Idiopathic pulmonary fibrosis: Diagnosis, epidemiology and natural history
Authors: Sgalla Giacomo , Biffi Alice , Richeldi Luca
Published: November 2015

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrosing lung disorder of unknown aetiology whose diagnosis involves the careful exclusion of secondary causes for pulmonary fibrosis and the presence of a pattern of usual interstitial pneumonia (UIP) at either high‐resolution computed tomography (HRCT) scan or surgical lung biopsy. Despite great efforts made in establishing precise, universally acknowledged diagnostic criteria for IPF, its ascertainment remains a challenge, especially in those individuals presenting with atypical HRCT patterns. With new drugs emerging, establishing a precise diagnosis is becoming a clinically relevant issue. Although regarded as a rare disease, IPF epidemiology is controversial due to studies relying on old data and adopting mixed, incomparable methodologies for cases definition. Overall, the prevalence and incidence appear to be increasing over the last decades, suggesting that in earlier studies they might have been underestimated because of diagnostic uncertainty. IPF is invariably progressive, although its clinical course might greatly vary on an individual basis, with episodes of severe acute respiratory deterioration (acute exacerbations) being unpredictable. A deeper understanding of the mechanisms responsible for an accelerated course of the disease and the identification of biomarkers of progression would lead to a better stratification of the disease, essential for delivering individualized therapeutic strategies.
Whither Risk Assessment: New Challenges and Opportunities a Third of a Century After the Red Book
Authors: Greenberg Michael , Goldstein Bernard D. , Anderson Elizabeth , Dourson Michael , Landis Wayne , North D. Warner
Published: November 2015

Six multi‐decade‐long members of SRA reflect on the 1983 Red Book in order to examine the evolving relationship between risk assessment and risk management; the diffusion of risk assessment practice to risk areas such as homeland security and transportation; the quality of chemical risk databases; challenges from other groups to elements at the core of risk assessment practice; and our collective efforts to communicate risk assessment to a diverse set of critical groups that do not understand risk, risk assessment, or many other risk‐related issues. The authors reflect on the 10 recommendations in the Red Book and present several pressing challenges for risk assessment practitioners.
Fitting Cox Models with Doubly Censored Data Using Spline‐Based Sieve Marginal Likelihood
Authors: Li Zhiguo , Owzar Kouros
Published: November 2015

In some applications, the failure time of interest is the time from an originating event to a failure event while both event times are interval censored. We propose fitting Cox proportional hazards models to this type of data using a spline‐based sieve maximum marginal likelihood, where the time to the originating event is integrated out in the empirical likelihood function of the failure time of interest. This greatly reduces the complexity of the objective function compared with the fully semiparametric likelihood. The dependence of the time of interest on time to the originating event is induced by including the latter as a covariate in the proportional hazards model for the failure time of interest. The use of splines results in a higher rate of convergence of the estimator of the baseline hazard function compared with the usual non‐parametric estimator. The computation of the estimator is facilitated by a multiple imputation approach. Asymptotic theory is established and a simulation study is conducted to assess its finite sample performance. It is also applied to analyzing a real data set on AIDS incubation time.
Estimating Abundance from Presence–Absence Maps via a Paired Negative‐Binomial Model
Authors: Hwang Wen‐Han , Huggins Richard
Published: November 2015

The estimation of abundance from presence–absence data is an intriguing problem in applied statistics. The classical Poisson model makes strong independence and homogeneity assumptions and in practice generally underestimates the true abundance. A controversialad hocmethod based on negative‐binomial counts (Am. Nat.) has been empirically successful but lacks theoretical justification. We first present an alternative estimator of abundance based on a paired negative binomial model that is consistent and asymptotically normally distributed. A quadruple negative binomial extension is also developed, which yields the previousad hocapproach and resolves the controversy in the literature. We examine the performance of the estimators in a simulation study and estimate the abundance of 44 tree species in a permanent forest plot.
A Necessary Condition for the Strong Oracle Property
Authors: Kim Yongdai , Jeon Jong‐June , Han Sangmi
Published: November 2015

A problem of using a non‐convex penalty for sparse regression is that there are multiple local minima of the penalized sum of squared residuals, and it is not known which one is a good estimator. The aim of this paper is to give a guide to design a non‐convex penalty that has the strong oracle property. Here, the strong oracle property means that the oracle estimator is the unique local minimum of the objective function. We summarize three definitions of the oracle property – the global, weak and strong oracle properties. Then, we give sufficient conditions for the weak oracle property, which means that the oracle estimator becomes a local minimum. We give an example of non‐convex penalties that possess the weak oracle property but not the strong oracle property. Finally, we give a necessary condition for the strong oracle property.
Sample acceptance time criteria, electronic issue and alloimmunisation in thalassaemia
Authors: Trompeter S. , Baxter L. , McBrearty M. , Zatkya E. , Porter J.
Published: November 2015

Objectives

To determine the safety of a 1‐week acceptance criteria of sample receipt in laboratory to transfusion commencement in transfusion dependent thalassaemia with respect to alloimmunisation. To determine the safety of electronic issue of blood components in such a setting.

Methods

Retrospective audit of alloimmunisation (1999–2012) and blood exposure in registered thalassaemia patients at a central London thalassaemia centre where the acceptance criteria for the group and save sample from arrival in the laboratory to the time of issue of blood for transfusion for someone who has been transfused in the last 28 days was 1 week, and there was electronic issue protocol for patients who have always had a negative antibody screen (other than temporary positivity in pregnant women receiving prophylactic anti‐D or anti Le‐a, Anti Le‐b and Anti P1 that are no longer detectable).

Results

There were 133 patients with thalassemia variants regularly attending UCLH for review. A total of 105 patients had transfusion dependent thalassaemia (TDT) (7 E‐beta thalassaemia, 98 beta thalassaemia major). Ten of the 84 patients who received their transfusions at UCLH were alloimmunised. Seven of them had been alloimmunised prior to arrival at UCLH. Only two patients developed antibodies at UCLH during this period.

Conclusion

The prevalence of alloantibody formation of 2% in UCLH transfused patients, with presumptive incidence of 0·01 alloantibodies per 100 units or 0·001 immunisations per person per year compares favourably with other reported series and suggests that 1 week interval with appropriate electronic issue is acceptable practice.
How do we develop and implement a preoperative anemia clinic designed to improve perioperative outcomes and reduce cost?
Authors: Guinn Nicole R. , Guercio Jason R. , Hopkins Thomas J. , Grimsley Aime , Kurian Dinesh J. , Jimenez Maria I. , Bolognesi Michael P , Schroeder Rebecca , Aronson Solomon ,   on behalf of the Duke Perioperative Enhancement Team (POET)
Published: November 2015

Treatment of anemia is one of the four pillars of patient blood management programs. Preoperative anemia is common and associated with increased perioperative morbidity after surgery and increased rates of blood transfusion. Effective treatment of preoperative anemia, however, requires advanced screening, diagnosis, and initiation of therapy weeks before elective surgery. Here we describe the development and implementation of a preoperative anemia screening and treatment program at Duke University Hospital.
Hypokalemia and suspected renal tubular acidosis associated with topical carbonic anhydrase inhibitor therapy in a cat
Authors: Thiessen Charlotte E. , Tofflemire Kyle L. , Makielski Kelly M. , Ben‐Shlomo Gil , Whitley R. David , Allbaugh Rachel A.
Published: November 2015

Objective

To describe the occurrence of hypokalemia, metabolic acidosis, and suspected renal tubular acidosis associated with the administration of topical ophthalmic carbonic anhydrase inhibitor (CAI) in a cat.

Case Summary

A 2‐year‐old, 5.3 kg, male, castrated, domestic short‐haired cat developed hyporexia 6 weeks after starting topical ophthalmic dorzolamide 2% therapy for treatment of ocular hypertension. Two weeks later, the cat was evaluated for severe weakness, cervical ventroflexion, and anorexia. Plasma electrolyte and acid–base measurement revealed hypokalemia (K+ = 2.9 mmol/L; reference interval 3.8–5.4 mmol/L) and metabolic acidosis (plasma HCO3− = 9.8 mmol/L; reference interval 15–23 mmol/L) in the presence of a urine pH of 7.5 (reference interval 6.5–7.5). The pH abnormalities were consistent with a renal tubular acidosis. Clinical and biochemical abnormalities resolved with short‐term supportive care, potassium supplementation, and discontinuation of dorzolamide therapy.

New or Unique Information Provided

This is the first report of hypokalemia and metabolic acidosis associated with topical CAI therapy in a cat.
Downregulation of prostaglandin E2 is involved in hindgut mucosal damage in lactating goats fed a high‐concentrate diet
Authors: Tao Shiyu , Han Zhengqiang , Tian Jing , Cong Rihua , Duanmu Yongqian , Dong Haibo , Ni Yingdong , Zhao Ruqian
Published: November 2015

New Findings

What is the central question of this study?

A high‐concentrate (HC) diet results in damage to the hindgut mucosa. The aim of the study was to investigate the status of epithelial proliferation in the hindgut mucosa of goats with subacute ruminal acidosis and, simultaneously, to evaluate prostaglandin E2 synthesis and the downstream signalling pathways.

What is the main finding and its importance?

The downregulation of local prostaglandin E2 synthesis and its downstream signalling pathway are involved in the process of inhibiting epithelial proliferation in the hindgut epithelium of HC‐fed goats. Our results provide new insight into the relationship between abnormal fermentation in the hindgut and damage to the intestinal mucosal barrier.

Our previous data demonstrated that feeding a high‐concentrate (HC) diet to lactating goats for a long time causes severe damage to the hindgut mucosa and parallels the activation of cell apoptosis and local oxidative stress. In the present study, changes in production of prostaglandin E2 (PGE2) and its signalling pathway were evaluated in the process of epithelial barrier disruption in the hindgut. Twelve goats in mid‐lactation were randomly assigned to either a HC diet group or a low‐concentrate (LC) diet group for 10 weeks. Cell proliferation markers, cyclooxygenase‐2 activity, PGE2 content and the relative signalling pathway, including CREB and AKT, were analysed by enzyme‐linked immunosorbent assay and Western blot, respectively. The mRNA and protein expressions of MKI67 and CCND2 (two proliferation markers) were significantly decreased in the caecal mucosa of HC‐ compared with LC‐fed goats (P < 0.05). The protein content of interleukin‐10 and β‐defensin in the caecal mucosa was also downregulated in HC‐fed goats (P < 0.05). The HC‐fed goats showed a tendency to a decrease in cyclooxygenase‐2 enzyme activity (P = 0.081) and a significant decrease of local PGE2 content and EP4 (PGE2 receptor) protein expression in caecal mucosa (P < 0.05). Moreover, the protein abundance of p‐CREB (P = 0.069) and p‐AKT (P < 0.05) and the mRNA expression of epidermal growth factor receptor (P < 0.05) were downregulated in caecal mucosa of HC‐ compared with LC‐fed goats. These results indicate that a reduction in epithelial cell proliferation was partly responsible for the damage to the epithelial barrier, which might be associated with the downregulation of PGE2 synthesis and its downstream signalling pathway.
Calcium signalling in salivary gland physiology and dysfunction
Authors: Ambudkar Indu S.
Published: November 2015

Studies over the past four decades have established that Ca2+ is a critical factor in control of salivary gland function and have led to identification of the critical components of this process. The major ion transport mechanisms and ion channels that are involved in fluid secretion have also been established. The key event in activation of fluid secretion is an increase in [Ca2+]i triggered by inositol 1,4,5‐trisphosphate (IP3)‐induced release of Ca2+ from ER via the IP3 receptor (IP3R). IP3Rs determine the site of initiation and the pattern of the [Ca2+]i signal in the cell. However, Ca2+ entry into the cell is required to sustain the elevation of [Ca2+]i and fluid secretion and is mediated by the store‐operated Ca2+ entry (SOCE) mechanism. Orai1, TRPC1, TRPC3 and STIM1 have been identified as critical components of SOCE in these cells. Cells finely tune the generation and amplification of [Ca2+]i signals for regulation of cell function. An important emerging area is the concept that unregulated [Ca2+]i signals in cells can directly cause cell damage, dysfunction and disease. Alternatively, aberrant [Ca2+]i signals can also amplify and increase the rates of cell damage. Such defects in Ca2+ signalling have been described in salivary glands in conjunction with radiation‐induced loss of salivary gland function as well as in the salivary defects associated with the autoimmune exocrinopathy Sjögren's syndrome. Such defects have been associated with altered function or expression of key Ca2+ signalling components, such as STIM proteins and TRP channels. These studies offer new avenues for examining the mechanisms underlying the disease and development of novel clinical targets and therapeutic strategies.

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Uso de la tierra y diversidades alfa, beta y gamma de diplópodos en la cuenca del río Otún, Colombia
Authors: Ruiz-Cobo Darío Hernán , Bueno-Villegas Julián , Feijoo-Martínez Alexander
Published: November 2015

 Objective: To determine the relationship between changes in ecosystems and agrosystems provoked by human intervention and the alpha, beta and gamma diversity of the Diplopoda in the middle basin of the Otún river. Materials and methods: In this research we used a stratified systematic design with seven sampling windows and 16 sampling points. Millipedes were divided into families and morphotypes to calculate the alpha, beta and gamma diversity related to the heterogeneity of land uses. Results: We identified 35 morphotypes from 12 families and five orders. Alpha diversity of Diplopoda revealed significant differences between land uses (P <0.05) and a decrease of richness from preserved areas to transformed areas by human activity. A high number of exclusive morphotypes were found in forest relicts and fallow with low species turnover between them, while the pastures, crop fields and plantations presented similar numbers of morphotypes but the species turnover between them was high (complementarity > 85%) in spite of the low diversity in the land uses, which determined the high contribution of the beta diversity to the gamma diversity of the landscape. Conclusion: The heterogeneity of land uses showed that the changes modify the structure of diversity in Diplopoda with gradients diverging from the preserved ones to the highly transformed ones.

Key words: alpha, beta, gamma diversity, Colombian Andes, soil Diplopoda.
Mecanismos antitumorales de la metformina: señalización, metabolismo, inmunidad y más allá.
Authors: Duque Jorge Eduardo , López Catalina , Cruz Nataly , Samudio Ismael
Published: November 2015

Metformin is a synthetic biguanide first described in the 1920´s as a side product of the synthesis of N,N-dimethylguanidine. Like other related biguanides, metformin displays antihyperglycemic properties, and has become the most widely prescribed oral antidiabetic medicine around the world. Intriguing recent evidence suggests that metformin has chemopreventive and direct antitumor properties, and several ongoing clinical studies around the world are using this agent alone or in combination with chemotherapeutic schemes to determine prospectively its safety and efficacy in the treatment of human cancer. Notably, immune activating effects of metformin have recently been described, and may support a notion put forth in the 1950s that this agent possessed antiviral and antimalarial effects. However, how these effects may contribute to its observed antitumor effects in retrospective studies has not been discussed. Mechanistically, metformin has been shown to activate liver kinase B1 (LKB1) and its downstream target AMP-activated kinase (AMPK). The activation of AMPK has been proposed to mediate metformin´s glucose lowering effect, although recent evidence suggests that this agent can inhibit electron transport in hepatocyte mitochondria resulting in AMPK-independent inhibition of hepatic gluconeogenesis. Likewise, albeit activation of AMPK and the resulting inhibition of the mammalian target of rapamycin (mTOR) signaling have been suggested to mediate the antitumor effects of metformin, AMPK-independent growth inhibitory properties of this agent in tumor cells have also been described. Here we present a brief review of the signaling, metabolic, and immune effects of metformin and discuss how their interplay may orchestrate the antitumor effects of this agent. In addition, we provide the rationale for a compassionate use study of metformin in combination with metronomic chemotherapy.

Key words: metformin, cáncer, AMPK, metabolism, diabetes
Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8
Authors: Sáenz-Suárez Homero , Lareo Leonardo René , Oribio-Quinto Carlos , Martínez-Mendoza Juan , Chávez-Zobel Aura
Published: November 2015

Objective: To make computational predictions of the structure of the human proteins Hsp27, αB-crystalline and HspB8. Materials and methods. The prediction of the secondary structure was obtained by a consensus of the programs for secondary prediction GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN and Psi-Pred. The models of tertiary structure were built from fragments homologous to proteins with tertiary known structure that were obtained by multiple alignments. Using the primary sequence we obtained the antigenicity profiles of native proteins and we analyzed the profiles of hydrophobicity, polarity, flexibility and accessibility of both native and mutant proteins. Results. Predictions of the secondary and tertiary structures of the studied proteins show that in the three cases, more than 65% are coil regions, 20-25 % are folded sheet and less than 10% are alpha helix. Analyses of the primary structure show that at least one of the studied profiles in every mutation is altered. Conclusions. The comparative analyses of structure suggest that mutations affect the solubility of the mutated proteins and hence affect their function as molecular chaperones

Key words: Hsp27, αB-cristalline, HspB8, prediction of secondary structure, computational model of tertiary structure
Anotaciones de la ecología alimentaria de monos aulladores negros en un fragmento con condiciones de hacinamiento (Balancán, Tabasco, México)
Authors: Aristizábal-Borja John , Pozo-Montuy Gilberto , Pérez-Torres Jairo , Serio-Silva Juan
Published: November 2015

We described the feeding behavior of Central-American black howler monkey (Alouatta pigra) in a fragment of less than one hectare of humid evergreen forest surrounded by grassland for livestock use, isolated trees and mango orchards, in the region of Balancán (Tabasco, México). Objective: To record the diet and activity of black howler monkeys in crowded conditions during the wettest month in Balancán (Tabasco, México). Methods: The behavioral observations (81 h) were made using the focal animal methodology with an A. pigra troop made up of three individuals (1 adult male, 1 adult female and 1 infant). Results: Feeding time represented 15.97%, rest 78% and locomotion 4.57% of total time. In the study area we recorded 14 plant species, with 10 being consumed by howler monkeys. 55% of feeding time was devoted to the consumption of fruits, 27% to leaves, 17% to stems, and 1% to sprouts. Spondias mombin was the tree species most consumed, with 61% of the time invested on it. Conclusion: Like other studies, we confirmed the frugivore-folivore feeding tendency of the genus Alouatta. We provide information on the black howler monkey flexibility to live and maintain themselves in extreme perturbation conditions, where their habitat is 0.1 ha with few tree species to use, forcing individuals to move around the ground.

Key words: Alouatta pigra, diet, pattern of activity, frugivory, fragmented habitat
Desempeño de juveniles del pez ángel Pterophyllum scalare alimentados con el oligoqueto Enchytraeus buchholzi
Authors: Jiménez-Rojas Jhon Edison , Alméciga-Díaz Paola Andrea , Herazo-Duarte Diego Mauricio
Published: November 2015

The angel fish Pterophyllum scalare is one of the main species of ornamental interest and widely exploited in Colombia for export. Objective. To evaluate the influence on growth and survival of juvenile P. scalare veil variety fed with Enchytraeus buchholzi. Materials and methods. Ten juveniles per fish tank were randomly distributed among nine fish tanks and then treated with three different diets (D1, D2 and D3): commercial feed containing 45% of crude protein (CP) (D1); commercial feed containing 45% of CP + E. buchholzi with 11.6% of CP (D2) and E. buchholzi alone with 11.6% of CP (D3). Animals were fed during 28 days and final weight (FW), final standard length (FSL), weight gain (WG), gain in standard length (GSL), specific growth rate (SGR), and survival were measured. Results. Significant differences were observed (p <0.05) for the variables FW and FSL. Individuals fed with diet D2 showed higher FW and FSL than those fed with diet D1. The best growth performance was in overall obtained with D2 and were not significantly different (p >0.05) to those observed in juveniles fed with D3. Conclusions. Based upon our results, we recommend E. buchholzi to be used as a supplement to the artificial diet instead of a diet on its own. The adequate proportion in the diet must be known for its optimal use.

Key words: growth, live food, angelfish, survival.
Selection of a bioassay battery to assess toxicity in the affluents and effluents of three water-treatment plants
Authors: Bohórquez-Echeverry Paola , Duarte-Castañeda Marcela , León-López Nubia , Caicedo-Carrascal Fabián , Vásquez-Vásquez Myriam , Campos-Pinilla Claudia
Published: November 2015

Objective. The assessment of water quality includes the analysis of both physical-chemical and microbiological parameters. However, none of these evaluates the biological effect that can be generated in ecosystems or humans. In order to define the most suitable organisms to evaluate the toxicity in the affluent and effluent of three drinking-water treatment plants, five acute toxicity bioassays were used, incorporating three taxonomic groups of the food chain. Materials and methods. The bioassays used were Daphnia magna and Hydra attenuata as animal models, Lactuca sativa and Pseudokirchneriella subcapitata as plant models, and Photobacterium leioghnathi as bacterial model. To meet this objective, selection criteria of the organisms evaluated and cluster analysis were used to identify the most sensitive in the affluent and effluent of each plant. Results. All organisms are potentially useful in the assessment of water quality by meeting four essential requirements and 17 desirable requirements equivalent to 100% acceptability, except P. leioghnathi which does not meet two essential requirements that are the IC50 for the toxic reference and the confidence interval. The animal, plant and bacterial models showed different levels of sensitivity at the entrance and exit of the water treatment systems. Conclusions. H. attenuata, P. subcapitata and P. leioghnathi were the most effective organisms in detecting toxicity levels in the affluents and D. magna, P. subcapitata and P. leioghnathi in the effluents.
Key words: bioassays, cluster analysis, drinking water, raw water, toxicity.
Nonlinear Recursive Estimation With Estimability Analysis for Physical and Semiphysical Engine Model Parameters
Authors: Souflas Ioannis , Pezouvanis Antonios , Ebrahimi Kambiz M.
Published: November 2015

A methodology for nonlinear recursive parameter estimation with parameter estimability analysis for physical and semiphysical engine models is presented. Orthogonal estimability analysis based on parameter sensitivity is employed with the purpose of evaluating a rank of estimable parameters given multiple sets of observation data that were acquired from a transient engine testing facility. The qualitative information gained from the estimability analysis is then used for estimating the estimable parameters by using two well-known nonlinear adaptive estimation algorithms known as extended Kalman filter (EKF) and unscented Kalman filter (UKF). The findings of this work contribute on understanding the real-world challenges which are involved in the effective implementation of system identification techniques suitable for online nonlinear estimation of parameters with physical interpretation.
Subject-Specific Computational Modeling of Evoked Rabbit Phonation
Authors: Chang Siyuan , Novaleski Carolyn K. , Kojima Tsuyoshi , Mizuta Masanobu , Luo Haoxiang , Rousseau Bernard
Published: November 2015

When developing high-fidelity computational model of vocal fold vibration for voice production of individuals, one would run into typical issues of unknown model parameters and model validation of individual-specific characteristics of phonation. In the current study, the evoked rabbit phonation is adopted to explore some of these issues. In particular, the mechanical properties of the rabbit's vocal fold tissue are unknown for individual subjects. In the model, we couple a 3D vocal fold model that is based on the magnetic resonance (MR) scan of the rabbit larynx and a simple one-dimensional (1D) model for the glottal airflow to perform fast simulations of the vocal fold dynamics. This hybrid three-dimensional (3D)/1D model is then used along with the experimental measurement of each individual subject for determination of the vocal fold properties. The vibration frequency and deformation amplitude from the final model are matched reasonably well for individual subjects. The modeling and validation approaches adopted here could be useful for future development of subject-specific computational models of vocal fold vibration.
Modeling and Temperature Analysis of the Nexa 1.2 kW Fuel Cell System
Authors: Salim R. I. , Noura H. , Nabag M. , Fardoun A.
Published: November 2015

The United Arab Emirates (UAE) has been exploring several renewable and green technologies to help reduce the increasing pollution rates. However, its coarse climate might impose some limitations toward the types of green technologies that can be effectively deployed in the region. In the first part of this work, an improved dynamic model of the Nexa 1.2 kW PEM fuel cell is developed using particle swarm optimization (PSO), and validated using experimental data. The developed model is then used to analyze the effect of the severe climate conditions of the UAE on the performance of the system to evaluate its operational compatibility with the region.
Atomic layer deposition of alternative glass microchannel plates
Authors: O'Mahony Aileen , Craven Christopher A. , Minot Michael J. , Popecki Mark A. , Renaud Joseph M. , Bennis Daniel C. , Bond Justin L. , Stochaj Michael E. , Foley Michael R. , Adams Bernhard W. , Mane Anil U. , Elam Jeffrey W. , Ertley Camden , Siegmund Oswald H. W.
Published: November 2015

The technique of atomic layer deposition (ALD) has enabled the development of alternative glass microchannel plates (MCPs) with independently tunable resistive and emissive layers, resulting in excellent thickness uniformity across the large area (20 × 20 cm), high aspect ratio (60:1 L/d) glass substrates. Furthermore, the use of ALD to deposit functional layers allows the optimal substrate material to be selected, such as borosilicate glass, which has many benefits compared to the lead-oxide glass used in conventional MCPs, including increased stability and lifetime, low background noise, mechanical robustness, and larger area (at present up to 400 cm2). Resistively stable, high gain MCPs are demonstrated due to the deposition of uniform ALD resistive and emissive layers on alternative glass microcapillary substrates. The MCP performance characteristics reported include increased stability and lifetime, low background noise (0.04 events cm−2 s−1), and low gain variation (±5%).
The Feasibility of Using Questionnaires and Accelerometers to Measure Physical Activity and Sedentary Behavior Among Inpatient Adults With Mental Illness
Authors: Fraser Sarah J. , Chapman Justin J. , Brown Wendy J. , Whiteford Harvey A. , Burton Nicola W.
Published: November 2015

Background:

The aim of this study was to assess the feasibility of using questionnaires and accelerometers to measure physical activity and sedentary behavior among inpatient adults with mental illness.

Methods:

Participants completed a physical activity and sitting time questionnaire and wore an accelerometer for 7 consecutive days. Feasibility was assessed in terms of participant engagement, self-reported ease/difficulty of completing study components, extreme self-report data values and adherence to accelerometer wear time criteria. Ease/difficulty ratings were examined by level of distress.

Results:

177 inpatients were invited to the study, 101 completed the questionnaires and 36 provided valid accelerometry data. Participants found it more difficult to complete sitting time and physical activity questionnaires than to wear the accelerometer during waking hours (z = 3.787, P < .001; z = 2.824, P = .005 respectively). No significant differences were found in ease/difficulty ratings by level of distress for any of the study components. Extreme values for self-reported sitting time were identified in 27% of participants.

Conclusion:

Inpatient adults with mental illness can engage with self-report and objective methods of measuring physical activity and sedentary behavior. They were initially less willing to participate in objective measurement, which may however be more feasible than self-report measures.
Bimatoprost (0.03%)-induced accommodative spasm and pseudomyopia
Authors: Padhy Debananda , Rao Aparna
Published: November 2015

Bimatoprost is a prostaglandin analogue used topically in the treatment of glaucoma. Commonly known side effects include eyelash growth, iris pigmentation and conjunctival hyperemia. While pseudomyopia is reported to be caused by parasympathomimetics, such an effect precipitated by bimatoprost has not yet been reported. We report a case demonstrating pseudomyopia and accommodative spasm caused after starting bimatoprost 0.03% in a young patient with glaucoma.
The theoretical foundations for size spectrum models of fish communities
Authors: Andersen Ken H. , Jacobsen Nis S. , Farnsworth K.D.
Published: November 2015

Size spectrum models have emerged from 40 years of basic research on how body size determines individual physiology and structures marine communities. They are based on commonly accepted assumptions and have a low parameter set, making them easy to deploy for strategic ecosystem-oriented impact assessment of fisheries. We describe the fundamental concepts in size-based models about food encounter and the bioenergetics budget of individuals. Within the general framework, three model types have emerged that differ in their degree of complexity: the food-web, the trait-based, and the community models. We demonstrate the differences between the models through examples of their response to fishing and their dynamic behavior. We review implementations of size spectrum models and describe important variations concerning the functional response, whether growth is food-dependent or fixed, and the density dependence imposed on the system. Finally, we discuss challenges and promising directions.
Unsupervised statistical learning applied to experimental high-energy physics and related areas
Authors: Simas Filho Eduardo F. , Seixas José M.
Published: November 2015

Unsupervised statistical learning (USL) techniques, such as self-organizing maps (SOMs), principal component analysis (PCA) and independent component analysis explore different statistical properties to efficiently process information from multiple variables. USL algorithms have been successfully applied in experimental high-energy physics (HEP) and related areas for different purposes, such as feature extraction, signal detection, noise reduction, signal-background separation and removal of cross-interference from multiple signal sources in multisensor measurement systems. This paper presents both a review of the theoretical aspects of these signal processing methods and examples of some successful applications in HEP and related areas experiments.
A modified full velocity difference model with the consideration of velocity deviation
Authors: Zhou Jie , Shi Zhong-Ke
Published: November 2015

In this paper, a modified full velocity difference model (FVDM) based on car-following theory is proposed with the consideration of velocity deviation which represents the inexact judgement of velocity. The stability condition is obtained by the use of linear stability analysis. It is shown that the stability of traffic flow varies with the deviation extent of velocity. The Burgers, Korteweg-de Vries (KdV) and modified K-dV (MKdV) equations are derived to describe the triangular shock waves, soliton waves and kink–antikink waves in the stable, metastable and unstable region, respectively. The numerical simulations show a good agreement with the analytical results, such as density wave, hysteresis loop, acceleration, deceleration and so on. The results show that traffic congestion can be suppressed by taking the positive effect of velocity deviation into account. By taking the positive effect of high estimate of velocity into account, the unrealistic high deceleration and negative velocity which occur in FVDM will be eliminated in the proposed model.
A Space Division Multiobjective Evolutionary Algorithm Based on Adaptive Multiple Fitness Functions
Authors: Wang Mingzhao , Wang Yuping , Wang Xiaoli
Published: November 2015

The weighted sum of objective functions is one of the simplest fitness functions widely applied in evolutionary algorithms (EAs) for multiobjective programming. However, EAs with this fitness function cannot find uniformly distributed solutions on the entire Pareto front for nonconvex and complex multiobjective programming. In this paper, a novel EA based on adaptive multiple fitness functions and adaptive objective space division is proposed to overcome this shortcoming. The objective space is divided into multiple regions of about the same size by uniform design, and one fitness function is defined on each region by the weighted sum of objective functions to search for the nondominated solutions in this region. Once a region contains fewer nondominated solutions, it is divided into several sub-regions and one additional fitness function is defined on each sub-region. The search will be carried out simultaneously in these sub-regions, and it is hopeful to find more nondominated solutions in such a region. As a result, the nondominated solutions in each region are changed adaptively, and eventually are uniformly distributed on the entire Pareto front. Moreover, the complexity of the proposed algorithm is analyzed. The proposed algorithm is applied to solve 13 test problems and its performance is compared with that of 10 widely used algorithms. The results show that the proposed algorithm can effectively handle nonconvex and complex problems, generate widely spread and uniformly distributed solutions on the entire Pareto front, and outperform those compared algorithms.
Axions/Axion-like particles and the CMB asymmetric dipole
Authors: Yang Qiaoli
Published: November 2015

Axions and axion-like particles (ALPs) are very attractive dark matter candidates. In this review, we briefly investigate how the cosmological observations reveal the existence of dark matter and some unique properties of axions/(ALPs) which make them more interesting.
Improved Gamma Process for Degradation Analysis Under Nonlinear Condition
Authors: Fan Zhao-Yi , Ju Hua , Sun Feng-Bin
Published: November 2015

Some life tests result in few or no failures. In such cases, we can, and should, consider using degradation measurements to assess reliability. In real world, product degradation is a stochastic process. Since such degradation is often seen as a monotonous process, literature widely uses Gamma Process to describe and quantify degradation. However, in these publications, scale parameter is considered constant over time and results under this assumption may have big deviation from the actual measurements under nonlinear condition. The purpose of this paper is to improve Gamma Process method to fit a broader class of degradation models. Firstly, we use MLE to estimate the parameters under the timely constant-scale-parameter assumption and analyze why the model does not fit data well. Then we propose an improved model to improve the method and use Monte Carlo simulation to verify the validity of the improved method.
A Fuzzy Linguistic Extended LibQUAL+ Model to Assess Service Quality in Academic Libraries
Authors: Cabrerizo F. J. , López-Gijón J. , Martínez M. A. , Morente-Molinera J. A. , Herrera-Viedma E.
Published: November 2015

LibQUAL+ model is the best-known method for the quality evaluation of library services, but it has two major drawbacks. First, to measure the quality, it is devised on a cardinal scale: the service levels range from 1 to 9. However, the standard representation of the concepts used by humans for communication is the natural language and, hence, users should express their judgments by using words instead of numbers. Second, it considers that all users’ opinions are equally important. Nevertheless, users do not play an equal role in assessing the service quality, i.e., the opinion given by some users should be more relevant than the opinion provided by others. To solve these drawbacks, we present an extended LibQUAL+ model representing the users’ perceptions by using a fuzzy linguistic modeling and taking into account that users’ opinions on the library services are not equally important.
A novel network-based computational method to predict protein phosphorylation on tyrosine sites
Authors: Wang Binghua , Wang Minghui , Jiang Yujie , Sun Dongdong , Xu Xiaoyi
Published: November 2015

Phosphorylation plays a great role in regulating a variety of cellular processes and the identification of tyrosine phosphorylation sites is fundamental for understanding the post-translational modification (PTM) regulation processes. Although a lot of computational methods have been developed, most of them only concern local sequence information and few studies focus on the tyrosine sites with in situ PTM information, which refers to different types of PTM occurring on the same modification site. In this study, by constructing the site-modification network that efficiently incorporates in situ PTM information, we introduce a novel network-based computational method, site-modification network-based inference (SMNBI) to predict tyrosine phosphorylation. In order to verify the effectiveness of the proposed method, we compare it with other network-based computational methods. The results clearly show the superior performance of SMNBI. Besides, we extensively compare SMNBI with other sequence-based methods including SVM and Bayesian decision theory. The evaluation demonstrates the power of site-modification network in predicting tyrosine phosphorylation. The proposed method is freely available at http://bioinformatics.ustc.edu.cn/smnbi/ .