Transrectal ultrasound image processing for brachytherapy applications

In this thesis, we propose a novel algorithm for detecting needles and their corresponding implanted radioactive seed locations in the prostate. The seed localization process is carried out efficiently using separable Gaussian filters in a probabilistic Gibbs random field framework. An approximation of the needle path through the prostate volume is obtained using a polynomial fit. The seeds are then detected and assigned to their corresponding needles by calculating local maxima of the voronoi region around the needle position. In our experiments, we were able to successfully localize over 85% of the implanted seeds. Furthermore, as a regular part of a brachytherapy cancer treatment, patient’s prostate is scanned using a trans-rectal ultrasound probe, its boundary is manually outlined, and its volume is estimated for dosimetry purposes. In this thesis, we also propose a novel semi-automatic segmentation algorithm for prostate boundary detection that requires a reduced amount of radiologist’s input, and thus speeds up the surgical procedure. Saved time can be used to re-scan the prostate during the operation and accordingly adjust the treatment plan. The proposed segmentation algorithm utilizes texture differences between ultrasound images of the prostate tissue and the surrounding tissues. It is carried out in 5 the polar coordinate system and it uses three-dimensional data correlation to improve the smoothness and reliability of the segmentation. Test results show that the boundary segmentation obtained from the algorithm can reduce manual input by the factor of 3, without significantly affecting the accuracy of the segmentation (i.e. semi-automatically estimated prostate volume is within 90% of the original estimate)

Genetic and Epigenetic Profiling Reveals EZH2-mediated Down Regulation of OCT-4 Involves NR2F2 during Cardiac Differentiation of Human Embryonic Stem Cells

Abstract Human embryonic (hES) stem cells are widely used as an in vitro model to understand global genetic and epigenetic changes that occur during early embryonic development. In-house derived hES cells (KIND1) were subjected to directed differentiation into cardiovascular progenitors (D12) and beating cardiomyocytes (D20). Transcriptome profiling of undifferentiated (D0) and differentiated (D12 and 20) cells was undertaken by microarray analysis. ChIP and sequential ChIP were employed to study role of transcription factor NR2F2 during hES cells differentiation. Microarray profiling showed that an alteration of about 1400 and 1900 transcripts occurred on D12 and D20 respectively compared to D0 whereas only 19 genes were altered between D12 and D20. This was found associated with corresponding expression pattern of chromatin remodelers, histone modifiers, miRNAs and lncRNAs marking the formation of progenitors and cardiomyocytes on D12 and D20 respectively. ChIP sequencing and sequential ChIP revealed the binding of NR2F2 with polycomb group member EZH2 and pluripotent factor OCT4 indicating its crucial involvement in cardiac differentiation. The study provides a detailed insight into genetic and epigenetic changes associated with hES cells differentiation into cardiac cells and a role for NR2F2 is deciphered for the first time to down-regulate OCT-4 via EZH2 during cardiac differentiation

Additional file 6: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

ChIP sequencing of occupancy of H3K79me2 on DMD gene during cardiac differentiation of KIND1 and HES3 cells showing occupancy of H3K79me2 methylation mark brought about by DOT1L on DMD gene during cardiac differentiation. Results clearly show significant peaks representing the DOT1L specific methylation mark on days 12 and 20 as compared to day 0 suggestive of its activation by DOT1L during cardiac differentiation in vitro. (PDF 614 kb

Additional file 2: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

Characterization of cardiac differentiation of HES3 cells by quantitative real-time PCR (qRT-PCR). Expression of transcripts representing pluripotency (OCT4), cardiac mesoderm (MESP1), cardiac progenitors (NKX2.5, MEF2C), and cardiomyocytes (CTNT) at days 0, 12, and 20 during 20 days of cardiac differentiation. Note OCT-4 expression in undifferentiated cells is downregulated as the cells initiate differentiation. Early cardiac markers detected on day 12 and mature markers upregulated on day 20. Similar changes in transcripts expression observed when KIND1 cells were differentiated into cardiac cells as described earlier [43]. Error bars represent ÂąSEM. (PDF 410 kb

Additional file 5: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

Dystrophin gene expression during cardiac differentiation of KIND1 hES cells on days 0, 12, and 20 during cardiac differentiation of KIND1 hES cell line. Expression of Dystrophin increased in cardiac progenitors and cardiomyocytes compared to undifferentiated KIND1 cells. Results in agreement with earlier reports in DOT1L conditional knockout mice heart concluding Dystrophin as a direct target of DOT1L [35]. Error bars represent ¹SEM. (PDF 329 kb

Additional file 1: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

Brightfield images of HES3 hES cells during directed differentiation into cardiac lineage. Differentiation results in distinct morphological changes leading to increased compaction among the cells as differentiation proceeds from day 0 to day 20. Similar changes observed when KIND1 cells were differentiated into cardiac cells as described earlier [43]. Magnification 10×. (PDF 554 kb

Additional file 4: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

ChIP sequencing in KIND1 and HES3 cells during cardiac differentiation visualized by Integrated Genome Viewer shows binding profile of H3K79me2 modification across genes HNF4A, LEFTY1, NOGGIN, NQO1, OTX2, and NPTX2 in KIND1 (green) and HES3 (red) cells at days 0, 12, and 20 of cardiac differentiation. (PDF 548 kb

Additional file 3: of Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage

Characterization of cardiac differentiation of HES3 cells by immunofluorescence studies. Expression of NKX2.5 (A) and CTNT (B) on days 12 and 20 observed by immunofluorescence. (A) Distinct nuclear expression of NKX2.5 observed and (B) CTNT cell surface expression. Similar changes observed when KIND1 cells were differentiated into cardiac cells as described earlier [43]. Counterstaining using DAPI. Magnifications 20×. (PDF 450 kb

Pharmacodynamics of cytarabine alone and in combination with 7-hydroxystaurosporine (UCN-01) in AML blasts in vitro and during a clinical trial

Chk1 and Akt signaling facilitate survival of cells treated with nucleoside analogues. Activation of Chk1 in response to cytarabine (ara-C) induced an S-phase checkpoint characterized by the inhibition of Cdk2, cell cycle arrest, no change in constitutively active Akt, or low-stress kinase signaling in ML-1 cells. However, inhibition of Chk1 by UCN-01 in S-phase-arrested cells resulted in an abrogation of the checkpoint, inhibition of Akt, activation of JNK, and a rapid induction of apoptosis. Similarly, primary acute myelogenous leukemia (AML) blasts exposed to ara-C and UCN-01 demonstrated a selective loss in cloning potential when compared with normal progenitors. Therefore, we evaluated a pilot clinical trial of ara-C in combination with UCN-01 in patients with relapsed AML. Blasts from some patients demonstrated a previously activated Chk1-Cdk2 DNA damage response pathway that decreased during therapy. Constitutively phosphorylated Akt kinase declined on addition of UCN-01 to the ara-C infusion, an action accompanied by an activation of JNK and reduction in absolute AML blast counts. Thus, use of UCN-01 in combination with ara-C decreases Chk1 phosphorylation, inhibits the Akt survival pathway, and activates JNK during the course of therapy, offering a rationale for the cytotoxic action of this combination during AML treatment. (Blood. 2006;107:2517-2524