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The government of Indonesia introduced new saving initiatives in National Housing Scheme through ‘Tabungan Pembangunan Rakyat’. Furthermore, the subsidies on housing finance increase access for low income people to purchase their first home. In the supply site, government provide supports through housing improvement programs, direct provision and cross-subsidy of mixed-income housing by private developers. Collaboration across government and private sector is essential to ensure housing is affordable especially for the low-income people. The lack of affordable housing in the city centre has put more pressure for transportation cost and time which affected the productivity and social development for vulnerable groups.

Introducción: Recientemente, los sistemas caóticos han llamado la atención de la comunidad científica internacional, debido a sus potenciales aplicaciones en varias ramas de la ciencia e ingeniería. Se han propuesto muchos trabajos con el fin de resolver algunos problemas interesantes, como la determinación de daños estructurales en los materiales o en sistemas de comunicaciones seguras. Sin embargo, la mayoría de estos trabajos se enfocan en sistemas caóticos en tiempo continuo, mientras que en muchos casos, es deseable que estos sistemas estén en el modo de tiempo discreto y puedan ser utilizados en tiempo real. Método: El presente trabajo propone la implementación experimental de tres osciladores caóticos discretizados en un microcontrolador simple. Los osciladores caóticos a implementar son muy conocidos y muy utilizados para ejemplificar posibles soluciones a diversos problemas: los osciladores de Lorenz, Rössler y Chen. Para lo cual, se utilizan tan solo un microcontrolador de bajo costo, unos cuantos resistores y un algoritmo de computación sencillo. Resultados: Se obtiene un sistema embebido de bajo costo y sencillo para implementar osciladores caóticos discretizados. Discusión o Conclusión: Se demuestra que los osciladores caóticos de Lorenz, Rössler y Chen pueden implementarse en cualquier microcontrolador de arquitectura basada en palabras de 18 bits o más. Además, se observa que el algoritmo propuesto se pude migrar de un oscilador a otro con solo sustituir el sistema caótico de ecuaciones., Introduction: Chaotic systems are of great interest in various branches of science and engineering. Many works have been proposed in order to solve some different interesting problems, such that determining structural damages in materials or for secure communications systems. However, several approaches are in continuous-time, whereas in many cases, the systems are desired to be in discrete-time mode and in real time. Method: In this work, an experimental implementation of three chaotic oscillators into a simple microcontroller is proposed. The chaotic oscillators to implement are Lorenz, Rössler and Chen. The implementation consists only of a low cost microcontroller, a few resistors and a simple algorithm. Results: An inexpensive and simple embedded system to generate chaotic oscillators was obtained. Discussion or Conclusion: The implementation of chaotic oscillators of Lorenz, Rössler and Chen into 18 bits microcontroller is demostrated. It is further noted that the proposed algorithm could migrate from one oscillator to another with only replace chaotic system equations.

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Background: Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.Results: We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets.Conclusions: Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases. © 2013 Swanson et al.; licensee BioMed Central Ltd.

BACKGROUND: Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS: We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS: AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories. CONCLUSIONS: We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.) Copyright © 2013 Massachusetts Medical Society.

Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of the identity and function of the genes affected by these alterations is limited. We performed exome sequencing on a discovery set of 16 oligodendrogliomas with 1p/19q co-deletion to identify new molecular features at base-pair resolution. As anticipated, there was a high rate of IDH mutations: all cases had mutations in either IDH1 (14/16) or IDH2 (2/16). In addition, we discovered somatic mutations and insertions/deletions in the CIC gene on chromosome 19q13.2 in 13/16 tumours. These discovery set mutations were validated by deep sequencing of 13 additional tumours, which revealed seven others with CIC mutations, thus bringing the overall mutation rate in oligodendrogliomas in this study to 20/29 (69%). In contrast, deep sequencing of astrocytomas and oligoastrocytomas without 1p/19q loss revealed that CIC alterations were otherwise rare (1/60; 2%). Of the 21 non-synonymous somatic mutations in 20 CIC-mutant oligodendrogliomas, nine were in exon 5 within an annotated DNA-interacting domain and three were in exon 20 within an annotated protein-interacting domain. The remaining nine were found in other exons and frequently included truncations. CIC mutations were highly associated with oligodendroglioma histology, 1p/19q co-deletion, and IDH1/2 mutation (p < 0.001). Although we observed no differences in the clinical outcomes of CIC mutant versus wild-type tumours, in a background of 1p/19q co-deletion, hemizygous CIC mutations are likely important. We hypothesize that the mutant CIC on the single retained 19q allele is linked to the pathogenesis of oligodendrogliomas with IDH mutation. Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co-deletion. Copyright © 2011 Pathologi

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4a. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-?B signalling in Group 4, suggest future avenues for rational, targeted therapy. © 2012 Macmillan Publishers Limited. All rights reserved.

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We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods. © 2010 Nature America, Inc. All rights reserved.

Contains fulltext : 57492.pdf (publisher's version ) (Open Access), Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human fingerprint map, 99% of the current assembled sequence and has an effective resolving power of 79 kb. We have made the clone set publicly available, anticipating that it will generally facilitate FISH or array-CGH-based identification and characterization of chromosomal alterations relevant to disease.