Abstract: De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.
Abstract: The relics of traditional folk culture in Kazakhstan are ceremonies or their fragments - such as weddings, funerals, shamanism. The world of spiritual creatures, spirits-protectors, spirits-helpers, injury spirits, spirits of illnesses, etc., is described in detail in shamanic rites (in Kazakh culture it is called bakslyk). The study of these displays of folk culture, which reflect the peoples` ethnic mentality or notions about the structure, values and hierarchies of the universe, includes collection and recording of the field materials and their interpretation, i.e. reconstruction of those meanings which were initially embodied or “coded" in folklore. A distinctive feature of Kazakh nomadic culture is its self-preservation and actualization, almost untouched the ancient mythologies of the world, in particular, the mythologies connected with music, musical instruments and the creator of music. Within the frameworks of the traditional culture the word and the music keep the sacral meaning. The ritual melodies and what they carry – the holly, and at the same time unexplored, powerful and threatening, uncontrolled by people world – keep on attributing the soul to all, connected with culture.
Abstract: Palestinian cities face the challenges of land scarcity,
high population growth rates, rapid urbanization, uneven
development and territorial fragmentation. Due to geopolitical
constrains and the absence of an effective Palestinian planning
institution, urban development in Palestinian cities has not followed
any discernable planning scheme. This has led to a number of
internal contradictions in the structure of cities, and adversely
affected land use, the provision of urban services, and the quality of
the living environment.
This paper explores these challenges, and the potential that exists
for introducing a more sustainable urban development pattern in
Palestinian cities. It assesses alternative development approaches
with a particular focus on sustainable development, promoting ecodevelopment
imperatives, limiting random urbanization, and meeting
present and future challenges, including fulfilling the needs of the
people and conserving the scarce land and limited natural resources.
This paper concludes by offering conceptual proposals and guidelines
for promoting sustainable physical development in Palestinian cities.
Abstract: The p53 tumor suppressor gene plays two important
roles in genomic stability: blocking cell proliferation after DNA
damage until it has been repaired, and starting apoptosis if the
damage is too critical. Codon 72 exon4 polymorphism (Arg72Pro) of
the P53 gene has been implicated in cancer risk. Various studies have
been done to investigate the status of p53 at codon 72 for arginine
(Arg) and proline (Pro) alleles in different populations and also the
association of this codon 72 polymorphism with various tumors. Our
objective was to investigate the possible association between P53
Arg72Pro polymorphism and susceptibility to colorectal cancer
among Isfahan and Chaharmahal Va Bakhtiari (a part of south west
of Iran) population. We investigated the status of p53 at codon 72 for
Arg/Arg, Arg/Pro and Pro/Pro allele polymorphisms in blood
samples from 145 colorectal cancer patients and 140 controls by
Nested-PCR of p53 exon 4 and digestion with BstUI restriction
enzyme and the DNA fragments were then resolved by
electrophoresis in 2% agarose gel. The Pro allele was 279 bp, while
the Arg allele was restricted into two fragments of 160 and 119 bp.
Among the 145 colorectal cancer cases 49 cases (33.79%) were
homozygous for the Arg72 allele (Arg/Arg), 18 cases (12.41%) were
homozygous for the Pro72 allele (Pro/Pro) and 78 cases (53.8%)
found in heterozygous (Arg/Pro).
In conclusion, it can be said that p53Arg/Arg genotype may be
correlated with possible increased risk of this kind of cancers in south
west of Iran.
Abstract: Personal name matching system is the core of
essential task in national citizen database, text and web mining,
information retrieval, online library system, e-commerce and record
linkage system. It has necessitated to the all embracing research in
the vicinity of name matching. Traditional name matching methods
are suitable for English and other Latin based language. Asian
languages which have no word boundary such as Myanmar language
still requires sounds alike matching system in Unicode based
application. Hence we proposed matching algorithm to get analogous
sounds alike (phonetic) pattern that is convenient for Myanmar
character spelling. According to the nature of Myanmar character, we
consider for word boundary fragmentation, collation of character.
Thus we use pattern conversion algorithm which fabricates words in
pattern with fragmented and collated. We create the Myanmar sounds
alike phonetic group to help in the phonetic matching. The
experimental results show that fragmentation accuracy in 99.32% and
processing time in 1.72 ms.
Abstract: Urbanization and related anthropogenic modifications
cause extent of habitat fragmentation and directly lead to decline of
local biodiversity. Conservation biologists advocate corridor creation
as one approach to rescue biodiversity. Here we examine the utility of
roads as corridors in preserving plant diversity by investigating
roadside vegetation in Yellow River Delta (YRD), China. We
examined the spatio-temporal distribution pattern of plant species
richness, diversity and composition along roadside. The results
suggest that roads, as dispersal conduits, increase occurrence
probability of new settlers to a new area, meanwhile, roads accumulate
the greater propagule pressure and favourable survival condition
during operation phase. As a result, more species, including native and
alien plants, non- halophyte and halophyte species, threatened and
cosmopolitic species, were found prosperous at roadside. Roadside
may be a refuge for more species, and the pattern of vegetation
distribution is affected by road age and the distance from road verge.
Abstract: Cancer becomes one of the leading cause of death in
many countries over the world. Fourier-transform infrared (FTIR)
spectra of human lung cancer cells (A549) treated with PMF (natural
product extracted from PM 701) for different time intervals were
examined. Second derivative and difference method were taken in
comparison studies. Cesium (Cs) and Rubidium (Rb) nanoparticles in
PMF were detected by Energy Dispersive X-ray attached to Scanning
Electron Microscope SEM-EDX. Characteristic changes in protein
secondary structure, lipid profile and changes in the intensities of
DNA bands were identified in treated A549 cells spectra. A
characteristic internucleosomal ladder of DNA fragmentation was
also observed after 30 min of treatment. Moreover, the pH values
were significantly increases upon treatment due to the presence of Cs
and Rb nanoparticles in the PMF fraction. These results support the
previous findings that PMF is selective anticancer agent and can
produce apoptosis to A549 cells.
Abstract: The major aim of this paper is to investigate the opposition politics in Africa. The paper also examines the status and the role, the contributions and the weaknesses of opposition1 political parties in Africa, particularly in transitional democracies that emerged in the 1990s. In Africa, many of the opposition parties appear or become active only during an election, and disappear when the election is over. It is found out that most of the opposition parties in Africa are established around the personalities of individuals, lack internal democracy, suffer from inter-party and intra-party conflicts, have severe shortage of finance, and lack strong base and experience. Their weaknesses also include bad organization and weak connection with the popular constituencies. The paper concludes that most of the weaknesses of the African opposition parties emanate from the incumbents- hostile policies, which are mostly aimed at fragmenting and weakening the opposition groups.
Abstract: Fourty one strains of ESBL producing P.aeruginosa
which were previously isolated from burn patients in Kerman
University general hospital, Iran were subjected to PCR, RFLP and
sequencing in order to determine the type of extended spectrum β-
lactamases (ESBL), the restriction digestion pattern and possibility of
mutation among detected genes. DNA extraction was carried out by
phenol chloroform method. PCR for detection of bla genes was
performed using specific primer for each gene. Restriction Fragment
Length Polymorphism (RFLP) for ESBL genes was carried out using
EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The
PCR products were subjected to direct sequencing of both the strands
for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1,
blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the
(n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29)
70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates
respectively. The RFLP analysis showed that each ESBL gene has
identical pattern of digestion among the isolated strains. Sequencing
of the ESBL genes confirmed the genuinety of PCR products and
revealed no mutation in the restriction sites of the above genes. From
results of the present investigation it can be concluded that blaVEB-1
and blaCTX-M were the most and the least frequently isolated ESBL
genes among the P.aeruginosa strains isolated from burn patients. The
RFLP and sequencing analysis revealed that same clone of the bla
genes were indeed existed among the antibiotic resistant strains.