Periimplantitis je jedan od kasnih neuspjeha implantoloske terapije. Za potrebe lijecenja ovog upalnog procesa razvijen je CIST protokol (engl. cumulative interceptive supportive therapy) koji sadrži 5 mjera, od A do E. Navedene se mjere primjenjuju u „paketima“ ovisno o težini klinicke slike. Prikazan je slucaj pacijenta nepusaca starosti 38 god. koji se 4 mjeseca nakon ugradnje implantata javio zbog krvarenja i neugodnog mirisa u podrucju oseointegriranog implantata postavljenog na mjestu zuba 36. Unatoc trendovima koji prednost daju primarno kirurskom pristupu lijecenju periimplantitisa, apsolutno je potrebno je pridržavati se CIST protokola. U njegovom provođenju znacajnu ulogu bi mogli igrati sustavi za svjetlosno aktiviranu dezinfekciju koji vjerojatno kompenziraju nemogucnost potpunog uklanjanja biofilma s povrsine implantata.

Motivation: Despite recent advances in algorithms design to characterize structural variation using high‐throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects. There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi‐sample data to “collectively” obtain a very high coverage dataset to accurately find insertions common in a given population. Result: Here, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one‐end‐anchored sequences to small‐scale de novo assemblies of unmapped reads, and conducting strand‐aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects. Availability and implementation: Pamir is available at https://github.com/vpc‐ccg/pamir. Contact: fhach@{sfu.ca, prostatecentre.com} or calkan@cs.bilkent.edu.tr Supplementary information: Supplementary data are available at Bioinformatics online.

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection. Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

Predmet istraživanja rada upravljanje je zasticenim prirodnim podrucjima u Bosni i Hercegovini sa svrhom iznalaženja modela održivog upravljanja

We investigate the global asymptotic stability and Naimark-Sacker bifurcation of the dierence equation xn+1 = F bxnxn 1 +cx 2 1 +f ; n = 0; 1;:::

The rural population in Bosnia and Herzegovina (BH), which constitutes more than half of the total population, experienced serious incidences of extreme weather events in the past two decades. This part of the population is vulnerable to climate change due to significant dependence on agriculture as a climate-sensitive livelihood option. However, the source of their vulnerability is due not only to the extent and magnitude of these extreme climate events, but also to the internal status within the vulnerable systems before the occurrence of such events. In order to explore the different dimensions of vulnerability, we used a set of 20 indicators to quantitatively assess the vulnerability of the rural population to climate change at the local level in BH. Two summarizing and two weighting methods were applied to assess vulnerability—Equal weights (EW) and principal component analysis (PCA). Based on the results obtained, we concluded that the current socio-economic conditions and the increased environmental pressure as a result of the present human-environment interactions are the main determinants of vulnerability in most vulnerable municipalities, rather than the degree to which these municipalities are exposed to significant climatic variations. Most vulnerable municipalities are located across the north, with a gradual decrease in vulnerability towards the central, north, and east of the country. Vulnerability increases again from here towards the south of the country. The number of municipalities classified as the highest and highly vulnerable increased when the second summarizing method and weighted indicators were used. However, the general geographic distribution of vulnerability did not change substantially compared to the first method. The approaches used in this study provide some valuable results at the local level, and are presented in a way that is practical for decision-making processes and may serve as a base for further research when designing effective adaptation and mitigation strategies, especially in the regions with similar climatic and socio-economic conditions.

We study the beginning of the Taylor tower, supplied by manifold calculus of functors, for the space of r-immersions, which are immersions without r-fold self-intersections. We describe the first r layers of the tower and discuss the connectivities of the associated maps. We also prove several results about r-immersions that are of independent interest.