Search results for: evolutionary PDE

Authors: Fernando C. Labouriau, Ricardo M. Naveiro

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This paper presents a model for mapping the evolutive pattern of products in order to generate new ideas, to perceive emerging technologies and to manage product’s portfolios in new product development (NPD). According to the proposed model, the information extracted from the patent system is filtered and analyzed with TRIZ tools to produce the input information to the NPD process. The authors acknowledge that the NPD process is well integrated within the enterprises business strategic planning and that new products are vital in the competitive market nowadays. In the other hand, it has been observed the proactive use of patent information in some methodologies for selecting projects, mapping technological change and generating product concepts. And one of these methodologies is TRIZ, a theory created to favor innovation and to improve product design that provided the analytical framework for the model. Initially, it is presented an introduction to TRIZ mainly focused on the patterns of evolution of technical systems and its strategic uses, a brief and absolutely non-comprehensive description as the theory has several others tools being widely employed in technical and business applications. Then, it is introduced the model for mapping the products evolutive pattern with its three basic pillars, namely patent information, TRIZ and NPD, and the methodology for implementation. Following, a case study of a Brazilian bike manufacturing is presented to proceed the mapping of a product evolutive pattern by decomposing and analyzing one of its assemblies along ten evolution lines in order to envision opportunities for further product development. Some of these lines are illustrated in more details to evaluate the features of the product in relation to the TRIZ concepts using a comparison perspective with patents in the state of the art to validate the product’s evolutionary potential. As a result, the case study provided several opportunities for a product improvement development program in different project categories, identifying technical and business impacts as well as indicating the lines of evolution that can mostly benefit from each opportunity.

Keywords: product development, patents, product strategy, systems evolution

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Authors: S. S. Singh, A. Bhattacharya, S. Bhattacharya

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The eukaryotic exosome complex plays a pivotal role in RNA biogenesis, maturation, surveillance and differential expression of various RNAs in response to varying environmental signals. The exosome is composed of evolutionary conserved nine core subunits and the associated exonucleases Rrp6 and Rrp44. Rrp6p is crucial for the processing of rRNAs, other non-coding RNAs, regulation of polyA tail length and termination of transcription. Rrp6p, a 3’-5’ exonuclease is required for degradation of 5’-external transcribed spacer (ETS) released from the rRNA precursors during the early steps of pre-rRNA processing. In the parasitic protist Entamoeba histolytica in response to growth stress, there occurs the accumulation of unprocessed pre-rRNA and 5’ ETS sub fragment. To understand the processes leading to this accumulation, we looked for Rrp6 and the exosome subunits in E. histolytica, by in silico approaches. Of the nine core exosomal subunits, seven had high percentage of sequence similarity with the yeast and human. The EhRrp6 homolog contained exoribonuclease and HRDC domains like yeast but its N- terminus lacked the PMC2NT domain. EhRrp6 complemented the temperature sensitive phenotype of yeast rrp6Δ cells suggesting conservation of biological activity. We showed 3’-5’ exoribonuclease activity of EhRrp6p with in vitro-synthesized appropriate RNAs substrates. Like the yeast enzyme, EhRrp6p degraded unstructured RNA, but could degrade the stem-loops slowly. Furthermore, immunolocalization revealed that EhRrp6 was nuclear-localized in normal cells but was diminished from nucleus during serum starvation, which could explain the accumulation of 5’ETS during stress. Our study shows functional conservation of EhRrp6p in E.histolytica, an early-branching eukaryote, and will help to understand the evolution of exosomal components and their regulatory function.

Keywords: entamoeba histolytica, exosome complex, rRNA processing, Rrp6

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Authors: Felermino D. M. A. Ali, S. C. Ng

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E-learning is an evolutionary form of distance learning and has become better over time as new technologies emerged. Today, efforts are still being made to embrace E-learning systems with emerging technologies in order to make them better. Among these advancements, Educational Data Mining (EDM) is one that is gaining a huge and increasing popularity due to its wide application for improving the teaching-learning process in online practices. However, even though EDM promises to bring many benefits to educational industry in general and E-learning environments in particular, its principal drawback is the lack of easy to use tools. The current EDM tools usually require users to have some additional technical expertise to effectively perform EDM tasks. Thus, in response to these limitations, this study intends to design and implement an EDM application framework which aims at automating and simplify the development of EDM in E-learning environment. The application framework introduces a Service-Oriented Architecture (SOA) that hides the complexity of technical details and enables users to perform EDM in an automated fashion. The framework was designed based on abstraction, extensibility, and interoperability principles. The framework implementation was made up of three major modules. The first module provides an abstraction for data gathering, which was done by extending Moodle LMS (Learning Management System) source code. The second module provides data mining methods and techniques as services; it was done by converting Weka API into a set of Web services. The third module acts as an intermediary between the first two modules, it contains a user-friendly interface that allows dynamically locating data provider services, and running knowledge discovery tasks on data mining services. An experiment was conducted to evaluate the overhead of the proposed framework through a combination of simulation and implementation. The experiments have shown that the overhead introduced by the SOA mechanism is relatively small, therefore, it has been concluded that a service-oriented architecture can be effectively used to facilitate educational data mining in E-learning environments.

Keywords: educational data mining, e-learning, distributed data mining, moodle, service-oriented architecture, Weka

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Authors: Ozgu Hafizoglu

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An analogy is an essential tool of human cognition that enables connecting diffuse and diverse systems with physical, behavioral, principal relations that are essential to learning, discovery, and innovation. The Cognitive Model of Analogy (CMA) leads and creates patterns of pathways to transfer information within and between domains in science, just as happens in the brain. The connectome of the brain shows how the brain operates with mental leaps between domains and mental hops within domains and the way how analogical reasoning mechanism operates. This paper demonstrates the CMA as an evolutionary approach to science, technology, and life. The model puts forward the challenges of deep uncertainty about the future, emphasizing the need for flexibility of the system in order to enable reasoning methodology to adapt to changing conditions in the new era, especially post-pandemic. In this paper, we will reveal how to draw an analogy to scientific research to discover new systems that reveal the fractal schema of analogical reasoning within and between the systems like within and between the brain regions. Distinct phases of the problem-solving processes are divided thusly: stimulus, encoding, mapping, inference, and response. Based on the brain research so far, the system is revealed to be relevant to brain activation considering each of these phases with an emphasis on achieving a better visualization of the brain’s mechanism in macro context; brain and spinal cord, and micro context: glia and neurons, relative to matching conditions of analogical reasoning and relational information, encoding, mapping, inference and response processes, and verification of perceptual responses in four-term analogical reasoning. Finally, we will relate all these terminologies with these mental leaps, mental maps, mental hops, and mental loops to make the mental model of CMA clear.

Keywords: analogy, analogical reasoning, brain connectome, cognitive model, neurons and glia, mental leaps, mental hops, mental loops

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Authors: Marius Gavrilescu, Sabina-Adriana Floria, Florin Leon, Silvia Curteanu, Costel Anton

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Natural sciences provide a wide range of experimental data whose related problems require study and modeling beyond the capabilities of conventional methodologies. Such problems have solution spaces whose complexity and high dimensionality require correspondingly complex regression methods for proper characterization. In this context, we propose an optimization method which consists in a hybrid dual optimizer setup: a global optimizer based on a modified variant of the popular Imperialist Competitive Algorithm (ICA), and a local optimizer based on a gradient descent approach. The ICA is modified such that intermediate solution populations are more quickly and efficiently pruned of low-fitness individuals by appropriately altering the assimilation, revolution and competition phases, which, combined with an initialization strategy based on low-discrepancy sampling, allows for a more effective exploration of the corresponding solution space. Subsequently, gradient-based optimization is used locally to seek the optimal solution in the neighborhoods of the solutions found through the modified ICA. We use this combined approach to find the optimal configuration and weights of a fully-connected neural network, resulting in regression models used to characterize the process of obtained bricks using silicon-based materials. Installations in the raw ceramics industry, i.e., bricks, are characterized by significant energy consumption and large quantities of emissions. Thus, the purpose of our approach is to determine by simulation the working conditions, including the manufacturing mix recipe with the addition of different materials, to minimize the emissions represented by CO and CH4. Our approach determines regression models which perform significantly better than those found using the traditional ICA for the aforementioned problem, resulting in better convergence and a substantially lower error.

Keywords: optimization, biologically inspired algorithm, regression models, bricks, emissions

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Authors: Mahmoud B. Rokaya

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The study of opinion mining and sentiment analysis includes analysis of opinions, sentiments, evaluations, attitudes, and emotions. The rapid growth of social media, social networks, reviews, forum discussions, microblogs, and Twitter, leads to a parallel growth in the field of sentiment analysis. The field of sentiment analysis tries to develop effective tools to make it possible to capture the trends of people. There are two approaches in the field, lexicon-based and corpus-based methods. A lexicon-based method uses a sentiment lexicon which includes sentiment words and phrases with assigned numeric scores. These scores reveal if sentiment phrases are positive or negative, their intensity, and/or their emotional orientations. Creation of manual lexicons is hard. This brings the need for adaptive automated methods for generating a lexicon. The proposed method generates dynamic lexicons based on the corpus and then classifies text using these lexicons. In the proposed method, different approaches are combined to generate lexicons from text. The proposed method classifies the tweets into 5 classes instead of +ve or –ve classes. The sentiment classification problem is written as an optimization problem, finding optimum sentiment lexicons are the goal of the optimization process. The solution was produced based on mathematical programming approaches to find the best lexicon to classify texts. A genetic algorithm was written to find the optimal lexicon. Then, extraction of a meta-level feature was done based on the optimal lexicon. The experiments were conducted on several datasets. Results, in terms of accuracy, recall and F measure, outperformed the state-of-the-art methods proposed in the literature in some of the datasets. A better understanding of the Arabic language and culture of Arab Twitter users and sentiment orientation of words in different contexts can be achieved based on the sentiment lexicons proposed by the algorithm.

Keywords: social media, Twitter sentiment, sentiment analysis, lexicon, genetic algorithm, evolutionary computation

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Authors: Celeste De Kock, Bruce Anderson, Corneile Minnaar

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Geographic variation in the floral morphology of a flower species has often been assumed to result from co-variation in the availability of regionally-specific functional pollinator types, giving rise to plant ecotypes that are adapted to the morphology of the main pollinator types in that area. Wachendorfia paniculata is a geographically variable enantiostylous (handed) flower with preliminary observations suggesting that differences in pollinator community composition might be driving differences in the degree of herkogamy (spatial separation of the stigma and anthers on the same flower) across its geographic range. This study aimed to determine if pollinator-related variables such as visitation rate and pollinator type could explain differences in floral morphology seen in different populations. To assess pollinator community compositions, pollinator visitation rates, and the degree of herkogamy and flower size, flowers from 13 populations were observed and measured across the Western Cape, South Africa. Multiple regression analyses indicated that pollinator-related variables had no significant effect on the degree of herkogamy between sites. However, the degree of herkogamy was strongly negatively associated with the time of measurement. It remains possible that pollinators have had an effect on the development of herkogamy throughout the evolutionary timeline of different W. paniculata populations, but not necessarily to the fine-scale degree, as was predicted for this study. Annual fluctuations in pollinator community composition, paired with recent disturbances such as urbanization and the overabundance of artificially introduced honeybee hives, might also result in the signal of pollinator adaptation getting lost. Surprisingly, differences in herkogamy between populations could largely be explained by the time of day at which flowers were measured, suggesting a significant narrowing of the distance between reproductive parts throughout the day. We propose that this floral movement could possibly be an adaptation to ensure pollination if pollinator visitation to a flower was not sufficient earlier in the day, and will be explored in subsequent studies.

Keywords: enantiostyly, floral movement, geographic variation, ecotypes

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Kehinde Agbele, Longe Olumide, Daniel Ekong, Dele Seluwa, Akintoye Onamade

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One major problem of most existing information retrieval systems (IRS) is that they provide even access and retrieval results to individual users specially based on the query terms user issued to the system. When using IRS, users often present search queries made of ad-hoc keywords. It is then up to IRS to obtain a precise representation of user’s information need, and the context of the information. In effect, the volume and range of the Internet documents is growing exponentially and consequently causes difficulties for a user to obtain information that precisely matches the user interest. Diverse combination techniques are used to achieve the specific goal. This is due, firstly, to the fact that users often do not present queries to IRS that optimally represent the information they want, and secondly, the measure of a document's relevance is highly subjective between diverse users. In this paper, we address the problem by investigating the optimization of IRS to individual information needs in order of relevance. The paper addressed the development of algorithms that optimize the ranking of documents retrieved from IRS. This paper addresses this problem with a two-fold approach in order to retrieve domain-specific documents. Firstly, the design of context of information. The context of a query determines retrieved information relevance using personalization and context-awareness. Thus, executing the same query in diverse contexts often leads to diverse result rankings based on the user preferences. Secondly, the relevant context aspects should be incorporated in a way that supports the knowledge domain representing users’ interests. In this paper, the use of evolutionary algorithms is incorporated to improve the effectiveness of IRS. A context-based information retrieval system that learns individual needs from user-provided relevance feedback is developed whose retrieval effectiveness is evaluated using precision and recall metrics. The results demonstrate how to use attributes from user interaction behavior to improve the IR effectiveness.

Keywords: context, document relevance, information retrieval, personalization, user search behaviors

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Authors: Rai Friedman

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The recent migrant crisis has revealed an unmet demand for increased international protection and promotion of migrant rights. Europe has found itself at the centre of the migration crisis, being the recipient to the largest number of asylum-seekers since the conclusion of the second World War. Rather than impart a unified humanitarian lens of offering legal protections, the Schengen territory is devising new, preventative measures to confront the influx of asylum-seekers. This paper will focus on the refugee crisis in Europe as it relates to the Central Mediterranean route. To do so, it will outline the increased need for international protection for migrant rights through analyzing historic human rights treaties and conventions; the formation of the current composition of the Schengen area; the evolutionary changes in policies and legal landscapes throughout Europe and the Central Mediterranean route; the vernacular transformation surrounding refugees, migrants, and asylum-seekers; and expose the gaps in international protection. It will also discuss Europe’s critical position, both geographically and conceptually, critiquing the notion of European victimization. Lastly, it will discuss the increased harm of preventative border measures and argue for tangible sustainability solutions through economic programming models in highly vulnerable countries. To do so, this paper will observe a case study in Algeria that has conceded to an economic programming model for forced migrants. In 2017 amid worker shortages, Algeria announced it would grant African migrants’ legal status to become agriculturalists and construction workers. Algeria is one of the few countries along the Central Mediterranean route that has adopted a law to govern foreign nationals’ conditions of entry, stay and circulation. Thereafter, it will provide recommendations for solutions for forced migration along the Central Mediterranean route and advocate for strengthened protections under international law.

Keywords: refugees, migrants, human rights, middle east, Africa, mediterranean, international humanitarian law, policy

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Authors: Maureen Royce, Joshi Jariwala, Sally Kah

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Change is inevitable, but the change process is progressive. Organisational change is the process in which an organisation changes strategies, operational methods, systems, culture, and structure to affect something different in the organisation. This process can be continuous or developed over a period and driven by internal and external factors. Organisational change is essential if organisations are to survive in dynamic and uncertain environments. However, evidence from research shows that many change initiatives fail, leading to severe consequences for organisations and their resources. The complex models of third sector organisations, i.e., social enterprise, compounds the levels of change in these organisations. Interestingly, innovation is associated with a change in social enterprises due to the hybridity of product and service development. Furthermore, the creation of social intervention has offered a new process and outcomes to the lifecycle of change. Therefore, different forms of organisational innovation are developed, i.e., total, evolutionary, expansionary, and developmental, which affect the interventions of social enterprises. This raises both theoretical and business concerns on how the competing hybrid nature of social enterprises change, how change is managed, and the impact on these organisations. These perspectives present critical questions for further investigation. In this study, we investigate the impact of organisational change on employees and organisational development at DaDaFest –a disability arts organisation with a social focus based in Liverpool. The three main objectives are to explore the drivers of change and the implementation process; to examine the impact of organisational change on employees and; to identify barriers to organisation change and development. To address the preceding research objectives, qualitative research design is adopted using semi-structured interviews. Data is analysed using a six-step thematic analysis framework, which enables the study to develop themes depicting the impact of change on employees and organisational development. This study presents theoretical and practical contributions for academics and practitioners. The knowledge contributions encapsulate the evolution of change and the change cycle in a social enterprise. However, practical implications provide critical insights into the change management process and the impact of change on employees and organisational development.

Keywords: organisational change, change management, organisational change system, social enterprise

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Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

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The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: zika, biomolecular interactions, electrostatic interactions, molecular mechanisms

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Authors: Valentina Dotto

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Climate change cases used to take the form of statutory disputes rather than constitutional or common law disputes. This changed in 2015, with the Urgenda Climate case in the Netherlands (Urgenda Foundation v. The State of the Netherlands, C/09/456689/HAZA 13-1396) and, the Juliana case in the U.S. (United States v. U.S. District Court for District of Oregon, 17-71692, 9th Cir.). The two cases represent a new type of climate litigation, the claims brought against the federal government were in fact grounded in constitutional rights. The complaints used the Doctrine of Public Trust as a cornerstone for the lawsuits asserting that government's actions against climate change failed to protect essential public trust resources; thus, violating a generation's constitutional rights to life, liberty, and property. The Public Trust Doctrine –a quintessentially American legal concept-, reserved to the States by virtue of the 9th and 10th amendment of the federal Constitution, gives them considerable jurisdiction over natural resources and has been refined by a number of Supreme Court rulings. The Juliana case exemplifies the Doctrine’s evolutionary nature because it attempts to apply it to the federal government, and establish a right to a climate system capable of sustaining human life as a fundamental right protected by a substantive due process. Furthermore, the flexibility of the Doctrine makes it permissible to be applied to a variety of different legal systems as in the Urgenda case. At the very heart of the lawsuits stands the question of who owns the Earth resources and, to what extent the general public can claim the services that the Earth provides as common property. By employing the widest possible definition of the Doctrine of Public Trust these lawsuits tried to redefine environmental resources as a collective right of all people. By doing case analysis, the paper explores how these cases can contribute to widening the public access to information and broadening the public voice in decision making as well as providing a precedent to equal access in seeking justice and redress from environmental failures.

Keywords: climate change, doctrine of public trust, environmental democracy, Juliana case, Urgenda climate case

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Authors: Ashhar Ahmed Shaikh, Ayush Tandon

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The swift reduction of fossil fuels from nature has crucial need for alternative energy sources to cater vital demand. It is essential to boost alternative energy sources to cover the continuously increasing demand for energy while minimizing the negative environmental impacts. Solar energy is one of the reliable sources that can generate energy. Solar energy is freely available in nature and is completely eco-friendly, and they are considered as the most promising power generating sources due to their easy availability and other advantages for the local power generation. This paper is to review the implementation of power electronic devices through Solar Energy Grid Integration System (SEGIS) to increase the efficiency. This paper will also concentrate on the future grid infrastructure and various other applications in order to make the grid smart. Development and implementation of a power electronic devices such as PV inverters and power controllers play an important role in power supply in the modern energy economy. Solar Energy Grid Integration System (SEGIS) opens pathways for promising solutions for new electronic and electrical components such as advanced innovative inverter/controller topologies and their functions, economical energy management systems, innovative energy storage systems with equipped advanced control algorithms, advanced maximum-power-point tracking (MPPT) suited for all PV technologies, protocols and the associated communications. In addition to advanced grid interconnection capabilities and features, the new hardware design results in small size, less maintenance, and higher reliability. The SEGIS systems will make the 'advanced integrated system' and 'smart grid' evolutionary processes to run in a better way. Since the last few years, there was a major development in the field of power electronics which led to more efficient systems and reduction of the cost per Kilo-watt. The inverters became more efficient and had reached efficiencies in excess of 98%, and commercial solar modules have reached almost 21% efficiency.

Keywords: solar energy grid integration systems, smart grid, advanced integrated system, power electronics

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Authors: Xianming Chen, Yu Lei, Meinan Wang

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The dikaryotic basidiomycete fungus, Puccinia striiformis, causes stripe rust, one of the most important diseases of wheat and barley worldwide. The pathogen is largely reproduced asexually, and asexual recombination has been hypothesized to be one of the mechanisms for the pathogen variations. To test the hypothesis and understand the genetic process of asexual recombination, somatic recombinant isolates were obtained under controlled conditions by inoculating susceptible host plants with a mixture of equal quantity of urediniospores of isolates with different virulence patterns and selecting through a series of inoculation on host plants with different genes for resistance to one of the parental isolates. The potential recombinant isolates were phenotypically characterized by virulence testing on the set of 18 wheat lines used to differentiate races of the wheat stripe rust pathogen, P. striiformis f. sp. tritici (Pst), for the combinations of Pst isolates; or on both sets of the wheat differentials and 12 barley differentials for identifying races of the barley stripe rust pathogen, P. striiformis f. sp. hordei (Psh) for combinations of a Pst isolate and a Psh isolate. The progeny and parental isolates were also genotypically characterized with 51 simple sequence repeat and 90 single-nucleotide polymorphism markers. From nine combinations of parental isolates, 68 potential recombinant isolates were obtained, of which 33 (48.5%) had similar virulence patterns to one of the parental isolates, and 35 (51.5%) had virulence patterns distinct from either of the parental isolates. Of the 35 isolates of distinct virulence patterns, 11 were identified as races that had been previously detected from natural collections and 24 were identified as new races. The molecular marker data confirmed 66 of the 68 isolates as recombinants. The percentages of parental marker alleles ranged from 0.9% to 98.9% and were significantly different from equal proportions in the recombinant isolates. Except for a couple of combinations, the greater or less contribution was not specific to any particular parental isolates as the same parental isolates contributed more to some of the progeny isolates but less to the other progeny isolates in the same combination. The unequal contributions by parental isolates appear to be a general role in somatic recombination for the stripe rust fungus, which may be used to distinguish asexual recombination from sexual recombination in studying the evolutionary mechanisms of the highly variable fungal pathogen.

Keywords: molecular markers, Puccinia striiformis, somatic recombination, stripe rust

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

Abstract:

Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: E. Syngelaki, C. C. F. Schinkel, S. Klatt, E. Hörandl

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Environmental influence can alter the conditions for plant development and can trigger changes in epigenetic variation. Thus, the exposure to abiotic environmental stress can lead to different DNA methylation profiles and may have evolutionary consequences for adaptation. Epigenetic control mechanisms may further influence mode of reproduction. The alpine species R. kuepferi has diploid and tetraploid cytotypes, that are mostly sexual and facultative apomicts, respectively. Hence, it is a suitable model system for studying the correlations of mode of reproduction, ploidy, and environmental stress. Diploid and tetraploid individuals were placed in two climate chambers and treated with low (+7°C day/+2°C night, -1°C cold shocks for three nights per week) and warm (control) temperatures (+15°C day/+10°C night). Subsequently, methylation sensitive-Amplified Fragment-Length Polymorphism (AFPL) markers were used to screen genome-wide methylation alterations triggered by stress treatments. The dataset was analyzed for four groups regarding treatment (cold/warm) and ploidy level (diploid/tetraploid), and also separately for full methylated, hemi-methylated and unmethylated sites. Patterns of epigenetic variation suggested that diploids differed significantly in their profiles from tetraploids independent from treatment, while treatments did not differ significantly within cytotypes. Furthermore, diploids are more differentiated than the tetraploids in overall methylation profiles of both treatments. This observation is in accordance with the increased frequency of apomictic seed formation in diploids and maintenance of facultative apomixis in tetraploids during the experiment. Global analysis of molecular variance showed higher epigenetic variation within groups than among them, while locus-by-locus analysis of molecular variance showed a high number (54.7%) of significantly differentiated un-methylated loci. To summarise, epigenetic variation seems to depend on ploidy level, and in diploids may be correlated to changes in mode of reproduction. However, further studies are needed to elucidate the mechanism and possible functional significance of these correlations.

Keywords: apomixis, cold stress, DNA methylation, Ranunculus kuepferi

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Authors: Arun Joshi

Abstract:

The present study deals with the report of Gangamopteriscyclopteroides from the Barakar Formation of Simlong Open Cast Mine, Rajmahal Area, Rajmahal Basin, Jharkhand, India. The genus Gangamopteriscomprises leaves which are simple, entire, symmetrical or asymmetrical, linear, lanceolate, elliptical, obovate in shape, apex broadly rounded, obtuse, acute, acuminate or mucronate, base petiolate or contracted, midrib absent. Median region occupied by subparallel veins with anastomoses of elongate or hexagonal outline. Secondary veins arise from median veins by repeated dichotomy, arched, bifurcating and anasotomosing network. The present work is significant as it represents the presence of Glossopteris flora (250- 290 ma) which is mainly responsible for the formation of coal. Coal is one of the major fuels for power production through thermal power plants. The Glossopteris flora is one of the major floras that occupied the southern continent during Carboniferous- Permian time. This southern continent is also known as Gondwana comprising Australia, South Africa, Antarctica, Madagascar and India. There is a vast geological reserve of coal with favorable stripping ratio available at the Simlong Block but the area comes under the most naxalite prone area and thus the mine has been running in an unplanned manner. It has got the potential of becoming a big project with higher capacity and is well suited for enhancing production which can be helpful in the economic growth of the country. Though, the present record is scanty, it shows the presence of Glossopteris flora responsible for the formation of coal in the Coalmine. However, there are fears of fossils disappearing from this area as the state government of Jharkhand has given out a mining lease in the area to private companies. Therefore, it is very necessary to study such coal forming vegetation and their systematic study from the area to generate a new palaeobotanical database, palaeoenvironmental interpretation, basinal correlation and for the understanding of evolutionary perspectives.

Keywords: Barakar formation, coal, Glossopteris flora, Gondwana, India, Naxalite, Rajmahal Basin

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Authors: German Hernandez-Alonso, Antonio Lazcano, Arturo Becerra

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Until today, viruses remain controversial and poorly understood; about their origin, this problem represents an enigma and one of the great challenges for the contemporary biology. Three main theories have tried to explain the origin of viruses: regressive evolution, escaped host gene, and pre-cellular origin. Under the perspective of the escaped host gene theory, it can be assumed a cellular origin of viral components, like protein RNA-binding domains. These universal distributed RNA-binding domains are related to the RNA metabolism processes, including transcription, processing, and modification of transcripts, translation, RNA degradation and its regulation. In the case of viruses, these domains are present in important viral proteins like helicases, nucleases, polymerases, capsid proteins or regulation factors. Therefore, they are implicated in the replicative cycle and parasitic processes of viruses. That is why it is possible to think that those domains present low levels of divergence due to selective pressures. For these reasons, the main goal for this project is to create a catalogue of the RNA-binding domains found in all the available viral proteomes, using bioinformatics tools in order to analyze its evolutionary process, and thus shed light on the general virus evolution. ProDom database was used to obtain larger than six thousand RNA-binding domain families that belong to the three cellular domains of life and some viral groups. From the sequences of these families, protein profiles were created using HMMER 3.1 tools in order to find distant homologous within greater than four thousand viral proteomes available in GenBank. Once accomplished the analysis, almost three thousand hits were obtained in the viral proteomes. The homologous sequences were found in proteomes of the principal Baltimore viral groups, showing interesting distribution patterns that can contribute to understand the evolution of viruses and their host-virus interactions. Presence of cellular RNA-binding domains within virus proteomes seem to be explained by closed interactions between viruses and their hosts. Recruitment of these domains is advantageous for the viral fitness, allowing viruses to be adapted to the host cellular environment.

Keywords: bioinformatics tools, distant homology, RNA-binding domains, viral evolution

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Authors: Maria E. Fortună, Elena Ungureanu, Răzvan Rotaru, Valeria Harabagiu

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Polymers are used in a variety of areas due to their unique mechanical and chemical properties. Natural polymers are biodegradable, whereas synthetic polymers are rarely biodegradable but can be modified. As a result, by combining the benefits of natural and synthetic polymers, composite materials that are biodegradable can be obtained with potential for biomedical and environmental applications. However, because of their strong resistance to degradation, it may be difficult to eliminate waste. As a result, interest in developing biodegradable polymers has risen significantly. This research involves obtaining and characterizing two biodegradable poly-ε-caprolactone-polydimethylsiloxane copolymers. A comparison study was conducted using an aminopropyl-terminated polydimethylsiloxane macroinitiator with two distinct molecular weights. The copolymers were obtained by ring-opening polymerization of poly (ɛ-caprolactone) in the presence of aminopropyl-terminated polydimethylsiloxane as initiator and comonomers and stannous 2-ethylhexanoate as a catalyst. The materials were characterized using a number of techniques, including NMR, FTIR, EDX, SEM, AFM, and DSC. Additionally, the water contact angle and water vapor sorption capacity were assessed. Furthermore, the copolymers were examined for environmental susceptibility by conducting biological tests on tomato plants (Lypercosium esculentum), with an accent on biological stability and metabolism. Subsequent to the copolymer's degradation, the dynamics of nitrogen experience evolutionary alterations, validating the progression of the process accompanied by the liberation of organic nitrogen. The biological tests performed (germination index, average seedling height, green and dry biomass) on Lypercosium esculentum, San Marzano variety tomato plants in direct contact with the copolymer indicated normal growth and development, suggesting a minimal toxic effect and, by extension, compatibility of the copolymer with the environment. The total chlorophyll concentration of plant leaves in contact with copolymers was determined, considering the pigment's critical role in photosynthesis and, implicitly, plant metabolism and physiological state.

Keywords: biodegradable, biological stability, copolymers, polydimethylsiloxane

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Tamara Zappaterra

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The Learning Difficulties have an evolutionary nature. The international research has focused its analysis on the characteristics of Learning Difficulties in childhood, but we are still far from a thorough understanding of the nature of such disorders in adolescence and adulthood. Such issues become even more urgent in the university context. Spelling, meaning, and appropriate use of the specific vocabulary of the various disciplines represent an additional challenge for the dyslexic student. This paper explores the characteristics of Learning Difficulties in adulthood and the impact with the university teaching. It presents the results of an interdisciplinary project (educational, medical and engineering area) at University of Florence. The purpose of project is to design of a protocol for usability of teaching and individual study at university level. The project, after a first reconnaissance of user needs that have been reached with the participation of the very same protagonists, is at the stage of guidelines drafting for inclusion and education, to be used by teachers, students and administrative staff. The methodologies used are a questionnaire built on purpose and a series of focus groups with users. For collecting data during the focus groups it was decided to use a method typical of the Quality Function Deployment, a tool originally used for quality management, whose versatility makes it easy to use in a number of different context. The paper presents furthermore the findings of the project, the most significant elements of the guidelines for teaching, i.e. the section for teachers, whose aim is to implement a Learning Difficulties-friendly teaching, even at the university level, in compliance with italian Law 170/2010. The Guidelines for the didactic and inclusion of Learning Difficulties students of the University of Florence are articulated around a global and systemic plan of action, meant to accompany and protect the students during their study career, even before enrolling at the University, with different declination: the logistical, relational, educational, and didactic levels have been considered. These guidelines in Italy received the endorsement of the CNUDD. It is a systemic intervention plan for Learning Difficulties students, which roused and keeps rousing the interest of all the university system, with a radical consideration on academic teaching. Since while we try to provide the best Learning Difficulties-friendly didactic in compliance with the rules, no one can be exempted from a wider consideration on the nature and the quality of university teaching offered to all students.

Keywords: didactic tools, learning difficulties, special and inclusive education, university teaching

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Authors: Huang Hao, Li Weiwen

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Global biodiversity continues to decline as a result of global climate change and various human activities, such as habitat destruction, pollution, introduction of alien species and overfishing. Although there are connections between global marine organisms more or less, it is better to have clear geographical boundaries in order to facilitate the assessment and management of different biogeographical zones. And so area based management tools (ABMT) are considered as the most effective means for the conservation and sustainable use of marine biodiversity. On a large scale, the geographical gap (or barrier) is the main factor to influence the connectivity, diffusion, ecological and evolutionary process of marine organisms, which results in different distribution patterns. On a small scale, these factors include geographical location, geology, and geomorphology, water depth, current, temperature, salinity, etc. Therefore, the analysis on geographic and environmental factors is of great significance in the study of biodiversity characteristics. This paper summarizes the marine spatial classification and ABMTs used in coastal area, open oceans and deep sea. And analysis principles and methods of marine spatial classification based on biogeographic related factors, and take China Near Sea (CNS) area as case study, and select key biogeographic related factors, carry out marine spatial classification at biological region scale, ecological regionals scale and biogeographical scale. The research shows that CNS is divided into 5 biological regions by climate and geographical differences, the Yellow Sea, the Bohai Sea, the East China Sea, the Taiwan Straits, and the South China Sea. And the bioregions are then divided into 12 ecological regions according to the typical ecological and administrative factors, and finally the eco-regions are divided into 98 biogeographical units according to the benthic substrate types, depth, coastal types, water temperature, and salinity, given the integrity of biological and ecological process, the area of the biogeographical units is not less than 1,000 km². This research is of great use to the coastal management and biodiversity conservation for local and central government, and provide important scientific support for future spatial planning and management of coastal waters and sustainable use of marine biodiversity.

Keywords: spatial classification, marine biodiversity, bio-geographical, conservation

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Authors: Ozlem Oral, Emre Taskin, Aysel Yuce, Serap Dokmeci, Devrim Gozuacik

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Autophagy is an evolutionary conserved lysosome-dependent catabolic pathway, responsible for the degradation of long-lived proteins, abnormal aggregates and damaged organelles which cannot be degraded by the ubiquitin-proteasome system. Lysosomes degrade the substrates through the activity of lysosomal hydrolases and lysosomal membrane-bound proteins. Mutations in the coding region of these proteins cause malfunctional lysosomes, which contributes to the pathogenesis of lysosomal storage diseases. Gaucher disease is a lysosomal storage disease resulting from the mutation of a lysosomal membrane-associated glycoprotein called glucocerebrosidase and its cofactor saposin C. The disease leads to intracellular accumulation of glucosylceramide and other glycolipids. Because of the essential role of lysosomes in autophagic degradation, Gaucher disease may directly be linked to this pathway. In this study, we investigated the expression of autophagy and/or lysosome-related genes and proteins in fibroblast cells isolated from patients with different mutations. We carried out confocal microscopy analysis and examined autophagic flux by utilizing the differential pH sensitivities of RFP and GFP in mRFP-GFP-LC3 probe. We also evaluated lysosomal pH by active lysosome staining and lysosomal enzyme activity. Beside lysosomes, we also performed proteasomal activity and cell death analysis in patient samples. Our data showed significant attenuation in the expression of key autophagy-related genes and accumulation of their proteins in mutant cells. We found decreased the ability of autophagosomes to fuse with lysosomes, associated with elevated lysosomal pH and reduced lysosomal enzyme activity. Proteasomal degradation and cell death analysis showed reduced proteolytic activity of the proteasome, which consequently leads to increased susceptibility to cell death. Our data indicate that the major degradation pathways are affected by multifunctional lysosomes in mutant patient cells and may underlie in the mechanism of clinical severity of Gaucher patients. (This project is supported by TUBITAK-3501-National Young Researchers Career Development Program, Project No: 112T130).

Keywords: autophagy, Gaucher's disease, glucocerebrosidase, mutant fibroblasts

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Authors: Husham Bayazed

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Purpose of presentation: Pregnancy represents the most important period for the conservation of the species. The immune system is one of the most important systems protecting the mother against the environment and preventing damage to the fetus. This presentation aims to review and discuss the role of the immune system during pregnancy, the evolutionary inflammatory process through pregnancy, infectious and environmental exposure influences on the mother and the fetus, and the impacts of sexual dimorphism of the placenta on offspring susceptibility to different disorders. Recent Findings: In 1960, Peter Medawar (Nobel Prize Winner) proposed that the fetus, a semi-allograft, is similar to a tissue graft that escapes rejection through a mechanism involving systemic immune suppression (Graft –Host response). However, recent researchers and studies have documented that implantation means inflammation, and the inflammatory process is considered a breach of tolerance in pregnancy with immune induction, which is necessary for the protection of the mother and the fetus against infections and environmental triggers. This inflammatory process should be maintained during different pregnancy phases till parturition, and any block at any phase will be associated with pregnancy complications, including pregnancy failure or loss, miscarriage, and preterm birth subsequently. Maternal immune activation following any trigger can have a positive effect on the fetus. The old concept of the placenta being asexual is inaccurate, and being with sexual dimorphism with clear differences in susceptibility to different factors that stimulate maternal immunity. Summary: The presence of different immune cells ((i.e., T cells, B cells, NK cells, etc.) at the implantation site is considered proof of a strong maternal immune response to the fetus. Therefore, human pregnancy is considered a unique immunological paradigm requiring maternal immune modulation rather than suppression. So Medawar's postulation of maternal systemic immunosuppression is wrong. Maternal immune system activation triggered by infections, stress, diet, and pollution can have a positive effect on the fetus, with the development of fetal-trained immunity necessary for survival. The sexual dimorphism of the placenta seems to have an impact on the differences in sex susceptible to the environment maternal risk stimuli. This link to why the incidence of autism is increasing more among boys than girls.

Keywords: pregnancy, maternal immunity, implantation and inflammation, placenta sexual dimorphism

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Authors: Deddi Nordiawan

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Effective public policy creation required a strong budget system, both in terms of design and implementation. Performance-based Budget is an evolutionary approach with two substantial characteristics; first, the strong integration between budgeting and planning, and second, its existence as guidance so that all activities and expenditures refer to measurable performance targets. There are four processes in the government that should be followed in order to make the budget become performance-based. These four processes consist of the preparation of a vision according to the bold aspiration, the formulation of outcome, the determination of output based on the analysis of organizational resources, and the formulation of Value Creation Map that contains a series of programs and activities. This is consistent with the concept of logic model which revealed that the budget performance should be placed within a relational framework of resources, activities, outputs, outcomes and impacts. Through the issuance of Law 17/2003 regarding State Finance, local governments in Indonesia have to implement performance-based budget. Central Government then issued Government Regulation 58/2005 which contains the detail guidelines how to prepare local governments budget. After a decade, implementation of performance budgeting in local government is still not fully meet expectations, though the guidance is completed, socialization routinely performed, and trainings have also been carried out at all levels. Accordingly, this study views the practice of performance-based budget at local governments as a problematic situation. This condition must be approached with a system approach that allows the solutions from many point of views. Based on the fact that the infrastructure of budgeting has already settled, the study then considering the situation as complexity. Therefore, the intervention needs to be done in the area of human activity system. Using Soft Systems Methodology, this research will reconstruct the process of performance-based budget at local governments is area of human activity system. Through conceptual models, this study will invite all actors (central government, local government, and the parliament) for dialogue and formulate interventions in human activity systems that systematically desirable and culturally feasible. The result will direct central government in revise the guidance to local government budgeting process as well as a reference to build the capacity building strategy.

Keywords: soft systems methodology, performance-based budgeting, Indonesia, public policy

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Authors: John McDowall, Lucy Lightfoot

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Stigma constitutes a significant barrier to the recovery and social integration of individuals affected by mental illness. Although there is some debate in the literature regarding the definition and utility of stigma as a concept, it is widely accepted that it comprises three components: stereotypical beliefs, prejudicial reactions, and discrimination. Stereotypical beliefs describe the cognitive knowledge-based component of stigma, referring to beliefs (often negative) about members of a group that is based on cultural and societal norms (e.g. ‘People with anxiety are just weak’). Prejudice refers to the affective/evaluative component of stigma and describes the endorsement of negative stereotypes and the resulting negative emotional reactions (e.g. ‘People with anxiety are just weak, and they frustrate me’). Discrimination refers to the behavioural component of stigma, which is arguably the most problematic, as it exerts a direct effect on the stigmatized person and may lead people to behave in a hostile or avoidant way towards them (i.e. refusal to hire them). Research exploring anti-stigma initiatives focus primarily on an educational approach, with the view that accurate information will replace misconceptions and decrease stigma. Many approaches take a biogenetic stance, emphasising brain and biochemical deficits - the idea being that ‘mental illness is an illness like any other.' While this approach tends to effectively reduce blame, it has also demonstrated negative effects such as increasing prognostic pessimism, the desire for social distance and perceptions of stereotypes. In the present study 144 participants were split into three groups and read one of three vignettes presenting causal explanations for Generalised Anxiety Disorder (GAD): One explanation emphasized biogenetic factors as being important in the etiology of GAD, another emphasised psychosocial factors (e.g. aversive life events, poverty, etc.), and a third stressed the adaptive features of the disorder from an evolutionary viewpoint. A variety of measures tapping the various components of stigma were administered following the vignettes. No difference in stigma measures as a function of causal explanation was found. People who had contact with mental illness in the past were significantly less stigmatising across a wide range of measures, but this did not interact with the type of causal explanation.

Keywords: generalised anxiety disorder, discrimination, prejudice, stigma

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Authors: Gobinathan Devathasan, Kezia Devathasan

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Objective: To improve the current modified Broca-Wernicke-Lichtheim-Kussmaul speech schema and provide insight into autism. Methods: We reviewed the pertinent literature. Current findings, involving Brodmann areas 22, 46, 9,44,45,6,4 are based on neuropathology and functional MRI studies. However, in primary autism, there is no lucid explanation and changes described, whether neuropathology or functional MRI, appear consequential. Findings: We forward an enhanced model which may explain the enigma related to autism. Vowel output is subcortical and does need cortical representation whereas consonant speech is cortical in origin. Left lateralization is needed to commence the circuitry spin as our life have evolved with L-amino acids and left spin of electrons. A fundamental species difference is we are capable of three syllable-consonants and bi-syllable expression whereas cetaceans and songbirds are confined to single or dual consonants. The 4 key sites for speech are superior auditory cortex, Broca’s two areas, and the supplementary motor cortex. Using the Argand’s diagram and Reimann’s projection, we theorize that the Euclidean three dimensional synaptic neuronal circuits of speech are quantized to coherent waves, and then decoherence takes place at area 6 (spherical representation). In this quantum state complex, 3-consonant languages are instantaneously integrated and multiple languages can be learned, verbalized and differentiated. Conclusion: We postulate that evolutionary human speech is elevated to quantum interaction unlike cetaceans and birds to achieve the three consonants/bi-syllable speech. In classical primary autism, the sudden speech switches off and on noted in several cases could now be explained not by any anatomical lesion but failure of coherence. Area 6 projects directly into prefrontal saccadic area (8); and this further explains the second primary feature in autism: lack of eye contact. The third feature which is repetitive finger gestures, located adjacent to the speech/motor areas, are actual attempts to communicate with the autistic child akin to sign language for the deaf.

Keywords: quantum neuronal paradigm, cetaceans and human speech, autism and rapid magnetic stimulation, coherence and decoherence of speech

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Authors: Debamitra Chakravorty, Pratap K. Parida

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Cold-adapted proteases enhance wash performance in low-temperature laundry resulting in a reduction in energy consumption and wear of textiles and are also used in the dehairing process in leather industries. Unfortunately, the possible drawbacks of using cold-adapted proteases are their instability at higher temperatures. Therefore, proteases with broad temperature stability are required. Unfortunately, wild-type cold-adapted proteases exhibit instability at higher temperatures and thus have low shelf lives. Therefore, attempts to engineer cold-adapted proteases by protein engineering were made previously by directed evolution and random mutagenesis. The lacuna is the time, capital, and labour involved to obtain these variants are very demanding and challenging. Therefore, rational engineering for cold stability without compromising an enzyme's optimum pH and temperature for activity is the current requirement. In this work, mutations were rationally designed with the aid of high throughput computational methodology of network analysis, evolutionary conservation scores, and molecular dynamics simulations for Savinase from Bacillus lentus with the intention of rendering the mutants cold stable without affecting their temperature and pH optimum for activity. Further, an attempt was made to incorporate a mutation in the most stable mutant rationally obtained by this method to introduce oxidative stability in the mutant. Such enzymes are desired in detergents with bleaching agents. In silico analysis by performing 300 ns molecular dynamics simulations at 5 different temperatures revealed that these three mutants were found to be better in cold stability compared to the wild type Savinase from Bacillus lentus. Conclusively, this work shows that cold adaptation without losing optimum temperature and pH stability and additionally stability from oxidative damage can be rationally designed by in silico enzyme engineering. The key findings of this work were first, the in silico data of H5 (cold stable savinase) used as a control in this work, corroborated with its reported wet lab temperature stability data. Secondly, three cold stable mutants of Savinase from Bacillus lentus were rationally identified. Lastly, a mutation which will stabilize savinase against oxidative damage was additionally identified.

Keywords: cold stability, molecular dynamics simulations, protein engineering, rational design

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Authors: Perizat Balkhimbekova

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Evolutionary changes in cognitive world view taking place in the last decades are followed by changes in perception of the key concepts which are related to the certain lingua-cultural sphere. Also, such concepts reflect the person’s attitude to essential processes in the sphere of concepts, e.g. the opposite operations like creation and destruction. These changes in people’s life and thinking are displayed in a language world view. In order to open the maintenance of mental structures and concepts we should use language means as observable results of people’s cognitive activity. Semantics of words, free phrases and idioms should be considered as an authoritative source of information concerning concepts. The regularized set of concepts in people consciousness forms the sphere of concepts. Cognitive linguistics widely discusses the sphere of concepts as its crucial category defining it as the field of knowledge which is made of concepts. It is considered that a sphere of concepts comprises the various types of association and forms conceptual fields. As a material for the given research, the data from Russian National Corpus and British National Corpus were used. In is necessary to point out that data provided by computational studies, are intrinsic and verifiable; so that we have used them in order to get the reliable results. The procedure of study was based on such techniques as extracting of the context containing concepts of creation|destruction from the Russian National Corpus (RNC), and British National Corpus (BNC); analyzing and interpreting of those context on the basis of cognitive approach; finding of correspondence between the given concepts in the Russian and English world view. The key problem of our study is to find the correspondence between the elements of world view represented by opposite concepts such as creation and destruction. Findings: The concept of "destruction" indicates a process which leads to full or partial destruction of an object. In other words, it is a loss of the object primary essence: structures, properties, distinctive signs and its initial integrity. The concept of "creation", on the contrary, comprises positive characteristics, represents the activity aimed at improvement of the certain object, at the creation of ideal models of the world. On the other hand, destruction is represented much more widely in RNC than creation (1254 cases of the first concept by comparison to 192 cases for the second one). Our hypothesis consists in the antinomy represented by the aforementioned concepts. Being opposite both in respect of semantics and pragmatics, and from the point of view of axiology, they are at the same time complementary and interrelated concepts.

Keywords: creation, destruction, concept, world view

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