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Kin T, Hirano M, Tonomura Y, Ueno S. Coexistence of Ramsay Hunt syndrome and varicella-zoster virus encephalitis. Infection 2007; 34:352-4. [PMID: 17180593 DOI: 10.1007/s15010-006-5669-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Accepted: 05/11/2006] [Indexed: 10/23/2022]
Abstract
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.
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Sasaki YTF, Sano M, Ideue T, Kin T, Asai K, Hirose T. Identification and characterization of human non-coding RNAs with tissue-specific expression. Biochem Biophys Res Commun 2007; 357:991-6. [PMID: 17451645 DOI: 10.1016/j.bbrc.2007.04.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
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.
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Kin T, Zhai X, Murdoch TB, Salam A, Shapiro AMJ, Lakey JRT. Enhancing the success of human islet isolation through optimization and characterization of pancreas dissociation enzyme. Am J Transplant 2007; 7:1233-41. [PMID: 17359501 DOI: 10.1111/j.1600-6143.2007.01760.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
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.
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Kiryu H, Tabei Y, Kin T, Asai K. Murlet: a practical multiple alignment tool for structural RNA sequences. ACTA ACUST UNITED AC 2007; 23:1588-98. [PMID: 17459961 DOI: 10.1093/bioinformatics/btm146] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
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.
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Sasaki YTF, Sano M, Kin T, Asai K, Hirose T. Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem Biophys Res Commun 2007; 357:724-30. [PMID: 17445766 DOI: 10.1016/j.bbrc.2007.03.200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 03/29/2007] [Indexed: 11/26/2022]
Abstract
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.
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Kiryu H, Kin T, Asai K. Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics 2006; 23:434-41. [PMID: 17182698 DOI: 10.1093/bioinformatics/btl636] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 2006; 35:D145-8. [PMID: 17099231 PMCID: PMC1669753 DOI: 10.1093/nar/gkl837] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
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
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Hamada M, Tsuda K, Kudo T, Kin T, Asai K. Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics 2006; 22:2480-7. [PMID: 16908501 DOI: 10.1093/bioinformatics/btl431] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Kin T, Hirano M, Taoka T, Furiya Y, Kataoka H, Kichikawa K, Ueno S. Global and region-specific analyses of apparent diffusion coefficient in dentatorubral-pallidoluysian atrophy. AJNR Am J Neuroradiol 2006; 27:1463-6. [PMID: 16908559 PMCID: PMC7977539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
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.
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Tabei Y, Tsuda K, Kin T, Asai K. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics 2006; 22:1723-9. [PMID: 16690634 DOI: 10.1093/bioinformatics/btl177] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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/.
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Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto KI, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama JI, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H. Genome sequencing and analysis of Aspergillus oryzae. Nature 2006; 438:1157-61. [PMID: 16372010 DOI: 10.1038/nature04300] [Citation(s) in RCA: 851] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 10/06/2005] [Indexed: 11/09/2022]
Abstract
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.
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Villiger P, Ryan EA, Owen R, O'Kelly K, Oberholzer J, Al Saif F, Kin T, Wang H, Larsen I, Blitz SL, Menon V, Senior P, Bigam DL, Paty B, Kneteman NM, Lakey JRT, Shapiro AMJ. Prevention of bleeding after islet transplantation: lessons learned from a multivariate analysis of 132 cases at a single institution. Am J Transplant 2005; 5:2992-8. [PMID: 16303015 DOI: 10.1111/j.1600-6143.2005.01108.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
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.
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O'Gorman D, Kin T, McGhee-Wilson D, Shapiro AMJ, Lakey JRT. Multi-lot analysis of custom collagenase enzyme blend in human islet isolations. Transplant Proc 2005; 37:3417-9. [PMID: 16298613 DOI: 10.1016/j.transproceed.2005.09.139] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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O'Gorman D, Kin T, Murdoch T, Richer B, McGhee-Wilson D, Ryan E, Shapiro AMJ, Lakey JRT. The standardization of pancreatic donors for islet isolation. Transplant Proc 2005; 37:1309-10. [PMID: 15848705 DOI: 10.1016/j.transproceed.2004.12.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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Abstract
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.
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Tsujimura T, Kuroda Y, Avila J, Kin T, Shapiro AM, Lakey J. THE INFLUENCE OF PANCREAS PRESERVATION ON HUMAN ISLET ISOLATION OUTCOMES: IMPACT OF THE TWO-LAYER METHOD. Transplantation 2004. [DOI: 10.1097/00007890-200407271-00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tsuda K, Uda S, Kin T, Asai K. Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data. Neural Process Lett 2004. [DOI: 10.1023/b:nepl.0000016845.36307.d7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Tsujimura T, Kuroda Y, Avila JG, Kin T, Churchill TA, Shapiro AMJ, Lakey JRT. Resuscitation of the ischemically damaged human pancreas by the two-layer method prior to islet isolation. Transplant Proc 2003; 35:2461-2. [PMID: 14611986 DOI: 10.1016/j.transproceed.2003.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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Kin T, Tsuda K, Asai K. Marginalized kernels for RNA sequence data analysis. GENOME INFORMATICS. INTERNATIONAL CONFERENCE ON GENOME INFORMATICS 2002; 13:112-22. [PMID: 14571380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
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.
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Lakey JR, Helms LM, Kin T, Korbutt GS, Rajotte RV, Shapiro AM, Warnock GL. Serine-protease inhibition during islet isolation increases islet yield from human pancreases with prolonged ischemia. Transplantation 2001; 72:565-70. [PMID: 11544413 DOI: 10.1097/00007890-200108270-00003] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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Ryan EA, Lakey JR, Rajotte RV, Korbutt GS, Kin T, Imes S, Rabinovitch A, Elliott JF, Bigam D, Kneteman NM, Warnock GL, Larsen I, Shapiro AM. Clinical outcomes and insulin secretion after islet transplantation with the Edmonton protocol. Diabetes 2001; 50:710-9. [PMID: 11289033 DOI: 10.2337/diabetes.50.4.710] [Citation(s) in RCA: 629] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
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.
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Aomatsu Y, Nakajima Y, Ohyama T, Kin T, Kanehiro H, Hisanaga M, Ko S, Nagao M, Tatekawa Y, Sho M, Ikeda N, Kanokogi H, Kobayashi T, Urizono Y, Yamada T, Shibaji T, Kanamura T, Ogawa S, Iwata H, Nakano H. Efficacy of agarose/polystyrene sulfonic acid microencapsulation for islet xenotransplantation. Transplant Proc 2000; 32:1071-2. [PMID: 10936363 DOI: 10.1016/s0041-1345(00)01129-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Kitsukawa SI, Kin T, Tsukamoto T, Yonese J, Ishikawa Y, Fukui I. Extragonadal germ cell tumor of mediastinum with high serum level of carcinoembryonic antigen and carbohydrate antigen 19-9. J Urol 2000; 163:912-3. [PMID: 10688012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Kin T, Aizawa T, Namiki K, Noda K, Oyama H, Samesima T, Arai Y, Miki M. [A case of epithelial membrane antigen-positive leiomyosarcoma of the urinary bladder]. HINYOKIKA KIYO. ACTA UROLOGICA JAPONICA 2000; 46:189-91. [PMID: 10806578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
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.
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Yoshida T, Yonese J, Kitsukawa S, Kin T, Tsukamoto T, Maeda Y, Fukui I. [Treatment results of VIP (etoposide, ifosfamide and cisplatin) chemotherapy as a first-line therapy in metastatic germ cell tumors]. Nihon Hinyokika Gakkai Zasshi 2000; 91:55-61. [PMID: 10723177 DOI: 10.5980/jpnjurol1989.91.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
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.
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