Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

<p>Abstract</p> <p>Background</p> <p>In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design.</p> <p>Results</p> <p>RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%.</p> <p>Conclusion</p> <p>To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (<it>ViennaPackage </it>– 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.</p

Patterns of Gene Expression in Western Corn Rootworm (\u3ci\u3eDiabrotica virgifera virgifera\u3c/i\u3e) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing

With Next Generation Sequencing technologies, high-throughput RNA sequencing (RNAseq) was conducted to examine gene expression in neonates of Diabrotica virgifera virgifera (LeConte) (Western Corn Rootworm, WCR) challenged with individual proteins of the binary Bacillus thuringiensis insecticidal proteins, Cry34Ab1 and Cry35Ab1, and the combination of Cry34/Cry35Ab1, which together are active against rootworm larvae. Integrated results of three different statistical comparisons identified 114 and 1300 differentially expressed transcripts (DETs) in the Cry34Ab1 and Cry34/35Ab1 treatment, respectively, as compared to the control. No DETs were identified in the Cry35Ab1 treatment. Putative Bt binding receptors previously identified in other insect species were not identified in DETs in this study. The majority of DETs (75% with Cry34Ab1 and 68.3% with Cry34/35Ab1 treatments) had no significant hits in the NCBI nr database. In addition, 92 DETs were shared between Cry34Ab1 and Cry34/35Ab1 treatments. Further analysis revealed that the most abundant DETs in both Cry34Ab1 and Cry34/35Ab1 treatments were associated with binding and catalytic activity. Results from this study confirmed the nature of these binary toxins against WCR larvae and provide a fundamental profile of expression pattern of genes in response to challenge of the Cry34/35Ab1 toxin, which may provide insight into potential resistance mechanisms

Cutaneous leukocytoclastic vasculitis due to anti-tuberculosis medications, rifampin and pyrazinamide

Anti-tuberculosis drugs frequently result in cutaneous adverse reactions, including pruritus, maculopapular exanthems, and urticaria. However, anti-tuberculosis drug-associated cutaneous leukocytoclastic vasculitis (CLV) has been rarely reported. We describe a case of CLV induced by rifampin and pyrazinamide. A 38-year-old male had been diagnosed with pulmonary tuberculosis two months ago and then he started standard anti-tuberculosis therapy with isoniazid, rifampin, ethambutol, and pyrazinamide. Purpuric lesions developed in the extremities after 1.5 months of anti-tuberculosis medication; the lesions progressively spread over the entire body. Histopathology of the purpuric skin lesion was consistent with leukocytoclastic vasculitis. The skin lesion improved after cessation of anti-tuberculosis medications and treatment with oral corticosteroids and antihistamines. Anti-tuberculosis drugs were rechallenged one at a time over 3 days. Purpura recurred on the right forearm and forehead after taking 300 mg of rifampin. The skin lesion disappeared after taking oral prednisolone. Finally, 1,500 mg of pyrazinamide was readministrated, and then purpuric lesions recurred on both forearms. This report describes a case of leukocytoclastic vasculitis secondary to rifampin and pyrazinamide therapy

A Case of Successful Selective Abortion Using Radio-frequency Ablation in Twin Pregnancy Suffering from Severe Twin to Twin Transfusion Syndrome

Twin to twin transfusion syndrome (TTTS) is one of the major complication of monochorionic twin pregnancy which is mainly understood by placental vascular anastomosis. Perinatal mortality and morbidity is high as 80-100% if untreated and even higher if the disease is developed at early stage. Variety of methods of isolating or intercepting placental vascular anastomosis are introduced, but they are only available in centers where all the required equipments are prepared. We report here a case of TTTS complicated with severe polyhydroamnios during the second trimester. The blood supply to donor twin was interrupted successfully at 19+2 weeks of gestation by minimally invasive radio-frequency cord ablation, under ultrasound guidance. The normal recipient twin was delivered successfully at 35 weeks of gestation and had no eventful neonatal course

Subclinical Infiltration of Basal Cell Carcinoma in Asian Patients: Assessment after Mohs Micrographic Surgery

Background: Several differences in basal cell carcinomas (BCCs) were found, according to the ethnic group; for example, pigmented BCCs was more common in Asian or Hispanic patients. However, there are few reports on the subclinical extension of the BCC in Asian patients. Objective: The aim of this study was to evaluate the subclinical infiltration of the basal cell carcinoma in Asian patients. Methods: All patients with BCC who visited the department of dermatology at Korea University Ansan Hospital were treated with Mohs micrographic surgery. In 81 patients, 83 tumors of BCC were completely eradicated by Mohs micrographic surgery (MMS) from April 2001 to August 2008, and were reviewed in this study. Information recorded included the total margin and the number of stages of Mohs micrographic surgery, anatomic location, tumor size, presence of pigmentation, clinical type, and pathological subtype. We divided the clinical types into nodular, ulcerated, and pigmented, and the pathological types into nodular, micronodular, morpheaform, and adenoid. The BCC was of pigmented type if pigmentation covered more than 25 % of the tumor, regardless of whether pigmentation was distinct, or if there was apparent pigmentation that covered more than 10 % of the tumor. Results: The nose and cheek were the most common sites requiring more than one stage of surgery. In tumors smaller than 1 cm, 91.7 % required only one stage of excision, compared with 60.6 % in tumor

Ruptured duodenal varices arising from the main portal vein successfully treated with endoscopic injection sclerotherapy: a case report

Duodenal varices result from retroperitoneal portosystemic shunts that usually come from the pancreaticoduodenal vein and drain into the inferior vena cava. Because they are a rare but fatal cause of gastrointestinal bleeding, a prompt hemostatic intervention is mandatory. A 62-year-old man who had a history of excessive alcohol consumption presented with massive hematemesis and melena. Emergent endoscopy revealed ruptured varices with an adhering whitish fibrin clot on the postbulbar portion of the duodenum. Abdominal computed tomography demonstrated a cirrhotic liver with venous collaterals around the duodenum and extravasated contrast in the second and third portions. The collaterals originated from the main portal vein and drained via the right renal vein into the inferior vena cava. Endoscopic injection sclerotherapy with cyanoacrylate was successful in achieving hemostasis, and resulted in the near eradication of duodenal varices at a 6-month follow-up

Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery

10.1371/journal.pone.0090133PLoS ONE93-POLN