Search results for: small whole genome sequencing

Authors: Yugander Arra, Florence Auguy, Melissa Stiebner, Sophie Chéron, Michael M. Wudick, Van Schepler-Luu, Sébastien Cunnac, Wolf B. Frommer, Laurence Albar

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Rice yellow mottle virus (RYMV) is one of the most important diseases affecting rice in Africa. The most promising strategy to reduce yield losses is the use of highly resistant varieties. The resistance gene RYMV2 is homolog of the Arabidopsis constitutive expression of pathogenesis related protein-5 (AtCPR5) nucleoporin gene. Resistance alleles are originating from African cultivated rice Oryza glaberrima, rarely cultivated, and are characterized by frameshifts or early stop codons, leading to a non-functional or truncated protein. Rice possesses two paralogs of CPR5 and function of these genes are unclear. Here, we evaluated the role of the two rice candidate nucleoporin paralogs OsCPR5.1 (pathogenesis-related gene 5; RYMV2) and OsCPR5.2 by CRISPR/Cas9 genome editing. Despite striking sequence and structural similarity, only loss-of-function of OsCPR5.1 led to full resistance, while loss-of-function oscpr5.2 mutants remained susceptible. Short N-terminal deletions in OsCPR5.1 also did not lead to resistance. In contrast to Atcpr5 mutants, neither OsCPR5.1 nor OsCPR5.2 knock out mutants showed substantial growth defects. Taken together, the candidate nucleoporin OsCPR5.1, but not its close homolog OsCPR5.2, plays a specific role for the susceptibility to RYMV, possibly by impairing the import of viral RNA or protein into the nucleus. Whereas gene introgression from O. glaberrima to high yielding O. sativa varieties is impaired by strong sterility barriers and the negative impact of linkage drag, genome editing of OsCPR5.1, while maintaining OsCPR5.2 activity, thus provides a promising strategy to generate O. sativa elite lines that are resistant to RYMV.

Keywords: CRISPR Cas9, genome editing, knock out mutant, recessive resistance, rice yellow mottle virus

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Authors: D. Hammad, D. P. Tonge

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Rheumatoid arthritis (RA) is a disabling and common autoimmune disease during which the body's immune system attacks healthy tissues. This results in complicated and long-lasting actions being carried out by the immune system, which typically only occurs when the immune system encounters a foreign object. In the case of RA, the disease affects millions of people and causes joint inflammation, ultimately leading to the destruction of cartilage and bone. Interestingly, the disease mechanism still remains unclear. It is likely that RA occurs as a result of a complex interplay of genetic and environmental factors including an imbalance in the microorganism population inside our body. The human microbiome or microbiota is an extensive community of microorganisms in and on the bodies of animals, which comprises bacteria, fungi, viruses, and protozoa. Recently, the development of molecular techniques to characterize entire bacterial communities has renewed interest in the involvement of the microbiome in the development and progression of RA. We believe that an imbalance in some of the specific bacterial species in the gut, mouth and other sites may lead to atopobiosis; the translocation of these organisms into the blood, and that this may lead to changes in immune system status. The aim of this study was, therefore, to characterize the microbiome of RA serum samples in comparison to healthy control subjects using 16S rRNA gene amplification and sequencing. Serum samples were obtained from healthy control volunteers and from patients with RA both prior to, and following treatment. The bacterial community present in each sample was identified utilizing V4 region 16S rRNA amplification and sequencing. Bacterial identification, to the lowest taxonomic rank, was performed using a range of bioinformatics tools. Significantly, the proportions of the Lachnospiraceae, Ruminococcaceae, and Halmonadaceae families were significantly increased in the serum of RA patients compared with healthy control serum. Furthermore, the abundance of Bacteroides and Lachnospiraceae nk4a136_group, Lachnospiraceae_UGC-001, RuminococcaceaeUCG-014, Rumnococcus-1, and Shewanella was also raised in the serum of RA patients relative to healthy control serum. These data support the notion of a blood microbiome and reveal RA-associated changes that may have significant implications for biomarker development and may present much-needed opportunities for novel therapeutic development.

Keywords: blood microbiome, gut and oral bacteria, Rheumatoid arthritis, 16S rRNA gene sequencing

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Authors: Guilherme Gorgulho, Carlos Roberto Camello Lima

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Due to the competitive market in which companies are currently engaged, the constant changes require companies to react quickly regarding the variability of demand and process. The changes are caused by customers, or by demand fluctuations or variations of products, or the need to serve customers within agreed delivery taking into account the continuous search for quality and competitive prices in products. These changes end up influencing directly or indirectly the activities of the Planning and Production Control (PPC), which does business in strategic, tactical and operational levels of production systems. One area of concern for organizations is in the short term (operational level), because this planning stage any error or divergence will cause waste and impact on the delivery of products on time to customers. Thus, this study aims to optimize the efficiency of production scheduling, using different sequencing strategies in an automotive company. Seeking to aim the proposed objective, we used the computer simulation in conjunction with lean manufacturing to build and validate the current model, and subsequently the creation of future scenarios.

Keywords: computational simulation, lean manufacturing, production scheduling, sequencing strategies

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Authors: Dong-Hyun Ha, Young-Min Ko, Chang-Bin Ha, Hyoung-Kyu Song

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In Heterogeneous network (HetNet) can provide high quality of a service in a wireless communication system by composition of small cell networks. The composition of small cell networks improves cell coverage and capacity to the mobile users.Recently, various techniques using small cell networks have been researched in the wireless communication system. In this paper, the cooperative scheme obtaining high reliability is proposed in the small cell networks. The proposed scheme suggests a cooperative small cell system and the new signal transmission technique in the proposed system model. The new signal transmission technique applies a cyclic delay diversity (CDD) scheme based on the multiple input multiple output-orthogonal frequency division multiplexing (MIMO-OFDM) system to obtain improved performance. The improved performance of the proposed scheme is confirmed by the simulation results.

Keywords: adaptive transmission, cooperative communication, diversity gain, OFDM

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Authors: Jerzy Banski

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The basic aim of this study is to discuss and assess different classifications and research approaches to small towns that take their social and economic functions into account, as well as relations with surrounding areas. The subject literature typically includes three types of approaches to the classification of small towns: 1) the structural, 2) the location-related, and 3) the mixed. The structural approach allows for the grouping of towns from the point of view of the social, cultural and economic functions they discharge. The location-related approach draws on the idea of there being a continuum between the center and the periphery. A mixed classification making simultaneous use of the different approaches to research brings the most information to bear in regard to categories of the urban locality. Bearing in mind the approaches to classification, it is possible to propose a synthetic method for classifying small towns that takes account of economic structure, location and the relationship between the towns and their surroundings. In the case of economic structure, the small centers may be divided into two basic groups – those featuring a multi-branch structure and those that are specialized economically. A second element of the classification reflects the locations of urban centers. Two basic types can be identified – the small town within the range of impact of a large agglomeration, or else the town outside such areas, which is to say located peripherally. The third component of the classification arises out of small towns’ relations with their surroundings. In consequence, it is possible to indicate 8 types of small-town: from local centers enjoying good accessibility and a multi-branch economic structure to peripheral supra-local centers characterised by a specialized economic structure.

Keywords: small towns, classification, functional structure, localization

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Authors: D. S. V. Barbieri, R. R. Gomes, G. D. Santos, P. F. Herkert, M. Moreira, E. S. Trindade, V. A. Vicente

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The importance of yeast infections has increased in recent decades. The monitoring of Candida yeasts has been relevant in the study of groups and populations. This research evaluated 31 Candida spp. isolates from oral microbiota of 12 Brazilian schoolchildren coinfected with Streptococcus mutans. The isolates were evaluated for their ability to form biofilm in vitro and molecularly characterized based on the sequencing of intergenic spacer regions ITS1-5,8S-ITS2 and variable domains of the large subunit (D1/D2) regions of the rDNA, as well as ABC system genotyping. The sequencing confirmed 26 lineages of Candida albicans, three Candida tropicalis, one Candida guillhermondii and one Candida glabrata. Genetic variability and differences on in biofilm formation were observed among Candida yeasts lineages. At least one Candida strain from each caries activity child was C.albicans genotype A or Candida non-albicans. C. tropicalis was associated with highest cavities rates. These results indicate that the presence of C. albicans genotype A or multi-colonization by non albicans species seem to be associates to the potentialization of caries risk.

Keywords: biofilm, Candida albicans, oral microbiota, caries

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Authors: E. Rak

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The aim of the paper is to identify some of the specific characteristics of employee development, as observed in the practice of small enterprises in Poland. Results suggest that a sizeable percentage of employers are not interested in improving the development of their employee base. This aspect is often perceived as insignificant. In addition, many employers have no theoretical or practical knowledge of employee development methods. Lack of sufficient financial support is reported as third on the list of the most important barriers to employee development. Employees, on the other hand, typically offload the responsibility of initiating this type of activities onto the employer. Employee development plans are typically flexible and accommodating. The original value offered by this research comes in the form of a detailed characteristics of employee development in small enterprises, accompanied by identification of specificity of human resource development in Polish companies.

Keywords: employee development, human resources development, small enterprises, trainings

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Authors: Scott A. Ochsner, Christopher M. Watkins, Apollo McOwiti, David L. Steffen Lauren B. Becnel, Neil J. McKenna

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Understanding signaling by nuclear receptors (NRs) requires an appreciation of their cognate ligand- and tissue-specific transcriptomes. While target gene regulation data are abundant in this field, they reside in hundreds of discrete publications in formats refractory to routine query and analysis and, accordingly, their full value to the NR signaling community has not been realized. One of the mandates of the Nuclear Receptor Signaling Atlas (NURSA) is to facilitate access of the community to existing public datasets. Pursuant to this mandate we are developing a freely-accessible community web resource, Transcriptomine, to bring together the sum total of available expression array and RNA-Seq data points generated by the field in a single location. Transcriptomine currently contains over 25,000,000 gene fold change datapoints from over 1200 contrasts relevant to over 100 NRs, ligands and coregulators in over 200 tissues and cell lines. Transcriptomine is designed to accommodate a spectrum of end users ranging from the bench researcher to those with advanced bioinformatic training. Visualization tools allow users to build custom charts to compare and contrast patterns of gene regulation across different tissues and in response to different ligands. Our resource affords an entirely new paradigm for leveraging gene expression data in the NR signaling field, empowering users to query gene fold changes across diverse regulatory molecules, tissues and cell lines, target genes, biological functions and disease associations, and that would otherwise be prohibitive in terms of time and effort. Transcriptomine will be regularly updated with gene lists from future genome-wide expression array and expression-sequencing datasets in the NR signaling field.

Keywords: target gene database, informatics, gene expression, transcriptomics

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Authors: Mohamed M. Bumadian, D. James Gilmour

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Three bacterial species were isolated from the River Wye (Derbyshire, England) and identified using 16S rRNA gene sequencing as Serratia proteamaculans, Aeromonas hydrophila and Klebsiella pneumoniae. Respiration rates of the strains were measured in order to determine the metabolic activity under salt stress. The highest respiration rates of all three strains were found at 0.17 M and 0.5 M NaCl and then the respiration rate decreased with increasing concentrations of NaCl. In addition, the effect of increasing concentrations of NaCl on malate dehydrogenase activity was determined using cell-free extracts of the three strains. Malate dehydrogenase activity was stimulated at NaCl concentrations up to 0.5 M, and a small level of activity remained even at 3.5 M NaCl. The pH optimum of the malate dehydrogenase in cell-free extracts of all strains was higher than pH 7.5.

Keywords: fresh water, halotolerant pathogenic bacteria, 16S rRNA gene, cell-free extracts, respiration rates, malate dehydrogenase

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Authors: Shameel Pervez, Saad Aziz Durrani, Ibatsam Khokhar

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Pectinase is an enzyme that breaks down pectin, a compound responsible for structural integrity of the plant. Pectin is difficult to break down mechanically and the cost is very high, that is why many industries including food industries use pectinase enzyme produced by microbes for pectin breakdown. Apple (Malus domestica) is an important fruit in terms of market value. Every year, millions of apples are wasted due to post-harvest rot caused by fungi. Fungi are natural decomposers of our ecosystem and are infamous for post-harvest rot of apple fruit but at the same time they are prized for their high production of valuable extracellular enzymes such as pectinase. In this study, fungi belonging to different genus were isolated from rotten apples. Rotten samples of apple were picked from different markets of Lahore. After surface sterilization, the rotten parts were cut into small pieces and placed onto MEA media plates for three days. Afterwards, distinct colonies were picked and purified by sub-culturing. The isolates were identified to genus level through the study of basic colony morphology and microscopic features. The isolates were then subjected to screening for pectinase activity on MS media to compare pectinase production and were then subsequently tested for pathogenic activity through wound suspension method to evaluate the pathogenic activity of isolates in comparison with their pectinolytic activity. A total of twelve fungal strains were isolates from rotten apples. They were belonging to genus Penicillium, Alternaria, Paecilomyces and Rhizopus. Upon screening for pectinolytic activity, isolates Pen 1, Pen 4, and Rz showed high pectinolytic activity and were further subjected to DNA isolation and partial sequencing for species identification. The results of partial sequencing were combined with in-depth study of morphological features revealing Pen 1 as Penicillium janthinellum, Pen 4 as Penicillium griseofulvum, and Rz as Rhizopus microsporus. Pathogenic activity of all twelve isolates was evaluated. Penicillium spp. were highly pathogenic and destructive and same was the case with Paecilomyces sp. and Rhizopus sp. However, Alternaria spp. were found to be more consistent in their pathogenic activity, on all types of apples.

Keywords: apple, pectinase, fungal pathogens, penicillium, rhizopus

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Authors: H. D. Duong, J. I. Rhee

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In this work, gold nanoparticles in star shape (called gold nanostars, GNS) were synthesized and coated by N-(3-aminopropyl) methacrylamide hydrochloride (PA) and mercaptopropionic acid (MPA) for functionalizing their surface by amine and carboxyl groups and then investigated for ROS production. The GNS with big size and multi-tips seem to be superior in singlet oxygen production as compared with that of small GNS and less tips. However, the functioned GNS in small size could also enhance efficiency of singlet oxygen production about double as compared with that of the intact GNS. In combination with methylene blue (MB+), the functioned GNS could enhance the singlet oxygen production of MB+ after 1h of LED750 irradiation and no difference between small size and big size in this reaction was observed. In combination with 5-aminolevulinic acid (ALA), only GNS coated PA could enhance the singlet oxygen production of ALA and the small size of GNS coated PA was a little higher effect than that of the bigger size. However, GNS coated MPA with small size had strong effect on hydroxyl radical production of ALA.

Keywords: 5-aminolevulinic acid, gold nanostars, methylene blue, ROS production

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Authors: Abul B. M. M. K. Islam, Nuria Lopez-Bigas, Elizaveta V. Benevolenskaya

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RBP2 has shown to be important for cell differentiation control through epigenetic mechanism. The main aim of the present study is genome-wide location analysis of human RBP2 isoforms that differ in a histone-binding domain by ChIPseq. It is conceivable that the larger isoform (LI) of RBP2, which contains a specific H3K4me3 interacting domain, differs from the smaller isoform (SI) in genomic location, may account for the observed diversity in RBP2 function. To distinguish the two RBP2 isoforms, we used the fact that the SI lacks the C-terminal PHD domain and hence used the antibodies detecting both RBP2 isoforms (AI) through a common central domain, and the antibodies detecting only LI but not SI, through a C-terminal PHD domain. Overall our analysis suggests that RBP2 occupies about 77 nucleotides and binds GC rich motifs of active genes, does not bind to centromere, telomere, or enhancer regions, and binding sites are conserved compare to random. A striking difference between the only-SI and only-LI is that a large number of only-SI peaks are located in CpG islands and close to TSS compared to only-LI peaks. Enrichment analysis of the related genes indicates that several oncogenic pathways and metabolic pathways/processes are significantly enriched among only-SI/AI targets, but not LI/only-LI peak’s targets.

Keywords: bioinformatics, cancer, ChIP-seq, KDM5A

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Authors: E. O. Fakoya, B. G. Abiona, W. O. Oyediran, A. M. Omoare

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This study examined the socio-economic effects of micro-credit on small scale poultry farmers’ livelihood in Ado Odo-Ota Local Government area of Ogun State. Purposive sampling method was used to select eighty (80) small scale poultry farmers that benefited in micro credit. Interview guide was used to obtain information on the respondents’ socio-economic characteristic, sources of micro-credit and the effects of micro-credit on their livelihood. The results revealed that most of the respondents (77.50 %) were males while half (40.00%) of the respondents were between the ages of 31-40 years. A high proportion (72.50%) of the respondents had formal education. The major sources of micro credit to small scale poultry farmers were cooperative society (47.50%) and personal savings (20.00%). The findings also revealed that micro-credit had positive effect on the assets and livelihoods of small scale poultry farmers’ livelihood. Results of t-test analysis showed a significant difference between the effects before and after micro-credit on small-scale poultry farmers’ Livelihood at p < 0.05. The study recommends that formal lending institution should be given necessary support by government to enable poultry farmers have access to credit facilities in the study area.

Keywords: micro-credit, effects, livelihood, poultry farmers, socio-economic, small scale

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Authors: Sahar Nasr, Lin Li, Edwin Wang

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Bladder cancer (BLCA) is known as the 13th cause of death among cancer patients worldwide, and ~575,000 new BLCA cases are diagnosed each year. Urothelial carcinoma (UC) is the most prevalent subtype among BLCA patients, which can be categorized into muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Currently, various therapeutic options are available for UC patients, including (1) transurethral resection followed by intravesical instillation of chemotherapeutics or Bacillus Calmette-Guérin for NMIBC patients, (2) neoadjuvant platinum-based chemotherapy (NAC) plus radical cystectomy is the standard of care for localized MIBC patients, and (3) systematic chemotherapy for metastatic UC. However, conventional treatments may lead to several challenges for treating patients. As an illustration, some patients may suffer from recurrence of the disease after the first line of treatment. Recently, immune checkpoint therapy (ICT) has been introduced as an alternative treatment strategy for the first or second line of treatment in advanced or metastatic BLCA patients. Although ICT showed lucrative results for a fraction of BLCA patients, ~80% of patients were not responsive to it. Therefore, novel treatment methods are required to augment the ICI response rate within BLCA patients. It has been shown that the infiltration of T-cells into the tumor microenvironment (TME) is positively correlated with the response to ICT within cancerous patients. Therefore, the goal of this study is to enhance the infiltration of cytotoxic T-cells into TME through the identification of target genes within the tumor that are responsible for the non-T-cell inflamed TME and their inhibition. BLCA bulk RNA-sequencing data from The Cancer Genome Atlas (TCGA) and immune score for TCGA samples were used to determine the Pearson correlation score between the expression of different genes and immune score for each sample. The genes with strong negative correlations were selected (r < -0.2). Thereafter, the correlation between the expression of each gene and survival in BLCA patients was calculated using the TCGA data and Cox regression method. The genes that are common in both selected gene lists were chosen for further analysis. Afterward, BLCA bulk and single-cell RNA-sequencing data were ranked based on the expression of each selected gene and the top and bottom 25% samples were used for pathway enrichment analysis. If the pathways related to the T-cell infiltration (e.g., antigen presentation, interferon, or chemokine pathways) were enriched within the low-expression group, the gene was included for downstream analysis. Finally, the selected genes will be used to calculate the correlation between their expression and the infiltration rate of the activated CD+8 T-cells, natural killer cells and the activated dendric cells. A list of potential target genes has been identified and ranked based on the above-mentioned analysis and criteria. SUN-1 got the highest score within the gene list and other identified genes in the literature as benchmarks. In conclusion, inhibition of SUN1 may increase the tumor-infiltrating lymphocytes and the efficacy of ICI in BLCA patients. BLCA tumor cells with and without SUN-1 CRISPR/Cas9 knockout will be injected into the syngeneic mouse model to validate the predicted SUN-1 effect on increasing tumor-infiltrating lymphocytes.

Keywords: data analysis, gene expression analysis, gene identification, immunoinformatic, functional genomics, transcriptomics

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Authors: Eno Jah Tabogo

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The aim of this research is to identify and examine current deficiencies in entrepreneurial training in improving the performance of small businesses in sub Saharan Africa economies. This research achieves this by examining the course content, training methods, and profiles of trainers and trainees of small business service providers in Sub Saharan Africa (SSA) to identify training deficiencies in improving small businesses. Data was for the analysis was collected from a sample of four entrepreneurial training providers in SSA. These four providers served an average of 1,500 trainees. Questionnaire was used to collect data via face to face and through telephone. Face validity was determined by distributing the questionnaire among a group of colleagues, followed by a group discussion to strengthen the validity of the questionnaire. Interviews were also held with managers of training programs. Content and descriptive statistics was used to analyse the data collected. The results indicated only 25% of the training content were entrepreneurial. In terms of service provided, both business, entrepreneurial, technical and after-care services were identified. It was also discovered that owners of training firms had no formal entrepreneurship background. The paper contributes by advocating for a comprehensive entrepreneurship-training program for successful small business enterprises. Recommendations that could help sustain emerging small business enterprises and direction for further research are presented.

Keywords: entrepreneurship, emerging markets, small business, training

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Authors: Yun Zhang, Zhu Wang

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Renewing ancient residential areas is an integral part of the sustainable development of modern cities. Compared with a metropolis, the old areas of small and medium-sized cities is more complicated to update, as the spatial form is more fragmented. In this context, the author takes as the research object, the ancient town of Changshu City, which is a small city representative in China with a history of more than 1,200 years. Through the analysis of urban research and update projects, the spatial evolution characteristics and renewal strategies of small ancient urban settlements are studied. On this basis, it is proposed to protect the residential area from the perspective of integrity and sustainability, strengthen the core public part, control the district building, and reshape the important interface. Renewing small and medium-sized urban areas should respect the rhythm of their own urban development and gradually complete the update, not blindly copying the experience of large cities.

Keywords: ancient residential area, Changshu, city renewal strategy, small and medium-sized cities

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Authors: Alexander Kelisek, Stanislava Strelcova

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Developing of business in small and medium-sized enterprises (SMEs) is a specific especially for its flexibility and rapid adaptation to the conditions of turbulent market environment compared to large enterprises. Therefore, an importance of SMEs is growing rapidly in Slovakia but also in other EU countries. Small and medium enterprises are characterized by transparent organizational structure, as it allows the realization of direct management and information flow without significant negative aspects. In the national economy small and medium-sized enterprises represent a significant potential when performs a several important functions (e.g. social, economic, export-import, etc.) The significance of these enterprises is not only at national, but also at transnational level. Importance of SMEs is also aware of the EU, which declared this statement in a key document for SMEs called Small Business Act. In this document, SMEs are characterized, as the backbone of the EU economy and also as a key source of jobs opportunities. In addition to these aspects, SMEs attaches high innovation and development potential. The authors of the article are dealing with the current status of SMEs development in the Slovak Republic and highlight the current challenges that entrepreneurs face in their small and medium enterprises.

Keywords: small and medium enterprises (SMEs), business support, SMEs development, SMEs funding

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Tian Xia, Yuan Yan Tang

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In order to obtain higher small target detection accuracy, this paper presents an effective algorithm inspired by the local contrast mechanism. The proposed method can enhance target signal and suppress background clutter simultaneously. In the first stage, a enhanced image is obtained using the proposed Weighted Laplacian of Gaussian. In the second stage, an adaptive threshold is adopted to segment the target. Experimental results on two changeling image sequences show that the proposed method can detect the bright and dark targets simultaneously, and is not sensitive to sea-sky line of the infrared image. So it is fit for IR small infrared target detection.

Keywords: small target detection, local contrast, human vision system, Laplacian of Gaussian

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Authors: Tugrul Oktay, Mehmet Konar, Mustafa Soylak, Firat Sal, Murat Onay, Orhan Kizilkaya

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In this paper, autonomous performance of a small manufactured unmanned helicopter is tried to be increased. For this purpose, a small unmanned helicopter is manufactured in Erciyes University, Faculty of Aeronautics and Astronautics. It is called as ZANKA-Heli-I. For performance maximization, autopilot parameters are determined via minimizing a cost function consisting of flight performance parameters such as settling time, rise time, overshoot during trajectory tracking. For this purpose, a stochastic optimization method named as simultaneous perturbation stochastic approximation is benefited. Using this approach, considerable autonomous performance increase (around %23) is obtained.

Keywords: small helicopters, hierarchical control, stochastic optimization, autonomous performance maximization, autopilots

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Authors: Ewa Rak

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This paper is part of a broader research project on employee development in small enterprises, financed by Polish National Science Centre. The project results will serve as basis for a doctoral dissertation. The paper utilises literature studies and qualitative research conducted in small enterprises operating in the Lower Silesia region of Poland. This paper aims to identify some of the factors that stimulate employee development in small companies operating in Poland. The great variety of business pursuits and applications represented by this sector makes it hard to determine a universal configuration of factors to offer best possible conditions for employee development. Research results suggest that each of the examined companies had one or two of such factors in focus, and serving as the basis for the entire pro-development system. These include: employment security (both for employee and entrepreneur) and extensive knowledge and experience of entrepreneurs, but only if it is combined with a willingness and ability to share it.

Keywords: employee development, factors that stimulate employee development, human resources development, Poland, small enterprises, training

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Authors: Kesavan Markkandan, Ha Young Park, Seung-Il Yoo, Sin-Gi Park, Junhyung Park

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For genetic identification of crop cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, PCR based, co-dominant and relatively abundant. However, new InDels need to be developed for genetic studies of new varieties due to the difference of allele frequencies in InDels among the population groups. These new varieties are evolved with low levels of genetic diversity in specific genome loci with high recombination rate. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a variation block (VB), where the genomes split by all assumed recombination sites. Firstly, VBs in crop cultivars were mined for transferability to VB-specific InDel markers. Secondly, putative InDels in the VB regions were identified for the development of barcode system by analyzing particular cultivar’s whole genome data. Thirdly, common VB-specific InDels from all cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the selected markers was assessed with other cultivars, and the barcode system that allows a clear distinction among those cultivars is described. The same approach can be applicable for other commercial crops. Hence, VB-based genetic identification not only minimize the molecular markers but also useful for assessing cultivars and for marker-assisted breeding in other crop species.

Keywords: variation block, polymorphism, InDel marker, genetic identification

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Authors: Yina F. Muñoz, Alexander Paz, Hanns De La Fuente-Mella, Joaquin V. Fariña, Guilherme M. Sales

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The primary approach for estimating bridge deterioration uses Markov-chain models and regression analysis. Traditional Markov models have problems in estimating the required transition probabilities when a small sample size is used. Often, reliable bridge data have not been taken over large periods, thus large data sets may not be available. This study presents an important change to the traditional approach by using the Small Data Method to estimate transition probabilities. The results illustrate that the Small Data Method and traditional approach both provide similar estimates; however, the former method provides results that are more conservative. That is, Small Data Method provided slightly lower than expected bridge condition ratings compared with the traditional approach. Considering that bridges are critical infrastructures, the Small Data Method, which uses more information and provides more conservative estimates, may be more appropriate when the available sample size is small. In addition, regression analysis was used to calculate bridge deterioration. Condition ratings were determined for bridge groups, and the best regression model was selected for each group. The results obtained were very similar to those obtained when using Markov chains; however, it is desirable to use more data for better results.

Keywords: concrete bridges, deterioration, Markov chains, probability matrix

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Authors: Tatsuya Otoshi, Masayuki Murata

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With the development and diversification of applications on the Internet, applications that require high responsiveness, such as video streaming, are becoming mainstream. Application responsiveness is not only a matter of communication delay but also a matter of time required to grasp changes in network conditions. The tradeoff between accuracy and measurement time is a challenge in network control. We people make countless decisions all the time, and our decisions seem to resolve tradeoffs between time and accuracy. When making decisions, people are known to make appropriate choices based on relatively small samples. Although there have been various studies on models of human decision-making, a model that integrates various cognitive biases, called ”quantum decision-making,” has recently attracted much attention. However, the modeling of small samples has not been examined much so far. In this paper, we extend the model of quantum decision-making to model decision-making with a small sample. In the proposed model, the state is updated by value-based probability amplitude amplification. By analytically obtaining a lower bound on the number of samples required for decision-making, we show that decision-making with a small number of samples is feasible.

Keywords: quantum decision making, small sample, MPEG-DASH, Grover's algorithm

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Authors: Melvin Mothoa

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Small Micro and Medium Enterprises are very significant for the development of their market economies. They are the main creators of the new working places, and they present a vital core of the market economy in countries across the globe. Access to finance is identified as crucial for small, micro, and medium-sized enterprises for their growth and innovation. This paper is conceived to propose a perception-based SMME framework to aid in access to financial support. Furthermore, the study will address issues that impede SMMEs in South Africa from obtaining finance from financial institutions. The framework will be tested against data collected from 200 Small Micro & Medium Enterprises in the Gauteng province of South Africa. The study adopts a quantitative method, and the delivery of self-administered questionnaires to SMMEs will be the primary data collection tool. Structural equation modeling will be used to further analyse the data collected.

Keywords: finance, small business, growth, development

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Authors: A. Lovascio, A. D’Orazio, V. Centonze

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From several years till now the aerospace industry is developing more and more small satellites for Low-Earth Orbit (LEO) missions. Such satellites have a low cost of making and launching since they have a size and weight smaller than other types of satellites. However, because of size limitations, small satellites need integrated electronic equipment based on digital logic. Moreover, the LEOs require telecommunication modules with high throughput to transmit to earth a big amount of data in a short time. In order to meet such requirements, in this paper we propose a Telemetry, Tracking & Command module optimized through the use of the Commercial Off-The-Shelf components. The proposed approach exploits the major flexibility offered by these components in reducing costs and optimizing the performance. The method has been applied in detail for the design of the front-end receiver, which has a low noise figure (1.5 dB) and DC power consumption (smaller than 2 W). Such a performance is particularly attractive since it allows fulfilling the energy budget stringent constraints that are typical for LEO small platforms.

Keywords: COTS, LEO, small-satellite, TT&C

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Authors: Akinwale Olusola Mokayode, Emaanuel Adu, Seriki Idowu Ibrahim

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Small business can serve as a tool for poverty reduction in South Africa, but it requires adequate support and development for its continuous sustenance in spite of rigorous challenges, especially in the rural environment. This study explored the challenges faced by the small business owners in the rural Eastern Cape Province of South Africa. The objective of the study is to identify the challenges faced by small business owners in the case study area and to examine the effects of those challenges on poverty rate. Survey research design was adopted, with the distribution of structured questionnaire for data collection through a simple random sampling method. Descriptive and inferential statistics was used to analyse the data. Findings showed that small business owners face various challenges in their commercial operations. It was also made clearer that these challenges have effects on the poverty rate as well as crime rate. In conclusion, in other for small businesses to be effective instrument to tackle poverty, certain measure must be taken into considerations. This therefore necessitates recommendation from the researcher that potential and current business owners must seek valuable advice from the more experienced business tycoon and seek information about the business assistance programmes provided by government and private sectors.

Keywords: eastern cape, poverty, poverty reduction, rural, small business, sustainable livelihood

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Authors: Mhaned Oubounyt, Jan Baumbach

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Differences in co-expression networks between two or multiple cells (sub)types across conditions is a pressing problem in single-cell RNA sequencing (scRNA-seq). A key challenge is to define those co-variations that differ between or among cell types and/or conditions and phenotypes to examine small regulatory networks that can explain mechanistic differences. To this end, we developed SCANet, an all-in-one Python package that uses state-of-the-art algorithms to facilitate the workflow of a combined single-cell GCN (Gene Correlation Network) and GRN (Gene Regulatory Networks) pipeline, including inference of gene co-expression modules from scRNA-seq, followed by trait and cell type associations, hub gene detection, co-regulatory networks, and drug-gene interactions. In an example case, we illustrate how SCANet can be applied to identify regulatory drivers behind a cytokine storm associated with mortality in patients with acute respiratory illness. SCANet is available as a free, open-source, and user-friendly Python package that can be easily integrated into systems biology pipelines.

Keywords: single-cell, co-expression networks, drug-gene interactions, co-regulatory networks

Procedia PDF Downloads 92

Authors: Lemuel David

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The importance of the Micro, Small, and Medium Enterprises sector is well recognized for its legitimate contribution to the Macroeconomic objectives of the Republic of Liberia, like generation of employment, input t, exports, and enhancing entrepreneurship. Right now, Medium and Small enterprises accounts for about 99 percent of the industrial units in the country, contributing 60 percent of the manufacturing sector output and approximately one-third of the nation’s exports. The role of various financial institutions like ECO bank and Non-financial Institutions like Bearch Limited support promoting the growth of Micro, Small, and Medium Enterprises is unique. A small enterprise or entrepreneur gets many types of assistance from different institutions for varied purposes in the course of his entrepreneurial journey. This paper focuses on the factors related to financial institutional support and non-financial institutional support entrepreneurs to the growth of Medium and Small enterprises in the Republic of Liberia. The significance of this paper is to support Policy and Institutional Support for Medium and Small enterprises to know the views of entrepreneurs about financial and non-financial support systems in the Republic of Liberia. This study was carried out through a survey method, with the use of questionnaires. The population for this study consisted of all registered Medium and Small enterprises which have been registered during the years 2004-2014 in the republic of Liberia. The sampling method employed for this study was a simple random technique and determined a sample size of 400. Data for the study was collected using a standard questionnaire. The questionnaire consisted of two parts: the first part consisted of questions on the profile of the respondents. The second part covers (1) financial, promotional factors and (2) non-financial promotional factors. The results of the study are based on financial and non-financial supporting activities provided by institutions to Medium and Small enterprises. After investigation, it has been found that there is no difference in the support given by Financial Institutions and non-financial Institutions. Entrepreneurs perceived “collateral-free schemes and physical infrastructure support factors are highest contributing to entry and growth of Medium and Small enterprises.

Keywords: micro, small, and medium enterprises financial institutions, entrepreneurship

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Authors: Maryam Zafar, Sajida Rasheed, Imran Hashmi

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Water as an environmental reservoir is reported to act as a habitat and transmission route to microaerophilic bacteria such as Heliobacter pylori. It has been studied that in biofilms are the predominant dwellings for the bacteria to grow in water and protective reservoir for numerous pathogens by protecting them against harsh conditions, such as shear stress, low carbon concentration and less than optimal temperature. In this study, influence of these and many other parameters was studied on H. pylori in stagnant and moving water biofilms both in surface and underground aquatic reservoirs. H. pylori were recovered from pipe of different materials such as Polyvinyl Chloride, Polypropylene and Galvanized iron pipe cross sections from an urban water distribution network. Biofilm swabbed from inner cross section was examined by molecular biology methods coupled with gene sequencing and H. pylori 16S rRNA peptide nucleic acid probe showing positive results for H. pylori presence. Studies showed that pipe material affect growth of biofilm which in turn provide additional survival mechanism for pathogens like H. pylori causing public health concerns.

Keywords: biofilm, gene sequencing, heliobacter pylori, pipe materials

Procedia PDF Downloads 326