ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences

<p>Abstract</p> <p>Background</p> <p>Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often performed before alignment to mask insertion sequences such as transposable elements (TEs). However, recently such TEs have been reported to influence the gene regulatory network evolution. Therefore, an alignment approach that is robust to TE insertions is meaningful for finding novel conserved TFBSs in TEs.</p> <p>Results</p> <p>We constructed a web server 'ReAlignerV' for complex alignment of genomic sequences. ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs. It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence. Furthermore, we evaluated false positive aligned sites by focusing on the species-specific TEs (SSTEs), and found that ReAlignerV has a higher specificity and robustness to insertions for sequences having more than 20% TE content, compared to LAGAN, AVID, MAVID and BLASTZ.</p> <p>Conclusion</p> <p>ReAlignerV can be applied successfully to TE-insertion-rich sequences without prior repeat masking, and this increases the chances of finding regulatory sequences hidden in TEs, which are important sources of the regulatory network evolution. ReAlignerV can be accessed through and downloaded from <url>http://genet.med.kagawa-u.ac.jp/</url>.</p

Calcium Phosphate Composition Affects Ureteroscopic Laser Lithotripsy

The effects of stone composition on transurethral lithotripsy (TUL) have not been sufficiently elucidated. The purpose of this study was to identify how calcium phosphate stone composition impacts TUL. Two hundred eighty-nine cases of semi-rigid and/or flexible TUL for upper urinary tract calculi were reviewed retrospectively. Inclusion criteria were a preoperative assessment by noncontrast computed tomography (NCCT) and a stone composition analysis. Small stones and those without calcium composition were excluded. Stone core radiodensity (SCR) was measured by taking the average of the upper 3 of 5 points in the proximity of the center of the stone on NCCT. Fifty-three patients with calcium phosphate composition (CaP) and 118 patients with calcium oxalate and without phosphate composition were eligible for analysis. SCR was significantly higher in the CaP group (p<0.01). The CaP patient group needed a significantly longer operation time (p=0.014) and more laser energy (p=0.085), and tended to have a lower rate of complete lithotripsy (p=0.096) and higher incidence of postoperative pyelonephritis (p=0.181). Stones containing calcium phosphate are harder, demand more laser energy, and require a longer operating time. NCCT evaluation can estimate stone composition preoperatively, and may be a useful tool for predicting operative outcomes

Observables suitable for restricting the fidelity to multipartite maximally entangled states

We present a class of observables which are suitable for determining the fidelity of a state to the multipartite Greenberger-Horne-Zeilinger (GHZ) state. Given an expectation value of an observable belonging to the class, we give a simple formula that gives a lower bound and an upper bound for the fidelity. Applying the formula to the GHZ-state preparation experiment by Pan {\it et al}. {[Nature (London) {\bf 403}, 515 (2000)]}, we show that the observed state lies outside of the class of biseparable mixed three-qubit states. We also show that for this class of operators, adopting the principle of minimum variance {[Phys. Rev. A {\bf 60}, 4338 (1999)]} in the state estimation always results in the state with the minimum fidelity.Comment: 6 page

Xanthogranuloma of the intrasellar region presenting in pituitary dysfunction: a case report

<p>Abstract</p> <p>Introduction</p> <p>Differentiation of cystic mass lesions of the sellar and parasellar regions may pose a diagnostic dilemma for physicians, neurosurgeons, radiologists and pathologists involved in treating patients with these entities. A considerable number of tumors previously identified as craniopharyngiomas may, in fact, have been xanthogranulomas. We report a case of pituitary dysfunction caused by xanthogranuloma of the intrasellar region.</p> <p>Case presentation</p> <p>A 47-year-old man of Japanese descent presented to our institution with a tumor located exclusively in the intrasellar region which manifested as severe hypopituitarism. MRI revealed a clearly defined intrasellar mass that was heterogeneously hyperintense on T1-weighted images and markedly hypointense on T2-weighted images. We preoperatively diagnosed the patient with Rathke's cleft cyst or non-functioning pituitary adenoma. Although the tumor was completely removed using a transsphenoidal approach, the improvement of the patient's endocrine function was marginal, and continued endocrine replacement therapy was needed. Postoperatively, a histological examination revealed the tumor to be a xanthogranuloma of the intrasellar region. His visual field defects and headache improved.</p> <p>Conclusion</p> <p>Because diagnosis depends on surgical intervention and xanthogranulomas of the intrasellar region are very rare, the natural history of xanthogranuloma is still unknown. Therefore, this entity is difficult to diagnose preoperatively. We suggest that xanthogranuloma should be included in the differential diagnosis, even in the case of sellar lesions, to formulate appropriate postoperative management and improve endocrine outcomes.</p

Platelet derived growth factor regulates ABCA1 expression in vascular smooth muscle cells

AbstractThe ATP-binding cassette transporter A1 (ABCA1) regulates lipid efflux from peripheral cells to High-density lipoprotein. The platelet-derived growth factor (PDGF) is a potent mitogen that enables vascular smooth muscle cells to participate in atherosclerosis. In this report, we showed that PDGF suppressed endogenous expression of ABCA1 in cultured vascular smooth muscle cells. Exposure of CRL-208 cells to PDGF elicited a rapid phosphorylation of a kinase downstream from PI3-K, Akt. The constitutively active form of both p110, a subunit of PI3-K, and Akt inhibited activity of the ABCA1 promoter. In conclusion, PI3-K-Akt pathways participate in PDGF-suppression of ABCA1 expression

Plasma brain natriuretic peptide as a surrogate marker for cardioembolic stroke

<p>Abstract</p> <p>Background</p> <p>Cardioembolic stroke generally results in more severe disability, since it typically has a larger ischemic area than the other types of ischemic stroke. However, it is difficult to differentiate cardioembolic stroke from non-cardioembolic stroke (atherothrombotic stroke and lacunar stroke). In this study, we evaluated the levels of plasma brain natriuretic peptide in acute ischemic stroke patients with cardioembolic stroke or non-cardioembolic stroke, and assessed the prediction factors of plasma brain natriuretic peptide and whether we could differentiate between stroke subtypes on the basis of plasma brain natriuretic peptide concentrations in addition to patient's clinical variables.</p> <p>Methods</p> <p>Our patient cohort consisted of 131 consecutive patients with acute cerebral infarction who were admitted to Kagawa University School of Medicine Hospital from January 1, 2005 to December 31, 2007. The mean age of patients (43 females, 88 males) was 69.6 ± 10.1 years. Sixty-two patients had cardioembolic stroke; the remaining 69 patients had non-cardioembolic stroke (including atherothrombotic stroke, lacunar stroke, or the other). Clinical variables and the plasma brain natriuretic peptide were evaluated in all patients.</p> <p>Results</p> <p>Plasma brain natriuretic peptide was linearly associated with atrial fibrillation, heart failure, chronic renal failure, and left atrial diameter, independently (F_4,126= 27.6, p < 0.0001; adjusted R²= 0.45). Furthermore, atrial fibrillation, mitral regurgitation, plasma brain natriuretic peptide (> 77 pg/ml), and left atrial diameter (> 36 mm) were statistically significant independent predictors of cardioembolic stroke in the multivariable setting (Χ²= 127.5, p < 0.001).</p> <p>Conclusion</p> <p>It was suggested that cardioembolic stroke was strongly predicted with atrial fibrillation and plasma brain natriuretic peptide. Plasma brain natriuretic peptide can be a surrogate marker for cardioembolic stroke.</p