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Gene tree species tree reconciliation with gene conversion [article]

Damir Hasic, Eric Tannier
2017 arXiv   pre-print
If a gene that is transfered replaces another gene, then we have transfer with replacement, which is to transfer what conversion is to duplication (see Hasić and Tannier (2017) for NP-hardness proof,  ... 
arXiv:1703.08950v2 fatcat:uzxr62mpyffyzezbytvqp7sxau

Gene tree species tree reconciliation with gene conversion

Damir Hasić, Eric Tannier
2019 Journal of Mathematical Biology  
If a gene that is transfered replaces another gene, then we have transfer with replacement, which is to transfer what conversion is to duplication (see Hasić and Tannier (2017) for NP-hardness proof,  ... 
doi:10.1007/s00285-019-01331-w pmid:30767052 fatcat:qy6d5sfx25eljkmzv36btp67ge

Criteria for Solar Car Optimized Route Estimation

Mehrija Hasicic, Damir Bilic, Harun Siljak
2017 Microprocessors and microsystems  
This paper gives a thorough overview of Solar Car Optimized Route Estimation (SCORE), novel route optimization scheme for solar vehicles based on solar irradiance and target distance. In order to conduct the optimization, both data collection and the optimization algorithm itself have to be performed using appropriate hardware. Here we give an insight to both stages, hardware and software used and present some results of the SCORE system together with certain improvements of its fusion and
more » ... ization criteria. Results and the limited applicability of SCORE are discussed together with an overview of future research plans and comparison with state-of-the-art solar vehicle optimization solutions.
doi:10.1016/j.micpro.2017.05.005 fatcat:2d5oeaol4nahpczsuigvczditq

Prognostic Parameters of Acute Myeloid Leukaemia at Presentation

Azra Jahic, Ermina Iljazovic, Samira Hasic, Aida Arnautovic, Damir Sabitovic, Semir Mesanovic, Haris Sahovic, Vlastimir Simendic
2017 Medicinski arhiv  
The treatment response and outcome in acute myeloid leukaemia (AML) is heterogeneous. Aim: To analyze the prognostic parameters of AML at presentation. Methods: The total sample of 44 AML patients was analyzed on the basis of age <55 and ≥55 years, sex, WBC count <50x10/ 9 /l and ≥50x10/ 9 /l, the Hb concentration <100 g/l and ≥100 g/l, PLT count <100x10/ 9 /l and ≥100x10/ 9 /l, Karnofsky score <60% and >60%, cytogenetics, CD56 expression, morphological type and types of treatment (standard and
more » ... reduced induction chemotherapy, high-dose chemotherapy/stem cell transplantationautologous and HLA matched, related, allogeneic, together and separately). Results: The age <55 years, Karnofsky score >60% and standard induction chemotherapy statistically correlated with the higher complete remission (CR) rates, longer relapse free survival (RFS), lower relapse rate (RR), and longer overall survival (OS) (p<0.01). The difference in terms of CR and RR between the sexes were not statistically significant (p<0.05), however women had statistically lower OS comparing to men (9.71±4.54 months vs. 38.03±9.17 months) (p<0.01). WBC count ≥ 50x10/ 9 /l and the Hb concentration <100 g/l statistically correlated with shorter OS (p<0.05), while the WBC count ≥50x10/ 9 /l statistically correlated with shorter RFS (p<0.05). The PLT count <100x10/ 9 /l and ≥100x10/ 9 /l was not found as prognostically significant for CR, RR, RFS, and OS (p<0.05). In comparison to the standard induction chemotherapy, both types of high dose chemotherapy/stem cell transplantation (HDT/SCT) (10/22), together and separately, resulted in longer RFS, lower RR, and longer OS (p<0.05). The frequency of cytogenetic risk was intermediate 81.6%, unfavorable 13.2%, and favorable 5.3%, respectively. CD56 + expression statistically correlated with the lower PLT count, higher RR, shorter RFS, and shorter OS (p<0.05). Statistical analysis of the cytogenetic risk and morphological types of AML were not possible due to the small number of patients in stratified groups. Conclusions: Female sex, the WBC count >50x10/ 9 /l, the concentration of Hb <100 g/l, and CD56 + expression, at presentation of AML, should be considered as parameters of adverse risk, especially in latter decisions considering post-remission treatment with HDT/SCT.
doi:10.5455/medarh.2017.71.20-24 pmid:28428668 pmcid:PMC5364786 fatcat:v6nyxwdi7vaw7ih4dwmwlbzga4

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations [article]

Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Gueguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier, David Parsons
2019 biorxiv/medrxiv   pre-print
Motivation: Gene and species tree reconciliation methods can be used to root gene trees and correct uncertainties that are due to scarcity of signal in coming from phylogenetic methods based uniquely on multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack of performance on certain functions, or usability for biologists. Results: We present Treerecs, a phylogenetic software based on duplication-loss
more » ... on. Treerecs is simple to install and to use, fast, versatile, with a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. Availability: Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from .
doi:10.1101/782946 fatcat:fqfsawdrrvfd5as3ublscpnaaq

An Exact Two-Phase Method For Optimal Camera Placement In Art Gallery Problem

Adis Alihodzic, Sead Delalić, Damir Hasic
2020 Proceedings of the 2020 Federated Conference on Computer Science and Information Systems  
It is well-known that determining the optimal number of guards which can cover the interior of a simple nonconvex polygon presents an NP-hard problem. The optimal guard placement can be described as a problem which seeks for the smallest number of guards required to cover every point in a complex environment. In this paper, we propose an exact twophase method as well as an approximate method for tackling the mentioned issue. The proposed exact approach in the first phase maps camera placement
more » ... oblem to the set covering problem, while in the second phase it uses famous state-of-the-art CPLEX solver to address set covering problem. The performance of our combined exact algorithm was compared to the performance of the approximate one. According to the results presented in the experimental analysis, it can be seen that the exact approach outperforms the approximate method for all instances.
doi:10.15439/2020f79 dblp:conf/fedcsis/AlihodzicDH20 fatcat:n35pwh562rewxduwbyqb7gupky

Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Damir Hasić, Eric Tannier
2019 Journal of combinatorial optimization  
However, note that duplications with replacement, i.e. conversions, were recently introduced by Hasić and Tannier (2017) .  ... 
doi:10.1007/s10878-019-00396-z fatcat:2tkm4snj6vemdgsykbbhv7scfe

Influence of Malondialdehyde and Matrix Metalloproteinase-9 on Progression of Carotid Atherosclerosis in Chronic Renal Disease with Cardiometabolic Syndrome

Senija Rašić, Damir Rebić, Sabaheta Hasić, Ismar Rašić, Marina Delić Šarac
2015 Mediators of Inflammation  
Objective was to assess whether the concentration of malondialdehyde (MDA) as a marker of lipid peroxidation and serum concentration of matrix metalloproteinase-9 (MMP-9) are involved in the process of atherosclerosis in chronic kidney disease (CKD) patients nondialysis-dependent and those on peritoneal dialysis (PD), both with signs of cardiometabolic syndrome (CMS). Thirty CKD and 22 PD patients were included in a study. All observed patients were divided into three subgroups depending on the
more » ... degree of atherosclerotic changes in the carotid arteries (CA). Severity of atherosclerotic changes in the CA was evaluated by ultrasonography. We confirmed significantly lower level of serum MDA throughout all the stages of atherosclerosis in PD patients compared with observed CKD patients (P<0.05) and increased serum concentration of MDA and MMP-9 with the progression of severity atherosclerotic changes in both groups of patients. The multiple regression analysis revealed that MDA and MMP-9 are significant predictors of changes in IMT-CA CKD patients (P<0.05) and plaque score on CA in these patients (P<0.05). The results suggest that MDA and MMP-9 could be mediators of CKD-related vascular remodeling in CMS.
doi:10.1155/2015/614357 pmid:26538831 pmcid:PMC4619965 fatcat:3sa6pveix5hshg2oqmyqiky4v4

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus (+10 others)
2018 Bioinformatics  
Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we
more » ... r a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. Availability: Contact: Supplementary information: There is no supplementary data associated with this publication.
doi:10.1093/bioinformatics/bty389 pmid:29762653 fatcat:4x5yhdsxvzex5fe3vvc3mml6gy

Putting the SC in SCORE: Solar Car Optimized Route Estimation and Smart Cities [article]

Mehrija Hasicic, Harun Siljak
2019 arXiv   pre-print
Acknowledgements We thank Mr Damir Bilic (Mlardalen University, Sweden) for his invaluable contribution in developing SCORE, and useful discussions in preparation of this chapter.  ... 
arXiv:1911.08940v1 fatcat:6dm5pdibpbhdlgjrwpcyepsocm

The Institutionalisation of Political Science in Post-Yugoslav States: Continuities and New Beginnings [chapter]

Davor Boban, Ivan Stanojević
2021 Opportunities and Challenges for New and Peripheral Political Science Communities  
Acknowledgement The authors would like to acknowledge and thank Professor Gabriella Ilonszki from Budapest's Corvinus University, Professor Dušan Pavlović from the University of Belgrade, Associate Professor Damir  ...  Kapidžić from the University of Sarajevo, and Assistant Professor Jasmin Hasić from the Sarajevo School of Science and Technology, for their invaluable comments and information regarding the state of  ... 
doi:10.1007/978-3-030-79054-7_4 fatcat:nywckjph6vbnfmkfwiqtj3lbzi


Nusreta Kepeš
2013 Zbornik radova Islamskog pedagoškog fakulteta u Bihaću  
potrebno analizirati političku propagandu kao djelovanje koje ima za cilj sadržaj političkog karaktera. 2 Besim Spahić, Kontroverze propagandnog djelovanja, NIŠRO Oslobođenje, Sarajevo, 1987. g., str. 92. 2 Damir  ...  u pokretima i kretanju, pravilnog odnosa prema ishrani i načinu života,11 Psihofizička sposobnost djece drugog razreda devetogodišnje osnovne škole da prate nastavu, seminarski rad studentice Medine Hasić  ... 
doi:10.52535/27441695.2013.6.121-151 fatcat:6cm5v3alwjhundbq225mimz25m

Normierungsprozesse in der modernen bosnischen Sprache

Azra Kmetas
2011 unpublished
Potom je Novka Agić ponovo imenovana na mjesto direktora, dok je za njenu zamjenicu imenovana Jasminka Hasić -Slijepčević. 31.  ...  određene preporuke, proći sigurnosne provjere itd, i ne radi se o velikom broju ljudi, a među onima koji su prošli svu potrebnu proceduru su spomenuti glumac Alban Ukaj, rukometaš Bojan Skoko, fudbaler Damir  ... 
doi:10.25365/thesis.15699 fatcat:nuwapjowg5b2paq6mfs3wou4zq