Abstract: The electroencephalograph (EEG) signal is one of the most widely signal used in the bioinformatics field due to its rich information about human tasks. In this work EEG waves classification is achieved using the Discrete Wavelet Transform DWT with Fast Fourier Transform (FFT) by adopting the normalized EEG data. The DWT is used as a classifier of the EEG wave's frequencies, while FFT is implemented to visualize the EEG waves in multi-resolution of DWT. Several real EEG data sets (real EEG data for both normal and abnormal persons) have been tested and the results improve the validity of the proposed technique.
Abstract: The noteworthy point in the advancement of Brain Machine Interface (BMI) research is the ability to accurately extract features of the brain signals and to classify them into targeted control action with the easiest procedures since the expected beneficiaries are of disabled. In this paper, a new feature extraction method using the combination of adaptive band pass filters and adaptive autoregressive (AAR) modelling is proposed and applied to the classification of right and left motor imagery signals extracted from the brain. The introduction of the adaptive bandpass filter improves the characterization process of the autocorrelation functions of the AAR models, as it enhances and strengthens the EEG signal, which is noisy and stochastic in nature. The experimental results on the Graz BCI data set have shown that by implementing the proposed feature extraction method, a LDA and SVM classifier outperforms other AAR approaches of the BCI 2003 competition in terms of the mutual information, the competition criterion, or misclassification rate.
Abstract: Scolothrips longicornis Priesner is one of the
important predators of tetranychid mites with a wide distribution
throughout Iran. Life table and population growth parameters of S.
longicornis feeding on two-spotted spider mite, Tetranychus
turkestani Ugarov & Nikolski were investigated under laboratory
condition (26±1ºC, 65±5% R.H. and 16L: 8D). To carry of these
experiments, S. longicornis collections reared on cowpea infested
with T. turkestani were prepared. The eggs with less than 24 hours
old were selected and reared. The emerged larvae feeding directly on
cowpea leaf discs which were infested with T. turkestani. Thirty
females of S. longicornis with 24 hours age were selected and
released on infested leaf discs. They replaced daily to a new leaf disc
and the laying eggs have counted. The experiment continued till the
last thrips had died. The result showed that the mean age mortality of
the adult female thrips were between 21-25 days which is nearly
equal life expectancy (ex) at the time of adult eclosion. Parameters
related to reproductive table including gross reproductive rate, net
reproductive rate, intrinsic rate of natural increase and finite rate of
increase were 48.91, 37.63, 0.26 and 2.3, respectively. Mean age per
female/day, mean fertile egg per female/day, gross hatch rate, mean
net age fertility, mean net age fecundity, net fertility rate and net
fecundity rate were 2.23, 1.76, 0.87, 13.87, 14.26, 69.1 and 78.5,
respectively. Sex ratio of offspring also recorded daily. The highest
sex ratio for females was 0.88 in first day of oviposition. The sex
ratio decreased gradually and reached under 0.46 after the day 26 and
the oviposition rate declined. Then it seems that maintenance of
rearing culture of predatory thrips for mass rearing later than 26 days
after egg-laying commence is not profitable.
Abstract: Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.
Abstract: Phytases are acid phosphatase enzymes, which
efficiently cleave phosphate moieties from phytic acid, thereby
generating myo-inositol and inorganic phosphate. Thirty four
isolates of endophytic fungi to produce of phytases were isolated
from leaf, stem and root fragments of soybean. Screening of 34
isolates of endophytic fungi identified the phytases produced by
Rhizoctonia sp. and Fusarium verticillioides . The phytase
production were the best induced by phytic acid and rice bran
compared the others inducer in submerged fermentation medium
used. The phytase produced by both Rhizoctonia sp. and F.
verticillioides have pH optimum at 4.0 and 5.0 respectively. The
characterization of phytase from Fusarium verticillioides showed that
temperature optimum was 500C and stability until 600C, the pH
optimum 5.0 and pH stability was 2.5 – 6.0, and substrate specificity
were rice bran>soybean meal>corn> coconut cake, respectively.
Abstract: In this study, lipase production has been investigated
using submerge fermentation by Aspergillus niger in Kilka fish oil as
main substrate. The Taguchi method with an L9 orthogonal array
design was used to investigate the effect of parameters and their
levels on lipase productivity. The optimum conditions for Kilka fish
oil concentration, incubation temperature and pH were obtained 3
gr./ml 35°C and 7, respectively. The amount of lipase activity in
optimum condition was obtained 4.59IU/ml. By comparing this
amount with the amount of productivity in the olive oil medium
based on the cost of each medium, it was that using Kilka fish oil is
84% economical. Therefore Kilka fish oil can be used as an
economical and suitable substrate in the lipase production and
industrial usages.
Abstract: The present study has been conducted to characterize
the prophenoloxidase (PPO) system of the desert locust, Schistocerca
gregaria following injection of Bacillus thuringiensis kurstaki (Bt).
The bulk of PPO system was associated with haemocytes and a little
amount was found in plasma. This system was activated by different
activators such as laminarin, lipopolysaccharide (LPS) and trypsin
suggesting that the stimulatory mechanism may involve an enzyme
cascade of one or more associated molecules. These activators did
not activate all the molecules of the cascade. Presence of
phenoloxidase activity (PO) coincides with the appearance of protein
band with molecular weight (MW) 70.154 KD (Kilo Dalton).
Abstract: Artemisinin is a potential antimalarial drug effective
against the multidrug resistant forms of Malarial Parasites. The
current production of artemisinin is insufficient to meet the global
demand. In the present study microbial biotransformation of
arteannuin B, a biogenetic precursor of artemisinin to the later has
been investigated. Screening studies carried out on several soil borne
microorganisms have yielded one novel species with the
bioconversion ability. Crude cell free extract of 72h old culture of the
isolate had shown the bioconversion activity. On incubation with the
substrate arteannuin B, crude cell free extract of the isolate had
shown a bioconversion of 18.54% to artemisinin on molar basis with
a specific activity of 0.18 units/mg.
Abstract: Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.
Abstract: In order to compare vertical stratification, floristic composition, and woody species diversity of subtropical evergreen broadleaf forests between the Ryukyu Archipelago, Japan, and South China, tree censuses in a 400 m2 plot in Ishigaki Island and a 1225 m2 plot in Dinghushan Nature Reserve were performed. Both of the subtropical forests consisted of five vertical strata. The floristic composition of the Ishigaki forest was quite different from that of the Dinghushan forest in terms of similarity on a species level (Kuno-s similarity index r0 = 0.05). The values of Shannon-s index H' and Pielou-s index J ' tended to increase from the bottom stratum upward in both forests, except H' for the top stratum in the Ishigaki forest and the upper two strata in the Dinghushan forest. The woody species diversity in the Dinghushan forest (H'= 3.01 bit) was much lower than that in the Ishigaki forest (H'= 4.36 bit).
Abstract: The entomopathogenic nematodes Steinernema
feltiaeare are components of many biological pesticides. The
biological pesticides are applicated by means a spraying machines.
The influence of high pressure operating time on viability of
nematodes has been experimentally investigated in order to explain if
static pressure inside of the sprayers installation was able to destroy
nematodes. The value of pressure was 55 MPa and its maximum
operating time was 3 hours. Changes were found in viability of
pressurized samples of nematodes, mixed with water.
Abstract: Protein structure determination and prediction has
been a focal research subject in the field of bioinformatics due to the
importance of protein structure in understanding the biological and
chemical activities of organisms. The experimental methods used by
biotechnologists to determine the structures of proteins demand
sophisticated equipment and time. A host of computational methods
are developed to predict the location of secondary structure elements
in proteins for complementing or creating insights into experimental
results. However, prediction accuracies of these methods rarely
exceed 70%.
Abstract: Aquatic and semi aquatic birds as a group are suited to
feed and breed in environments in which water forms a fundamental
part. These birds are biological indicator in aquatic environment,
because these birds belong to the top level of food chain in aquatic
ecosystems. There are 61 species in 14 families of aquatic and semi
aquatic birds in Iran. The birds of the Sattarkhan Lake belong to 16
species in 8 families which include 26.2 percent of total Aquatic and
semi aquatic bird species and 57% of Aquatic and semi aquatic bird's
family of Iran. Study was carried out monthly at Sattarkhan Lake
show the existence of Phalacrocorax carbo, Ardea cinerea, Egretta
alba, Egretta garzetta, Bubulcus ibis, Botaurus stellaris, Sterna
hirundo, Chlidonias leucopterus, Larus minutus, Larus argentatus,
Larus ridibunbus, Alcedo atthis, Ciconia ciconia, Plegadis
falcinellus, Circus aeruginosus, Corvus frugilegus
Abstract: This study investigated morphology of the Spanner Barb (Puntius lateristriga Valenciennes, 1842) and water quality at Thepchana waterfall. This study was conducted at Thepchana Waterfall, Khao Nan National Park from March to May 2007. There were 40 Spanner Barb collected with 20 males and 20 females. Males had an average of 5.57 cm in standard length, 6.62 cm in total length and 5.18 g in total body weight. Females had an average of 7.25 cm in standard length, 8.24 cm in total length and 10.96 g in total body weight. The length (L) – weight (W) relationships for combining sexes, males and females were LogW = -2.137 + 3.355logL, log W = -0.068 + 3.297logL, and log W = -2.068 + 3.297logL, respectively. The Spanner Barb were smaller size fish with a compressed form; terminal mouth; villiform teeth; ctenoid scale; concave tail; general body color yellowish olive, with slight reddish tint to fins; vertical band beginning below dorsal and horizontal stripe from base of tail almost to vertical band. They also had a vertical band midway between the eye and first vertical band. There was a black spot above anal fin. The bladder looked like J-shape. Inside of the bladder was found small insects and insect lava. The body length and the bowels length was 1:1 ratio. The water temperature ranged from 25.00 – 27.00 °C which was appropriate for their habitat characteristics. Acid - alkalinity ranged from 6.65 – 6.90 mg/l. Dissolved oxygen ranged from 4.55 – 4.70 mg/l. Water hardness ranged from 31.00 – 48.00 mg/l. The amount of ammonia was about 0.25 mg/l.
Abstract: The growing health hazardous impact of arsenic (As)
contamination in environment is the impetus of the present
investigation. Application of lactic acid bacteria (LAB) for the
removal of toxic and heavy metals from water has been reported.
This study was performed in order to isolate and characterize the Asresistant
LAB from mud and sludge samples for using as efficient As
uptaking probiotic. Isolation of As-resistant LAB colonies was
performed by spread plate technique using bromocresol purple
impregnated-MRS (BP-MRS) agar media provided with As @ 50
μg/ml. Isolated LAB were employed for probiotic characterization
process, acid and bile tolerance, lactic acid production, antibacterial
activity and antibiotic tolerance assays. After As-resistant and
removal characterizations, the LAB were identified using 16S rDNA
sequencing. A total of 103 isolates were identified as As-resistant
strains of LAB. The survival of 6 strains (As99-1, As100-2, As101-3,
As102-4, As105-7, and As112-9) was found after passing through the
sequential probiotic characterizations. Resistant pattern pronounced
hollow zones at As concentration >2000 μg/ml in As99-1, As100-2,
and As101-3 LAB strains, whereas it was found at ~1000 μg/ml in
rest 3 strains. Among 6 strains, the As uptake efficiency of As102-4
(0.006 μg/h/mg wet weight of cell) was higher (17 – 209%)
compared to remaining LAB. 16S rDNA sequencing data of 3 (As99-
1, As100-2, and As101-3) and 3 (As102-4, As105-7, and As112-9)
LAB strains clearly showed 97 to 99% (340 bp) homology to
Pediococcus dextrinicus and Pediococcus acidilactici, respectively.
Though, there was no correlation between the metal resistant and
removal efficiency of LAB examined but identified elevated As
removing LAB would probably be a potential As uptaking probiotic
agent. Since present experiment concerned with only As removal
from pure water, As removal and removal mechanism in natural
condition of intestinal milieu should be assessed in future studies.
Abstract: There was studied dynamic of the number of
nematodes fauna of various ecosystems of Gombori Mountain Ridge
that belongs to peak of fauna dynamic. The nature of dynamic is in
general similar in all six biotypes and the difference is evident only in
total number of nematodes.
Abstract: Two species of Physalis, P.angulataL. and P.
peruviana L. were used as models for comparative study to
understand the values of micro-morphological, -anatomical and
architectural characteristics of leaf for taxonomic purposes and
possibly breeding and commercial applications. Both speciespossess
amphistomaticleaves with 1-layer epidermis, 3-4-layer spongy
mesophyll andbicollateral bundle midrib. Palisade parenchyma cells
of P. angulatawere almost twice longer (65-75 μm) than the other
one. Type of stomata was similar as anomocyticbut stomatal
index(SI) at adaxial surface and abaxial surface of P. angulata were
less than of P. peruvianaas 3.57, 4.00 and6.25, 6.66 respectively.
Some leaf architectural characteristics such as leaf shape, order of
venationalsoprovided information of taxonomic significance
Abstract: Phytophthora cinnamomi (P. c) is a plant pathogenic
oomycete that is capable of damaging plants in commercial production
systems and natural ecosystems worldwide. The most common
methods for the detection and diagnosis of P. c infection are
expensive, elaborate and time consuming. This study was carried out
to examine whether species specific and life cycle specific volatile
organic compounds (VOCs) can be absorbed by solid-phase
microextraction fibers and detected by gas chromatography that are
produced by P. c and another oomycete Pythium dissotocum. A
headspace solid-phase microextraction (HS-SPME) together with gas
chromatography (GC) method was developed and optimized for the
identification of the VOCs released by P. c. The optimized parameters
included type of fiber, exposure time, desorption temperature and
desorption time. Optimization was achieved with the analytes of P.
c+V8A and V8A alone. To perform the HS-SPME, six types of fiber
were assayed and compared: 7μm Polydimethylsiloxane (PDMS),
100μm Polydimethylsiloxane (PDMS), 50/30μm
Divinylbenzene/CarboxenTM/Polydimethylsiloxane
DVB/CAR/PDMS), 65μm Polydimethylsiloxane/Divinylbenzene
(PDMS/DVB), 85μm Polyacrylate (PA) fibre and 85μm CarboxenTM/
Polydimethylsiloxane (Carboxen™/PDMS). In a comparison of the
efficacy of the fibers, the bipolar fiber DVB/CAR/PDMS had a higher
extraction efficiency than the other fibers. An exposure time of 16h
with DVB/CAR/PDMS fiber in the sample headspace was enough to
reach the maximum extraction efficiency. A desorption time of 3min
in the GC injector with the desorption temperature of 250°C was
enough for the fiber to desorb the compounds of interest. The chromatograms and morphology study confirmed that the VOCs from
P. c+V8A had distinct differences from V8A alone, as did different
life cycle stages of P. c and different taxa such as Pythium dissotocum.
The study proved that P. c has species and life cycle specific VOCs,
which in turn demonstrated the feasibility of this method as means of
Abstract: Statistical analysis of electrophysiological recordings
obtained under, e.g. tactile, stimulation frequently suggests participation
in the network dynamics of experimentally unobserved “hidden"
neurons. Such interneurons making synapses to experimentally
recorded neurons may strongly alter their dynamical responses to
the stimuli. We propose a mathematical method that formalizes this
possibility and provides an algorithm for inferring on the presence
and dynamics of hidden neurons based on fitting of the experimental
data to spike trains generated by the network model. The model
makes use of Integrate and Fire neurons “chemically" coupled
through exponentially decaying synaptic currents. We test the method
on simulated data and also provide an example of its application to
the experimental recording from the Dorsal Column Nuclei neurons
of the rat under tactile stimulation of a hind limb.
Abstract: Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.