Nonparametric approaches for population structure analysis

The analysis of population structure has many applications in medical and population genetic research. Such analysis is used to provide clear insight into the underlying genetic population substructure and is a crucial prerequisite for any analysis of genetic data. The analysis involves grouping individuals into subpopulations based on shared genetic variations. The most widely used markers to study the variation of DNA sequences between populations are single nucleotide polymorphisms. Data preprocessing is a necessary step to assess the quality of the data and to determine which markers or individuals can reasonably be included in the analysis. After preprocessing, several methods can be utilized to uncover population substructure, which can be categorized into two broad approaches: parametric and nonparametric. Parametric approaches use statistical models to infer population structure and assign individuals into subpopulations. However, these approaches suffer from many drawbacks that make them impractical for large datasets. In contrast, nonparametric approaches do not suffer from these drawbacks, making them more viable than parametric approaches for analyzing large datasets. Consequently, nonparametric approaches are increasingly used to reveal population substructure. Thus, this paper reviews and discusses the nonparametric approaches that are available for population structure analysis along with some implications to resolve challenges.

Cluster ensemble based on Random Forests for genetic data

Background

Clustering plays a crucial role in several application domains, such as bioinformatics. In bioinformatics, clustering has been extensively used as an approach for detecting interesting patterns in genetic data. One application is population structure analysis, which aims to group individuals into subpopulations based on shared genetic variations, such as single nucleotide polymorphisms. Advances in DNA sequencing technology have facilitated the obtainment of genetic datasets with exceptional sizes. Genetic data usually contain hundreds of thousands of genetic markers genotyped for thousands of individuals, making an efficient means for handling such data desirable.

Results

Random Forests (RFs) has emerged as an efficient algorithm capable of handling high-dimensional data. RFs provides a proximity measure that can capture different levels of co-occurring relationships between variables. RFs has been widely considered a supervised learning method, although it can be converted into an unsupervised learning method. Therefore, RF-derived proximity measure combined with a clustering technique may be well suited for determining the underlying structure of unlabeled data. This paper proposes, RFcluE, a cluster ensemble approach for determining the underlying structure of genetic data based on RFs. The approach comprises a cluster ensemble framework to combine multiple runs of RF clustering. Experiments were conducted on high-dimensional, real genetic dataset to evaluate the proposed approach. The experiments included an examination of the impact of parameter changes, comparing RFcluE performance against other clustering methods, and an assessment of the relationship between the diversity and quality of the ensemble and its effect on RFcluE performance.

Conclusions

This paper proposes, RFcluE, a cluster ensemble approach based on RF clustering to address the problem of population structure analysis and demonstrate the effectiveness of the approach. The paper also illustrates that applying a cluster ensemble approach, combining multiple RF clusterings, produces more robust and higher-quality results as a consequence of feeding the ensemble with diverse views of high-dimensional genetic data obtained through bagging and random subspace, the two key features of the RF algorithm.

Subjective Text Mining for Arabic Social Media

The need for designing Arabic text mining systems for the use on social media posts is increasingly becoming a significant and attractive research area. It serves and enhances the knowledge needed in various domains. The main focus of this paper is to propose a novel framework combining sentiment analysis with subjective analysis on Arabic social media posts to determine whether people are interested or not interested in a defined subject. For those purposes, text classification methods—including preprocessing and machine learning mechanisms—are applied. Essentially, the performance of the framework is tested using Twitter as a data source, where possible volunteers on a certain subject are identified based on their posted tweets along with their subject-related information. Twitter is considered because of its popularity and its rich content from online microblogging services. The results obtained are very promising with an accuracy of 89%, thereby encouraging further research.

Electron spin resonance and magnetic studies on some copper(II) azobarbituric and azothiobarbituric acid complexes

Electron spin resonance and magnetic susceptibility on some copper(II) complexes prepared from phenylazobarbituric and phenylazothiobarbituric acid compounds containing 2,5-dichloro and 2,5-dimethyl groups were discussed. The thio complexes exist in dimer-monomer mixture. The corresponding copper(II) complexes of the oxygen homologous failed to exhibit association. Singlet-triplet separation values equal to -321 and -263 cm(-1) for the 2,5-dimethyl and 2,5-dichloro complexes, respectively, of the thio series. An empirical measure of the amount of tetrahedral deformation based on the values of g||/A|| assigned the square-planar geometry of the dimethyl-oxygen complex while the other complexes are with tetrahedral planar geometries. The effect of temperature on the ESR data was discussed. The diamagnetic properties of the complexes derived from 2,5-dichloro and 2,5-dimethyl thiobarbituric acid suggested the formation of Cu(I) complexes.

Histological study of necrolytic acral erythema

Described in 1996, necrolytic acral erythema remains the sole diagnostic cutaneous marker for hepatitis C virus infection. To date only eight cases have been described in literature, a fact that makes full histological description and appreciation of the disease process inadequate. Thirty necrolytic acral erythema cases were biopsied and detailed histological description was performed by three separate dermatopathologists who were blinded as to clinical presentation. Clinicopathological correlation was used to evaluate the disease progress. In the early stage, there is moderate regular acanthosis with variable spongiosis and inflammation, progressing to a picture resembling nummular eczema. In its fully evolved form, necrolytic acral erythema shows psoriasiform epidermal hyperplasia with marked papillomatosis. Associated findings include parakeratosis, focal hypergranulosis, subcorneal pustule, epidermal pallor, necrotic keratinocytes, which sometimes become confluent in the upper epidermis and/or track along the acrosyringia, vascular ectasia and papillary dermal inflammation. Late stage samples display some remaining acanthosis with variable inflammation. Pigment incontinence is seen in all stages.

Asymmetric catalysis on sequentially-linked columns

We report a catalytic asymmetric reaction process that involves the use of solid-phase reagents and catalysts that constitute the packing of a series of "reaction columns". This process was applied to the catalytic asymmetric synthesis of beta-lactams, to yield pure products with excellent enantio- and diastereoselectivity. We have identified several advantages to conducting chemical reactions on sequential columns, including ease of catalyst and reagent recovery and simplified purification steps that preclude the need for chromatography.

Reactive ketenes through a carbonate/amine shuttle deprotonation strategy: catalytic, enantioselective alpha-bromination of acid chlorides

[reaction: see text] We have developed an efficient methodology for the generation of ketenes by employing a catalytic shuttle base and potassium carbonate as a stoichiometric base. We have applied this technology to the catalytic, asymmetric alpha-bromination of acid chlorides.

Column asymmetric catalysis for beta-lactam synthesis

[structure] A catalytic asymmetric reaction process was designed involving the use of solid-phase reagents and catalysts that constitute the packing of a series of "reaction columns". This process was applied to the catalytic asymmetric synthesis of beta-lactams, yielding pure product after crystallization with exceptional enantio- and diastereoselectivity.

Susceptibility of Biomphalaria alexandrina to the plant Azolla pinnata and some herbicides in relation to infection with Schistosoma mansoni miracidia

Molluscicidal activity of the herebicides 2,4-D and Graminol, as well as both extracts and dry powder of the plant Azolla pinnata were evaluated against B. alexandrina snails. It was observed that 2,4-D proved to be the most toxic compound among he tested ones, showing LC90 of 52 ppm after 24 h of exposure. Ethanol extract of Azolla showed the highest molluscicidal activity against the tested snails compared with the other extracts and dry powder (LC90 = 3300 ppm). Ethanol extract at 6600 ppm after 3 h of exposure killed 100% and 19.4% of S. mansoni miracidia and cercariae, respectively. The molluscicidal activity of 2,4-D was not influenced by the presence of Azolla (900 plants/liter) for 7 days, while Graminol effect was significantly reduced. However, the infectivity of S. mansoni miracidia to B. alexandrina snails was not affected by Azolla existence.

Thyroid hormones, cholesterol and triglyceride levels in the camel

Thyroxine, tri-iodothyronine, triglyceride and cholesterol were measured in the serum of clinically healthy male camels. Thyroxine and tri-iodothyronine levels, which were assayed by an immunoabsorbent method, were not correlated with either age or cholesterol levels.

EPR study of hydrated testosterone monoclinic and orthorhombic single crystals gamma-irradiated at 295 K

The molecular structure of free radicals formed in gamma-irradiated monoclinic and orthorhombic single crystals of hydrated testosterone were investigated by EPR spectroscopy. Two different types of radical were observed. In the monoclinic form, the radical arises by the loss of a hydrogen atom from the carbon atom C(2), whereas, in the orthorhombic form, it arises by addition of a hydrogen atom to the oxygen atom O(3). The hyperfine spectrum of the radical formed in the monoclinic single crystal originates from the interaction of the unpaired electron with one alpha-proton in position 2 and two non equivalent beta-protons in position 1. In the orthorhombic single crystal, we observed interaction of the unpaired electron, which is delocalized on the carbons C(3), C(4) and C(5) with one alpha-proton in position 4 and with four nonequivalent beta-protons connected with the carbon atoms C(2) and C(6). The hyperfine tensors of the coupling and the g-tensor of the radicals are given.