HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (NSF/NIH BIGDATA Grant R01GM108348-01)National Science Foundation (U.S.) (Graduate Research Fellowship)Simons Foundatio

Times of Minima of Some Eclipsing Binaries

We present new times of minima in the light curves of some eclipsing binarie

Malignant mixed Mullerian tumor of the uterus with prominent neuroectodermal differentiation - A case report

A case of malignant mixed Mullerian tumor of the uterus with prominent neuroectodermal differentiation is reported. The most notable feature of the tumor was its large component of primitive neuroepithelium lining tubules. The islands of neuroectodermal tissue were admired with conventional endometrioid adenocarcinoma and sarcomatous elements resembling malignant fibrous histiocytoma only in a small focus

Bilateral epididymal Candida abscesses: Sonographic findings and sonographically guided fine-needle aspiration

We report the case of a 67-year-old diabetic man who presented 2 months after transurethral prostate surgery with impaired consciousness, urinary incontinence, and recurrent urinary tract infections that did not respond to antibiotic treatment. Sonographic findings suggested abscess formation (enlarged, heterogeneous epididymides and a central hypoechoic area in the head of the left epididymis). Aspirates obtained from sonographically guided needle biopsy were purulent. Staining showed budding yeast forms, and Candida albicans grew in culture. Systemic candidiasis was diagnosed. The patient underwent bilateral epididymo-orchiectomy, and pathologic analysis of resected specimens showed bilateral epididymal necrosis and disseminated abscess formation. (C) 1998 John Wiley & Sons, Inc

Significance of heat shock protein-27 expression in patients with renal cell carcinoma

Objectives. To investigate heat shock protein (HSP)-27 expression in patients with renal cell carcinoma (RCC) and examine its biologic significance. HSPs were first defined as proteins induced by heat shock and other environmental and pathophysiologic stresses. They are implicated in protein-protein interactions and are thought to play an important role in cancer. The expression of HSP-27 has been demonstrated in some human tumors

Estrogen and progesterone receptor manipulations in castrated rat uterus models and the clinical adaptation.

To investigate the influence of tamoxifen, danazol and triptorelin (a GnRH agonist) on estrogen and progesterone receptors of rat endometrium, 44 castrated Sprague-Dawley rats were divided into four equal groups, and each group received either no treatment or one of the agents. After administration of the agents, estrogen and progesterone receptor levels, detected by immunohistochemical methods, were compared with the controls. Estrogen and progesterone receptors were significantly higher in the tamoxifen group than the controls (p0.05). Receptor levels were higher in the danazol group than the controls, but it was significant only in the estrogen receptors. Among the 3 groups, receptor levels were higher than in the control group. There was not any correlation among the estrogen and progesterone receptor levels in all groups

Three cases of diffuse mullerian neoplasia

Three cases with simultaneous neoplasms in multiple sites of female reproductive tract, followed up in our university clinic are reported

Primary non-Hodgkin's T-cell lymphoma of the thyroid gland complicating Hashimoto's thyroiditis: Case report

This case report presents an extremely rare case of primary non-Hodgkin's T-cell lymphoma of the thyroid gland complicating Hashimoto's thyroiditis and discusses the clinical history, findings, treatment, and prognosis. Although the place of surgery in the treatment of thyroid lymphoma is controversial, in this case, surgery followed by three rounds of chemotherapy with cyclophosphamide, doxorubicin, vincristine, and prednisone, and radiation therapy to neck and mediastinum were a very effective treatment for the disease so that no relapse has been detected during 3-year follow-up

changes for osteogenesis: In a rat model

The aim of this study is to investigate the effects of type I collagen on bone defects and on genes specifically for osteogenesis in a rat model. Two millimeter drill hole bone defect was created in the femur of rats. In the experimental group, type I collagen was applied in bone defects whereas in control group defects were left empty. Inflammation, development of connective tissue, osteogenesis, and foreign body reaction parameters evaluated with histologically and genes evaluated by blood samples. In the experimental group, the histopathologically significant change was found in favor of bone healing only at the first week. A significant increase was found in genetic expressions of BMP-1, 2, 3, 4, 5, 6, 7, TGF-RII, Smad-1, IL-6, BMPR-IA, BMPR-IB, Eng, BMPR-II, c-fos, Cdkn1a, Chrd, Gdf-5, Id-1, PDGF-, IGF-1, Serpine-1, and TGF-RI at the first hour. At the first, third, and sixth week, no significant increase was found in any of the gene expressions. Type I collagen is found to be effective in favor of bone healing through increased inflammatory cytokines and expression of BMP genes in the early stages of fracture healing.C1 [Yigiter, Ozgur] Denizli State Hosp, Dept Orthoped & Traumatol, Denizli, Turkey.[Yorukoglu, Ali Cagdas; Demirkan, Ahmet Fahir] Pamukkale Univ, Dept Orthoped & Traumatol, Fac Med, TR-20070 Denizli, Turkey.[Sentuerk, Nilay] Pamukkale Univ, Dept Pathol, Fac Med, Denizli, Turkey.[Dodurga, Yavuz] Pamukkale Univ, Dept Med Biol, Denizli, Turkey