We propose a novel single polarization photonic band gap fiber (SP-PBGF) with an anisotropic air hole lattice in the core. An SP-PBGF with an elliptical air hole lattice in the core recently proposed ...can easily realize SP guidance utilizing the large difference of cutoff frequency for the x- and y-polarized modes. In this paper, in order to achieve SP guidance based on the same principle of this PBGF, we utilize an anisotropic lattice of circular air holes instead of elliptical air holes to ease the fabrication difficulty. After investigating the influence of the structural parameters on SP guidance, it is numerically demonstrated that the designed SP-PBGF has 381 nm SP operating band.
Epigenetic modifications are essential for controlling gene expression. Recent studies have shown that not only single epigenetic modifications but also combinations of multiple epigenetic ...modifications play vital roles in gene regulation. A striking example is the long hypomethylated regions enriched with modified H3K27me3 (called, "K27HMD" regions), which are exposed to suppress the expression of key developmental genes relevant to cellular development and differentiation during embryonic stages in vertebrates. It is thus a biologically important issue to develop an effective optimization algorithm for detecting long DNA regions (e.g., >4 kbp in size) that harbor a specific combination of epigenetic modifications (e.g., K27HMD regions). However, to date, optimization algorithms for these purposes have received little attention, and available methods are still heuristic and ad hoc.
In this paper, we propose a linear time algorithm for calculating a set of non-overlapping regions that maximizes the sum of similarities between the vector of focal epigenetic states and the vectors of raw epigenetic states at DNA positions in the set of regions. The average elapsed time to process the epigenetic data of any of human chromosomes was less than 2 seconds on an Intel Xeon CPU. To demonstrate the effectiveness of the algorithm, we estimated large K27HMD regions in the medaka and human genomes using our method, ChromHMM, and a heuristic method.
We confirmed that the advantages of our method over those of the two other methods. Our method is flexible enough to handle other types of epigenetic combinations. The program that implements the method is called "CSMinfinder" and is made available at: http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/Segmentation/
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Epilepsy is a common neurological disorder, and mutations in genes encoding ion channels or neurotransmitter receptors are frequent causes of monogenic forms of epilepsy. Here we show that abnormal ...expansions of TTTCA and TTTTA repeats in intron 4 of SAMD12 cause benign adult familial myoclonic epilepsy (BAFME). Single-molecule, real-time sequencing of BAC clones and nanopore sequencing of genomic DNA identified two repeat configurations in SAMD12. Intriguingly, in two families with a clinical diagnosis of BAFME in which no repeat expansions in SAMD12 were observed, we identified similar expansions of TTTCA and TTTTA repeats in introns of TNRC6A and RAPGEF2, indicating that expansions of the same repeat motifs are involved in the pathogenesis of BAFME regardless of the genes in which the expanded repeats are located. This discovery that expansions of noncoding repeats lead to neuronal dysfunction responsible for myoclonic tremor and epilepsy extends the understanding of diseases with such repeat expansion.
k -means clustering has been widely used to gain insight into biological systems from large-scale life science data. To quantify the similarities among biological data sets, Pearson correlation ...distance and standardized Euclidean distance are used most frequently; however, optimization methods have been largely unexplored. These two distance measurements are equivalent in the sense that they yield the same k -means clustering result for identical sets of k initial centroids. Thus, an efficient algorithm used for one is applicable to the other. Several optimization methods are available for the Euclidean distance and can be used for processing the standardized Euclidean distance; however, they are not customized for this context. We instead approached the problem by studying the properties of the Pearson correlation distance, and we invented a simple but powerful heuristic method for markedly pruning unnecessary computation while retaining the final solution. Tests using real biological data sets with 50-60K vectors of dimensions 10-2001 ( similar to 400 MB in size) demonstrated marked reduction in computation time for k = 10-500 in comparison with other state-of-the-art pruning methods such as Elkan's and Hamerly's algorithms. The BoostKCP software is available at http://mlab.cb.k.u-tokyo.ac.jp/ similar to ichikawa/boostKCP/.
Small luminescent molecular probes based on the iridium(III) complex BTP, (btp)2Ir(acac) (btp = benzothienylpyridine, acac = acetylacetone) have been developed for sensing intracellular and in vivo ...O2. These compounds are BTPSA (containing an anionic carboxyl group), BTPNH2 (containing a cationic amino group), and BTPDM1 (containing a cationic dimethylamino group); all substituents are incorporated into the ancillary acetylacetonato ligand of BTP. Introduction of the cationic dimethylamino group resulted in an almost 20-fold increase in cellular uptake efficiency of BTPDM1 by HeLa cells compared with BTP. The phosphorescence intensity of BTPDM1 internalized in living cells provided a visual representation of the O2 gradient produced by placing a coverslip over cultured monolayer cells. The intracellular O2 levels (pO2) inside and outside the edge of the coverslip could be evaluated by measuring the phosphorescence lifetime of BTPDM1. Furthermore, intravenous administration of 25 nmol BTPDM1 to tumor-bearing mice allowed the tumor region to be visualized by BTPDM1 phosphorescence. The lifetime of BTPDM1 phosphorescence from tumor regions was much longer than that from extratumor regions, thereby demonstrating tumor hypoxia (pO2 = 6.1 mmHg for tumor and 50 mmHg for extratumor epidermal tissue). Tissue distribution studies showed that 2 h after injection of BTPDM1 into a mouse, the highest distribution was in liver and kidney, while after 24 h, BTPDM1 was excreted in the feces. These results demonstrate that BTPDM1 can be used as a small molecular probe for measuring intracellular O2 levels in both cultured cells and specific tissues and organs.
Formula Omitted-means clustering has been widely used to gain insight into biological systems from large-scale life science data. To quantify the similarities among biological data sets, Pearson ...correlation distance and standardized Euclidean distance are used most frequently; however, optimization methods have been largely unexplored. These two distance measurements are equivalent in the sense that they yield the same Formula Omitted-means clustering result for identical sets of Formula Omitted initial centroids. Thus, an efficient algorithm used for one is applicable to the other. Several optimization methods are available for the Euclidean distance and can be used for processing the standardized Euclidean distance; however, they are not customized for this context. We instead approached the problem by studying the properties of the Pearson correlation distance, and we invented a simple but powerful heuristic method for markedly pruning unnecessary computation while retaining the final solution. Tests using real biological data sets with 50-60K vectors of dimensions 10-2001 (∼400 MB in size) demonstrated marked reduction in computation time for Formula Omitted = 10-500 in comparison with other state-of-the-art pruning methods such as Elkan's and Hamerly's algorithms. The BoostKCP software is available at http://mlab.cb.k.u-tokyo.ac.jp/∼ichikawa/boostKCP/.
We presented a spatial parallel manipulator with redundant actuators for gross and fine motions to achieve fine positioning together with gross motion in three dimensional space. Four types of ...parallel mechanisms with redundancy for such a manipulator were proposed and their infinitesimal displacement characteristics were investigated. Of the four mechanisms, a mechanism was chosen, and a kinematic synthesis was carried out. A prototype parallel manipulator was designed and built based on the synthesis result. A control system to achieve a fine motion together with a gross motion and a procedure to determine desired input of gross and fine motion drive systems for a specified pose of the output link were presented. We showed experimental results of fine positioning achieved by our prototype manipulator. A high ratio greater than 106 of total stroke of gross motion to positioning resolution and repeatability was achieved by our prototype manipulator.
Chromatin architecture governs cell lineages by regulating the specific gene expression; however, its role in the diversity of cancer development remains unknown. Among pancreatic cancers, pancreatic ...ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasms (IPMN) with an associated invasive carcinoma (IPMNinv) arise from 2 distinct precursors, and their fundamental differences remain obscure. Here, we aimed to assess the difference of chromatin architecture regulating the transcriptional signatures or biological features in pancreatic cancers.
We established 28 human organoids from distinct subtypes of pancreatic tumors, including IPMN, IPMNinv, and PDAC. We performed exome sequencing (seq), RNA-seq, assay for transposase-accessible chromatin-seq, chromatin immunoprecipitation-seq, high-throughput chromosome conformation capture, and phenotypic analyses with short hairpin RNA or clustered regularly interspaced short palindromic repeats interference.
Established organoids successfully reproduced the histology of primary tumors. IPMN and IPMNinv organoids harbored GNAS, RNF43, or KLF4 mutations and showed the distinct expression profiles compared with PDAC. Chromatin accessibility profiles revealed the gain of stomach-specific open regions in IPMN and the pattern of diverse gastrointestinal tissues in IPMNinv. In contrast, PDAC presented an impressive loss of accessible regions compared with normal pancreatic ducts. Transcription factor footprint analysis and functional assays identified that MNX1 and HNF1B were biologically indispensable for IPMN lineages. The upregulation of MNX1 was specifically marked in the human IPMN lineage tissues. The MNX1-HNF1B axis governed a set of genes, including MYC, SOX9, and OLFM4, which are known to be essential for gastrointestinal stem cells. High-throughput chromosome conformation capture analysis suggested the HNF1B target genes to be 3-dimensionally connected in the genome of IPMNinv.
Our organoid analyses identified the MNX1-HNF1B axis to be biologically significant in IPMN lineages.
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Integrative molecular and biological assays were performed on human pancreatic cancer organoids. Chromatin conformation stratified the lineage differences in pancreatic cancers and reflected their biological features.
The process and molecular mechanisms underlying the formation and destruction of a pseudo-capsule (PC) in clear cell renal cell carcinoma (ccRCC) are poorly understood. In the present study, the PCs ...of surgical specimens from primary tumors and metastatic lesions in 169 patients with ccRCC, and carcinogen-induced ccRCC rat models were semi-quantified using the invasion of PC (i-Cap) score system. This was based on the relationship among the tumor, PC and adjacent normal tissue (NT) as follows: i-Cap 0, tumor has no PC and does not invade NT; i-Cap 1, tumor has a complete PC and does not invade into the PC; i-Cap 2, tumor with focal absences in the PC, which partially invades the PC but not completely through the PC; i-Cap 3, tumor crosses the PC and invades the NT; i-Cap 4, tumor directly invades the NT without a PC. The study suggested that PC formation was not observed without physical compression, and also revealed that tumor invasion into the PC was a prognostic factor for postoperative oncological outcomes. Higher i-Cap, Fuhrman grade and tumor size were independent poor prognostic factors for postoperative disease-free survival. mRNA expression arrays generated from carcinogen-induced ccRCC rat models were used to explore genes potentially associated with the formation and destruction of a PC. Subsequently, human ccRCC specimens were validated for four genes identified via expression array; the results revealed that collagen type 4A2, matrix metal-loproteinase-7 and l-selectin were upregulated alongside the progression of i-Cap score. Conversely, endoglin was down-regulated. In conclusion, the present study provides insights into the formation and destruction of a PC, and the results may aid the treatment and management of patients with ccRCC. Key words: RCC, PC, prognostic factor, molecular mechanism, rat model
Because of the increasing number of car accidents, it is very important to provide safety systems for car drivers. In this paper, we propose a method for synthesizing virtual blind corner images by ...using multiple vehicle cameras, so that drivers can see the other side of the blind corner. The existing methods require position sensors such as GPS and calibrated cameras. In this paper we propose a method for generating virtual views of blind corners from uncalibrated cameras mounted on multiple vehicles. The proposed method is tested by using real vehicles. The accuracy and the stability of the proposed method is also evaluated.
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