Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Performance Enhancement of Multiuser Time Reversal UWB Communication System

UWB communication is a recent research area for indoor propagation channels. Time Reversal (TR) communication in UWB has shown promising results for improving the system performance. In multiuser environment, the system performance is significantly degraded due to the interference among different users. TR reduces the interference caused by multiusers due to its spatial focusing property. The performance of a multiuser TR communication system is further improved if the TR filter is modified. In this paper, multiuser TR in UWB communication is investigated using simple TR filter and a modified TR filter with circular shift operation. The concept of circular shift in TR is analytically studied. Thereafter, the channel impulse responses (CIR) of a typical indoor laboratory environment are measured. The measured CIRs are used to analyze the received signal peak power and signal to interference ratio (SIR) with and without performing the circular shift operation in a multiuser environment

Taxonomic and environmental annotation of bacterial 16S rRNA gene sequences via Shannon entropy and database metadata terms

Microbial ecology seeks to describe the diversity and distribution of microorganisms in various habitats within the context of environmental variables. High throughput sequencing has greatly boosted the number and scope of projects aiming to study and analyse these organisms, with ever-increasing amounts of data being generated. Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. This data is then used to study the distribution of biodiversity as well as the response of microbial communities to stressors. However, the 16S rRNA gene displays varying degrees of sequence conservation along its length and is therefore prone to provide different results depending on the part of 16S rRNA gene used for sequencing and analysis. Furthermore, sequence alignment is primarily performed using the popular BLAST sequence alignment tool, which incurs a great computational performance penalty although newer, more efficient tools are being developed. A new approach that is fast and more accurate is critically needed to process the avalanche of data. Additionally, repositories of environmental metadata can provide contextual information to sequence annotations, potentially enhancing analysis if they can be incorporated into bioinformatics pipelines. The overarching aim of this work was to enhance the taxonomic annotation of bacterial sequences by developing a weighted scheme that utilizes inherent evolutionary conservation in the bacterial 16S rRNA gene sequences and by adding contextual, environmental information pertaining to these sequences in a systematic fashion

Frequency distribution of HCV genotypes among chronic hepatitis C patients of Khyber Pakhtunkhwa

<p>Abstract</p> <p>Background</p> <p>Hepatitis C Virus (HCV) genotypes frequency is important for the predication of response to therapy and duration of treatment. Despite variable response rates experienced in the case of Interferon (IFN) -based therapies, there was scarcity of data on HCV genotypes frequency in Khyber Pakhtunkhwa (KPK).</p> <p>Study Design</p> <p>A total of 200 blood samples were collected from chronic HCV patients prior to the initiation of anti-viral therapy. The study population included patients from 6 districts of KPK. Active HCV infection was confirmed in case of all the patients by real time PCR. HCV genotypes were determined in each case by Type-specific PCR.</p> <p>Results</p> <p>The analysis revealed that out of 200 PCR positive samples; 78 (39%) were 2a, 62 (31%) were 3a, 16 (8%) were 3b, 34 (17%) were untypable while 1a, 2b and 1b were 3 (1.5%), 2 (1%) and 5 (2.5%), respectively.</p> <p>Conclusion</p> <p>Genotype determination is not carried out prior to therapy in KPK. Although, the abundantly prevalent types (2a and 3a) of HCV in KPK are susceptible to combination therapy, yet resistance experienced in some of the chronic HCV patients may partly be attributed to the prevalence of less prevalent resistant genotypes (1a, 1b) of HCV among the population.</p

Antibacterial, Antifungal, and Insecticidal Potentials of Oxalis corniculata

Oxalis corniculata is a common medicinal plant widely used against numerous infectious diseases. The agrochemical potential of methanolic extract, n-hexane, chloroform, ethyl acetate, and n-butanol fractions were assessed to measure the antibacterial, antifungal, and insecticidal activities of the plant. The crude, chloroform, and n-butanol soluble fractions showed excellent activities against Escherichia coli, Shigella dysenteriae, Salmonella typhi, and Bacillus subtilis but have no activity against Staphylococcus aureus. Similarly the crude, n-hexane, and chloroform fractions were also found to have significant activity against fungal strains including Fusarium solani, Aspergillus flexneri, and Aspergillus flavus and have no activity against Aspergillus niger. Chemical pesticides have shown very good results at the beginning, but with the passage of time the need was realized to use the natural plant sources for the safe control of insects. The current study will provide minor contribution towards it. High mortality rate was recorded for the crude extract and chloroform fraction against Tribolium castaneum. The two isolated compounds 5-hydroxy-6,7,8,4′-tetramethoxyflavone (1) and 5,7,4′-trihydroxy-6,8-dimethoxyflavone (2) were evaluated for antibacterial, antifungal, and insecticidal activities. The results showed that compound 2 was more active than compound 1 against the tested bacterial strains and insects

A New Weighting Scheme in Weighted Markov Model for Predicting the Probability of Drought Episodes

Drought is a complex stochastic natural hazard caused by prolonged shortage of rainfall. Several environmental factors are involved in determining drought classes at the specific monitoring station. Therefore, efficient sequence processing techniques are required to explore and predict the periodic information about the various episodes of drought classes. In this study, we proposed a new weighting scheme to predict the probability of various drought classes under Weighted Markov Chain (WMC) model. We provide a standardized scheme of weights for ordinal sequences of drought classifications by normalizing squared weighted Cohen Kappa. Illustrations of the proposed scheme are given by including temporal ordinal data on drought classes determined by the standardized precipitation temperature index (SPTI). Experimental results show that the proposed weighting scheme for WMC model is sufficiently flexible to address actual changes in drought classifications by restructuring the transient behavior of a Markov chain. In summary, this paper proposes a new weighting scheme to improve the accuracy of the WMC, specifically in the field of hydrology

Multiuser Time Reversal UWB Communication System: A Modified Transmission Approach

International audienceIn this paper, ultra-wideband (UWB), time reversal (TR) communication is investigated by modifying the transmission prefilter. Mathematical expressions for received signal and the interference in the modified transmission scheme are derived. It is shown that the modified transmission approach reduces multi-user interference which eventually translates into a better bit error rate (BER) performance than simple TR multiuser scheme. Channel impulse responses (CIR) of a typical indoor channel are measured. In a multi-user scenario, both TR and the modified TR schemes are studied using the measured CIRs. It is shown that the proposed modified TR scheme outperforms the original TR scheme

Multi-operation data encryption mechanism using dynamic data blocking and randomized substitution

Existing cryptosystems deal with static design features such as fixed sized data blocks, static substitution and apply identical set of known encryption operations in each encryption round. Fixed sized blocks associate several issues such as ineffective permutations, padding issues, deterministic brute force strength and known-length of bits which support the cracker in formulating of modern cryptanalysis. Existing static substitution policies are either not optimally fit for dynamic sized data blocks or contain known S-box transformation and fixed lookup tables. Moreover, static substitution does not directly correlate with secret key due to which it has not been shown safer especially for Advanced Encryption Standard (AES) and Data Encryption Standard (DES). Presently, entire cryptosystems encrypt each data block with identical set of known operations in each iteration, thereby lacked to offer dynamic selection of encryption operation. These discussed, static design features are fully known to the cracker, therefore caused the practical cracking of DES and undesirable security pitfalls against AES as witnessed in earlier studies. Various studies have reported the mathematical cryptanalysis of AES up to full of its 14 rounds. Thus, this situation completely demands the proposal of dynamic design features in symmetric cryptosystems. Firstly, as a substitute to fixed sized data blocks, the Dynamic Data Blocking Mechanism (DDBM) has been proposed to provide the facility of dynamic sized data blocks. Secondly, as an alternative of static substitution approach, a Randomized Substitution Mechanism (RSM) has been proposed which can randomly modify session-keys and plaintext blocks. Finally, Multi-operation Data Encryption Mechanism (MoDEM) has been proposed to tackle the issue of static and identical set of known encryption operations on each data block in each round. With MoDEM, the encryption operation can dynamically be selected against the desired data block from the list of multiple operations bundled with several sub-operations. The methods or operations such as exclusive-OR, 8-bit permutation, random substitution, cyclic-shift and logical operations are used. Results show that DDBM can provide dynamic sized data blocks comparatively to existing approaches. Both RSM and MoDEM fulfill dynamicity and randomness properties as tested and validated under recommended statistical analysis with standard tool. The proposed method not only contains randomness and avalanche properties but it also has passed recommended statistical tests within five encryption rounds (significant than existing). Moreover, mathematical testing shows that common security attacks are not applicable on MoDEM and brute force attack is significantly resistive

Microbial profiling and risk factors assessment for Otitis Media and Otitis Externa

Background: Otitis media and otitis externa are common otological manifestations in all generations especially in children. There is lack of accurate identification of the causative agent and thus poor diagnosis for such infections. Therefore, it leads to permanent anatomical disabilities including poor speech and defects in balancing and hearing. The study was conducted to isolate, characterize and identify the microbes causing otitis media and otitis externa. Methods: A total of 250 patients having otitis media and otitis externa were enrolled in the study from March 2011 to October 2011. All patients were examined through clinical examination and detailed history was collected. Pus samples from the discharging ears were plated on MacConkey’s, Chocolate and Blood agar for 24 to 48 hours. Isolates were identified on the basis of morphology, staining reactions and various biochemical tests. Results: In this study, only 6% cases yielded no growth, 14% yielded mixed cultures while 80% cases yielded pure cultures. The presumptive diagnosis for ear swabbing was otitis media (76%) and otitis externa (24%). The most common bacterial isolates obtained were Staphylococcus aureus (43.3%) followed byPseudomonas aeruginosa (25%) in the diagnosed cases of otitis media. While for the cases of otitis externa,Pseudomonas aeruginosa was the predominant organism with 52.2%. Infection of otitis media was most common among children and the persons having low socioeconomic conditions. Conclusion: Pseudomonas aeruginosa was identified as the principal pathogen followed by Staphylococcus aureus. To circumvent the painful effects of acute and chronic ear infections, an accurate microbial profiling may play pivotal role