bluuebunny/crossref_metadata_2025 huggingface dataset:
Fault detection and identification of non‐linear hybrid system using self‐switched sigma point filter bank
Authors: Chatterjee Sayanti , Sadhu Smita , Ghoshal T.K.
Published: January 2015

This study proposes a scheme for fault detection and identification (FDI) of a class of non‐linear hybrid systems. For fault detection, the proposed method uses a self‐switched unscented Kalman filter (UKF) where a component filter with the appropriate dynamic model is chosen to suit the current mode of the hybrid plant. The mode of the hybrid plant, usually defined by system states, is deduced based on the state estimates. The statistical tests of measured datasets are used to detect and identify the fault parameters. For fault identification, a bank of such switched UKF filters is used. A three‐tank system has been used to demonstrate the effectiveness of the scheme. Different types of faults, that is, leakage, clogging and abrupt changes in inflow (actuator fault) have been considered. t‐Statistical test has been performed on the residuals for FDI and threshold calculation purposes. It is shown that all the types of faults can be successfully detected and identified by the proposed method. The performance of the proposed system is compared with the same for an extended Kalman filter‐based FDI system. It has been shown that the UKF‐based scheme has lower latency and higher range coverage.
Data‐driven fault‐tolerant control design for wind turbines with robust residual generator
Authors: Wang Guang , Huang Zenghui
Published: January 2015

In this study, a fault‐tolerant control (FTC) system is proposed and applied on a wind turbine benchmark. The significant characteristic of the FTC system is the data‐driven fault‐tolerant architecture whose core is embedding residual generators into control loop. To begin with, the authors introduce a method for constructing residual generators with parity vectors, which are directly identified from measurements. Then an optimal scheme is proposed for selecting parity vectors that are sensitive to specific variables. Besides, several residual generators are applied in the FTC system for multiple failures, and a switching mechanism is elaborately designed. At last, the effectiveness of the proposed FTC scheme is demonstrated by the simulation results of the wind turbine model.
Computer‐aided analysis of fluorescein angiograms using colour leakage maps
Authors: Magdy Eman , Ibrahim Mohamed , Nguyen Quan D. , Fahmy Ahmed S.
Published: January 2015

Fundus fluorescein angiography (FFA) is a standard screening and diagnosis technique for several retinal diseases. The analysis of FFA images is performed qualitatively by skilled observers, and thus is vulnerable to inter‐ and intra‐observer variability. In this study, the authors present a method for computer‐aided analysis of FFA images. The method is based on generating quantitative colour fluorescein leakage maps (FLM) that mimic the thickness maps generated by the optical coherence tomography (OCT). Results from 64 patients show strong correlation between the FLM and OCT thickness maps (r = 0.8). The method was found to be reproducible and robust to variability in the image acquisition times.
Influence of landscape properties on stream water quality in agricultural catchments in Southeastern Brazil
Authors: Mori Gisele Biem , de Paula Felipe Rossetti , de Barros Ferraz Silvio Frosini , Camargo Antonio Fernando Monteiro , Martinelli Luiz Antônio
Published: January 2015

Changes in land cover, especially the replacement of forest by agricultural activities affect the hydrological processes of river catchments, resulting in physical and chemical compositional changes of water draining from affected basins. The aim of this study was to evaluate landscape influences at different spatial scales (catchment and riparian) on the physical and chemical composition of stream water in 15 agricultural catchments, belonging to the Corumbataí basin (Brazil). We calculated the average slope (%), average elevation (m), soil classes (%), major land use classes (%), average distance from the forest cover in relation to the hydrographic network (m), largest patch index (%) at the catchment scale and riparian zone of drainage network scale within a 30 m buffer. Water samples were collected in two seasons (dry and rainy) to characterize physical and chemical properties: turbidity, suspended solids, total nitrogen, nitrate and total phosphorus. Our results showed higher concentration of nitrate in sugarcane fields and larger amount of suspended solids and turbidity in pasture areas. We concluded that degraded and highly fragmented forests may not be effectively contributing toward the protection of aquatic ecosystems.
Wind power curve modeling in complex terrain using statistical models
Authors: Bulaevskaya V. , Wharton S. , Clifton A. , Qualley G. , Miller W. O.
Published: January 2015

The simplest power curves model wind power only as a function of the wind speed at the turbine hub height. While the latter is an essential predictor of power output, wind speed information in other parts of the vertical profile, as well as additional atmospheric variables, are also important determinants of power. The goal of this work was to determine the gain in predictive ability afforded by adding wind speed information at other heights, as well as other atmospheric variables, to the power prediction model. Using data from a wind farm with a moderately complex terrain in the Altamont Pass region in California, we trained three statistical models—a neural network, a random forest and a Gaussian process model—to predict power output from various sets of aforementioned predictors. The comparison of these predictions to the observed power data revealed that considerable improvements in prediction accuracy can be achieved both through the addition of predictors other than the hub-height wind speed and the use of statistical models. To our knowledge, the use of the Gaussian process model in this context is new, in contrast to neural networks and random forests. The advantage of this model over the other two models is that it provides a much more natural way to estimate the uncertainty associated with its predictions. In addition, this study presents one of the most comprehensive analyses to date of the relative importance of various wind power curve inputs.
A compact 100 kV high voltage glycol capacitor
Authors: Wang Langning , Liu Jinliang , Feng Jiahuai
Published: January 2015

A high voltage capacitor is described in this paper. The capacitor uses glycerol as energy storage medium, has a large capacitance close to 1 nF, can hold off voltages of up to 100 kV for μs charging time. Allowing for low inductance, the capacitor electrode is designed as coaxial structure, which is different from the common structure of the ceramic capacitor. With a steady capacitance at different frequencies and a high hold-off voltage of up to 100 kV, the glycol capacitor design provides a potential substitute for the ceramic capacitors in pulse-forming network modulator to generate high voltage pulses with a width longer than 100 ns.
The study of electromagnetic cusp solitons
Authors: Verma Deepa , Das Amita , Kaw Predhiman , Tiwari Sanat Kumar
Published: January 2015

The formation of a cusp structure in the envelope of electromagnetic solitons for electron-ion plasma at the ion wave breaking point has been shown by Farina and Bulanov [Phys. Rev. Lett. 86, 5289 (2001)]. The analytical form of the cusp structure has been obtained here. The analytical form of the cusp is shown to compare well with the exact numerically obtained solutions. Such cusp solitons occurring at the ion wave breaking point may have relevance to ion acceleration mechanism. In an effort towards studying the dynamical stability of such structures, the time evolution studies have been carried out which show that the structure survives for several plasma periods. However, ultimately it breaks apart due to the instability associated with the forward Raman scattering.
Phase retarder based on one-dimensional photonic crystals composed of plasma and mu-negative materials
Authors: Liu Yang , Yi Lin , Hu Xin-Guang , Duan Yong-Fa , Yang Zhi-Zong
Published: January 2015

By using transfer matrix method, a systematic study on the properties of the reflection phase shifts and the reflection phase difference between TE and TM waves in a finite one-dimensional (1D) photonic crystal containing plasma and mu-negative materials is presented. It is found that the reflection phase difference between the two polarizations remains constant in a rather wide frequency range for a given incident angle. More specifically, the reflection phase difference increases gradually from 0 to π rad with the increase of the incident angle. That is to say, the finite 1D structure can serve as a broadband phase retarder. It is also evident that the working frequency range of the phase retarder can be adjusted by altering the plasma frequency and the thickness of the plasma layers without changing the structure of the photonic crystal.
Heat transfer mechanisms in pulsating heat-pipes with nanofluid
Authors: Gonzalez Miguel , Kelly Brian , Hayashi Yoshikazu , Kim Yoon Jo
Published: January 2015

In this study, the effect of silver nanofluid on a pulsating heat-pipe (PHP) thermal performance was experimentally investigated to figure out how nanofluid works with PHP. A closed loop PHP was built with 3 mm diameter tubes. Thermocouples and pressure transducers were installed for fluid and surface temperature and pressure measurements. The operating temperature of the PHP varied from 30–100 °C, with power rates of 61 W and 119 W. The fill ratio of 30%, 50%, and 70% were tested. The results showed that the evaporator heat transfer performance was degraded by the addition of nanoparticles due to increased viscosity at high power rate, while the positive effects of high thermal conductivity and enhanced nucleate boiling worked better at low power rate. In the condenser section, owing to the relatively high liquid content, nanofluid more effectively improved the heat transfer performance. However, since the PHP performance was dominantly affected by evaporator heat transfer performance, the overall benefit of enhanced condenser section performance was greatly limited. It was also observed that the poor heat transfer performance with nanofluid at the evaporator section led to lower operating pressure of PHP.
A record flexible piezoelectric KNN ultrafine-grained nanopowder-based nanogenerator
Authors: Xue Qing-tang , Wang Zhe , Tian He , Huan Yu , Xie Qian-Yi , Yang Yi , Xie Dan , Li Cheng , Shu Yi , Wang Xiao-Hui , Ren Tian-Ling
Published: January 2015

We explore a type piezoelectric material 0.9525(K0.5Na0.5NbO3)-0.0475LiTaO3 (KNN-LTS) which can be used to fabricate nanogenerator with high output voltage and current due to its high piezoelectric constant (d33). Because of its unique structure mixed with multi-wall carbon nanotube and polydimethylsiloxane, the output voltage is up to 53 V and the output current is up to 15 uA (current density of 12.5 uA/cm2) respectively. The value of the output voltage and output current represent the highest level in the piezoelectric field reported to date. The KNN-LTS nanopowder-based nanogenerator can also be used as a sensitive motion detection sensor.
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Authors: Li Xiaowei , Ke Peiling , Wang Aiying
Published: January 2015

Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Molecular Docking and Spectroscopic Study on the Interaction of Serum Albumin with Iron(III) Diamine Sarcophagine
Authors: Farahani Bahman Vasheghani , Bardajee Ghasem Rezanejade , Rajabi Farzaneh Hosseinpour , Hooshyar Zari
Published: January 2015

Iron(iii) diamine sarcophagine (DiAmsar) has attracted great attention in biological and medical applications. In particular, for any potential in vivo application, knowledge about the interaction of iron(iii) DiAmsar with serum albumin is crucial. As a step towards the elucidation of the fate of iron(iii) DiAmsar introduced into an organism, first, iron(iii) DiAmsar was synthesised and characterised. In the next step, interactions of iron(iii) DiAmsar with human serum albumin (HSA) and bovine serum albumin (BSA) were systematically investigated by various spectroscopic methods (Fourier-transform infrared, UV-visible, fluorescence) and cyclic voltammetry and molecular docking techniques under simulated physiological conditions. The fluorescence intensities of HSA and BSA decreased remarkably with increasing concentration of iron(iii) DiAmsar. The Stern–Volmer quenching constant KSV at different temperatures and corresponding thermodynamic parameters such as ΔHo, ΔGo, and ΔSo were calculated. The binding distance of iron(iii) DiAmsar with HSA and BSA was also determined using the theory of fluorescence energy transfer. Further, the conformational changes of HSA and BSA induced by iron(iii) DiAmsar were analysed by means of Fourier-transform (FT)-IR. In addition, molecular docking was performed to explore the possible binding sites and the microenvironment conditions around the bound iron(iii) DiAmsar.
Comparison of teosinte (Zea mexicana L.) and inter-subspecific hybrids (Zea mays L.×Zea mexicana) for high forage yield under two sowing regimes
Authors: Niazi Imtiaz Akram Khan , Rauf Saeed , Teixeira da Silva Jaime A. , Munir Hassan
Published: January 2015

This study was undertaken to evaluate the response of teosinte (Zea mexicana L.) and intersubspecific hybrids to heat stress, in particular productivity. Unlike maize (Zea mays L.), teosinte demonstrated thermophilic properties, namely lower heat injury, sustained chlorophyll content under heat stress (36−45°C) and high percentage survival of seedlings (at 55°C). Teosinte also had the ability to produce large plant biomass (27% and 55% higher yield than maize under non-stressed and stress conditions, respectively) and therefore could be exploited as a forage crop. However, teosinte forage had low animal intake (1.48 kg day–1) because of high pubescence density (10.38 view–1) and low sweetness (9.90°Brix). There was a high percentage of heterosis in variable intersubspecific crosses and traits, and a high magnitude of over-dominance for many traits, for example 5.93–7.06 for total biomass plant–1. Hybrids showed additional advantages, including high oil (20% and 4%) and protein (14% and 25%) contents compared with teosinte under non-stressed and stress conditions, respectively. Moreover, inter-subspecific hybrids were also resistant to heat stress, with the capacity for sustaining growth for a longer period (20% and 33% higher than maize under non-stressed and stress conditions, respectively). Genetic distance between parents—calculated from stable agronomic traits—could be used to select parents for high heterosis under both heat stress and non-stressed conditions.
Uncoupling lifespan and healthspan in
Caenorhabditis elegans
longevity mutants
Authors: Bansal Ankita , Zhu Lihua J. , Yen Kelvin , Tissenbaum Heidi A.
Published: January 2015

Significance

Genetic and environmental manipulations have been identified that result in lifespan extension. The underlying assumption that lifespan extension would also result in an increase in healthspan is seemingly valid but infrequently examined. Here, we examined multiple pathways that modulate lifespan to investigate the relationship between lifespan extension and health. We analyzed wild-type and four long-lived mutants in an unbiased cross-sectional study with multiple assays until animals reached 80% maximum lifespan. We show lifespan and healthspan can be separated and all of the long-lived mutants extend the period of frailty as a consequence. If applied to humans, this would likely lead to unsustainable healthcare costs and demonstrates the importance of examining healthspan as opposed to lifespan for future research.
Plant functional traits and the multidimensional nature of species coexistence
Authors: Kraft Nathan J. B. , Godoy Oscar , Levine Jonathan M.
Published: January 2015

Significance

Biologists have long understood that differences between species in traits such as bill shape or rooting depth can maintain diversity in communities by promoting specialization and reducing competition. Here we test the assumption that phenotypic differences drive the stabilizing niche differences that promote coexistence. Using advances in ecological theory and detailed experiments we quantify average fitness and stabilizing niche differences between 102 plant species pairs and relate these differences to 11 functional traits. Individual traits were correlated with fitness differences that drive competitive exclusion but not stabilizing niche differences that promote coexistence. Stabilizing niche differences could only be described by combinations of traits, representing differentiation in multiple dimensions. This challenges the simplistic use of trait patterns to infer community assembly.
A generation at risk: Young investigators and the future of the biomedical workforce
Authors: Daniels Ronald J.
Published: January 2015

A number of distressing trends, including a decline in the share of key research grants going to younger scientists, as well as a steady rise in the age at which investigators receive their first funding, are now a decades-long feature of the US biomedical research workforce. Working committees have proposed recommendations, policy makers have implemented reforms, and yet the trajectory of our funding regime away from young scientists has only worsened. An investigation of some of the major factors and their geneses at play in explaining the increasing average age to first RO1 is presented. Recommendations related to funding, peer review, career paths, and the university–government partnership are provided.
Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets
Authors: Norris Laura C. , Main Bradley J. , Lee Yoosook , Collier Travis C. , Fofana Abdrahamane , Cornel Anthony J. , Lanzaro Gregory C.
Published: January 2015

Significance

We report that during a recent period of hybridization between two major African malaria mosquitoes,
Anopheles gambiae
and
Anopheles coluzzii
, an island of divergence on chromosome 2 introgressed from the
A. gambiae
into the
A. coluzzii
genome and its frequency subsequently increased. This introgression was coincident with the start of a major insecticide-treated bed net campaigns in Mali. These observations suggest that increased insecticide exposure acted as a selective force sufficient to drive introgression of an entire genomic island of divergence across the reproductive barrier separating these two species. This study provides a rare example of adaptive introgression in an animal species and elucidates the dynamics of how insecticide resistance evolved in
A. coluzzii
.
Atmospheric record in the Hadean Eon from multiple sulfur isotope measurements in Nuvvuagittuq Greenstone Belt (Nunavik, Quebec)
Authors: Thomassot Emilie , O’Neil Jonathan , Francis Don , Cartigny Pierre , Wing Boswell A.
Published: January 2015

Significance

Sulfur isotopes in ancient Earth sediments have peculiar compositions resulting from photochemical reactions of sulfur-bearing gaseous species with UV photons in the anoxic early Earth's atmosphere. High-precision measurements of sediments from distinct localities have revealed that these isotopic anomalies are sensitive to the abundances of atmospheric gases. They thus appear as promising metrics of ancient atmospheric composition. In the present study, we focus on the origin and extent of this atmospheric memory. We analyzed the multiple S-isotope compositions of some of the oldest metasediments preserved on Earth (originating from the >3.8-Ga Nuvvuagittuq Greenstone Belt, Canada) and found that this unusual atmospheric fingerprint has been present since the end of the Hadean, the earliest eon of Earth history.
Gamma irradiated chitosan and its derivatives as antioxidants for minced chicken
Authors: Abd El-Rehim Hassan A , Zahran Dalia A , El-Sawy Naeem M , Hegazy El-Sayed A , Elbarbary Ahmed M
Published: January 2015

Ionizing radiation and oxidizing agent like H2O2 were used to degrade chitosan (CS) and its derivatives; N-maleoylchitosan (NMCS), and N-phthaloylchitosan (NPhCS). The structure changes were detected using gel permeation chromatography (GPC). The results revealed that ionizing radiation degraded CS, MNCS, NPhCS and altered their molecular weights and antioxidant activity. The higher the irradiation dose, the lower the molecular weight and the higher antioxidant activity. The addition of irradiated CS and NMCS to minced chicken resulted in highly significant reduction in malondialdehyde (MDA) content (50 and 70%, respectively) if compared with the control. The irradiated NMCS toxicity study did not show strong proliferative effect at small concentrations or cytotoxic effects at higher concentrations. The obtained results suggested that CS and NMCS could be used as natural antioxidant for improving the oxidative deterioration of minced chicken during refrigerated storage.
An N-terminal region of a Myb-like protein is involved in its intracellular localization and activation of a gibberellin-inducible proteinase gene in germinated rice seeds
Authors: Sutoh Keita , Washio Kenji , Imai Ryozo , Wada Masamitsu , Nakai Tomonori , Yamauchi Daisuke
Published: January 2015

The expression of the gene for a proteinase (Rep1) is upregulated by gibberellins. The CAACTC regulatory element (CARE) of the Rep1 promoter is involved in the gibberellin response. We isolated a cDNA for a CARE-binding protein containing a Myb domain in its carboxyl-terminal region and designated the gene Carboxyl-terminal Myb1 (CTMyb1). This gene encodes two polypeptides of two distinctive lengths, CTMyb1L and CTMyb1S, which include or exclude 213 N-terminal amino acid residues, respectively. CTMyb1S transactivated the Rep1 promoter in the presence of OsGAMyb, but not CTMyb1L. We observed an interaction between CTMyb1S and the rice prolamin box-binding factor (RPBF). A bimolecular fluorescence complex analysis detected the CTMyb1S and RPBF complex in the nucleus, but not the CTMyb1L and RPBF complex. The results suggest that the arrangement of the transfactors is involved in gibberellin-inducible expression of Rep1.
Rab31 and APPL2 enhance FcγR-mediated phagocytosis through PI3K/Akt signaling in macrophages
Authors: Yeo Jeremy C. , Wall Adam A. , Luo Lin , Stow Jennifer L.
Published: January 2015

Rab31 recruits APPL2 to regulate phagocytic cup closure and FcγR signaling pathways via production of PI(3,4,5)P3in macrophages. APPL2 is poised to activate macrophages and act as a counterpoint to APPL1 in FcγR-mediated PI3K/Akt signaling. New locations and roles are found for Rab31 and APPL2 by which they contribute to innate immune functions.
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome
Authors: Li Fuyi , Li Chen , Wang Mingjun , Webb Geoffrey I. , Zhang Yang , Whisstock James C. , Song Jiangning
Published: January 2015

Motivation: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular recognition. It is estimated that >50% of the entire human proteome is glycosylated. However, it is still a significant challenge to identify glycosylation sites, which requires expensive/laborious experimental research. Thus, bioinformatics approaches that can predict the glycan occupancy at specific sequons in protein sequences would be useful for understanding and utilizing this important PTM.

Results: In this study, we present a novel bioinformatics tool called GlycoMine, which is a comprehensive tool for the systematic in silico identification of C-linked, N-linked, and O-linked glycosylation sites in the human proteome. GlycoMine was developed using the random forest algorithm and evaluated based on a well-prepared up-to-date benchmark dataset that encompasses all three types of glycosylation sites, which was curated from multiple public resources. Heterogeneous sequences and functional features were derived from various sources, and subjected to further two-step feature selection to characterize a condensed subset of optimal features that contributed most to the type-specific prediction of glycosylation sites. Five-fold cross-validation and independent tests show that this approach significantly improved the prediction performance compared with four existing prediction tools: NetNGlyc, NetOGlyc, EnsembleGly and GPP. We demonstrated that this tool could identify candidate glycosylation sites in case study proteins and applied it to identify many high-confidence glycosylation target proteins by screening the entire human proteome.

Availability and implementation: The webserver, Java Applet, user instructions, datasets, and predicted glycosylation sites in the human proteome are freely available at http://www.structbioinfor.org/Lab/GlycoMine/.

Contact:  Jiangning.Song@monash.edu or James.Whisstock@monash.edu or zhangyang@nwsuaf.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis
Authors: Chen Rui , Wei Qiang , Zhan Xiaowei , Zhong Xue , Sutcliffe James S. , Cox Nancy J. , Cook Edwin H. , Li Chun , Chen Wei , Li Bingshan
Published: January 2015

Motivation: A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models.

Results: In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants.

Availability and implementation: We implemented gTDT in C++ and the source code and the detailed usage are available on the authors’ website (https://medschool.vanderbilt.edu/cgg).

Contact:  bingshan.li@vanderbilt.edu or wei.chen@chp.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The price of conserving avian phylogenetic diversity: a global prioritization approach
Authors: Nunes Laura A. , Turvey Samuel T. , Rosindell James
Published: January 2015

The combination of rapid biodiversity loss and limited funds available for conservation represents a major global concern. While there are many approaches for conservation prioritization, few are framed as financial optimization problems. We use recently published avian data to conduct a global analysis of the financial resources required to conserve different quantities of phylogenetic diversity (PD). We introduce a new prioritization metric (ADEPD) that After Downlisting a species gives the Expected Phylogenetic Diversity at some future time. Unlike other metrics, ADEPD considers the benefits to future PD associated with downlisting a species (e.g. moving from Endangered to Vulnerable in the International Union for Conservation of Nature Red List). Combining ADEPD scores with data on the financial cost of downlisting different species provides a cost–benefit prioritization approach for conservation. We find that under worst-case spending $3915 can save 1 year of PD, while under optimal spending $1 can preserve over 16.7 years of PD. We find that current conservation spending patterns are only expected to preserve one quarter of the PD that optimal spending could achieve with the same total budget. Maximizing PD is only one approach within the wider goal of biodiversity conservation, but our analysis highlights more generally the danger involved in uninformed spending of limited resources.
Conserving the functional and phylogenetic trees of life of European tetrapods
Authors: Thuiller Wilfried , Maiorano Luigi , Mazel Florent , Guilhaumon François , Ficetola Gentile Francesco , Lavergne Sébastien , Renaud Julien , Roquet Cristina , Mouillot David
Published: January 2015

Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.
Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia
Authors: Toyama Hironori , Kajisa Tsuyoshi , Tagane Shuichiro , Mase Keiko , Chhang Phourin , Samreth Vanna , Ma Vuthy , Sokh Heng , Ichihashi Ryuji , Onoda Yusuke , Mizoue Nobuya , Yahara Tetsukazu
Published: January 2015

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using
rbcL
and
matK
gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.
The future of evolutionary diversity in reef corals
Authors: Huang Danwei , Roy Kaustuv
Published: January 2015

One-third of the world's reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.
Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses
Authors: Faith Daniel P.
Published: January 2015

The phylogenetic diversity measure, (‘PD’), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas.
Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?
Authors: Brooks T. M. , Cuttelod A. , Faith D. P. , Garcia-Moreno J. , Langhammer P. , Pérez-Espona S.
Published: January 2015

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgróet al.(2011Evol. Appl.4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.
Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)
Authors: Richman Nadia I. , Böhm Monika , Adams Susan B. , Alvarez Fernando , Bergey Elizabeth A. , Bunn John J. S. , Burnham Quinton , Cordeiro Jay , Coughran Jason , Crandall Keith A. , Dawkins Kathryn L. , DiStefano Robert J. , Doran Niall E. , Edsman Lennart , Eversole Arnold G. , Füreder Leopold , Furse James M. , Gherardi Francesca , Hamr Premek , Holdich David M. , Horwitz Pierre , Johnston Kerrylyn , Jones Clive M. , Jones Julia P. G. , Jones Robert L. , Jones Thomas G. , Kawai Tadashi , Lawler Susan , López-Mejía Marilu , Miller Rebecca M. , Pedraza-Lara Carlos , Reynolds Julian D. , Richardson Alastair M. M. , Schultz Mark B. , Schuster Guenter A. , Sibley Peter J. , Souty-Grosset Catherine , Taylor Christopher A. , Thoma Roger F. , Walls Jerry , Walsh Todd S. , Collen Ben
Published: January 2015

Rates of biodiversity loss are higher in freshwater ecosystems than in most terrestrial or marine ecosystems, making freshwater conservation a priority. However, prioritization methods are impeded by insufficient knowledge on the distribution and conservation status of freshwater taxa, particularly invertebrates. We evaluated the extinction risk of the world's 590 freshwater crayfish species using the IUCN Categories and Criteria and found 32% of all species are threatened with extinction. The level of extinction risk differed between families, with proportionally more threatened species in the Parastacidae and Astacidae than in the Cambaridae. Four described species were Extinct and 21% were assessed as Data Deficient. There was geographical variation in the dominant threats affecting the main centres of crayfish diversity. The majority of threatened US and Mexican species face threats associated with urban development, pollution, damming and water management. Conversely, the majority of Australian threatened species are affected by climate change, harvesting, agriculture and invasive species. Only a small proportion of crayfish are found within the boundaries of protected areas, suggesting that alternative means of long-term protection will be required. Our study highlights many of the significant challenges yet to come for freshwater biodiversity unless conservation planning shifts from a reactive to proactive approach.
A theoretical framework for requirements engineering and process improvement in small and medium software companies
Authors: Kabaale Edward , Kituyi Geoffrey Mayoka
Published: January 2015

Purpose

– Requirements engineering (RE) and process improvement has been identified as one of the key factors for improving software quality. Despite this, little scholarly work has been done on developing ways to improve the RE process. The situation of RE and process improvement is even worse in small and medium enterprises that produce software. Consequently, the quality of software being produced by these companies has kept deteriorating. The purpose of this paper is to design a framework that will help small and medium software companies improve their RE processes in order to compete favorably with larger software companies, more especially in terms of software quality.

Design/methodology/approach

– A qualitative research approach was adapted. Four software companies in Uganda were purposively selected to participate in the study. Data were collected using questionnaires. The requirements for designing the framework were gathered and refined from both primary and secondary data.

Findings

– The key requirements for process improvement in small and medium software companies were identified as user involvement, use of evolutionary requirements engineering process improvement (REPI) strategy, change management, training and education, management support and commitment.

Practical implications

– The designed framework was validated to ensure that it can be applied in RE and process improvement in small and medium software companies. Validation results show that the proposed framework is applicable and can be used to improve RE and process improvement in small and medium software companies.

Originality/value

– The paper presents an improvement of the systematic approach to REPI by Kabaale and Nabukenya which is decomposed for easy understanding by non-technical readers and users.
Data perspectives of workflow schema evolution
Authors: Arunagiri Aravindhan , Ramachandran Parthasarathy
Published: January 2015

Purpose

– Most literature on workflow (WF) adaptation considered the control flow correctness like absence of dead lock, live-lock, etc. during adaptation. The data aspect of WF adaptation like data flow, database schema changes and their correctness are less studied. When the WF schema is modified, their data flow and the database schema changes. The existing approaches used for adapting these data changes in the underlying database schema are time consuming and/or affect the old data persistence. The purpose of this paper is to concern the dynamic adaptation of the WF schema and implementing its data changes in the existing database schema.

Design/methodology/approach

– A conceptual framework developed to adapt on-the-fly, the concomitant data changes during WF adaptation. The framework consists a set of data schema compliance criteria (DSC) which identify the data changes that can be directly accommodated in the existing database schema. Data adaptation algorithm (DAA) is developed to handle the data changes that does not conform to the DSC in the existing database schema.

Findings

– In this approach the existing database schema is dynamically evolved without re-creating it, after WF schema adaptation. Therefore the WF schema changes can be implemented on-the-fly without stopping the running system. It also ensures the persistence of old data residing in the existing database.

Originality/value

– A novel approach developed to adapt the data changes in the existing database schema, without requiring recreation or migration the data. This automated consistency checking of data attribute changes in the database schema and implement them dynamically.
Detecting potential weaknesses in business processes
Authors: Bergener Philipp , Delfmann Patrick , Weiss Burkhard , Winkelmann Axel
Published: January 2015

Purpose

– Automating the task of identifying process weaknesses using process models is promising, as many organizations have to manage a large amount of process models. The purpose of this paper is to introduce a pattern-based approach for automatically detecting potential process weaknesses in semantic process models, thus supporting the task of business process improvement.

Design/methodology/approach

– Based on design research, combined with a case study, the authors explore the design, application and evaluation of a pattern-based process weakness detection approach within the setting of a real-life case study in a German bank.

Findings

– Business process weakness detection can be automated to a remarkable extent using pattern matching and a semantic business process modeling language. A case study provided evidence that such an approach highly supports business process analysts.

Research limitations/implications

– The presented approach is limited by the fact that not every potential process weakness detected by pattern matching is really a weakness but just gives the impression to be one. Hence, after detecting a weakness, analysts still have to decide on its authenticity.

Practical implications

– Applying weakness patterns to semantic process models via pattern matching allows organizations to automatically and efficiently identify process improvement potentials. Hence, this research helps to avoid time- and resource-consuming manual analysis of process model landscapes.

Originality/value

– The approach is not restricted to a single modeling language. Furthermore, by applying the pattern matching approach to a semantic modeling language, the authors avoid ambiguous search results. A case study proves the usefulness of the approach.
Proposal for a framework for quality measurement to the SPB – Brazilian Public Software
Authors: Alves Angela Maria , Pessoa Marcelo , Salviano Clênio F
Published: January 2015

Purpose

– The purpose of this paper is to address the development of a conceptual framework to drive and assess the quality of software production in the digital ecosystem domain.

Design/methodology/approach

– This research used action research paradigm, the soft methodology SSM and the framework PRO2PI-MFMOD. The methodologies were applied at Brazilian Public Software Ecosystem.

Findings

– The results of this research shows: the dimension of the capacity, as suggested by ISO/IEC 15504, is insufficient for quality treatment in certain domains; SSM methodology is suitable for scope and domain clarification in digital ecosystems; and PRO2PI-MFMOD framework is suitable to create a reference model process for digital ecosystems software production.

Research limitations/implications

– A complete SSM cycle was conducted, but with only one research cycle. In that sense, the results obtained in this research can be interpreted as boundaries to reflections regarding the learning occurred in the system.

Practical implications

– The research offers an empirical contribution, mapping and defining maturity framework elements that can be used by the software production digital ecosystems, aiming the description and understanding of the phenomenon through the theoretical views of complexity theory, systemic thinking, digital ecosystems and maturity models.

Social implications

– The contributions can be summarized in the following aspects: the maturity models evolution, shifting from command and control basis to cooperation and connection basis; the maturity models scope, drifting from organizational units to collaborative networks of software production; the assimilation and broadcast of digital ecosystems concept by MCTI; and the maturity levels introduced in the research can be used as a particular case of capacity dimension of the further ISO/IEC 33000 standards.

Originality/value

– Through the results obtained with systematic revision of the literature, one can notice the absence of publications that approach all the four axes that ground this research simultaneously. The proposed subject is original and relevant to the software community in the matter of software process improvement and to the current and further public digital ecosystems of software development.