Hemodynamic Analysis of Cerebral AVMs with 3D Phase-Contrast MR Imaging

BACKGROUND AND PURPOSE

The hemodynamics associated with cerebral AVMs have a significant impact on their clinical presentation. This study aimed to evaluate the hemodynamic features of AVMs using 3D phase-contrast MR imaging with dual velocity-encodings.

MATERIALS AND METHODS

Thirty-two patients with supratentorial AVMs who had not received any previous treatment and had undergone 3D phase-contrast MR imaging were included in this study. The nidus diameter and volume were measured for classification of AVMs (small, medium, or large). Flow parameters measured included apparent AVM inflow, AVM inflow index, apparent AVM outflow, AVM outflow index, and the apparent AVM inflow-to-outflow ratio. Correlation coefficients between the nidus volume and each flow were calculated. The flow parameters between small and other AVMs as well as between nonhemorrhagic and hemorrhagic AVMs were compared.

RESULTS

Patients were divided into hemorrhagic (n = 8) and nonhemorrhagic (n = 24) groups. The correlation coefficient between the nidus volume and the apparent AVM inflow and outflow was .83. The apparent AVM inflow and outflow in small AVMs were significantly smaller than in medium AVMs (P < .001 for both groups). The apparent AVM inflow-to-outflow ratio was significantly larger in the hemorrhagic AVMs than in the nonhemorrhagic AVMs (P = .02).

CONCLUSIONS

The apparent AVM inflow-to-outflow ratio was the only significant parameter that differed between nonhemorrhagic and hemorrhagic AVMs, suggesting that a poor drainage system may increase AVM pressure, potentially causing cerebral hemorrhage.

Integrating 3D Rotational Angiography into Gamma Knife Planning

3D rotational angiography provides remarkable spatial resolution for cerebrovascular disorders; however, it cannot be integrated directly into gamma knife planning due to the discrepancy of DICOM "tag" information, and most physicians still cannot benefit from 3D rotational angiography. Here, we describe a simple and easy technique to enable the integration of 3D rotational angiography.

Abstract P5-16-24: Prognostic factors after neoadjuvant chemotherapy in breast cancer: Surgery type as a new prognostic factor

Background: Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) is not necessarily linked to long-term survival. Response to chemotherapy and outcomes after NAC differ among breast cancer subtypes, so we analyzed prognostic factors by subtype.

Methods: We retrospectively analyzed 451 patients treated with anthracycline and taxane-based NAC between 2007 and 2015. Trastuzumab was added for human epidermal growth factor receptor (HER)-2-positive breast cancer. pCR was defined as no residual invasive breast carcinoma; noninvasive residuals and infiltrated lymph nodes were allowed. In our institute, mastectomy was performed in patients in whom the breast could not be preserved, such as patients with large residual tumors and diffusely spread tumors throughout the breast after NAC. Kaplan–Meier and univariate and multivariate cox regression analyses were used to evaluate disease-free interval (DFI) and DFI prognostic values, respectively.

Results: Median follow-up was 43 months; median age was 56 (range, 23–88) years. The 3-year DFI and OS were 82.1% and 94.4%, respectively. In total, 85 patients had recurrence (18.8%) and 31 patients died (6.9%). Response rate (RR) was 93.4% (421/457).pCR rate was 26.2% (118/451) in all cases: 0% (0/82), luminal A; 10.9% (14/128), luminal B HER2(−); 43.1% (31/71), luminal B HER2(+); 59.4% (38/64), HER2; and 34% (36/106), triple negative (TN). For all subtypes, patients who achieved pCR had a non-significantly higher DFI.

Multivariate cox regression showed these associations with DFI: surgery type and Ki-67 &gt; 30% for all cases and luminal B HER2(-); ypN (lymph node status after NAC), luminal B HER2(+);ypN and menopausal status, HER2; and age, surgery type, and clinical lymph node status (cN), TN.

Kaplan–Meier analysis showed that surgery type was strongly associated with DFI after NAC. Mastectomy patients had significantly poorer prognoses than partial mastectomy patients for all subtypes except HER2. For all cases, the median DFI in mastectomy patients was 73 months, but DFI was not reached in partial mastectomy patients (p &lt; 0.0001). Compared with partial mastectomy patients, mastectomy patients had more advanced disease in terms of tumor size, lymph node status, and stage and showed lesser clinical and pathological responses to NAC and effects on ypN. Furthermore, first recurrences in mastectomy patients were often distant metastases, leading to poor prognosis.

Moreover, we analyzed the prognostic factors in 118 patients who achieved pCR. Univariate Cox regression analysis showed the association of the following with DFI: age (≤40, &gt;40), cN, stage, surgery type, and ypN for all cases; decreasing Ki-67 values after NAC, luminal B HER2(−); clinical tumor size (cT), cN, surgery type, and luminal B HER2(+); ypN and HER2; age (≤40, &gt;40), cN, stage, surgery type, and TN. In multivariate cox regression analysis, age (≤40, &gt;40), surgery type, and ypN were independent predicting factors for all cases.

Conclusions: Prognostic factors after NAC differ among subtypes. Surgery type was strongly associated with outcomes after NAC, so it could be an independent prognostic factor.

Citation Format: Fujihara M, Kin T, Yoshimura Y, Kajiwara Y, Ito M, Ohtani S. Prognostic factors after neoadjuvant chemotherapy in breast cancer: Surgery type as a new prognostic factor [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-16-24.

Abstract P3-01-04: Potential clinical application of mammography conducted immediately after contrast enhanced CT as contrast enhanced subtraction mammography

【Background】

Contrast Enhanced Subtraction Mammography (CESM) has gained worldwide popularity. It is said that CESM can not only identify tumors but also delineate high-density lesions of the mammary gland that are difficult to be identified by normal mammography (MMG), as well as intraductal progress, and tumor hemodynamics.

一In general, imaging is commenced two minutes after injection of the contrast medium, and is conducted in two directions, i.e., left to right craniocaudal view and mediolateral oblique view in the similar manner to the normal MMG.

【Subjects and purpose】

The study was performed upon the approval of the institutional review board, and included 70 patients who had undergone CESM during the nine-month period from August 2015 to April 2016 using the method that MMG was performed within 2-8 minutes after injection of the contrast medium during contrast enhanced computed tomography. The scan was performed as postoperative follow-up in 29 patients, and as preoperative testing in 41 patients. This method allowed us to obtain additional data with contrast imaging without placing financial burden on the patient, and we investigated whether this method was effective as CESM in the present study.

【Results】

Of the 41 patients who had undergone the scan as a preoperative test (bilateral scans in 3 patients, and 44 breasts), it was in 43 breasts (97.7 %) that lesions could be identified by MMG, and in 42 breasts (95.5 %) that lesions could be identified by CESM. Of the 44 breasts, three breasts showed high-density mammary glands, in two of which the mass was lateral to the margin of the mammary gland, and therefore could be identified by normal MMG; however, in one breast the mass was medial to the margin of the mammary gland and difficult to be identified by MMG, and could only be identified by CESM. The lesions in the two breasts that were difficult to be identified by CESM exhibited the histological type of DCIS, and the lesions were able to be identified as calcification with normal MMG.

The tumor diameter was compared using invasion size determined by CESM, contrast-enhanced MRI, and postoperative pathological specimen, respectively. The correlation coefficient for CESM and contrast-enhanced MRI was 0.9668, and the correlation coefficient for CESM and postoperative pathological specimen was 0.984887, with a strong correlation observed (Pearson's correlation coefficient test).

【Conclusion】

To the best of our knowledge, no reports of CESM in which MMG is performed immediately after contrast-enhanced CT have been published to date, and thus this is the world's first attempt of such method performed at our hospital. CESM ensures diagnosability without being invasive or placing financial burden on the patient. It was suggested that CESM can be clinically useful particularly for those who cannot undergo contrast-enhanced MRI due to hardware problems, financial difficulties, or metal embedded within the body.

Citation Format: Ohtani S, Yoshimura Y, Kin T, Fujihara M, Kajiwara Y, Ito M, Okada N, Urashima M. Potential clinical application of mammography conducted immediately after contrast enhanced CT as contrast enhanced subtraction mammography [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-01-04.

Islet product characteristics and factors related to successful human islet transplantation from the Collaborative Islet Transplant Registry (CITR) 1999-2010

The Collaborative Islet Transplant Registry (CITR) collects data on clinical islet isolations and transplants. This retrospective report analyzed 1017 islet isolation procedures performed for 537 recipients of allogeneic clinical islet transplantation in 1999-2010. This study describes changes in donor and islet isolation variables by era and factors associated with quantity and quality of final islet products. Donor body weight and BMI increased significantly over the period (p<0.001). Islet yield measures have improved with time including islet equivalent (IEQ)/particle ratio and IEQs infused. The average dose of islets infused significantly increased in the era of 2007-2010 when compared to 1999-2002 (445.4±156.8 vs. 421.3±155.4×0(3) IEQ; p<0.05). Islet purity and total number of β cells significantly improved over the study period (p<0.01 and <0.05, respectively). Otherwise, the quality of clinical islets has remained consistently very high through this period, and differs substantially from nonclinical islets. In multivariate analysis of all recipient, donor and islet factors, and medical management factors, the only islet product characteristic that correlated with clinical outcomes was total IEQs infused. This analysis shows improvements in both quantity and some quality criteria of clinical islets produced over 1999-2010, and these parallel improvements in clinical outcomes over the same period.

Islet oxygen consumption rate dose predicts insulin independence for first clinical islet allotransplants

BACKGROUND

Human islet allotransplantation for the treatment of type 1 diabetes is in phase III clinical trials in the U.S. and is the standard of care in several other countries. Current islet product release criteria include viability based on cell membrane integrity stains, glucose-stimulated insulin release, and islet equivalent (IE) dose based on counts. However, only a fraction of patients transplanted with islets that meet or exceed these release criteria become insulin independent following 1 transplant. Measurements of islet oxygen consumption rate (OCR) have been reported as highly predictive of transplant outcome in many models.

METHOD

In this article we report on the assessment of clinical islet allograft preparations using OCR dose (or viable IE dose) and current product release assays in a series of 13 first transplant recipients. The predictive capability of each assay was examined and successful graft function was defined as 100% insulin independence within 45 days post-transplant.

RESULTS

OCR dose was most predictive of CTO. IE dose was also highly predictive, while glucoses stimulated insulin release and membrane integrity stains were not.

CONCLUSION

OCR dose can predict CTO with high specificity and sensitivity and is a useful tool for evaluating islet preparations prior to clinical human islet allotransplantation.

Autologous islet transplantation after total pancreatectomy for renal cell carcinoma metastases

Pancreatic metastases from renal cell carcinoma (RCC) may have a chronic and highly indolent course, and may be resected for cure after considerable delay following treatment of the primary tumor, in contrast to other more common pancreatic tumors. Surgical resection is the treatment of choice, which may lead to postpancreatectomy diabetes mellitus in the case of extensive resection. We present a 70-year-old patient with multifocal pancreatic metastases from RCC causing obstructive jaundice. A total pancreatectomy was required to excise two distant tumors in the head and tail of the pancreas, together with a segment VI liver resection. An autologous islet transplant (AIT) prepared from the central, uninvolved pancreas was carried out to prevent postpancreatectomy diabetes. The patient was rendered insulin-free and remains so with excellent glycemic control for 1 year of follow-up, and there is no evidence of tumor recurrence. The patient has been treated with adjuvant sunitinib to minimize risk of further recurrence. In conclusion, AIT after pancreatectomy may represent a useful option to treat patients with metastatic RCC. A critical component of this approach was dependent upon elaborate additional testing to exclude contamination of the islet preparation by cancerous cells.

Distinct and opposing roles for the phosphatidylinositol 3-OH kinase catalytic subunits p110α and p110β in the regulation of insulin secretion from rodent and human beta cells

AIMS/HYPOTHESIS

Phosphatidylinositol 3-OH kinases (PI3Ks) regulate beta cell mass, gene transcription, and function, although the contribution of the specific isoforms is unknown. As reduced type 1A PI3K signalling is thought to contribute to impaired insulin secretion, we investigated the role of the type 1A PI3K catalytic subunits α and β (p110α and -β) in insulin granule recruitment and exocytosis in rodent and human islets.

METHODS

The p110α and p110β subunits were inhibited pharmacologically or by small hairpin (sh)RNA-mediated knockdown, and were directly infused or overexpressed in mouse and human islets, beta cells and INS-1 832/13 cells. Glucose-stimulated insulin secretion (GSIS), single-cell exocytosis, Ca(2+) signalling, plasma membrane granule localisation, and actin density were monitored.

RESULTS

Inhibition or knockdown of p110α increased GSIS. This was not due to altered Ca(2+) responses, depolymerisation of cortical actin or increased cortical granule density, but to enhanced Ca(2+)-dependent exocytosis. Intracellular infusion of recombinant PI3Kα (p110α/p85β) blocked exocytosis. Conversely, knockdown (but not pharmacological inhibition) of p110β blunted GSIS, reduced cortical granule density and impaired exocytosis. Exocytosis was rescued by direct intracellular infusion of recombinant PI3Kβ (p110β/p85β) even when p110β catalytic activity was inhibited. Conversely, both the wild-type p110β and a catalytically inactive mutant directly facilitated exocytosis.

CONCLUSIONS/INTERPRETATION

Type 1A PI3K isoforms have distinct and opposing roles in the acute regulation of insulin secretion. While p110α acts as a negative regulator of beta cell exocytosis and insulin secretion, p110β is a positive regulator of insulin secretion through a mechanism separate from its catalytic activity.

The voltage-dependent potassium channel subunit Kv2.1 regulates insulin secretion from rodent and human islets independently of its electrical function

AIMS/HYPOTHESIS

It is thought that the voltage-dependent potassium channel subunit Kv2.1 (Kv2.1) regulates insulin secretion by controlling beta cell electrical excitability. However, this role of Kv2.1 in human insulin secretion has been questioned. Interestingly, Kv2.1 can also regulate exocytosis through direct interaction of its C-terminus with the soluble NSF attachment receptor (SNARE) protein, syntaxin 1A. We hypothesised that this interaction mediates insulin secretion independently of Kv2.1 electrical function.

METHODS

Wild-type Kv2.1 or mutants lacking electrical function and syntaxin 1A binding were studied in rodent and human beta cells, and in INS-1 cells. Small intracellular fragments of the channel were used to disrupt native Kv2.1-syntaxin 1A complexes. Single-cell exocytosis and ion channel currents were monitored by patch-clamp electrophysiology. Interaction between Kv2.1, syntaxin 1A and other SNARE proteins was probed by immunoprecipitation. Whole-islet Ca(2+)-responses were monitored by ratiometric Fura red fluorescence and insulin secretion was measured.

RESULTS

Upregulation of Kv2.1 directly augmented beta cell exocytosis. This happened independently of channel electrical function, but was dependent on the Kv2.1 C-terminal syntaxin 1A-binding domain. Intracellular fragments of the Kv2.1 C-terminus disrupted native Kv2.1-syntaxin 1A interaction and impaired glucose-stimulated insulin secretion. This was not due to altered ion channel activity or impaired Ca(2+)-responses to glucose, but to reduced SNARE complex formation and Ca(2+)-dependent exocytosis.

CONCLUSIONS/INTERPRETATION

Direct interaction between syntaxin 1A and the Kv2.1 C-terminus is required for efficient insulin exocytosis and glucose-stimulated insulin secretion. This demonstrates that native Kv2.1-syntaxin 1A interaction plays a key role in human insulin secretion, which is separate from the channel's electrical function.

Anakinra potentiates the protective effects of etanercept in transplantation of marginal mass human islets in immunodeficient mice

Anti-inflammatory agents are used routinely in clinical islet transplantation in an attempt to promote islet engraftment. Infliximab, and more recently etanercept, is being used to neutralize tumor necrosis factor alpha, but this tenet is based on limited preclinical data. One group has promoted the potential of combined etanercept with an IL-1 receptor antagonist, anakinra in a small clinical study, but without strong preclinical data to justify this approach. We therefore sought to evaluate the impact of combined anakinra and etanercept in a marginal islet mass transplant model using human islets in immunodeficient mice. The combination of anakinra and etanercept led to remarkable improvement in islet engraftment (control 36.4%; anakinra 53.9%; etanercept 45.45%; anakinra and etanercept 87.5% euglycemia, p < 0.05 by log-rank) compared to single-drug treated mice or controls. This translated into enhanced metabolic function (area under curve glucose tolerance), improved graft insulin content and marked reduction in beta-cell specific apoptotis (0.67% anakinra + etanercept vs. 23.5% control, p < 0.001). These results therefore strongly justify the combined short-term use of anakinra and etanercept in human islet transplantation.

Late cytomegalovirus transmission and impact of T-depletion in clinical islet transplantation

The epidemiology of cytomegalovirus infection (CMV) in islet transplantation (IT) is not well defined. This study defines incidence, transmission and clinical sequelae of CMV reactivation or disease in 121 patients receiving 266 islet infusions at a single institution. The donor (D)/recipient (R) serostatus was D+/R- 31.2%, D+/R+ 26.3%, D-/R+ 13.2% and D-/R- 29.3%. CMV prophylaxis with oral ganciclovir/valganciclovir was given in 68%. CMV infection occurred in 14/121 patients (11.6%); six had asymptomatic seroconversion and eight others had positive viremia (six asymptomatic and two with CMV febrile symptoms). Median peak viral loads were 1755 copies/mL (range 625-9 100 000). Risk factors for viremia included lymphocyte depletion (thymoglobulin or alemtuzumab, p < 0.001). Viremia was more common in D+/R+ versus D+/R- (p = 0.12), occurring mostly late after transplant (median 306 days). Presumed transmission from IT occurred in 8/83 of D+/R- procedures (9.6%). Of the two cases of CMV disease, one resulted from islet transmission from a CMV positive donor (D+/R-); the other was due to de novo exogenous infection (D-/R-). Therefore, CMV transmission presents rarely after IT and with low incidence compared to solid organ transplantation, but occurs late posttransplant. The use of lymphocyte depleting therapies is a primary risk factor.

Human islet distribution program for basic research at a single center

The Clinical Islet Laboratory at the University of Alberta/Alberta Health Services distributes human islets for basic research when islet preparations fail to meet defined release criteria for transplantation. This report highlights our islet distribution activity for diabetes research over a 3-year period. Shipments of the acinar-enriched fraction for research were not included in this report. In 2010, we distributed 6.3 million islet equivalents (IEQs) of islets through 127 shipments to 8 researchers, locally, nationally, and internationally. The number of preparations for research use was stable over the 3-year period (26, 23, and 29 preparations in 2008, 2009, and 2010, respectively). Islet yield distributed for research per isolation was 201, 212, and 218 × 10(3) IEQs, respectively. The number of basic researchers was stable as well, although there were only 2 researchers before 2007. Recently, each researcher has received fewer islets per shipment (49,820 IEQs in 2010 vs 75,635 IEQs in 2008) but more frequently (21.5 in 2010 vs 11.2 times per year in 2008). This paradigm shift would be desirable for researchers, because in our experience, most require <30,000 IEQs per shipment, and more frequent islet shipments results in a larger sample size for experimentation. After an initial expansion in the number of researchers requesting islets, our islet distribution activity has remained stable over the years in terms of total productivity of islets utilized for research. The current supply-versus-demand ratio in our program appears to be appropriate.

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence-specific gene silencing by guiding Argonaute complexes to target RNAs by means of base pairing. RNA silencing is thought to have evolved as a form of nucleic-acid-based immunity to inactivate viruses and transposable elements. Although the activity of transposable elements in animals has been thought largely to be restricted to the germ line, recent studies have shown that they may also actively transpose in somatic cells, creating somatic mosaicism in animals. In the Drosophila germ line, Piwi-interacting RNAs arise from repetitive intergenic elements including retrotransposons by a Dicer-independent pathway and function through the Piwi subfamily of Argonautes to ensure silencing of retrotransposons. Here we show that, in cultured Drosophila S2 cells, Argonaute 2 (AGO2), an AGO subfamily member of Argonautes, associates with endogenous small RNAs of 20-22 nucleotides in length, which we have collectively named endogenous short interfering RNAs (esiRNAs). esiRNAs can be divided into two groups: one that mainly corresponds to a subset of retrotransposons, and the other that arises from stem-loop structures. esiRNAs are produced in a Dicer-2-dependent manner from distinctive genomic loci, are modified at their 3' ends and can direct AGO2 to cleave target RNAs. Mutations in Dicer-2 caused an increase in retrotransposon transcripts. Together, our findings indicate that different types of small RNAs and Argonautes are used to repress retrotransposons in germline and somatic cells in Drosophila.

A fast structural multiple alignment method for long RNA sequences

BACKGROUND

Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses.

RESULTS

We propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA). The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory.

CONCLUSION

The proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.

Rfold: an exact algorithm for computing local base pairing probabilities

MOTIVATION

Base pairing probability matrices have been frequently used for the analyses of structural RNA sequences. Recently, there has been a growing need for computing these probabilities for long DNA sequences by constraining the maximal span of base pairs to a limited value. However, none of the existing programs can exactly compute the base pairing probabilities associated with the energy model of secondary structures under such a constraint.

RESULTS

We present an algorithm that exactly computes the base pairing probabilities associated with the energy model under the constraint on the maximal span W of base pairs. The complexity of our algorithm is given by O(NW2) in time and O(N+W2) in memory, where N is the sequence length. We show that our algorithm has a higher sensitivity to the true base pairs as compared to that of RNAplfold. We also present an algorithm that predicts a mutually consistent set of local secondary structures by maximizing the expected accuracy function. The comparison of the local secondary structure predictions with those of RNALfold indicates that our algorithm is more accurate. Our algorithms are implemented in the software named 'Rfold.'

AVAILABILITY

The C++ source code of the Rfold software and the test dataset used in this study are available at http://www.ncrna.org/software/Rfold/.

miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity

The identification of novel miRNAs has significant biological and clinical importance. However, none of the known miRNA features alone is sufficient for accurately detecting novel miRNAs. The aim of this paper is to integrate these features in a straightforward manner for detecting miRNAs with better accuracy. Since most miRNA regions are highly conserved among vertebrates for the ability to form stable hairpin structures, we implemented a hidden Markov model that outputs multidimensional feature vectors composed of both evolutionary features and secondary structural ones. The proposed method, called miRRim, outperformed existing ones in terms of detection/prediction performance: The total number of predictions was smaller than with existing methods when the number of miRNAs detected was adjusted to be the same. Moreover, there were several candidates predicted only by our method that are clustered with the known miRNAs, suggesting that our method is able to detect novel miRNAs. Genomic coordinates of predicted miRNA can be obtained from http://mirrim.ncrna.org/.

Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat

SUMMARY

We have launched a web server, which serves as a general-purpose idiogram rendering service, and allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface. The generated idiograms are suitable not only for visualizing summaries of genome-wide analysis but also for many types of presentation material including web pages, conference posters, oral presentations, etc.

AVAILABILITY

Idiographica is freely available at http://www.ncrna.org/idiographica/

Coexistence of Ramsay Hunt syndrome and varicella-zoster virus encephalitis

We describe a patient with Ramsay Hunt syndrome and varicella-zoster virus encephalitis. The coexistence of these conditions is rare and to our knowledge has not been clearly documented in the English-language literature. We summarize the clinical characteristics of our patient and seven similar patients described in previous reports, including those published in Japanese. Although concomitant diseases such as diabetes and chronic renal failure may lead to an aggressive course, all patients described in detail have had good outcomes.

Identification and characterization of human non-coding RNAs with tissue-specific expression

We have examined the expression profile of selected non-coding RNAs (ncRNAs) in 11 human tissues. Among 5489 full-length cDNA clones annotated as non-protein-coding transcripts in the H-Invitational database, we chose 150 clones for further analysis based on their gene structure and EST information. Expression profiling using quantitative RT-PCR and Northern blot hybridization revealed that the majority of the selected ncRNAs exhibited tissue specificity: 67% are predominantly expressed in a restricted subset of tissues. The absolute quantification of representative ncRNAs revealed that the majority of ncRNAs are expressed as low abundance transcripts. A comparative genomic analysis revealed that only 27% of the selected ncRNAs have mouse counterparts. Since the expression patterns of the human ncRNAs having no mouse counterparts remain to be similar to those of the mouse ncRNAs, the expression patterns of the selected ncRNAs may be conserved between human and mouse.

Enhancing the success of human islet isolation through optimization and characterization of pancreas dissociation enzyme

A major obstacle to successful human islet isolation has been the variability of the enzymatic digestion phase. The aim of this study was to define optimal enzyme activity ranges normalized by the pancreas weight and to identify valid parameters for the optimal selection of successful lots of collagenase enzyme blends. Our results from 251 islet isolations showed that optimization of thermolysin dosage based on Caseinase unit/g pancreas contributed considerably to islet isolation outcome but that collagenase dosage measured by the manufacturer (Wünsch unit/g pancreas) was not a major determinant of islet isolation outcome. We also found that lot-to-lot inconsistency of enzyme performance was not explained by the activity values provided by the manufacturer, but rather by an in-house assay of class I collagenase (CI) and class II collagenase (CII); using a lot with a lower CII/CI resulted in a higher success rate. The odds of successful isolation was 8.67 times higher when a vial with CII/CI ratio <0.204 was used than when a vial with CII/CI >or=0.204 was used, suggesting that CII/CI ratio may be a strong predictor to distinguish potential lot success. This study provides a framework for improved enzymatic digestion in human islet isolation.

Murlet: a practical multiple alignment tool for structural RNA sequences

MOTIVATION

Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken into account while constructing accurate multiple alignments of RNA genes. The Sankoff algorithm is a natural alignment algorithm that includes the effect of base-pair covariation in the alignment model. However, the extremely high computational cost of the Sankoff algorithm precludes its application to most RNA sequences.

RESULTS

We propose an efficient algorithm for the multiple alignment of structural RNA sequences. Our algorithm is a variant of the Sankoff algorithm, and it uses an efficient scoring system that reduces the time and space requirements considerably without compromising on the alignment quality. First, our algorithm computes the match probability matrix that measures the alignability of each position pair between sequences as well as the base pairing probability matrix for each sequence. These probabilities are then combined to score the alignment using the Sankoff algorithm. By itself, our algorithm does not predict the consensus secondary structure of the alignment but uses external programs for the prediction. We demonstrate that both the alignment quality and the accuracy of the consensus secondary structure prediction from our alignment are the highest among the other programs examined. We also demonstrate that our algorithm can align relatively long RNA sequences such as the eukaryotic-type signal recognition particle RNA that is approximately 300 nt in length; multiple alignment of such sequences has not been possible by using other Sankoff-based algorithms. The algorithm is implemented in the software named 'Murlet'.

AVAILABILITY

The C++ source code of the Murlet software and the test dataset used in this study are available at http://www.ncrna.org/papers/Murlet/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus

In the human HOXA locus a number of ncRNAs are transcribed from the intergenic regions in the opposite direction to HOXA mRNAs. We observed that the genomic organization of genes for the ncRNAs and HOXA proteins is highly conserved between human and mouse. We examined the expression profiles of these ncRNAs and HOXA mRNAs in various human tissues. The expression patterns of ncRNAs in human tissues coincide with those of the adjacent HOXA mRNAs that are collinearly expressed along the anteroposterior axis. This coordinated expression was observed even in transformed tumors and cancer cell lines, suggesting that the expression of ncRNAs is prerequisite for the regulated expression of HOXA genes. HIT18844 ncRNA transcribed from the most upstream position of the HOXA cluster possesses an ultra-conserved short stretch which potentially forms an evolutionarily conserved secondary structure. Our data suggest a critical role for ncRNAs in the regulation of HOXA gene expression.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices

MOTIVATION

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures.

RESULTS

We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs.

AVAILABILITY

The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences

There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized. Some of these transcripts may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation of such transcripts to find functional non-coding RNA candidates is very costly. Therefore, our primary interest is to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts. We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc. fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available at

Mining frequent stem patterns from unaligned RNA sequences

MOTIVATION

In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly.

RESULTS

Our method RNAmine employs a graph theoretic representation of RNA sequences and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

AVAILABILITY

The software is available upon request.

Global and region-specific analyses of apparent diffusion coefficient in dentatorubral-pallidoluysian atrophy

BACKGROUND AND PURPOSE

Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant spinocerebellar ataxia. Techniques for the quantitative assessment of neurodegenerative lesions remain to be established in this disease. We attempted to quantify global and region-specific neurodegeneration in DRPLA using analysis of apparent diffusion coefficient (ADC) maps.

METHODS

Diffusion-weighted images (b = 1000 s/mm(2)) by echo-planar sequences were obtained with the use of a 1.5T clinical scanner. Whole-brain histogram and region of interest (ROI) analyses of ADC values as well as conventional MR imaging studies were performed in 6 patients with genetically confirmed DRPLA.

RESULTS

Histograms demonstrated significantly higher mean ADC values in the patients than in age- and sex-matched control subjects (P < .01). ROI analysis revealed that the patients had significantly higher ADC values in the cerebellum and globus pallidus, preferentially affected regions (P < .05), but not in the thalamus, the region relatively spared in this disease. ADC values in the white matter were higher only in patients with adult-onset disease. Histogram analyses could more sensitively identify abnormalities than ROI analyses, because the former avoided errors associated with setting ROIs and thus had smaller P values on statistical analysis than the latter.

CONCLUSIONS

Histogram ADC analyses were more sensitive for the detection of neurodegeneration in DRPLA than ROI analyses, whereas ROI analyses revealed regional alterations reflecting the distribution of pathologic changes. Thus, histogram and ROI analyses complement each other and may permit the sensitive, quantitative evaluation of neurodegeneration in DRPLA, especially that involving the globus pallidus showing normal T2 signals.

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments

MOTIVATION

The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but also their potential secondary structures. Sankoff's algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required.

RESULTS

We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable with the much slower existing algorithms.

AVAILABILITY

The web server of SCARNA with graphical structural alignment viewer is available at http://www.scarna.org/.

Genome sequencing and analysis of Aspergillus oryzae

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.

Prevention of bleeding after islet transplantation: lessons learned from a multivariate analysis of 132 cases at a single institution

Islet transplantation is being offered increasingly for selected patients with unstable type 1 diabetes. Percutaneous transhepatic portal access avoids a need for surgery, but is associated with potential risk of bleeding. Between 1999 and 2005, we performed 132 percutaneous transhepatic islet transplants in 67 patients. We encountered bleeding in 18/132 cases (13.6%). In univariate analysis, the risk of bleeding in the absence of effective track ablation was associated with an increasing number of procedures (2nd and 3rd procedures with an odds ratio (OR) of 9.5 and 20.9, respectively), platelets count <150,000 (OR 4.4), elevated portal pressure (OR 1.1 per mm Hg rise), heparin dose > or =45 U/kg (OR 9.8) and pre-transplant aspirin (81 mg per day) (OR 2.6, p = 0.05). A multivariate analysis further confirmed the cumulative transplant procedure number (p < 0.001) and heparin dose > or =45 U/kg (p = 0.02) as independent risk factors for bleeding. Effective mechanical sealing of the intrahepatic portal catheter tract with thrombostatic coils and tissue fibrin glue completely prevented bleeding in all subsequent procedures (n = 26, p = 0.02). We conclude that bleeding after percutaneous islet implantation is an avoidable complication provided the intraparenchymal liver tract is sealed effectively.

Multi-lot analysis of custom collagenase enzyme blend in human islet isolations

INTRODUCTION

Variability currently in Liberase HI from lot to lot limits the ability to effectively isolate islets with consistency. Roche Diagnostics Inc (Indianapolis, Ind, USA) has developed a Custom Collagenase enzyme blend in hopes that producing collagenase II and I and thermolysin separately will eliminate variability. In this study we examined the variability in Custom Collagenase lots in respect to isolation results and isolation success rates and compared those to Liberase HI.

METHODS

We retrospectively analyzed records from 68 islet isolations where either Liberase HI (lot A: n = 23, Lot B: n = 20) or Custom Collagenase blend (Lot C: n = 10, Lot D: n = 15) was employed. Human islets were isolated from cadaveric pancreata using standardized methods performed in a controlled islet isolation facility.

RESULTS

Analysis of Liberase HI and Custom Collagenase using Student t test showed no difference between the two groups. Comparison of the two Custom Collagenase lots using the t test showed a statistical difference between undigested pancreas weight and pancreas digestion times. Using chi-square test, no statistical significance was found in isolation success rates from lot to lot.

CONCLUSION

Although the Custom Collagenase blend is comparable to Liberase HI in its ability to isolate human islets, variability still exists from lot to lot when used conventionally as Liberase HI is. The ability to predetermine doses is beneficial, and as techniques to manipulate the activity levels prior to isolations improve so to will the enzymes' ability to isolate islets on a consistent basis.

The standardization of pancreatic donors for islet isolation

INTRODUCTION

Islet transplantation has proven to be a successful treatment for insulin-dependent diabetes mellitus (IDDM). The aim of this study was to establish an algorithm by which the combination of the donor quality and pancreas quality was given a numerical score from 0 to 100 for use in determining the quality of a pancreas for islet isolation.

METHODS

In this study we retrospectively analyzed 326 pancreata and the outcomes of their respective isolations. Specific donor variables and physical characteristics were identified and weighted according to their influence on the success of the isolation. For each variable, ranges and point weightings were established based on our laboratory experience and literature review.

RESULTS

Analysis of the data showed a strong association of the donor point with isolation outcome. Pancreata with lower donor point scores had lower transplant success rates, while higher donor point scores in turn produced higher transplant rates.

CONCLUSION

This scoring system has proven to be effective in assessing the potential of pancreata for a favorable isolation outcome. By analyzing the final score of the pancreas, a standardized decision can be made on whether to accept or decline the pancreas. Another benefit of the scoring system is that it is a quick and efficient way to trend the quality of donor organs.

Marginalized kernels for biological sequences

MOTIVATION

Kernel methods such as support vector machines require a kernel function between objects to be defined a priori. Several works have been done to derive kernels from probability distributions, e.g., the Fisher kernel. However, a general methodology to design a kernel is not fully developed.

RESULTS

We propose a reasonable way of designing a kernel when objects are generated from latent variable models (e.g., HMM). First of all, a joint kernel is designed for complete data which include both visible and hidden variables. Then a marginalized kernel for visible data is obtained by taking the expectation with respect to hidden variables. We will show that the Fisher kernel is a special case of marginalized kernels, which gives another viewpoint to the Fisher kernel theory. Although our approach can be applied to any object, we particularly derive several marginalized kernels useful for biological sequences (e.g., DNA and proteins). The effectiveness of marginalized kernels is illustrated in the task of classifying bacterial gyrase subunit B (gyrB) amino acid sequences.

Resuscitation of the ischemically damaged human pancreas by the two-layer method prior to islet isolation

A two-layer cold storage method (TLM) allows sufficient oxygen delivery to pancreata during preservation and resuscitates the viability of ischemically damaged pancreata. This study determined the effect of additional preservation of ischemically damaged human pancreata by the TLM before islet isolation. Human pancreata were procured from cadaveric organ donors and preserved by the TLM for 3.2 +/- 0.5 hours (mean +/- SEM) at 4 degrees C after 11.1 +/- 0.9 hours of cold storage in University of Wisconsin solution (UW) (TLM group), or by cold UW alone for 11.0 +/- 0.3 hours (UW group). Islet isolations of all pancreata were performed using the Edmonton protocol. Islet recovery and in vitro function of isolated islets were significantly increased in the TLM group compared with the UW group. In the metabolic assessment of human pancreata, ATP levels were significantly increased after the TLM preservation. This study showed that additional short-term preservation by the TLM resuscitates the viability of ischemically damaged human pancreata before islet isolation, leading to improvements in islet recovery and in vitro function of isolated islets.

Marginalized kernels for RNA sequence data analysis

We present novel kernels that measure similarity of two RNA sequences, taking account of their secondary structures. Two types of kernels are presented. One is for RNA sequences with known secondary structures, the other for those without known secondary structures. The latter employs stochastic context-free grammar (SCFG) for estimating the secondary structure. We call the latter the marginalized count kernel (MCK). We show computational experiments for MCK using 74 sets of human tRNA sequence data: (i) kernel principal component analysis (PCA) for visualizing tRNA similarities, (ii) supervised classification with support vector machines (SVMs). Both types of experiment show promising results for MCKs.

Serine-protease inhibition during islet isolation increases islet yield from human pancreases with prolonged ischemia

BACKGROUND

Islet isolation from the pancreatic tissue matrix remains highly variable. Recent evidence suggests that intrinsic human pancreatic proteases, including trypsin, may inhibit effective collagenase enzymatic activity during islet isolation, thereby impairing the isolation success. In this study we have hypothesized that serine protease inhibition applied during pancreatic digestion, could improve yield and/or functional viability of islets isolated from human pancreases.

METHODS

Twelve organ donor pancreases with 12.9+/-0.6 hr cold storage (mean+/-SEM) were perfused via their ducts with Liberase-HI enzyme in the presence (n=6) or absence (n=6) of 0.4 mM Pefabloc. All were then gently dissociated and their purified islets separated with Ficoll density gradient centrifugation.

RESULTS

Donor-related factors (age, gender, cold storage time, body mass index, and pancreas weight) did not differ significantly between the two experimental groups. Pefabloc supplementation did not affect the digestion time, islets remaining trapped in exocrine tissue, or final islet purity. Islet recovery was increased in the Pefabloc-treated group (mean+/-SEM yield 323.8+/-80.8 x 10(3) islet equivalents vs. 130.8+/-13.6 x 10(3) islet equivalents, P<0.05). Cellular composition, DNA and insulin content, and insulin secretory activity of the isolated islets was similar.

CONCLUSIONS

Inhibition of intrinsic protease activity within pancreases after prolonged cold storage improves isolation of viable islets.

Clinical outcomes and insulin secretion after islet transplantation with the Edmonton protocol

Islet transplantation offers the prospect of good glycemic control without major surgical risks. After our initial report of successful islet transplantation, we now provide further data on 12 type 1 diabetic patients with brittle diabetes or problems with hypoglycemia previous to 1 November 2000. Details of metabolic control, acute complications associated with islet transplantation, and long-term complications related to immunosuppression therapy and diabetes were noted. Insulin secretion, both acute and over 30 min, was determined after intravenous glucose tolerance tests (IVGTTs). The median follow-up was 10.2 months (CI 6.5-17.4), and the longest was 20 months. Glucose control was stable, with pretransplant fasting and meal tolerance-stimulated glucose levels of 12.5+/-1.9 and 20.0+/-2.7 mmol/l, respectively, but decreased significantly, with posttransplant levels of 6.3+/-0.3 and 7.5+/-0.6 mmol/l, respectively (P < 0.006). All patients have sustained insulin production, as evidenced by the most current baseline C-peptide levels 0.66+/-0.06 nmol/l, increasing to 1.29+/-0.25 nmol/l 90 min after the meal-tolerance test. The mean HbA1c level decreased from 8.3+/-0.5% to the current level of 5.8+/-0.1% (P < 0.001). Presently, four patients have normal glucose tolerance, five have impaired glucose tolerance, and three have post-islet transplant diabetes (two of whom need oral hypoglycemic agents and low-dose insulin (<10 U/day). Three patients had a temporary increase in their liver-function tests. One patient had a thrombosis of a peripheral branch of the right portal vein, and two of the early patients had bleeding from the hepatic needle puncture site; but these technical problems were resolved. Two patients had transient vitreous hemorrhages. The two patients with elevated creatinine levels pretransplant had a significant increase in serum creatinine in the long term, although the mean serum creatinine of the group was unchanged. The cholesterol increased in five patients, and lipid-lowering therapy was required for three patients. No patient has developed cytomegalovirus infection or disease, posttransplant lymphoproliferative disorder, malignancies, or serious infection to date. None of the patients have been sensitized to donor antigen. In 11 of the 12 patients, insulin independence was achieved after 9,000 islet equivalents (IEs) per kilogram were transplanted. The acute insulin response and the insulin area under the curve (AUC) after IVGTT were consistently maintained over time. The insulin AUC from the IVGTT correlated to the number of islets transplanted, but more closely correlated when the cold ischemia time was taken into consideration (r = 0.83, P < 0.001). Islet transplantation has successfully corrected labile type 1 diabetes and problems with hypoglycemia, and our results show persistent insulin secretion. After a minimum of 9,000 IEs per kilogram are provided, insulin independence is usually attained. An elevation of creatinine appears to be a contraindication to this immunosuppressive regimen. For the subjects who had labile type 1 diabetes that was difficult to control, the risk-to-benefit ratio is in favor of islet transplantation.

[A case of epithelial membrane antigen-positive leiomyosarcoma of the urinary bladder]

A 41-year-old woman was admitted with gross hematuria and pain on urination. Cystoscopy showed a huge and lobulated submucosal non-papillary bladder tumor. Pelvic computed tomography demonstrated a heterogeneous and enhanced lobulated mass, 8 cm in diameter, with extravesical invasion but there appeared to be no metastatic lesions. Transurethral biopsy revealed leiomyosarcoma pathologically. Total cystectomy and construction of an ileal conduit were performed. The tumor was histologically diagnosed as leiomyosarcoma. Immunohistochemical studies revealed the tumor to be positive for epithelial membrane antigen (EMA) and muscle actin but negative for desmin, and S-100. We reviewed 102 cases of vesical leiomyosarcoma reported in Japan. Among these 102 cases, there were no EMA-positive cases. Immunohistochemical and electromicroscopic evaluation should be performed to evaluate this disease.

[Treatment results of VIP (etoposide, ifosfamide and cisplatin) chemotherapy as a first-line therapy in metastatic germ cell tumors]

PURPOSE

We investigated the effectiveness and toxicity of VIP therapy as a first-line chemotherapy for patients with metastatic germ cell tumor.

PATIENTS AND METHODS

From March 1994 to October 1997, we treated 16 patients with VIP therapy consisting of etoposide (100 mg/m2), ifosfamide, (1.2 g/m2) and cisplatin (20 mg/m2), all of which were generally given daily for 5 consecutive days every 3 weeks. Of the 16 patients, 6 were classified into a good, 5 into an intermediate, and 5 into a poor prognostic group according to the International Germ Cell Consensus Classification.

RESULTS

Thirteen patients (81%) achieved complete response with VIP alone or VIP plus surgery. Three-year survival rate was 100% in good and intermediate prognostic group, while 40% in poor prognostic group. Although all patients had Grade 3 or higher myelosuppression, the treatment was well tolerated and no patient died of treatment-related complications.

CONCLUSIONS

VIP appears to be an effective and safe regimen as an induction chemotherapy for good and intermediate risk patients with germ cell tumor. However, more intensive regimen may be necessary for poor-risk patients.