Involvement of MicroRNA Families in Cancer

Collecting representative sets of cancer microRNAs (miRs) from the literature we show that their corresponding families are enriched in sets of highly interacting miR families. Targeting cancer genes on a statistically significant level, such cancer miR families strongly intervene with signaling pathways that harbor numerous cancer genes. Clustering miR family-specific profiles of pathway intervention, we found that different miR families share similar interaction patterns. Resembling corresponding patterns of cancer miRs families, such interaction patterns may indicate a miR family’s potential role in cancer. As we find that the number of targeted cancer genes is a naı¨ve proxy for a cancer miR family, we design a simple method to predict candidate miR families based on gene-specific interaction profiles. Assessing the impact of miR families to distinguish between (non-)cancer genes, we predict a set of 84 potential candidate families, including 75% of initially collected cancer miR families. Further confirming their relevance, predicted cancer miR families are significantly indicated in increasing, non-random numbers of tumor types

Genome-Wide Associations of Signaling Pathways in Glioblastoma Multiforme

Background: eQTL analysis is a powerful method that allows the identification of causal genomic alterations, providing an explanation of expression changes of single genes. However, genes mediate their biological roles in groups rather than in isolation, prompting us to extend the concept of eQTLs to whole gene pathways. Methods: We combined matched genomic alteration and gene expression data of glioblastoma patients and determined associations between the expression of signaling pathways and genomic copy number alterations with a non-linear machine learning approach. Results: Expectedly, over-expressed pathways were largely associated to tag-loci on chromosomes with signature alterations. Surprisingly, tag-loci that were associated to under-expressed pathways were largely placed on other chromosomes, an observation that held for composite effects between chromosomes as well. Indicating their biological relevance, identified genomic regions were highly enriched with genes having a reported driving role in gliomas. Furthermore, we found pathways that were significantly enriched with such driver genes. Conclusions: Driver genes and their associated pathways may represent a functional core that drive the tumor emergence and govern the signaling apparatus in GBMs. In addition, such associations may be indicative of drug combinations for the treatment of brain tumors that follow similar patterns of common and diverging alterations

Molekularna dijagnostika i serološka istraživanja pestivirusa u ovaca.

In this research, the virological and serological presence of pestiviruses, such as border disease virus (BDV) was investigated in a sheep in the Central and Eastern Black Sea Regions of Turkey. The study material consisted of 40 organ materials collected from 13 aborted lambs, which were suspected to have pestiviruses, BDV and Bovine Viral Diarrhoea Virus (BVDV). Viral nucleic acids were investigated by using the reverse transcription polymerase chain reaction (RT-PCR). Nine of 13 aborted lambs (69.2%) and 24 of 40 organ samples (60%) obtained from those sheep were BDV RNA positive, whilst all the animals and organ samples were BVDV-RNA negative. Serum samples collected from 401 randomly selected sheep were investigated for pestivirus antibodies using competitive ELISA (cELISA) and the serum microneutralisation test (SNT) using BVDV-NADL strain. Seropositivity was found in between 7.22 and 74.38% with cELISA and 4.81 and 67.76% with SNT. Seropositivity rates in Amasya and Tokat provinces were higher than in Samsun and Giresun. The obtained data indicated that pestivirus infection in sheep is widespread in the Central and Eastern Black Sea Region.U radu su prikazana virološka i serološka istraživanja pestivirusa odnosno borderske bolesti u ovaca na središnjem i istočnom području Crnoga mora u Turskoj. Ukupno je bilo pretraženo 40 uzoraka tkiva različitih organa uzetih od 13 pobačenih plodova pod sumnjom da je uzročnik bio virus borderske bolesti ili virus virusnog proljeva goveda. Uzorci su bili pretraženi na prisutnost virusne nukleinske kiseline lančanom reakcijom polimerazom uz prethodnu reverznu transkripciju (RT-PCR). Devet od 13 pobačenih plodova (69,2%) i 24 od 40 uzoraka tkiva organa (60%) sadržavalo je RNA virusa borderske bolesti. Svi pretraženi uzorci bili su negativni na virus virusnoga proljeva. Uzorci seruma nasumce prikupljeni od 401 ovce bili su pretraženi na prisutnost specifičnih protutijela uporabom kompetitivnoga imunoenzimnoga testa (cELISA) i serum neutralizacijskoga testa (SNT) sa sojem NADL virusa virusnoga proljeva goveda. Ustanovljeno je da sepostotak serološki pozitivnih cELISA-om kretao od 7,22 do 74,38%, a SNT-om od 4,81 do 67,76%. Postotak serološki pozitivnih životinja u provincijama Amasya i Tokat bio je veći nego u provincijama Samsun i Giresun. Rezultati upućuju na zaključak da su pestivirusne zaraze rasprostranjene u ovaca na središnjem i istočnom području Crnoga mora

Computational modeling of growth: systemic and pulmonary hypertension in the heart

We introduce a novel constitutive model for growing soft biological tissue and study its performance in two characteristic cases of mechanically induced wall thickening of the heart. We adopt the concept of an incompatible growth configuration introducing the multiplicative decomposition of the deformation gradient into an elastic and a growth part. The key feature of the model is the definition of the evolution equation for the growth tensor which we motivate by pressure-overload-induced sarcomerogenesis. In response to the deposition of sarcomere units on the molecular level, the individual heart muscle cells increase in diameter, and the wall of the heart becomes progressively thicker. We present the underlying constitutive equations and their algorithmic implementation within an implicit nonlinear finite element framework. To demonstrate the features of the proposed approach, we study two classical growth phenomena in the heart: left and right ventricular wall thickening in response to systemic and pulmonary hypertension

Effects of E‐textbook Instructor Annotations on Learner Performance

With additional features and increasing cost advantages, e-textbooks are becoming a viable alternative to paper textbooks. One important feature offered by enhanced e-textbooks (e-textbooks with interactive functionality) is the ability for instructors to annotate passages with additional insights. This paper describes a pilot study that examines the effects of instructor e-textbook annotations on student learning as measured by multiple-choice and open-ended test items. Fifty-two college students in a business course were randomly assigned either a paper or an electronic version of a textbook chapter. Results show that the e-textbook group outperformed the paper textbook group on the open-ended test item, while both groups performed equally on the multiple-choice subject test. These results suggest that the instructional affordances that an interactive e-textbook provides may lead to higher-level learning

Astronomical Site Selection for Turkey Using GIS Techniques

A site selection of potential observatory locations in Turkey have been carried out by using Multi-Criteria Decision Analysis (MCDA) coupled with Geographical Information Systems (GIS) and satellite imagery which in turn reduced cost and time and increased the accuracy of the final outcome. The layers of cloud cover, digital elevation model, artificial lights, precipitable water vapor, aerosol optical thickness and wind speed were studied in the GIS system. In conclusion of MCDA, the most suitable regions were found to be located in a strip crossing from southwest to northeast including also a diverted region in southeast of Turkey. These regions are thus our prime candidate locations for future on-site testing. In addition to this major outcome, this study has also been applied to locations of major observatories sites. Since no goal is set for \textit{the best}, the results of this study is limited with a list of positions. Therefore, the list has to be further confirmed with on-site tests. A national funding has been awarded to produce a prototype of an on-site test unit (to measure both astronomical and meteorological parameters) which might be used in this list of locations.Comment: 17 pages, 10 figures, accepted by Experimental Astronom

Ab Initio Structural Energetics of Beta-Si3N4 Surfaces

Motivated by recent electron microscopy studies on the Si3N4/rare-earth oxide interfaces, the atomic and electronic structures of bare beta-Si3N4 surfaces are investigated from first principles. The equilibrium shape of a Si3N4 crystal is found to have a hexagonal cross section and a faceted dome-like base in agreement with experimental observations. The large atomic relaxations on the prismatic planes are driven by the tendency of Si to saturate its dangling bonds, which gives rise to resonant-bond configurations or planar sp^2-type bonding. We predict three bare surfaces with lower energies than the open-ring (10-10) surface observed at the interface, which indicate that non-stoichiometry and the presence of the rare-earth oxide play crucial roles in determining the termination of the Si3N4 matrix grains.Comment: 4 Pages, 4 Figures, 1 tabl

Risk Assessment of Human Exposure to Pesticides in Food

U ovome preglednom radu prikazane su metode procjene rizika od akutne i kronične izloženosti ljudi ostacima pesticida unesenih hranom. U hrani su često prisutni ostaci više različitih pesticida. Međutim rizik od istodobne izloženosti ostacima različitih pesticida nije moguće utvrditi jer trenutačno ne postoji međunarodno prihvaćeni postupak kumulativne procjene rizika. Stoga se procjena rizika temelji na toksikološkoj procjeni pojedinačnog spoja u određenoj vrsti hrane. Za izračun akutnog unosa najčešće se upotrebljava tzv. međunarodna procjena kratkoročnog unosa (engl. international estimation of short-term intake, IESTI). Model izračuna IESTI temelji se na tzv. metodi najgoreg scenarija uz pretpostavke da će osoba u kratkom vremenu konzumirati veliku količinu hrane koja sadržava najveći određeni maseni udio pesticida te uzimajući u obzir i nehomogenost distribucije ostataka pesticida u hrani. Kronična izloženost ostacima pesticida procjenjuje se uz primjenu tzv. determinističkog modela koji je analogan izračunu maksimalnoga dnevnog unosa.This review presents methods for the assessment of acute and chronic risk from pesticide residues in food. Multiple pesticide residues can often be found in food. Currently, there is no internationally accepted procedure for the assessment of cumulative exposure to multiple pesticide residues in food. Therefore, risk assessment is based on toxicological evaluation of single compounds in a food matrix. The international estimation of short-term intake model (IESTI) has been used to calculate acute intake. IESTI is based on "the worst-case scenario" and addresses the possibility that consumers sometimes eat large amounts of a food item, and such a large amount might contain residues at highest levels. However, it should take into account uneven distribution of pesticide residues in food. Chronic exposure is based on a deterministic approach, analogous to the calculation of the theoretical maximum daily intake

Effect of pathologic fractures on survival in multiple myeloma patients: a case control study

<p>Abstract</p> <p>Background</p> <p>Multiple Myeloma (MM) is a B cell neoplasm characterized by the clonal proliferation of plasma cells. Skeletal complications are found in up to 80% of myeloma patients at presentation and are major cause of morbidity.</p> <p>Methods</p> <p>49 patients were enrolled with MM admitted to Black Sea Technical University Hospital between 2002–2005. Pathologic fractures (PFs) were determined and the patients with or without PF were followed up minumum 3 years for survival analysis.</p> <p>Results</p> <p>PF was observed in 24 patients (49%) and not observed in 25 patients (51%). The risk of death was increased in the patients with PF compared with patients who had no fractures. While overall survival was 17.6 months in the patients with PFs, it was 57.3 months in the patients with no PFs.</p> <p>Conclusion</p> <p>These findings suggest that PFs may induce reduced survival and increased mortality in the MM patients, however, larger sample size is essential to draw clearer conclusions added to these data.</p

Postresectional lung injury in thoracic surgery pre and intraoperative risk factors: a retrospective clinical study of a hundred forty-three cases

<p>Abstract</p> <p>Introduction</p> <p>Acute respiratory dysfunction syndrome (ARDS), defined as acute hypoxemia accompanied by radiographic pulmonary infiltrates without a clearly identifiable cause, is a major cause of morbidity and mortality after pulmonary resection. The aim of the study was to determine the pre and intraoperative factors associated with ARDS after pulmonary resection retrospectively.</p> <p>Methods</p> <p>Patients undergoing elective pulmonary resection at Adnan Menderes University Medical Faculty Thoracic Surgery Department from January 2005 to February 2010 were included in this retrospective study. The authors collected data on demographics, relevant co-morbidities, the American Society of Anesthesiologists (ASA) Physical Status classification score, pulmonary function tests, type of operation, duration of surgery and intraoperative fluid administration (fluid therapy and blood products). The primary outcome measure was postoperative ARDS, defined as the need for continuation of mechanical ventilation for greater than 48-hours postoperatively or the need for reinstitution of mechanical ventilation after extubation. Statistical analysis was performed with Fisher exact test for categorical variables and logistic regression analysis for continuous variables.</p> <p>Results</p> <p>Of one hundred forty-three pulmonary resection patients, 11 (7.5%) developed postoperative ARDS. Alcohol abuse (p = 0.01, OR = 39.6), ASA score (p = 0.001, OR: 1257.3), resection type (p = 0.032, OR = 28.6) and fresh frozen plasma (FFP)(p = 0.027, OR = 1.4) were the factors found to be statistically significant.</p> <p>Conclusion</p> <p>In the light of the current study, lung injury after lung resection has a high mortality. Preoperative and postoperative risk factor were significant predictors of postoperative lung injury.</p