MODEL OF CROATIAN SEA PASSENGER PORTS MANAGEMENT RATIONALIZATION

Predmet istraživanja u ovome znanstvenom radu je razvitak pomorskoputničkih luka u Republici Hrvatskoj do 2012. godine. Za definiranje svojstava i determinanti pomorskoputničkih luka koristilo se modelom na bazi matrice rasta. Analiza i vrednovanje pojedinih elemenata modela i dobivene izravne stope rasta imale su za cilj znanstveno formulirati rezultate istraživanja, prema najvažnijim teorijskim zakonitostima razvitka pomorskoputničkih luka u Republici Hrvatskoj. Autori su se u znanstvenom istraživanju i prezentiranju rezultata istraživanja ovog rada služili kombinaciju znanstvenih metoda kao što su: metoda analize i sinteze, metoda konkretizacije, komparativna metoda i metoda modeliranja (matrica rasta). Glavna znanstvena hipoteza dokazana je izravnim stopama rasta odabranih elemenata modela a ona glasi: Znanstveno utemeljenim spoznajama o funkcioniranju i poslovanju sustava pomorskoputničkih luka moguće je predložiti model, mjere i aktivnosti za racionalno upravljanje tim lukama kako bi se osigurao rast i razvoj sustava pomorskoputničkih luka.This paper analyses the sustainable development of sea passenger ports in the Republic of Croatia until 2012. A model of growth was used in order to define the main characteristics and determinants of sea passenger ports. The purpose of the paper was to present a scientifically-based formulation of sustainable development analysis of sea passenger ports in Croatia, based on the evaluation and analysis of relevant elements and resulting direct rates. The authors in their scientific research and presentation used a various combination of scientific methods like: analysis and syntheses method, concretization method, comparative method and modeling method (growth matrix). The main scientific hypothesis is: By using scientifically based acknowledgments about functioning and management of sea passenger port system it is possible to suggest a model, measurements and activities for the rational management of sea passenger ports in Croatia in order to secure their growth and development. This scientific hypothesis was confirmed by the direct rates of growth of the model elements

Expression patterns of <i>GhMDHs</i> in vegetative tissues of <i>G</i>. <i>hirsutum</i>.

<p>A. Quantitative RT-PCR and semi-quantitative PCR results. B. RNA sequence data analysis results. Sequence Read Archive available under accession numbers SRX797899, SRX797900, SRX797901, SRX797903, SRX797904 and SRX797918 were retrieved from the public repository database for expression analysis in cotton roots, stems, leaves, petals, stamens and 10 DPA fibers, respectively. The color bar in the top of the left column of the heat map represents the relative signal intensity, while that in the top of right column indicates the FPKM-normalized log² transformed counts.</p

Orthologous MDH genes pairs identified between <i>G</i>. <i>arboretum</i>, <i>G</i>. <i>raimondii</i> and <i>G</i>. <i>hirsutum</i>.

<p>The chromosomes of <i>G</i>. <i>arboretum</i> (Ga1-Ga13), <i>G</i>. <i>raimondii</i> (Gr1-Gr13), and <i>G</i>. <i>hirsutum</i> (A1-A13 and D1-D13) are filled with light peach, green and ice blue color, respectively. The orthologous MDH genes are connected by black, red and green lines, while segmental duplicated MDH genes are connected by purple line. The duplicated gene pairs and orthologous relationships between the genomes are represented by Circos figure.</p

Phylogenetic relationships, gene structure and conserved motif analysis of MDH genes in <i>G</i>. <i>arboretum</i>, <i>G</i>. <i>raimondii</i>, and <i>G</i>. <i>hirsutum</i>.

<p>A. The unrooted phylogenetic tree was constructed using MEGA 6.0 with the Neighbor-Joining method, and a bootstrap analysis was performed with 1000 replicates. The MDH genes from <i>G</i>. <i>arboretum</i>, <i>G</i>. <i>raimondii</i>, and <i>G</i>. <i>hirsutum</i> were highlighted in red, green and black dots, respectively. The branches of each subgroup are presented in a specific color. M-MDH, Px-MDH, Pd-MDH, Ch-MDH, and C-MDH indicate mitochondrial, peroxisomal, plastidial, chloroplastic and cytoplasmic MDH subgroup, respectively. B. The exon-intron structures of MDH genes from <i>G</i>. <i>arboretum</i>, <i>G</i>. <i>raimondii</i>, and <i>G</i>. <i>hirsutum</i>. The green boxes, and the gray line indicates exons and introns. C. Different motifs are indicated in different colors. The regular expression and sequences of motifs 1–10 are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166341#pone.0166341.s005" target="_blank">S3 Table</a>.</p

A conserved glycine motif and a catalytic active site were present in <i>G</i>. <i>arboretum</i> (A) <i>G</i>. <i>raimondii</i> (B) and <i>G</i>. <i>hirsutum</i> (C).

<p>The highly conserved amino acids are indicated by <i>arrows</i>. Two inversions of the second and third conserved residue are marked a <i>rectangle</i>. The sequence position of each domain and the information content measured in bits are shown on the x and y axes, respectively.</p

Putative regulatory <i>cis</i>-elements in the PLD gene promoters of cotton.

<p>The relative positions of elements are labeled with capital letters in the figure and are denoted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156281#pone.0156281.s009" target="_blank">S6 Table</a>. The hormone response <i>cis</i>-elements are in orange, the stress response <i>cis</i>-elements are in blue, and the high transcription <i>cis</i>-elements are in red.</p

Expression patterns of <i>GhMDHs</i> in developing fibers of <i>G</i>. <i>hirsutum</i>.

<p>A. Quantitative RT-PCR and semi-quantitative PCR results. B. RNA sequence data analysis results. Sequence Read Archive available under accession numbers SRX797909, SRX797917, SRX797918, SRX797919 and SRX797920; this information was retrieved from a public repository database for expression analysis in developing fibers (0, 5, 10, 20 and 25 DPA, respectively). The color bar at the top left column of the heat map represents the relative signal intensity, while that at the top right column heat map indicates the FPKM-normalized log² transformed counts.</p

Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors

<div><p>In this study, 40 phospholipase D (PLD) genes were identified from allotetraploid cotton <i>Gossypium hirsutum</i>, and 20 PLD genes were examined in diploid cotton <i>Gossypium raimondii</i>. Combining with 19 previously identified <i>Gossypium arboreum</i> PLD genes, a comparative analysis was performed among the PLD gene families among allotetraploid and two diploid cottons. Based on the orthologous relationships, we found that almost each <i>G</i>. <i>hirsutum PLD</i> had a corresponding homolog in the <i>G</i>. <i>arboreum</i> and <i>G</i>. <i>raimondii</i> genomes, except for <i>GhPLDβ3A</i>, whose homolog <i>GaPLDβ3</i> may have been lost during the evolution of <i>G</i>. <i>arboreum</i> after the interspecific hybridization. Phylogenetic analysis showed that all of the cotton PLDs were unevenly classified into six numbered subgroups: α, β/γ, δ, ε, ζ and φ. An N-terminal C2 domain was found in the α, β/γ, δ and ε subgroups, while phox homology (PX) and pleckstrin homology (PH) domains were identified in the ζ subgroup. The subgroup φ possessed a single peptide instead of a functional domain. In each phylogenetic subgroup, the PLDs showed high conservation in gene structure and amino acid sequences in functional domains. The expansion of GhPLD and GrPLD gene families were mainly attributed to segmental duplication and partly attributed to tandem duplication. Furthermore, purifying selection played a critical role in the evolution of PLD genes in cotton. Quantitative RT-PCR documented that allotetraploid cotton PLD genes were broadly expressed and each had a unique spatial and developmental expression pattern, indicating their functional diversification in cotton growth and development. Further analysis of <i>cis</i>-regulatory elements elucidated transcriptional regulations and potential functions. Our comparative analysis provided valuable information for understanding the putative functions of the PLD genes in cotton fiber.</p></div

Image1_EMILIN2 is associated with prognosis and immunotherapy in clear cell renal cell carcinoma.pdf

Background: EMILIN2 is a platelet-associated elastin that regulates angiogenesis. It has recently been found to play an essential role in various tumors. Nevertheless, the mechanism of action of EMILIN2 in clear cell renal cell carcinoma (ccRCC) remains unclear.Methods: Samples from 33 cancers were obtained from UCSC Xena and The Cancer Genome Atlas (TCGA) database. The relationship between EMILIN2 expression and the clinicopathological characteristics and immune infiltration of ccRCC was investigated. Nonnegative matrix factorization (NMF) was used to classify ccRCC patients. A multigene risk prediction model of ccRCC was constructed using LASSO regression and multivariate regression analysis. A nomogram survival probability prediction map and calibration curve were constructed based on clinical information.Results: EMILIN2 is significantly overexpressed in ccRCC, a phenomenon that is associated with poor prognosis. Meanwhile, EMILIN2 expression is closely related to tumor immune infiltration in ccRCC. Patients with clear cell renal cell carcinoma were divided into two subtypes using NMF, with subtype 2 showed poor prognosis. Next, we established a risk score model for ccRCC based on the common differentially expressed genes (DEGs) between subtypes and groups based on EMILIN2 expression. The results indicated poor prognosis in the high-risk group in the training set and were confirmed in the validation set.Conclusion: Our findings suggest that EMILIN2 expression is closely associated with immune infiltration in ccRCC. EMILIN2 expression is negatively correlated with the prognosis of ccRCC patients. Here, we developed a tool that could predict the prognosis of ccRCC patients.</p

Syntenic relationship of the PLD genes in <i>G</i>. <i>hirsutum</i>.

<p>The syntenic relationships between <i>GhPLDxAs</i> and <i>GhPLDxDs</i> according to the CottonGen database are illustrated using the program Circos. Tandem and segmental duplicated PLD genes are connected by red and blue lines. The chromosomes of <i>G</i>. <i>hirsutum</i> are designated as GhA01—GhA13 and GhD01—GhD13.</p