bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance evaluation of classifier ensembles in terms of diversity and performance of individual systems
Authors: Chung Yun‐Sheng , Hsu D. Frank , Liu Chun‐Yi , Tang Chun‐Yi 
Published: December 2010

PurposeMultiple classifier systems have been used widely in computing, communications, and informatics. Combining multiple classifier systems (MCS) has been shown to outperform a single classifier system. It has been demonstrated that improvement in ensemble performance depends on either the diversity among or the performance of individual systems. A variety of diversity measures and ensemble methods have been proposed and studied. However, it remains a challenging problem to estimate the ensemble performance in terms of the performance of and the diversity among individual systems. The purpose of this paper is to study the general problem of estimating ensemble performance for various combination methods using the concept of a performance distribution pattern (PDP).Design/methodology/approachIn particular, the paper establishes upper and lower bounds for majority voting ensemble performance with disagreement diversity measure Dis, weighted majority voting performance in terms of weighted average performance and weighted disagreement diversity, and plurality voting ensemble performance with entropy diversity measure D.FindingsBounds for these three cases are shown to be tight using the PDP for the input set.Originality/valueAs a consequence of the authors' previous results on diversity equivalence, the results of majority voting ensemble performance can be extended to several other diversity measures. Moreover, the paper showed in the case of majority voting ensemble performance that when the average of individual systems performance P is big enough, the ensemble performance Pm resulting from a maximum (information‐theoretic) entropy PDP is an increasing function with respect to the disagreement diversity Dis. Eight experiments using data sets from various application domains are conducted to demonstrate the complexity, richness, and diverseness of the problem in estimating the ensemble performance.
A framework for evaluating pervasive systems
Authors: Yang Hen‐I , Chen Chao , Abdulrazak Bessam , Helal Sumi 
Published: December 2010

PurposeA decade and a half after the debut of pervasive computing, a large number of prototypes, applications, and interaction interfaces have emerged. However, there is a lack of consensus about the best approaches to create such systems or how to evaluate them. To address these issues, this paper aims to develop a performance evaluation framework for pervasive computing systems.Design/methodology/approachBased on the authors' experience in the Gator Tech Smart House – an assistive environment for the elderly, they established a reference scenario that was used to guide the analysis of the large number of systems they studied. An extensive survey of the literature was conducted, and through a thorough analysis, the authors derived and arrived at a broad taxonomy that could form a basic framework for evaluating existing and future pervasive computing systems.FindingsA taxonomy of pervasive systems is instrumental to their successful evaluation and assessment. The process of creating such taxonomy is cumbersome, and as pervasive systems evolve with new technological advances, such taxonomy is bound to change by way of refinement or extension. This paper found that a taxonomy for something so broad as pervasive systems is very complex. It overcomes the complexity by focusing the classifications on key aspects of pervasive systems, decided purely empirically and based on the authors own experience in a real‐life, large‐scale pervasive system project.Originality/valueThere are currently no methods or frameworks for comparing, classifying, or evaluating pervasive systems. The paper establishes a taxonomy – a first step toward a larger evaluation methodology. It also provides a wealth of information, derived from a survey of a broad collection of pervasive systems.
Timing and mechanisms controlling evaporite diapirism on Ellef Ringnes Island, Canadian Arctic Archipelago
Authors: Boutelier Jennifer , Cruden Alexander , Brent Tom , Stephenson Randell 
Published: December 2010

ABSTRACTThe Permo‐Carboniferous to Eocene Sverdrup Basin in Canada's Arctic Archipelago is strongly influenced by evaporite diapirism. However, salt structures within the basin have not been extensively investigated recently due to their remote location. This study includes the interpretation of legacy seismic reflection and borehole data to characterize the geometry of selected evaporite domes, and 1D backstripping of wells to investigate tectonic and sedimentary influences on diapirism. Extensional rift‐structures appear to have played a significant role in the formation of evaporite domes by triggering and directing salt movement. Diapirism was initiated by at least the Middle Triassic and continued to develop during the Mesozoic. Differential loading of salt on opposing east–west dome margins led to their present day asymmetric geometries. Diapir growth rates in the Mesozoic were closely linked to the rate of sedimentation and influenced by regional tectonism.
Issues with modelling the current and future distribution of invasive pathogens
Authors: Murray Kris A. , Retallick Richard W. R. , Puschendorf Robert , Skerratt Lee F. , Rosauer Dan , McCallum Hamish I. , Berger Lee , Speare Rick , VanDerWal Jeremy 
Published: December 2010

Summary1. Correlative species distribution models can be used to produce spatially explicit estimates of environmental suitability for organisms. This process can provide meaningful information for a range of purposes (e.g. estimating a species’ current or future distribution, estimating dispersal limits, predicting occupancy for conservation planning) but, like all statistical exercises, is subject to numerous assumptions and can be influenced by several sources of potential bias.2. In this issue of Journal of Applied Ecology, we (Murray et al. 2011) employ a correlative species distribution model for infection with the pathogen Batrachochytrium dendrobatidis (Bd), cause of amphibian chytridiomycosis, to derive useful information for the immediate management and research of this pathogen in Australia. Also in this issue, Rohr, Halstead & Raffel (2011) comment on some of the potential limitations of our approach and the value of our results in practice.3.
Synthesis and applications. Here we show that while a focus on mechanisms of dispersal and transmission among hosts, as advocated in both studies, is an important objective for modelling Bd distribution under climate change or at invasion fronts, correlative models can be of immediate value for their ability to generate a baseline hypothesis about the current potential distribution of this lethal pathogen and for efficiently identifying gaps in current knowledge. As demonstrated in our paper, this should help improve the immediate allocation of limited research and management resources for future surveillance efforts and proactive species conservation.
A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding
Authors: Goff Stephen A. 
Published: December 2010

SummaryHybrids between genetically diverse varieties display enhanced growth, and increased total biomass, stress resistance and grain yield. Gene expression and metabolic studies in maize, rice and other species suggest that protein metabolism plays a role in the growth differences between hybrids and inbreds. Single trait heterosis can be explained by the existing theories of dominance, overdominance and epistasis. General multigenic heterosis is observed in a wide variety of different species and is likely to share a common underlying biological mechanism. This review presents a model to explain differences in growth and yield caused by general multigenic heterosis. The model describes multigenic heterosis in terms of energy‐use efficiency and faster cell cycle progression where hybrids have more efficient growth than inbreds because of differences in protein metabolism. The proposed model is consistent with the observed variation of gene expression in different pairs of inbred lines and hybrid offspring as well as growth differences in polyploids and aneuploids. It also suggests an approach to enhance yield gains in both hybrid and inbred crops via the creation of an appropriate computational analysis pipeline coupled to an efficient molecular breeding program.ContentsSummary923I.Introduction924II.Early studies of heterosis924III.Heterosis in diverse species926IV.Gene expression studies926V.Protein metabolism927VI.Allele‐specific gene expression928VII.Quality control929VIII.A synthesis model930IX.Putting the model to work932Acknowledgements933References933
Measuring Platelet Aggregation in Dialysis Patients With a Whole Blood Aggregometer by the Screen Filtration Pressure Method
Authors: Waki Kayo , Hayashi Aki , Ikeda Shigeo , Ikeda Sadao , Nagatsuka Kazuhiro , Honma Yoshiyuki , Kadowaki Takashi , Yoshinoya Sadayoshi 
Published: December 2010

AbstractA semi‐automatic, whole‐blood aggregometer based on the screen filtration pressure (SFP) method is now widely used clinically and in research, but has not been used with hemodialysis (HD) patients. We measured whole‐blood platelet aggregation in HD patients by the SFP method. This retrospective cross‐sectional study included 62 HD patients, of whom 47 were non‐diabetic and 15 were diabetic; we also included a control group of healthy, non‐uremic subjects. With the t‐test, we examined differences in the platelet aggregation threshold index (PATI) in meaningful sub‐groupings of the HD patients, depending on whether or not they had diabetes, and whether or not they had been given antiplatelet agents. Considering the non‐diabetic HD patients first, their PATI values were significantly higher than those values in the control subjects (3.1 [1.0–5.2] vs. 1.8 [1.3–2.3] µM, P < 0.001). The non‐diabetic HD patients taking antiplatelet agents showed significantly (1.9 times) higher PATI values than the non‐diabetic HD patients without antiplatelet agents (4.4 [1.8–7.0] vs. 2.3 [1.3–3.3] µM, P = 0.003). We observed similar trends among diabetic HD patients. Whole‐blood analysis by the SPF method seems to be a promising way of monitoring platelet function for HD patients.
Heterologously Expressed Family 51 α-
l
-Arabinofuranosidases from
Oenococcus oeni
and
Lactobacillus brevis
Authors: Michlmayr Herbert , Schümann Christina , Kulbe Klaus D. , del Hierro Andrés M. 
Published: December 2010

ABSTRACT

Putative α-
l
-arabinofuranosidases of
Oenococcus oeni
and
Lactobacillus brevis
were heterologously expressed and characterized. We report the basic functional properties of the recombinant enzymes in comparison to those of a commercial family 51 arabinosidase of
Aspergillus niger.
Developmental Penalties Associated with Inducible Tolerance in
Helicoverpa armigera
to Insecticidal Toxins from
Bacillus thuringiensis
Authors: Rahman Mahbub , Glatz Richard , Roush Rick , Schmidt Otto 
Published: December 2010

ABSTRACT

Exposure of insect larvae to sublethal concentrations of crystal toxins from the soil bacterium
Bacillus thuringiensis
(Bt toxins) causes the induction of immune and metabolic responses that can be transmitted to offspring by epigenetic inheritance mechanisms. Given that the elevated immune status carries significant developmental penalties, we wanted to establish the relationships between immune induction, tolerance to the toxin and developmental penalties. A laboratory culture of
Helicoverpa armigera
was induced by a sublethal bacterial suspension containing crystal toxin Cry1Ac in one generation and maintained in the presence of toxin, acquiring significant levels of tolerance to the toxin within 12 generations of continuous exposure. Comparing tolerant and susceptible insects, we show that the induction of larval immune response and the coincident alteration of development-related metabolic activities by elicitors in the larval gut (larval induction) differs from the elevated immune status transmitted by epigenetic mechanisms (embryonic induction). Because the damaging effects of larval induction processes are higher compared to embryonic induction, it is likely that overall developmental penalties depend on the relative contribution of the two induction processes. When insects are kept with the same amount of toxin in the diet for subsequent generations, the embryonic induction process increases its contribution compared to the larval induction, resulting in reduced overall developmental penalty, while tolerance to the toxin is maintained.
Autophagy Deficiency Promotes β-Lactam Production in
Penicillium chrysogenum
Authors: Bartoszewska Magdalena , Kiel Jan A. K. W. , Bovenberg Roel A. L. , Veenhuis Marten , van der Klei Ida J. 
Published: December 2010

ABSTRACT

We have investigated the significance of autophagy in the production of the β-lactam antibiotic penicillin (PEN) by the filamentous fungus
Penicillium chrysogenum
. In this fungus PEN production is compartmentalized in the cytosol and in peroxisomes. We demonstrate that under PEN-producing conditions significant amounts of cytosolic and peroxisomal proteins are degraded via autophagy. Morphological analysis, based on electron and fluorescence microscopy, revealed that this phenomenon might contribute to progressive deterioration of late subapical cells. We show that deletion of the
P. chrysogenum
ortholog of
Saccharomyces cerevisiae
serine-threonine kinase
atg1
results in impairment of autophagy. In
P. chrysogenum atg1
cells, a distinct delay in cell degeneration is observed relative to wild-type cells. This phenomenon is associated with an increase in the enzyme levels of the PEN biosynthetic pathway and enhanced production levels of this antibacterial compound.
Transcriptional and Proteomic Responses ofPseudomonas aeruginosaPAO1 to Spaceflight Conditions Involve Hfq Regulation and Reveal a Role for Oxygen
Authors: Crabbé Aurélie , Schurr Michael J. , Monsieurs Pieter , Morici Lisa , Schurr Jill , Wilson James W. , Ott C. Mark , Tsaprailis George , Pierson Duane L. , Stefanyshyn-Piper Heidi , Nickerson Cheryl A. 
Published: December 2010

ABSTRACTAssessing bacterial behavior in microgravity is important for risk assessment and prevention of infectious diseases during spaceflight missions. Furthermore, this research field allows the unveiling of novel connections between low-fluid-shear regions encountered by pathogens during their natural infection process and bacterial virulence. This study is the first to characterize the spaceflight-induced global transcriptional and proteomic responses ofPseudomonas aeruginosa, an opportunistic pathogen that is present in the space habitat.P. aeruginosaresponded to spaceflight conditions through differential regulation of 167 genes and 28 proteins, with Hfq as a global transcriptional regulator. Since Hfq was also differentially regulated in spaceflight-grownSalmonella entericaserovar Typhimurium, Hfq represents the first spaceflight-induced regulator acting across bacterial species. The majorP. aeruginosavirulence-related genes induced in spaceflight were thelecAandlecBlectin genes and the gene for rhamnosyltransferase (rhlA), which is involved in rhamnolipid production. The transcriptional response of spaceflight-grownP. aeruginosawas compared with our previous data for this organism grown in microgravity analogue conditions using the rotating wall vessel (RWV) bioreactor. Interesting similarities were observed, including, among others, similarities with regard to Hfq regulation and oxygen metabolism. While RWV-grownP. aeruginosamainly induced genes involved in microaerophilic metabolism,P. aeruginosacultured in spaceflight presumably adopted an anaerobic mode of growth, in which denitrification was most prominent. Whether the observed changes in pathogenesis-related gene expression in response to spaceflight culture could lead to an alteration of virulence inP. aeruginosaremains to be determined and will be important for infectious disease risk assessment and prevention, both during spaceflight missions and for the general public.
Different Substrate Recognition Requirements for Cleavage of Synaptobrevin-2 byClostridium baratiiandClostridium botulinumType F Neurotoxins
Authors: Kalb Suzanne R. , Baudys Jakub , Egan Christina , Smith Theresa J. , Smith Leonard A. , Pirkle James L. , Barr John R. 
Published: December 2010

ABSTRACTBotulinum neurotoxins (BoNTs) cause botulism, which can be fatal if it is untreated. BoNTs cleave proteins necessary for nerve transmission, resulting in paralysis. Thein vivoprotein target has been reported for all seven serotypes of BoNT, i.e., serotypes A to G. Knowledge of the cleavage sites has led to the development of several assays to detect BoNT based on its ability to cleave a peptide substrate derived from itsin vivoprotein target. Most serotypes of BoNT can be subdivided into subtypes, and previously, we demonstrated that three of the currently known subtypes of BoNT/F cleave a peptide substrate, a shortened version of synaptobrevin-2, between Q58 and K59. However, our research indicated thatClostridium baratiitype F toxin did not cleave this peptide. In this study, we detail experiments demonstrating thatClostridium baratiitype F toxin cleaves recombinant synaptobrevin-2 in the same location as that cleaved by proteolytic F toxin. In addition, we demonstrate thatClostridium baratiitype F toxin can cleave a peptide substrate based on the sequence of synaptobrevin-2. This peptide substrate is an N-terminal extension of the original peptide substrate used for detection of other BoNT/F toxins and can be used to detect four of the currently known BoNT/F subtypes by mass spectrometry.
Rapid, Semiautomated Quantification of Bacterial Cells in Freshwater by Using a Microfluidic Device for On-Chip Staining and Counting
Authors: Yamaguchi Nobuyasu , Torii Masashi , Uebayashi Yuko , Nasu Masao 
Published: December 2010

ABSTRACT

A microfluidic device-based system for the rapid and semiautomated counting of bacteria in freshwater was fabricated and examined. Bacteria in groundwater and in potable water, as well as starved
Escherichia coli
O157:H7 spiked in pond water, were able to be on-chip stained and enumerated within 1 h using this system.
β-1,3-Glucanase from
Delftia tsuruhatensis
Strain MV01 and Its Potential Application in Vinification
Authors: Blättel V. , Larisika M. , Pfeiffer P. , Nowak C. , Eich A. , Eckelt J. , König H. 
Published: December 2010

ABSTRACT

During vinification microbial activities can spoil wine quality. As the wine-related lactic acid bacterium
Pediococcus parvulus
is able to produce slimes consisting of a β-1,3-glucan, must and wine filtration can be difficult or impossible. In addition, the metabolic activities of several wild-type yeasts can also negatively affect wine quality. Therefore, there is a need for measures to degrade the exopolysaccharide from
Pediococcus parvulus
and to inhibit the growth of certain yeasts. We examined an extracellular β-1,3-glucanase from
Delftia tsuruhatensis
strain MV01 with regard to its ability to hydrolyze both polymers, the β-1,3-glucan from
Pediococcus
and that from yeast cell walls. The 29-kDa glycolytic enzyme was purified to homogeneity. It exhibited an optimal activity at 50°C and pH 4.0. The sequencing of the N terminus revealed significant similarities to β-1,3-glucanases from different bacteria. In addition, the investigations indicated that this hydrolytic enzyme is still active under wine-relevant parameters such as elevated ethanol, sulfite, and phenol concentrations as well as at low pH values. Therefore, the characterized enzyme seems to be a useful tool to prevent slime production and undesirable yeast growth during vinification.
Global Gene Expression Patterns in
Clostridium thermocellum
as Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose
Authors: Riederer Allison , Takasuka Taichi E. , Makino Shin-ichi , Stevenson David M. , Bukhman Yury V. , Elsen Nathaniel L. , Fox Brian G. 
Published: December 2010

ABSTRACT

A microarray study of chemostat growth on insoluble cellulose or soluble cellobiose has provided substantial new information on
Clostridium thermocellum
gene expression. This is the first comprehensive examination of gene expression in
C. thermocellum
under defined growth conditions. Expression was detected from 2,846 of 3,189 genes, and regression analysis revealed 348 genes whose changes in expression patterns were growth rate and/or substrate dependent. Successfully modeled genes included those for scaffoldin and cellulosomal enzymes, intracellular metabolic enzymes, transcriptional regulators, sigma factors, signal transducers, transporters, and hypothetical proteins. Unique genes encoding glycolytic pathway and ethanol fermentation enzymes expressed at high levels simultaneously with previously established maximal ethanol production were also identified. Ranking of normalized expression intensities revealed significant changes in transcriptional levels of these genes. The pattern of expression of transcriptional regulators, sigma factors, and signal transducers indicates that response to growth rate is the dominant global mechanism used for control of gene expression in
C. thermocellum.
Heterogeneity of
Aspergillus niger
Microcolonies in Liquid Shaken Cultures
Authors: de Bekker Charissa , van Veluw G. Jerre , Vinck Arman , Wiebenga L. Ad , Wösten Han A. B. 
Published: December 2010

ABSTRACT

The fungus
Aspergillus niger
forms (sub)millimeter microcolonies within a liquid shaken culture. Here, we show that such microcolonies are heterogeneous with respect to size and gene expression. Microcolonies of strains expressing green fluorescent protein (GFP) from the promoter of the glucoamlyase gene
glaA
or the ferulic acid esterase gene
faeA
were sorted on the basis of diameter and fluorescence using the Complex Object Parametric Analyzer and Sorter (COPAS) technology. Statistical analysis revealed that the liquid shaken culture consisted of two populations of microcolonies that differ by 90 μm in diameter. The population of small microcolonies of strains expressing GFP from the
glaA
or
faeA
promoter comprised 39% and 25% of the culture, respectively. Two populations of microcolonies could also be distinguished when the expression of GFP in these strains was analyzed. The population expressing a low level of GFP consisted of 68% and 44% of the culture, respectively. We also show that mRNA accumulation is heterogeneous within microcolonies of
A. niger
. Central and peripheral parts of the mycelium were isolated with laser microdissection and pressure catapulting (LMPC), and RNA from these samples was used for quantitative PCR analysis. This analysis showed that the RNA content per hypha was about 45 times higher at the periphery than in the center of the microcolony. Our data imply that the protein production of
A. niger
can be improved in industrial fermentations by reducing the heterogeneity within the culture.
Induction of a State of Iron Limitation in Uropathogenic
Escherichia coli
CFT073 by Cranberry-Derived Proanthocyanidins as Revealed by Microarray Analysis
Authors: Hidalgo Gabriela , Ponton André , Fatisson Julien , O'May Che , Asadishad Bahareh , Schinner Tim , Tufenkji Nathalie 
Published: December 2010

ABSTRACT

Transcriptional profiles of uropathogenic
Escherichia coli
CFT073 exposed to cranberry-derived proanthocyanidins (PACs) were determined. Our results indicate that bacteria grown on media supplemented with PACs were iron deprived. To our knowledge, this is the first time that PACs have been shown to induce a state of iron limitation in this bacterium.