Enhanced international prognostic index in Japanese patients with diffuse large B-cell lymphoma

To evaluate the National Comprehensive Cancer Network (NCCN) International Prognostic Index (IPI), we analyzed 284 patients treated with the combination of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in our institution in Japan. Their 5-year overall survival (OS) by risk level was 80.7%, 74.8%, 55.4% and 67.5% (P=0.005); and their 5-year progression-free survival (PFS) was 76.8%, 78.6%, 63.7% and 58.3% (P=0.0722). The NCCN-IPI is a simple scale that uses conventional clinical factors, but did not reflect survival in our cohort. The NCCN-IPI may require further evaluation for different regions and ethnicities before adopting it for routine clinical use.

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The NCCN-IPI is developed to predict survival in the rituximab era.

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The NCCN-IPI failed to predict survival in our cohort.

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The NCCN-IPI may require further evaluation before routine clinical use.

Disseminated intravascular coagulation observed following treatment with gemtuzumab ozogamicin for relapsed/refractory acute promyelocytic leukemia

Gemtuzumab ozogamicin (GO) is a recombinant humanized immunoglobulin G4 anti-cluster of differentiation (CD)33 monoclonal antibody conjugated to N-acetyl-γ calicheamicin dimethylhydrazide, a naturally potent antibiotic. It has been introduced for the treatment of acute promyelocytic leukemia (APL), since large quantities of CD33 are commonly expressed on the surface of APL cells. The present study reported two cases with prominent disseminated intravascular coagulation (DIC), which was transiently observed following treatment with GO with relapsed/refractory APL. Very limited information exists regarding DIC occurring following GO, and its mechanism remains to be elucidated. In the present study, recombinant human soluble thrombomodulin was used for DIC treatment, and the patients recovered promptly. Since DIC is the most serious adverse event associated with GO treatment, elucidation of its mechanism and establishment of a treatment strategy are warranted.

Retrospective analysis of bevacizumab-induced hypertension and clinical outcome in patients with colorectal cancer and lung cancer

Bevacizumab(Avastin^®), a humanized therapeutic monoclonal antibody that targets vascular endothelial growth factor, is widely used in cancer treatment. Patients who are treated with bevacizumab have an increased risk of developing systemic hypertension. However, the relationship between bevacizumab‐induced hypertension and clinical outcome remains unclear. We aimed to evaluate the effect of bevacizumab‐induced hypertension in terms of prognosis in patients with colorectal cancer and non‐small cell lung cancer. The study included 632 patients, 317 patients with non‐small cell lung cancer and 315 patients with colorectal cancer. All patients were treated with bevacizumab in combination with standard chemotherapy protocols, between April 2007 and December 2014. Blood pressure was measured before each treatment cycle. In the patient group with colorectal cancer, treated with bevacizumab, Grade 2–3 hypertension was present in 27.6%. In hypertensive patients with colorectal cancer, median overall survival was 42.6 months, compared with 20.6 months for normotensive patients in this group (P = 0.00071). In the patient group with non‐small cell lung cancer, treated with bevacizumab, Grade 2–3 hypertension was present in 20.5%. In hypertensive patients with non‐small cell lung cancer, median overall survival was 43.0 months, compared with 26.3 months for normotensive patients in this group (P = 0.00451). Patients who developed hypertension during treatment with bevacizumab for colorectal cancer and non‐small cell lung cancer had significantly prolonged overall survival when compared with normotensive patients. Bevacizumab‐induced hypertension may represent a biomarker for clinical benefit in cancer patients treated with bevacizumab.

Mogamulizumab treatment of refractory peripheral T-cell lymphoma following autologous stem cell transplantation: A case report

Peripheral T-cell lymphoma (PTCL) represents a small heterogeneous group of non-Hodgkin lymphoma (NHL) that accounts for ~10% of NHLs in western countries and ~25% of NHLs in Japan. The disease remains extremely difficult to treat. Therefore, novel treatment modalities are required. Mogamulizumab is a humanized immunoglobulin G1 monoclonal antibody that targets CC chemokine receptor 4. To the best of our knowledge, the efficacy of mogamulizumab in patients who are refractory to conventional chemotherapy following autologous stem cell transplantation has not been investigated previously. The present study reports a patient with PTCL who relapsed following autologous stem cell transplantation and became resistant to salvage chemotherapy, in whom mogamulizumab showed evident efficacy without severe adverse event.

[Primary Central Nervous System Post-Transplant Lymphoproliferative Disorder in a Patient with Acute Lymphocytic Leukemia]

A 27-year-old woman with acute lymphocytic leukemia, who underwent allogeneic hematopoietic stem cell transplantation, complained of nausea and blurred vision 288 days after the transplantation. Intracranial tumors were identified on brain MRI. She received whole brain radiation after open biopsy, but she died. The tumors had characteristics of diffuse large B cell lymphoma, and she was finally diagnosed with primary central nervous system post-transplant lymphoproliferative disorder. This disease is rare and has a poor outcome. Therefore, accumulation of cases and establishment of treatments for this condition are urgently needed.

Genes associated with the progression of neurofibrillary tangles in Alzheimer's disease

The spreading of neurofibrillary tangles (NFTs), intraneuronal aggregates of highly phosphorylated microtubule-associated protein tau, across the human brain is correlated with the cognitive severity of Alzheimer's disease (AD). To identify genes relevant to NFT expansion defined by the Braak stage, we conducted whole-genome exon array analysis with an exploratory sample set consisting of 213 human post-mortem brain tissue specimens from the entorinal, temporal and frontal cortices of 71 brain-donor subjects: Braak NFT stages 0 (N=13), I-II (N=20), III-IV (N=19) and V-VI (N=19). We identified eight genes, RELN, PTGS2, MYO5C, TRIL, DCHS2, GRB14, NPAS4 and PHYHD1, associated with the Braak stage. The expression levels of three genes, PHYHD1, MYO5C and GRB14, exhibited reproducible association on real-time quantitative PCR analysis. In another sample set, including control subjects (N=30), and in patients with late-onset AD (N=37), dementia with Lewy bodies (N=17) and Parkinson disease (N=36), the expression levels of two genes, PHYHD1 and MYO5C, were obviously associated with late-onset AD. Protein-protein interaction network analysis with a public database revealed that PHYHD1 interacts with MYO5C via POT1, and PHYHD1 directly interacts with amyloid beta-peptide 42. It is thus likely that functional failure of PHYHD1 and MYO5C could lead to AD development.

[Retrospective analysis of Charlson comorbidity index (CCI)]

Owing to the advance of supportive care and the development of molecular targeted therapies, the elderlies or patients who have comorbidities have been treated more than before. The assessment of the comorbidity is indispensable to select the appropriate treatment or the control of following therapy. Some indices to determine them have been developed in western countries but not in Japan. The index which is used most is the Charlson comorbidity index (CCI). This index has never been evaluated in Japan. So we investigated the utility of the index for Japanese population. We surveyed retrospectively 498 patients aged 65 or more patients with colon cancer, breast cancer, lung cancer that have been treated in our hospital during 2002-2007. According to CCI, patients are classified into three groups and verified 1-year and 3-year survival rate. 1-year survival rate was 76.9% in groups of 0 points, 83.5% in groups of1 -5 points, 75.0% in the group of six or more points respectively (p=0.19). 3-year survival rate were 59.0%, 63.1%, 75.0%, respectively (p=0.46). Multivariate analysis identified age (≥ 50), Sex (man), stage (III and IV) as significant predictors for worse OS at 3-year. However, there was no significant difference in CCI. There are some items which frequency is zero, so the items of CCI may not match to Japanese population. Presence of existing disease is an important factor for the cancer therapy, and it should be evaluated accurately. It is urgently necessary to develop an evaluation method and establish the scale.

[Are the Japanese guidelines for the management of hepatitis B virus reactivation being properly implemented ?]

Hepatitis B virus(HBV)reactivation has been reported as a fatal complication following systemic chemotherapy or other immunosuppressive therapies. The Japanese Guidelines for HBV reactivation were published in 2009. Despite the publication of these guidelines, there have been some reports of fulminant hepatitis B. Therefore, it was suggested that the guidelines were not yet been widely implemented. We investigated whether the guidelines had been implemented in our hospital. After the evaluation, it was determined that 89%of HBV cases were screened for the HBV surface antigen(HBs-Ag). Additionally, the screening for HBV surface antibody(HBs-Ab)and HBV core antibody(HBc-Ab)should be performed in cases negative for HBs-Ag, which was performed in only 17% of HBs-Ag-negative cases. It was concluded that the guidelines had not been implemented in our hospital. Therefore, we conducted educational activities to promote the implementation of the guidelines. Screening tests were performed in all 270 HBV cases between January and June 2013. Two antigen-positive carriers were identified. The rate of HBs-Ag-negative and/or HBc antibody -positive cases was 20.3%. Of these, 76.4%were tested using a DNA quantitative test, but DNA quantification did not increase in any case. HBV reactivation is expected to increase due to the development of new drugs and the use of diverse regimens. All physicians who perform immunotherapy and chemotherapy should immediately participate in educational activities.

[Marked improvement of anemia during treatment with deferasirox in patients with primary myelofibrosis and acute myeloid leukemia with myelodysplasia-related changes]

We report two patients who achieved a marked improvement of hematopoiesis with the use of deferasirox (DSX) for transfusional iron overload. Case 1 is an 81-year-old male who was diagnosed with primary myelofibrosis in July, 2007. He required regular red blood cell (RBC) transfusion of 4 units/month when he was started on DSX treatment in June, 2009. Four months after the treatment, he became transfusion independent, and has maintained hemoglobin levels of around 13 g/dl until today. Case 2 is a 70-year-old female with acute myeloid leukemia with myelodysplasia-related changes. She had been on RBC transfusion of 4 units/month when she was started on DSX treatment in January, 2010. Two months after the treatment, she became transfusion-independent, and 5 months after treatment, blast cells completely disappeared in the peripheral blood, together with normalization of white blood cell and neutrophil counts. Achieving durable transfusion-independency and normalization of white blood cell count and differential with a single use of DSX is a very rare event. Prospective accumulation of more patients and research to understand the mechanism underlying these effects are clearly warranted.

[Epidural abscess in the spine extended from pulmonary zygomycosis during consolidation chemotherapy for acute lymphoblastic leukemia]

A 37-year-old woman with acute lymphoblastic leukemia developed fever and pneumonia during persistent neutropenia after consolidation chemotherapy. Pneumonia was rapidly followed by the formation of abscess in adjacent subcutaneous tissues, muscles and bones. She subsequently developed sudden onset of paraplegia and loss of all sensation below Th4. Epidural abscess was detected by MRI. Emergency drainage was performed, but the patient died 4 days after the operation. Rhizopus oryzae grew from culture of the epidural abscess. Since the incidence of zygomycosis appears to have increased over the recent years, clinicians should be aware of the possibility of zygomycosis in case of any infection that is resistant to antibiotics.

Successful treatment of adult onset Langerhans cell histiocytosis with multi-drug combination therapy

Adult onset Langerhans cell histiocytosis (LCH) is a rare disorder. Its clinical features have been well described in children, however remain poorly defined in adults. Optimal treatment strategy is still under debate. We have encountered two cases of adult onset LCH, which obtained a durable disease control by combination chemotherapy using prednisone, vinblastine and 6-mercaptopurine. Herein, we report their clinical features together with a review of the current literature.

The gold compound auranofin induces apoptosis of human multiple myeloma cells through both down-regulation of STAT3 and inhibition of NF-κB activity

Constitutive activation of NF-κB and STAT3 plays an important role in the cellular proliferation and survival of multiple myeloma cells. We first found that auranofin (AF), a coordinated gold compound, induced a significant level of cell cycle arrest at G1 phase and subsequent apoptosis of myeloma cells. Further, AF inhibited constitutive and IL-6-induced activation of JAK2 and phosphorylation of STAT3 followed by the decreased expression of Mcl-1. AF down-regulated the activation of NF-κB, and the combination of AF and a specific NF-κB inhibitor resulted in a marked decrease of Mcl-1 expression. These results suggest that AF inhibits both IL-6 induced-JAK/STAT pathway and NF-κB activation in myeloma cells.

[Usefulness of serum plasminogen activator inhibitor-1 for diagnosis and monitoring of late-onset sinusoidal obstruction syndrome after allogeneic stem cell transplantation]

Sinusoidal obstruction syndrome (SOS) was originally defined as a clinical syndrome occurring by three weeks after transplantation; however, it occurs even after three or more weeks, and such cases are called late-onset SOS. We report here a case of late-onset SOS. The patient was a 17-year-old male with acute myeloid leukemia in second complete remission. He received a preparative regimen including busulfan followed by allo-peripheral blood stem cell transplantation from an HLA-matched sibling donor. On day 28 after transplantation, he developed hepatomegaly with pain. On day 33 PAI-1 level was increased. Two days later ascites developed, leading to a diagnosis of late-onset SOS. The symptoms improved with conservative therapy and the level of PAI-1 was normalized. When hepatic impairment appears three or more weeks after transplantation, late-onset SOS should be considered. PAI-1 is a useful marker for the diagnosis and follow up of late-onset SOS.

Plasma cell leukemia presenting with diplopia due to unilateral abducens paralysis and complex chromosomal abnormalities

Involvement of cranial nerves is rare in plasma cell leukemia (PCL). Here, we report a case of PCL presenting with unilateral abducens paralysis. Cranial magnetic resonance imaging (MRI) disclosed a mass in the sphenoid sinus. Although the patient showed an initial response to chemotherapy, he died of disease progression 5 months later. Cytogenetic analysis showed translocation of chromosomes 11 and 14, t(11;14) (q13;q32), with additional complex abnormalities. This case implies an association between clinical manifestations and chromosomal abnormalities.

[Hematopoietic stem cell transplantation in the second or later complete remission in acute promyelocytic leukemia initially treated with all-trans retinoic acid]

Despite the use of all-trans retinoic acid (ATRA) as the first-line treatment for acute promyelocytic leukemia (APL), relapse occurs in about 20% of cases. Most relapsing APL patients can achieve second remission (CR2) following ATRA combined with chemotherapy or arsenic trioxide. Stem cell transplantation (SCT) has been widely adopted in CR2, but optimal SCT (auto- or allo-SCT) remains controversial. We analyzed the outcomes for 8 APL patients initially treated using ATRA, who relapsed, achieved CR2 and underwent auto-SCT (n = 4) or allo-SCT (n = 4). The mean age of patients who underwent allo-SCT was 39 years. Minimal residual disease (MRD) just prior to SCT was positive in 1 patient and negative in 3. Engraftment was achieved in all patients, but 2 patients died of transplantation-related complications within 6 months. Complete molecular remission has been maintained in the remaining 2 patients. The mean age of patients who underwent auto-SCT was 48 years. MRD just prior to SCT was negative in all 4 patients. Complete molecular remission has been maintained in all 4 patients (mean follow-up, 3 years 9 months). The results for auto-SCT are favorable in patients with MRD-negative APL.

Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis

MOTIVATION

A major issue in computational biology is the reconstruction of pathways from several genomic datasets, such as expression data, protein interaction data and phylogenetic profiles. As a first step toward this goal, it is important to investigate the amount of correlation which exists between these data.

RESULTS

These methods are successfully tested on their ability to recognize operons in the Escherichia coli genome, from the comparison of three datasets corresponding to functional relationships between genes in metabolic pathways, geometrical relationships along the chromosome, and co-expression relationships as observed by gene expression data.

[Complex additional chromosomal abnormalities of del(5q), del(7q), and +22 in a patient with acute myelomonocytic leukemia carrying inv(16)]

A 37-year-old man with acute myelomonocytic leukemia (AML) M4E who exhibited the complex karyotype of 5q-, 7q-, and +22 in addition to inv(16), relapsed soon after complete remission. As previously reported, AML M4E carrying inv(16) is associated with a good prognosis, even when co-occurring with chromosomal abnormalities, which alone are considered to have poor outcome. Cytogenetic prognosis studies, such as CALGB or SWOG, have reported that certain additional chromosomal abnormalities or complex karyotypes might affect the prognosis of patients with AML M4E with inv(16). Our case suggests that, in general, AML M4E carrying inv(16) is in the favorable risk category, while cases with additional chromosomal abnormalities or complex karyotypes might be classified in the poor risk group and thus should be given additional clinical attention.

Extraction of correlated gene clusters by multiple graph comparison

This paper presents a new method to extract a set of correlated genes with respect to multiple biological features. Relationships among genes on a specific feature are encoded as a graph structure whose nodes correspond to genes. For example, the genome is a graph representing positional correlations of genes on the chromosome, the pathway is a graph representing functional correlations of gene products, and the expression profile is a graph representing gene expression similarities. When a set of genes are localized in a single graph, such as a gene cluster on the chromosome, an enzyme cluster in the metabolic pathway, or a set of coexpressed genes in the microarray gene expression profile, this may suggest a functional link among those genes. The functional link would become stronger when the clusters are correlated; namely, when a set of corresponding genes form clusters in multiple graphs. The newly introduced heuristic algorithm extracts such correlated gene clusters as isomorphic subgraphs in multiple graphs by using inter-graph links that are defined based on biological relevance. Using the method, we found E.coli correlated gene clusters in which genes are related with respect to the positions in the genome and the metabolic pathway, as well as the 3D structural similarity. We also analyzed protein-protein interaction data by two-hybrid experiments and gene coexpression data by microarrays in S.cerevisiae, and estimated the possibility of utilizing our method for screening the datasets that are likely to contain many false positive relations.

Helicobacter pylori alters n-6 fatty acid metabolism and prostaglandin E2 synthesis in rat gastric mucosal cells

BACKGROUND AND AIMS

Little is known about whether Helicobacter pylori infection alters fatty acid metabolism in gastric mucosal cells. By using cultured rat gastric mucosal cells (RGM-1), we investigated the effect of H. pylori broth culture filtrates on this point. Furthermore, our study aimed to find out whether n-6 long chain polyunsaturated fatty acids from linoleic acid are formed in RGM-1 cells.

METHODS

Rat gastric mucosal cells were incubated with 10, 20 and 40 microg/mL of linoleic acid or medium alone. Phosphatidylcholine content extracted from whole RGM-1 cells was quantitated by using a densitometer, and its fatty acid composition was analyzed by using gas chromatography. Prostaglandin E2 concentration in the culture medium was measured by using radioimmunoassay. The expression of cyclooxygenase (COX)-1 and COX-2 was examined by using reverse transcription-polymerase chain reaction. In addition, after incubation with [1-14C] linoleic acid, radioactivities of both linoleic acid and arachidonic acid components of the PC fraction were counted. The effects of H. pylori broth culture filtrates on PC content, its fatty acid composition and prostaglandin (PG)E2 synthesis were also assessed.

RESULTS

Linoleic acid addition caused an increase in the composition of arachidonic acid, as well as linoleic acid, and also in PGE2 concentration. Cyclo-oxygenase-2 expression was induced in RGM-1 cells by the addition of linoleic acid. In addition, [1-14C] linoleic acid added to the culture medium was converted to [1-14C] arachidonic acid in RGM-1 cells. Helicobacter pylori broth culture filtrates decreased linoleic acid composition and increased arachidonic acid composition. Moreover, after incubation with H. pylori broth culture filtrates, PGE2 concentrations were higher than that of the controls.

CONCLUSIONS

These findings suggest the presence of fatty acid elongase and Delta5- and Delta6-desaturases synthesize arachidonic acid from linoleic acid in RGM-1 cells. Thus, H. pylori infection may enhance PGE2 synthesis and accelerate n-6 fatty acid metabolism in gastric mucosal cells, which could make the gastric mucosal barrier more fragile.

Effect of Helicobacter pylori eradication on gastric mucosal phospholipid content and its fatty acid composition

BACKGROUND AND AIMS

Whether Helicobacter pylori eradication alters gastric mucosal phospholipid contents and their fatty acid composition remains unclear. The aim of the present study was to clarify the effect of H. pylori eradication on gastric mucosal phosphatidylcholine (PC) content and its fatty acid composition.

METHODS

Endoscopic biopsy specimens were taken from the antrum and body of each of 19 asymtomatic male volunteers for detection of H. pylori, histopathological assessment of gastritis, phospholipid determination and fatty acid analysis. All the subjects with H. pylori infection were treated with eradication therapy. Endoscopy and tissue sampling were repeated again 1 and 6 months after all treatment.

RESULTS

In eight subjects, H. pylori infection was evident and was successfully eradicated. Pretreatment degrees of lymphocytes and plasma cells (inflammation) and polymorphonuclear neutrophils (activity) were greater in H. pylori-positive subjects compared with H. pylori-negative subjects (P<0.001), whereas the degree of inflammation decreased (P<0.001), and neutrophils had completely disappeared at 6 months after eradication. Moreover, the gastric mucosal PC contents at the antrum and body were unchanged within 1 month after cessation of treatment, but increased at 6 months after eradication (P<0.05). At 6 months after cessation of treatment, H. pylori-eradicated subjects had an increase (+30% at antrum, +18% at body) in linoleic acid composition and a decrease (-37%, -43%) in arachidonic acid composition of PC at the antrum and body, respectively.

CONCLUSIONS

These findings suggest that H. pylori eradication reduces the production of various eicosanoids, resulting in the normalization of gastric mucosal PC content and its fatty acid composition, which may consequently cause the gastric mucosal hydrophobicity to be normalized.

Mining the quantitative trait loci associated with oral glucose tolerance in the OLETF rat

Although the synergetic effects of multiple marker loci regarding quantitative traits such as blood glucose level have attracted interest, previous conclusions have been based on assumptions that each marker locus behaves independently of the other, leading to approximation. To cope with this problem, this paper focuses on the effects of multiple genetic factors and tries to find significant marker combinations by using conjunctive rules regarding genotypes at multiple marker loci. Application of the proposed method on the OLETF model rat of non-insulin dependent diabetes mellitus (NIDDM) has found significant combinations of marker loci with respect to oral glucose tolerance (OGT).

[Home medical care from our hospital]

From April, 1996 to March, 1999, our hospital provided home medical care on a 24-hour basis for fifty patients with advanced or terminal cancer. Eventually, twenty-four patients died at home and twenty-six in the hospital. Stability of health status, the presence of willing and able caregivers, as well as a greater number of house-calls are suggested factors in facilitating a death at home. However, the patients who died in the hospital were obliged to readmit themselves until the time of death due to caregivers' reasons such as fatigue, emotional stress and/or health problems. In addition to timely availability and accessibility of respite care, psychosocial support for family caregivers by liaison nurses remains an issue to be solved in future.

Effect of Helicobacter pylori infection on gastric mucosal phospholipid contents and their fatty acid composition

To investigate the effect of Helicobacter pylori infection on the 'gastric mucosal barrier', phospholipid contents and the fatty acid composition of endoscopic biopsy specimens of the gastric mucosa were analysed in healthy volunteers with and without H. pylori infection. The gastric corporeal phosphatidylcholine (PC) content of H. pylori-positive healthy volunteers was less than that of H. pylori-negative healthy volunteers (P < 0.05). Moreover, H. pylori-positive healthy volunteers had a decrease in linoleic acid composition (P < 0.0001) and an increase in arachidonic acid composition (P < 0.0001) and in the arachidonic acid/linoleic acid ratio (P < 0.0001) of antral and corporeal PC compared with H. pylori-negative healthy volunteers. These findings suggest that H. pylori infection enhances production of various eicosanoids, resulting in changes in the gastric mucosal phospholipid contents and their fatty acid composition, that may consequently cause the gastric mucosal barrier to be weakened.

Classification of RNA secondary structures using the techniques of cluster analysis

An RNA molecule has a lot of suboptimal secondary structures. Some of these suboptimal structures are very similar and some are entirely different. In some cases, the free energy of these suboptimal structures does not differ much from that of the optimal structure. In order to characterize this relationship more clearly, we defined a metric among the secondary structures by the unweighted pair group method, using the arithmetic average and extended this metric to the sets of secondary structures. We report two applications of this metric. First, we developed a method for the classification of these suboptimal secondary structures of a given RNA sequence. Results of classification are presented with the secondary structures of cadang-cadang coconut viroid, potato spindle tuber viroid and polio virus as examples. Second, we applied this metric to the classification of the secondary structures derived from a set of mutant RNA sequences. We discuss that the mutation of a given RNA sequence changes not only the optimal secondary structure, but also the population of the cluster of the secondary structures.

Visualization of RNA secondary structures using highly parallel computers

Results of RNA secondary structure prediction algorithm are usually given as a set of hydrogen bonds between bases. However, we cannot know the precise structure of an RNA molecule by only knowing which bases form hydrogen bonds. One way to understand the structure of an RNA molecule is to visualize it using a planar graph so that we can easily know the geometric relations among the substructures such as stacking regions and loops. To do this, we consider bases to be particles on a plane and introduce a repulsive force and an attractive force among these particles and determine their positions according to these forces. A naive algorithm requires O(N2) time but we can reduce it to O(NlogN) with an approximation algorithm which is often used in the area of N-body simulation. Our program is written in parallel object-oriented language 'Schematic' which is recently developed. Efficiency of our implementation on a parallel computer and results of visualization of secondary structures are presented using cadang-cadang coconut viroid as an example.

RNA secondary structure prediction using highly parallel computers

An RNA secondary structure prediction method using a highly parallel computer is reported. We focus on finding thermodynamically stable structures of a single-stranded RNA molecule. Our approach is based on a parallel combinatorial method which calculates the free energy of a molecule as the sum of the free energies of all the physically possible hydrogen bonds. Our parallel algorithm finds many highly stable structures all at once, while most of the conventional prediction methods find only the most stable structure. The important idea in our algorithm is search tree pruning, with dynamic load balancing across the processor elements in a parallel computer. Software tools for visualization and classification of secondary structures are also presented using the sequence of cadang-cadang coconut viroid as an example. Our software system runs on CM-5.