A VHDL code generator for Reed-Solomon encoders and decoders

Reed-Solomon codes are error correcting codes that are used in many applications such as satellite communications, digital audio tape, and in CDROMs. Such diverse applications call for the use of many different Reed-Solomon codes. The topic of this thesis is the development of a program to produce synthesizable VHDL code for an arbitrary Reed-Solomon encoder or decoder. A novel extension of the Massey-Berlekamp algorithm for solving the key equation is presented. This modified algorithm is a key aspect of the Reed-Solomon decoder designs discussed in this thesis. The details of the design of both RS encoders and decoders are presented in detail. A program written in a high level language was designed so as to generate the VHDL code that corresponds to the algorithms for encoding and decoding. Several encoders and decoders were synthesized for the Xilinx XCV1000 series of field programmable gate arrays (FPGAs). The resulting area and speed metrics are presented for several designs of Reed-Solomon encoders and decoders

Accumulation of heavy metals from soil in medicinal plants

Medicinal plants accumulate heavy metals from contaminated soil, and their consumption can cause poisoning. Our objective was to determine the levels of Pb, Cd, Zn, Cu, Fe, and Mn in four medicinal plant species (Achillea millefolium, Hypericum perforatum, Plantago lanceolata, and Urtica dioica) and their native soil, all sampled at a former smelter. The highest soil Cd, Pb, and Zn levels surpassed the maximum allowed limit 75-fold, 48-fold, and 14-fold, respectively. Their soil levels correlated with those in the plants, but this was not the case with Cu, Fe, and Mn. Heavy metal accumulation seems to depend on the plant species, yet even so, medicinal herbs should be cultivated and gathered only from controlled (uncontaminated) areas. Polluted areas should be monitored on a regular basis, while further research should investigate the connection between the heavy metal levels in the soil, their levels available for plants, and the levels extractable from plants

Treatment of benign prostatic hyperplasia by natural drugs

Benign prostatic hyperplasia (BPH) is one of the most common urinary diseases affecting men, generally after the age of 50. The prevalence of this multifactorial disease increases with age. With aging, the plasma level of testosterone decreases, as well as the testosterone/estrogen ratio, resulting in increased estrogen activity, which may facilitate the hyperplasia of the prostate cells. Another theory focuses on dihydrotestosterone (DHT) and the activity of the enzyme 5α-reductase, which converts testosterone to DHT. In older men, the activity of this enzyme increases, leading to a decreased testosterone/DHT ratio. DHT may promote prostate cell growth, resulting in hyperplasia. Some medicinal plants and their compounds act by modulating this enzyme, and have the above-mentioned targets. This review focuses on herbal drugs that are most widely used in the treatment of BPH, including pumpkin seed, willow herb, tomato, maritime pine bark, Pygeum africanum bark, rye pollen, saw palmetto fruit, and nettle root, highlighting the latest results of preclinical and clinical studies, as well as safety issues. In addition, the pharmaceutical care and other therapeutic options of BPH, including pharmacotherapy and surgical options, are discussed, summarizing and comparing the advantages and disadvantages of each therapy

Disaster resilience in Australia: A geographic assessment using an index of coping and adaptive capacity

This paper reports a national-scale assessment of disaster resilience, using the Australian Disaster Resilience Index. The index assesses resilience at three levels: overall capacity for disaster resilience; coping and adaptive capacity; and, eight themes of disaster resilience across social, economic and institutional domains. About 32% of Australia's population (7.6 million people) live in an area assessed as having high capacity for disaster resilience. About 52% of Australia's population (12.3 million people) live in an area assessed as having moderate capacity for disaster resilience. The remaining 16% of Australia's population (3.8 million people) live in an area assessed as having low capacity for disaster resilience. Distribution of disaster resilience in Australia is strongly influenced by a geography of remoteness. Most metropolitan and inner regional areas were assessed as having high capacity for disaster resilience. In contrast, most outer regional, remote and very remote areas were assessed as having low capacity for disaster resilience, although areas of low capacity for disaster resilience can occur in metropolitan areas. Juxtaposed onto this distribution, themes of disaster resilience highlight strengths and barriers to disaster resilience in different communities. For example, low community capital and social cohesion is a disaster resilience barrier in many metropolitan areas, but higher community capital and social cohesion in outer regional and some remote areas supports disaster resilience. The strategic intent of a shared responsibility for disaster resilience can benefit from understanding the spatial distribution of disaster resilience, so that policies and programmes can address systemic influences on disaster resilience

The Australian Natural Disaster Resilience Index: Annual project report 2017-18

Natural hazard management policy directions in Australia – and indeed internationally – are increasingly being aligned to ideas of resilience. However, the definition and conceptualization of resilience in relation to natural hazards is keenly contested within academic literature (Klein et al., 2003; Wisner et al., 2004; Boin et al., 2010; Tierney, 2014). Broadly speaking, resilience to natural hazards is the ability of individuals and communities to cope with disturbances or changes and to maintain adaptive behaviour (Maguire and Cartwright, 2008). Building resilience to natural hazards requires the capacity to cope with the event and its aftermath, as well as the capacity to learn about hazard risks, change behaviour, transform institutions and adapt to a changing environment (Maguire and Cartwright, 2008). The Australian Natural Disaster Resilience Index is a tool for assessing the resilience of communities to natural hazards at a large scale. Using a top down approach, the assessment will provide input to macro-level policy, strategic planning, community planning and community engagement activities at National, State and local government levels. First, it is a snapshot of the current state of natural hazard resilience at a national scale. Second, it is a layer of information for use in strategic policy development and planning. Third, it provides a benchmark against which to assess future change in resilience to natural hazards. Understanding resilience strengths and weaknesses will help communities, governments and organizations to build the capacities needed for living with natural hazards. Design of the Australian Natural Disaster Resilience Index The Australian Natural Disaster Resilience Index will assess resilience based on two sets of capacities – coping capacity and adaptive capacity. We have used a hierarchical structure for the Australian Natural Disaster Resilience Index. Indicators provide the data for a theme – together the indicators measure the status of the theme. We collected approximately 90 indicators across the eight coping and adaptive capacity themes. Indicators were collected at Statistical Area 2 (SA2) resolution where possible. Results of the Australian Natural Disaster Resilience Index The results and initial trends in the eight themes of the Australian Natural Disaster Resilience Index are presented below. It should be noted that these interpretations and maps are subject to further change as the State of Disaster Resilience Report is developed. What is presented here is an overview of the pattern of index values. In all maps, lower index values in brown represent lower disaster resilience and higher index values in green represent higher disaster resilience. Each of the sections is an SA2 division of the ABS

Presence of activating KRAS mutations correlates significantly with expression of tumour suppressor genes DCN and TPM1 in colorectal cancer

<p>Abstract</p> <p>Background</p> <p>Despite identification of the major genes and pathways involved in the development of colorectal cancer (CRC), it has become obvious that several steps in these pathways might be bypassed by other as yet unknown genetic events that lead towards CRC. Therefore we wanted to improve our understanding of the genetic mechanisms of CRC development.</p> <p>Methods</p> <p>We used microarrays to identify novel genes involved in the development of CRC. Real time PCR was used for mRNA expression as well as to search for chromosomal abnormalities within candidate genes. The correlation between the expression obtained by real time PCR and the presence of the <it>KRAS </it>mutation was investigated.</p> <p>Results</p> <p>We detected significant previously undescribed underexpression in CRC for genes <it>SLC26A3</it>, <it>TPM1 </it>and <it>DCN</it>, with a suggested tumour suppressor role. We also describe the correlation between <it>TPM1 </it>and <it>DCN </it>expression and the presence of <it>KRAS </it>mutations in CRC. When searching for chromosomal abnormalities, we found deletion of the <it>TPM1 </it>gene in one case of CRC, but no deletions of <it>DCN </it>and <it>SLC26A3 </it>were found.</p> <p>Conclusion</p> <p>Our study provides further evidence of decreased mRNA expression of three important tumour suppressor genes in cases of CRC, thus implicating them in the development of this type of cancer. Moreover, we found underexpression of the <it>TPM1 </it>gene in a case of CRCs without <it>KRAS </it>mutations, showing that <it>TPM1 </it>might serve as an alternative path of development of CRC. This downregulation could in some cases be mediated by deletion of the <it>TPM1 </it>gene. On the other hand, the correlation of <it>DCN </it>underexpression with the presence of <it>KRAS </it>mutations suggests that <it>DCN </it>expression is affected by the presence of activating <it>KRAS </it>mutations, lowering the amount of the important tumour suppressor protein decorin.</p

Improved Detection of Germline Mutations in Korean VHL Patients by Multiple Ligation-dependent Probe Amplification Analysis

von Hippel-Lindau (VHL) disease is an autosomal dominant inherited tumor syndrome characterized by the development of tumors in the eye, brain, spinal cord, inner ear, adrenal gland, pancreas, kidney, and epididymis, associated with germline mutations in the VHL gene. We used sequentially sequencing method and multiple ligation-dependent probe amplification (MLPA) analysis and detected germline mutations in the VHL in 15/15 (100%) of VHL patients fulfilling the clinical criteria. Of the 15 distinct mutations detected, large deletions were detected in 5/15 (33.3%) patients, including 4/15 (26.7%) partial deletions and 1/15 (6.6%) deletion of the entire VHL gene by MLPA and the remainder were point mutations detected by sequencing method, of which five mutations were novel. Using MLPA analysis, we detected large deletions including both partial deletions and complete gene deletion, which has not been reported in Korean VHL patients. In conclusion, sequential application of sequencing method and MLPA analysis might make possible to identify germline mutations in most patients with VHL

Molecular analysis using DHPLC of cystic fibrosis: increase of the mutation detection rate among the affected population in Central Italy

BACKGROUND: Cystic fibrosis (CF) is a multisystem disorder characterised by mutations of the CFTR gene, which encodes for an important component in the coordination of electrolyte movement across of epithelial cell membranes. Symptoms are pulmonary disease, pancreatic exocrine insufficiency, male infertility and elevated sweat concentrations. The CFTR gene has numerous mutations (>1000) and functionally important polymorphisms (>200). Early identification is important to provide appropriate therapeutic interventions, prognostic and genetic counselling and to ensure access to specialised medical services. However, molecular diagnosis by direct mutation screening has proved difficult in certain ethnic groups due to allelic heterogeneity and variable frequency of causative mutations. METHODS: We applied a gene scanning approach using DHPLC system for analysing specifically all CFTR exons and characterise sequence variations in a subgroup of CF Italian patients from the Lazio region (Central Italy) characterised by an extensive allelic heterogeneity. RESULTS: We have identified a total of 36 different mutations representing 88% of the CF chromosomes. Among these are two novel CFTR mutations, including one missense (H199R) and one microdeletion (4167delCTAAGCC). CONCLUSION: Using this approach, we were able to increase our standard power rate of mutation detection of about 11% (77% vs. 88%)

Ser80Ile mutation and a concurrent Pro25Leu variant of the VHL gene in an extended Hungarian von Hippel-Lindau family

Von Hippel-Lindau disease (VHL) is a rare autosomal dominant disease characterized by development of cystic and tumorous lesions at multiple sites, including the brain, spinal cord, kidneys, adrenals, pancreas, epididymis and eyes. The clinical phenotype results from molecular abnormalities of the VHL tumor suppressor gene, mapped to human chromosome 3p25-26. The VHL gene encodes two functionally active VHL proteins due to the presence of two translational initiation sites separated by 53 codons. The majority of disease-causing mutations have been detected downstream of the second translational initiation site, but there are conflicting data as to whether few mutations located in the first 53 codons, such as the Pro25Leu could have a pathogenic role. In this paper we report a large Hungarian VHL type 2 family consisting of 32 members in whom a disease-causing AGT80AAT (Ser80Ile) c.239G>A, p.Ser80Ile mutation, but not the concurrent CCT25CTT (Pro25Leu) c.74C>T, p.Pro25Leu variant co-segregated with the disease. To our knowledge, the Ser80Ile mutation has not been previously described in VHL type 2 patients with high risk of pheochromocytoma and renal cell cancer. Therefore, this finding represents a novel genotype-phenotype association and VHL kindreds with Ser80Ile mutation will require careful surveillance for pheochromocytoma. We concluded that the Pro25Leu variant is a rare, neutral variant, but the presence such a rare gene variant may make genetic counseling difficult