Distributed sequence alignment applications for the public computing architecture

The public computer architecture shows promise as a platform for solving fundamental problems in bioinformatics such as global gene sequence alignment and data mining with tools such as the basic local alignment search tool (BLAST). Our implementation of these two problems on the Berkeley open infrastructure for network computing (BOINC) platform demonstrates a runtime reduction factor of 1.15 for sequence alignment and 16.76 for BLAST. While the runtime reduction factor of the global gene sequence alignment application is modest, this value is based on a theoretical sequential runtime extrapolated from the calculation of a smaller problem. Because this runtime is extrapolated from running the calculation in memory, the theoretical sequential runtime would require 37.3 GB of memory on a single system. With this in mind, the BOINC implementation not only offers the reduced runtime, but also the aggregation of the available memory of all participant nodes. If an actual sequential run of the problem were compared, a more drastic reduction in the runtime would be seen due to an additional secondary storage I/O overhead for a practical system. Despite the limitations of the public computer architecture, most notably in communication overhead, it represents a practical platform for grid- and cluster-scale bioinformatics computations today and shows great potential for future implementations.

Optical antenna effect in semiconducting nanowires

We report on investigations of the interaction of light with nanoscale antennae made from crystalline GaP nanowires (NWs). Using Raman scattering, we have observed strong optical antenna effects which we identify with internal standing wave photon modes of the wire. The antenna effects were probed in individual NWs whose diameters are in the range 40 < d < 300 nm. The data and our calculations show that the nature of the backscattered light is critically dependent on the interplay between a photon confinement effect and bulk Raman scattering. At small diameter, d < 65 nm, the NWs are found to act like a nearly perfect dipole antenna and the bulk Raman selection rules are masked leading to a polarized scattering intensity function I R approximately cos4 theta. Underscoring the importance of this work is the realization that a fundamental understanding of the "optical antenna effect" in semiconducting NWs is essential to the analysis of all electro-optic effects in small diameter filaments.

DH1, a LOB domain-like protein required for glume formation in rice

T-DNA tagging is a high throughput strategy for identifying and cloning functional genes in plants. In this study, we screened 4416 lab-created T(1) rice T-DNA tagged lines and identified a mutant, designated dh1 (degenerated hull1), with phenotype of degenerated hull and naked pistils and stamens. Approximately 60% florets on the dh1 panicle defected in forming normal palea and lemma. Instead, they formed degenerative velum-like or filamentous organs accompanying with the lack of lodicules, stamens and pistils at different degree. A 361 bp of genomic sequence flanking the T-DNA isolated using TAIL-PCR (Thermal asymmetric interlaced PCR) co-segregated with the mutation phenotype. Results of blastn and gene prediction revealed the T-DNA inserted into the promoter region of a function-predicted gene at 283 bp upstream of its transcription start site (TSS). The predicted gene encoded a LOB (Lateral Organ Boundaries) domain-like protein. RT-PCR analyses indicated the transcription level of target candidate gene, DH1, decreased significantly in dh1 mutant. RNAi aimed at DH1 in wild type plants could partially result in the mutation phenotype of dh1. DH1 could also rescue the mutation phenotype in the complement experiment. The result of transformation by a fused expression vector, pDH1::GFP, revealed that DH1 had the keen spatial and temporal characteristics of expressing at axillary bud, young panicle and floral organs but not at root, leaf, node and culm, and strongly expressing at young tissues but weakly at mature organs. The dh1 presented severer mutation phenotype under relatively longer daylight than under shorter daylight implied that shorter daylight induced the expression of gene(s) redundant to DH1 in function and partially compensated for the loss-of-function. It is the first time to report the LOB-domain gene participating in the development of floral organs in rice.

Bowel perforation secondary to ventriculoperitoneal shunt: case report and clinical analysis

Bowel perforation is an unusual complication of ventriculoperitoneal shunting. This article describes a case of bowel perforation associated with a ventriculoperitoneal shunt inserted in an 8-month-old male infant for meningocoele and hydrocephalus. Ten months after insertion of the shunt the infant presented with the shunting tube protruding through the anus. There were no signs of meningitis or peritonitis. At laparotomy the tube was seen to enter the transverse colon and was encapsulated by the greater omentum. The tube was cut and the distal end removed via the anus. The transverse colon was repaired. The catheter continued to function effectively and the patient remained asymptomatic. The literature on this rare complication is reviewed and the therapeutic options are discussed.

Relationship between serum sodium level and brain ventricle size after aneurysmal subarachnoid hemorrhage

OBJECTIVE

To study the relationship of serum sodium levels and brain ventricle size after aneurysmal subarachnoid hemorrhage (SAH).

METHODS

Serum sodium levels and brain computed tomography (CT) scans were obtained simultaneously and within 21 days from onset of SAH in 69 patients. Serum sodium levels were compared with brain ventricle size on CT. The index of third ventricle was calculated from brain CT, and we studied its relationship to GOS (Glasgow Outcome Scale) scores.

RESULTS

There was obvious correlation between serum sodium levels and index of third ventricle (r = -0.753). GOS scores correlated with serum sodium levels in patients with hypernatremia.

CONCLUSION

There was a negative correlation between serum sodium levels and cerebral ventricle size in SAH patients. Hypernatremia is one factor leading an unfavorable prognosis in SAH patients.

Lidocaine abolishes the myocardial protective effect of sevoflurane post-conditioning

BACKGROUND

Post-ischemic administration of volatile anesthetics activates ischemia-reperfusion injury salvage process and decreases myocardial damage. However, the mechanisms underlying anesthetic post-conditioning and effects of lidocaine on it remain unclear. Here we report the cardioprotection of sevoflurane-induced post-conditioning and the effects of lidocaine on it.

METHODS

Isolated perfused rat hearts were exposed to 40 min of ischemia followed by 1 h of reperfusion. Volatile anesthetic post-conditioning was induced by 15 min of 3 vol% sevourane (1.5 minimum alveolar concentration) administered at the onset of reperfusion. In some experiments, lidocaine was coadministered with sevoflurane in different concentrations (2, 10 and 20 microg/ml). Infarct size was determined by dividing the total necrotic area of the left ventricle by the total left ventricular slice area (percent necrotic area).

RESULTS

Sevoflurane-induced post-conditioning signicantly improved post-ischemia functional recovery and decreased infarct size (47.3+/-5.6% in unprotected hearts vs. 18.6+/-3.1% in anesthetic post-conditioning, P<0.05). Sevourane-mediated cardioprotection was abolished by 20 microg/ml lidocaine.

CONCLUSIONS

Sevourane-induced post-conditioning effectively protected myocardium against reperfusion damage and its cytoprotection was reversed by 20 microg/ml lidocaine.

Diagnostic yield of capsule endoscopy in ulcerative colitis and inflammatory bowel disease of unclassified type (IBDU)

BACKGROUND AND STUDY AIMS

Capsule endoscopy is increasingly reported as an important diagnostic procedure in patients with known or suspected Crohn's disease, but its clinical utility in patients with ulcerative colitis or unclassified type inflammatory bowel disease (IBDU) is unclear. The aim of our study was to determine the diagnostic yield of capsule endoscopy for small-bowel disease in patients with ulcerative colitis and IBDU.

PATIENTS AND METHODS

All data from patients with a history of ulcerative colitis or IBDU who underwent capsule endoscopy between October 2001 and August 2005 were analyzed for procedure indications and findings. Images were reviewed by an experienced capsule endoscopist. The finding of multiple ulcerations (three or more) on capsule endoscopy was classified as diagnostic of small-bowel Crohn's disease.

RESULTS

120 patients had undergone 122 capsule endoscopy procedures. Overall, 19 of 120 patients (15.8 %) had capsule endoscopy findings consistent with the diagnosis of Crohn's disease. The proportion of patients with small-bowel disease was significantly higher among patients with a history of colectomy (7 of 21 patients, 33 %) compared with those without colectomy (12/99, 12 %) ( P = 0.04). Among patients with positive findings on capsule endoscopy, 18 had also previously undergone a small-bowel follow-through study and only one showed findings consistent with Crohn's disease.

CONCLUSIONS

Many patients with a diagnosis of ulcerative colitis and atypical features or IBDU may have small-bowel findings on capsule endoscopy that are consistent with Crohn's disease. Capsule endoscopy should be considered in ulcerative colitis patients with atypical clinical features particularly after colectomy.

Numerical simulation of municipal solid waste combustion in a novel two-stage reciprocating incinerator

A mathematical model was presented in this paper for the combustion of municipal solid waste in a novel two-stage reciprocating grate furnace. Numerical simulations were performed to predict the temperature, the flow and the species distributions in the furnace, with practical operational conditions taken into account. The calculated results agree well with the test data, and the burning behavior of municipal solid waste in the novel two-stage reciprocating incinerator can be demonstrated well. The thickness of waste bed, the initial moisture content, the excessive air coefficient and the secondary air are the major factors that influence the combustion process. If the initial moisture content of waste is high, both the heat value of waste and the temperature inside incinerator are low, and less oxygen is necessary for combustion. The air supply rate and the primary air distribution along the grate should be adjusted according to the initial moisture content of the waste. A reasonable bed thickness and an adequate excessive air coefficient can keep a higher temperature, promote the burnout of combustibles, and consequently reduce the emission of dioxin pollutants. When the total air supply is constant, reducing primary air and introducing secondary air properly can enhance turbulence and mixing, prolong the residence time of flue gas, and promote the complete combustion of combustibles. This study provides an important reference for optimizing the design and operation of municipal solid wastes furnace.