55 research outputs found
HeatMapper Expansion
No full textExpansion of an existing visualization tool for genomic data.Software TechnologyElectrical Engineering, Mathematics and Computer Scienc
Predict Radiotherapy Plan Quality
No full textA person with cancer has several treatment options. One of which is radiotherapy. Radiotherapy is treatment of cancer with radiation. To minimize the damage to healthy tissue, radiation is applied from several directions into the body. When treating cancer with radiotherapy, the organs nearby the tumor are at high risk of getting damaged. In the treatment plan the dose to the organs at risk has to be balanced with the dose given to the target. These calculations are nowadays done by medical personnel. Although a lot of treatments succeed, without much damage to healthy tissue, a lot of treatments do serious damage to the organs at risk. Can treatment plans be optimized in terms of organ sparing? To reach optimization, several methods have been executed in order to create groups within a patient set. 115 patients of prostate cancer have been analyzed using Principal Component Analysis and Agglomerative Clustering. The data consist of Overlap Volume Histogram values of the bladder and rectum in a CSV file. Each CSV file contains 201 values. These CSVs are used as an input for both methods. This led to several figures as results. The principal component analysis showed that 80% of the data is covered by the first principal component and 92% by the first and second. Also, a scatterplot has been made, which shows the transformed data. This scatterplot shows no subgroups can be identified with the bladder and rectum data of the patient. The Agglomerative Clustering method results in six plots. A variation in linkages and connectivity has been used, but all six led to no clear distinction within the data. These results led to the conclusion that no subgroups are distinguishable based only on OVH data and no prediction can be made that optimizes radiotherapy plans based solely on OVH data of patients.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc
Existence of global solutions for a multidimensional Boussinesq-type equation with supercritical initial energy
No full text1st International Conference on Analysis and Applied Mathematics (ICAAM) -- OCT 18-21, 2012 -- Gumushane, TURKEYIn this work, global weak solutions of the multidimensional Boussinesq-type equation with power type nonlinearity gamma vertical bar u vertical bar(p), gamma > 0 and supercritical initial energy is given by potential well method. Classical energy methods can not guarantee the global existence for this type of nonlinearity. As is known the functional I (u) defined for potential well method includes only the initial displacement, and by use of sign invariance of this functional one can only prove the global existence for critical and subcritical initial energy. In the case of supercritical initial energy such a functional fails to prove the global existence. A new functional is defined, which contains not only initial displacement, but also initial velocity.Sci & Technol Res Council Turkey (TUBITAK),Gumushane Univ,Fatih Uni
SURGICAL MANAGEMENT OF TEMPOROMANDIBULAR JOINT ANKYLOSIS: INITIAL EXPERIENCES
No full textObjective: The aim of this study is to introduce our initial clinical experience in the operative management of temporomandibular joint (TMJ) ankylosis. Study design: This retrospective study assessed 8 patients with TMJ ankylosis who underwent different surgical procedures. Gap arthroplasty with temporalis muscle and fascia flap repositioning was performed in 6 patients, transport distraction osteogenesis was performed to form a neocondyle in one patient and TMJ prosthesis was replaced in one patient. Patients were followed weekly at first month and at months 3rd, 6th, 12th, and 24th postoperatively. Patients were evaluated in terms of maximum interincisal opening and occlusal stability in each appointment. Results: Mean preoperative Maximum interincisal opening (MIO) of 11 mm (2-14 mm) was improved to 31mm (26-35 mm). All patients had satisfactory mandibular motions 2 years after the operation and reankylosis was not observed in patients. Conclusion: Radiological and clinical evaluation should be carefully performed to avoid possible intraoperative and postoperative complications in the management of TMJ ankylosis. Consistent with the literature, it was observed that temporalis musculofascial flap repositioning is successful to avoid reankylosi
2D Representation of Transcriptomes by t-SNE Exposes Relatedness between Human Tissues
No full textThe GTEx Consortium reported that hierarchical clustering of RNA profiles from 25 unique tissue types among 1641 individuals accurately distinguished the tissue types, but a multidimensional scaling failed to generate a 2D projection of the data that separates tissue-subtypes. In this study we show that a projection by t-Distributed Stochastic Neighbor Embedding is in line with the cluster analysis which allows a more detailed examination and visualization of human tissue relationships.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc
An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia
No full textBackground The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number of genes of the WNT pathway are analyzed by using either gene expression or DNA-methylation profiles for the identification of prognostic markers and potential candidate targets for drug therapy. It is known that mRNA expression is controlled by DNA-methylation and that specific patterns can infer the ability to differentiate biological differences, thus a combined analysis using all WNT annotated genes could provide more insight in the WNT signaling. Approach We created a computational approach that integrates gene expression and DNA promoter methylation profiles. The approach represents the continuous gene expression and promoter methylation profiles with nine discrete mutually exclusive scenarios. The scenario representation allows for a refinement of patient groups by a more powerful statistical analysis, and the construction of a co-expression network. We focused on 268 WNT annotated signaling genes that are derived from the molecular signature database. Results Using the scenarios we identified seven prognostic markers for overall survival and event-free survival. Three genes are novel prognostic markers; two with favorable outcome (PSMD2, PPARD) and one with unfavorable outcome (XPNPEP). The remaining four genes (LEF1, SFRP2, RUNX1, and AXIN2) were previously identified but we could refine the patient groups. Three AML risk groups were further analyzed and the co-expression network showed that only the good risk group harbors frequent promoter hypermethylation and significantly correlated interactions with proteasome family members. Conclusion Our results provide novel insights in WNT signaling in AML, we discovered new and previously identified prognostic markers and a refinement of the patient groups.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc
Elevated expression levels of COX-2, IL-8 and VEGF in colon adenocarcinoma
No full textThere is growing evidence of a connection between inflammation and tumor development and NF-kappa B is an important transcription factor in the inflammation pathway. Genetic approaches have proven the role of NF-kappa B responsive genes in tumorigenesis. The NF-kappa B responsive genes products such as IL-8, VEGF and COX-2 are the key components of angiogenesis. MMP-2 and MMP-9 are playing important roles in the disruption of the extracellular matrix that may contribute to the metastasis of tumor cells. This study aimed to investigate gene expression levels of COX-2, IL-8, VEGF, MMP-2 and MMP-9 in colon tumors. A total of 34 fresh colon carcinoma specimens and paired normal adjacent tissues (NAT) were collected during the surgery and RNA isolations were carried out from specimens. Synthesis of cDNA was carried out from these RNAs with oligo dT18 primers. The transcribed cDNA was used for PCR amplification reactions for the investigated genes with beta-actin being the internal reference via the semi-quantitative RT-PCR method. A statistically significant difference was observed for COX-2, IL-8 and VEGF which were all upregulated in colon tumors compared with adjacent normal tissues (p0.05). Upregulated expression levels of COX-2, IL-8 and VEGF might occur in the early stages of tumorigenesis and detection of these mRNA levels may be beneficial for early diagnosis and management of colon tumors.Dicle University Scientific Research Projects Coordination Unit; [11-VF-76]This work was supported by Dicle University Scientific Research Projects Coordination Unit. Project Number: 11-VF-76
Endoscopic pilonidal sinus treatment (EPSIT) versus sinus laser therapy (SiLaT) for sacrococcygeal pilonidal sinus
No full textIntroduction: New surgical treatment methods are being investigated in sacrococcygeal pilonidal sinus disease. Minimal invasive methods such as endoscopic pilonidal sinus treatment (EPSIT) and sinus laser therapy (SiLaT) have promising results and advantages of laparoscopic surgery. Aim: To compare the efficiency and safety of EPSIT with SiLaT. Material and methods: Seventy-three patients with pilonidal sinus who had undergone EPSIT or SiLaT within 2 years were evaluated retrospectively. Data of patients’ demographics, complications and postoperative course were collected and compared between the two groups. Results: We analyzed seventy-three patients who underwent EPSIT or SiLaT, with a mean age of 23.4 ±8.4 (12–46) years and body mass index (BMI) of 25.5 ±4.5 (18–38) kg/m2. Among them, 36 patients (26 males, ten females) underwent EPSIT and 37 patients (27 males, ten females) underwent SiLaT. Mean operative time was similar for both groups (32.3 ±14.8 vs. 31.0 ±14.8; p = 0.757). Early complications (minimal bleeding) were recorded in 2 patients in the SiLaT group. The duration of analgesic use was significantly lower in the EPSIT group compared to the SiLaT group (1.3 ±0.5 (1–3) vs. 1.9 ±1.1 (1–5); p = 0.005). The mean postoperative time of total wound healing was similar for both groups: 23.6 ±14.7 (12–90) vs. 25.2 ±14.5 (14–90) days (p = 0.385). There was no significant difference in the average time of return to total daily activity (3.4 ±0.9 (2–5) vs. 3.6 ±1.2 (2–7) days, p = 0.679). There were no significant differences between the groups regarding late postoperative complications (recurrence: 7). Conclusions: Both methods have similar early and late complications. The duration of need for analgesic usage was shorter in EPSIT patients
Hypergeometric analysis of tiling-array and sequence data: Detection and interpretation of peaks
No full textProbing protein-deoxyribonucleic acid (DNA) is gaining popularity as it sheds light on molecular mechanisms that regulate the expression of genes. Currently, tiling-arrays and next-generation sequencing technology can be used to measure these interactions. Both methods generate a signal over the genome in which contiguous regions of peaks on the genome represent the presence of an interacting molecule. Many methods do exist to identify functional regions of interest (ROIs) on the genome. However the detection of ROIs are often not an end-point in research questions and it therefore requires data dragging between tools to relate the ROIs to information present in databases, such as gene-ontology, pathway information, or enrichment of certain genomic content. We introduce hypergeometric analysis of tiling-array and sequence data (HATSEQ), a powerful tool that accurately identifies functional ROIs on the genome where a genomic signal significantly deviates from the general genome-wide behavior. HATSEQ also includes a number of built-in post-analyses with which biological meaning can be attached to the detected ROIs in terms of gene pathways and de-novo motif analysis, and provides different visualizations and statistical summaries for the detected ROIs. In addition, HATSEQ has an intuitive graphic user interface that lowers the barrier for researchers to analyze their data without the need of scripting languages. We compared the results of HATSEQ against two other popular chromatin immunoprecipitation sequencing (ChIP-Seq) methods and observed overlap in the detected ROIs but HATSEQ is more specific in delineating the peak boundaries. We also discuss the versatility of HATSEQ by using a Signal Transducer and Activator of Transcription 1 (STAT1) ChIP-Seq data-set, and show that the detected ROIs are highly specific for the expected STAT1 binding motif.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc
Prevalence and characteristics of supernumerary teeth in east-northern Turkish population
No full textObjectives: The aim of the present study was to determine the frequency and the distribution of supernumerary teeth (ST) in patients from east-northern Turkey.Materials and Methods: A retrospective study was performed using panoramic radiographs of 1876 patients [673 females (mean age: 13.05±2.79 years) and 1203 males (mean age: 13.63±3.18 years)] ranging in age from 7 to 34 years (mean age: 13.39±3.05 years). Demographic variables including age and sex, the type, number, eruption status of the ST were recorded. In addition, associated pathologies or complications (displacement, eruption failure, resorption of adjacent tooth, and cyst formation) caused by ST were also recorded. The Pearson chi-squared test was used to determine potential differences between genders.Results: ST were detected in 15 patients (0.75 %). The frequency of males and females with ST was 1.16 % and 0.49 %, respectively (P= 0.944). The most commonly observed ST was premolar (33.33%) followed by mesiodens (26.67%), distomolar (20.0%), lateral (13.33%), paramolar (6.67%), respectively. Most of the ST were found to be unilateral, impacted, and in the maxilla. Complications associated with ST were observed in 20.0% of the patients with ST.Conclusions: The frequency of ST in east-northern Turkish general population was found to be 0.75% with no gender difference (p>0.05). The most commonly observed ST was premolar followed by mesiodens
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