Computational Tools for Analyzing Correlations Between Microbial Biological Diversity and Ecosystems

Metagenomics has developed into a reliable mechanism to analyze microbial diversity of microbial communities in the recent years. Through the use of next-generation sequencing, metagenomic studies can generate billions of short sequencing reads that are processed by computational tools. However, with the rapid adoption of metagenomics, a large amount of data has been produced. This high level of data production requires the development of computational tools and pipelines to manage data scalability and performance. In this thesis, we developed several tools that will aid in the exploration of the large amount of DNA sequence data, and we further developed a bioinformatic pipeline that will enhance the use of the developed tools by researchers with minimum computational background while also making them available for widespread use across the field of microbiology so that the research community can further contribute to development of these tools to overcome the growing computational challenges resultant from continued technological advances in high throughput DNA sequencing

Solitary Plasmacytoma of the Parotid Gland with Crystalline Inclusions: A Case Report

BACKGROUND: Solitary extramedullary plasmacytoma of the parotid gland is a rare condition. Intracytoplasmic Crystalline inclusions in the tumor are even rarer and have been reported only once in the parotid gland. CASE PRESENTATION: We report here, a case of plasmacytoma of the parotid gland with intracellular crystalline inclusions in a 73-year-old woman CONCLUSION: Solitary extramedullary plasmacytoma of the parotid gland and crystalline inclusions in the tumor is of rare occurrence. The importance of such a finding with relation to tumor progression, clinical course of the disease or prognosis in general remains to be understood

Application of the oxycodone templated molecular imprinted polymer in adsorption of the drug from human blood plasma as the real biological environment; a joint experimental and density functional theory study

In this project, we have synthesized and used a molecular imprinted polymer (MIP) for adsorption of oxycodone residue from the biological samples. Indeed, this study aims to develop a suitable method for determination of oxycodone drug residue in the human plasma using the common analysis methods. Therefore, the MIP was used for the solid phase extraction (MIP-SPE) approach in order to collect the oxycodone opioid and to concentrate it in the blood plasma samples. The extraction parameters such as adsorption time, pH, and the amount of sorbent in blood plasma were optimized and the capacity of loading amount (LA) for adsorbing it was determined. Moreover, a high performance liquid chromatography (HPLC)-UV detector method was validated and used for analyzing of the mentioned opioid extracted from plasma. The results showed that the limit of detection (LOD), and the limit of quantization (LOQ) for the developed MIP-SPE method were 1.24 ppb, and 3.76 ppb, respectively. Moreover, both of the MIP-, and non-imprinted polymers (NIP)-drug complexes were designed and were then optimized by the density functional theory (DFT) method. The results showed that the theoretical calculations supported the experimental data, confirming the favorability of adsorption of the drug by MIP compared to NIP

Evidence for magma mixing/mingling process in the plutonic intrusive bodies of Qorveh (Kurdistan Province): with emphasis on textural and geochemical characteristics

The Qorveh batholith, in the N-Sanandaj-Sirjan Zone, comprises several gabbroic, dioritic and granitic masses intruded the Jurassic metamorphic assemblage (i.e., schist, amphibolite and marble). In spite of a number of studies which have been carried out on the various aspects of these rocks, but none of them has been studied the Mixing/Mingling model. Thus, the purpose of present study is to examine the development of the magmatic mixing process in the rocks under study based on geochemical data obtained from the enclaves and their host rocks as well as their field relationship.Analytical MethodIn order to study the geochemical properties of intrusive rocks, 10 samples of enclaves and their host rocks. The rock composition with the least amount of alteration was selected and sent to the Pennsylvania State University of (USA) to determine the amounts of major elements by ICP-AES method, and rare and rare earth elements by ICP-MS method.Field observationsThe enclaves, in the intrusive masses under study, are finer than that of their host rock. Therefore, they belong to the group of mafic fine-grained enclaves or microgranular mafic enclaves. (MMEs). The (MMEs) are in rounded and elliptical shapes in the host rocks and generally they have a sharp contact with their host and are composed of igneous minerals.PetrographyThe host rocks include granite, granodiorite and monzonite, and the enclaves are dioritic and gabbroic in composition. There are similar minerals in the enclaves and their host rocks, but they often differ in the amount of minerals. They are mainly composed of mafic mineral and plagioclase. While their host rocks are characterized by smaller amounts of these minerals, the host rocks instead have higher amounts of quartz alkali feldspar. The transfer of plagioclase crystals at the common boundary of the enclave and the host rock is evidence of the magmatic mixing process in the nature of the intrusive masses studied. A number of enclaves contain megacrystals of feldspar potassium and quartz taken from the host rocks. This supports the formation of enclaves by mixing.GeochemistryGeochemical studies indicate that these rocks are metaluminous, belonging to calc-alkaline magma series, having I-type characteristics. In Harker diagrams, mafic enclaves have higher MgO, TiO2, P2O5, Na2O, FeO(t), Al2O3, MnO and CaO contents than that of the host rocks, and lower K2O and SiO2 contents. The higher contents of CaO, MgO and FeO(t) in the enclaves, compared to their host, confirms their more mafic nature, which is usually proportional to the higher contents of mafic minerals in the modal of the enclaves than that of the host. The enrichment of the studied enclaves in Co, Cr, Ni display that these rocks are globules of mafic magmas mingling to felsic type.DiscussionAccording to field observations as well as petrographic studies, the effective factor in the evolution of magma forming intrusive masses has been mentioned as magmatic mixing. The presence of mafic fine-grained enclaves with evidence of disequilibrium textures such as feldspar with poikilitic texture, the presence of mafic masses and needle apatite, small blades-shaped plagioclase within large plagioclase or two types of plagioclases, and zoning all confirm magmatic mingling/ mixing processes. Considering that the magnesium number (Mg#) in the mantle is about 0.7 and the studied enclaves with a high magnesium number of 0.52-0.62 are evidence of the involvement of mantle-derived mafic magma. High values of Mg# in enclaves compared to their host rock (0.34-0.48) shows the mixing of magmas from the mantle with the crustal magmas. Magma mixing model has also been considered by geochemical differentiation diagrams. The trend of the samples is a curve and indicates that the effective process in magma evolution is most likely magmatic fusion. Numerous studies have shown that mafic microgranular enclaves are globules of a mantle derived mafic magma that crystallize rapidly in the injected felsic magma from the crust and, as a result, become more viscous, forming separated magmatic bubbles. In addition to the mentioned geochemical features, the enclaves are poor in LREE and LILE and enriched in Ti compared to the host rocks. Therefore, they seem to have originated from two different magmas and are placed together due to magmatic mixing.ConclusionThe host rock units in the studied intrusions include granite, granodiorite, monzonite and gabbroic, dioritic enclaves. The constituent magma of this complex is in I- type, metaluminous and is in the calc-alkaline series. Based on the studies, the dominant process in the evolution of magmatic mixing. Some new findings include the presence of reversals in submerged slabs and the penetration of fleshy compounds. Which naturally have different temperatures and compositions compared to higher crustal horizon magmas, provides conditions for the occurrence and the development of the magmatic mixing process.AcknowledgementsThis paper is a part of the dissertation of the first author and therefore the authors acknowledge the financial support of the research assistant, Bu Ali Sina University

Impacts of nano-clay particles and heat-treating on out-of-phase thermo-mechanical fatigue characteristics in piston aluminum-silicon alloys

Abstract. In this article, the effect of nano-clay particles and heat-treating on thermo-mechanical fatigue (TMF) behaviors and failures of piston aluminum-silicon (AlSi) alloys was investigated. For this purpose, thermo-mechanical fatigue tests were conducted under out-of-phase (OP) loading conditions. Two loading conditions were checked based on different maximum temperatures (250, 300, and 350 °C) and various thermo-mechanical loading factors (100, 125, and 150%). The minimum temperature was constant in all tests at 50 °C under a heating/cooling rate of 10 °C/s and a dwell time of 5 s. Results showed that the nano-composites had a longer fatigue lifetime, at least 2 times higher, compared to the Al alloy, when the maximum temperature was 250 °C and the thermo-mechanical loading factor was 100%. However, no effective change was seen for the stress value and the plastic strain. At higher maximum temperatures, the change in the material behavior was lower. The fracture analysis by scanning electron microscopy (SEM) demonstrated that both materials had a brittle behavior due to cleavage and quasi-cleavage marks. The damage mechanism was also due to the Si-rich phase and intermetallics, respectively for the crack propagation and the micro-crack initiation

Low Iris and Anterior Chamber Volume Associated with Deepening after Laser Peripheral Iridotomy in Primary Angle Closure Suspects

Purpose: To evaluate the association between baseline ocular variables and the opening of the anterior chamber angle by laser peripheral iridotomy (LPI) in primary angle closure suspects (PACS) using a new Fourier-domain swept-source anterior segment optical coherence tomography (FD-ASOCT). Method: Sixty-six PACS eyes of 41 individuals were included in this prospective interventional case series. An FD-ASOCT (Casia SS-1000 OCT; Tomey, Nagoya, Japan) was used to measure biometric baseline variables and at one month after the LPI. Paired t-test was used to compare the difference between pre-and post-LPI measurements. Multivariate regression analysis was used to test for an association between baseline iris thickness and volume, anterior chamber depth and volume, and lens vault with a widening of the angle after an LPI. Results: The mean age of participants was 58.6 ± 8.7 years, 682% of whom were female. The angle opening distance, recess area and trabecular iris surface area at 500 microns increased by 48 to 73% (all p<0.001). Lens vault and iris volume did not change. A low anterior chamber volume and low iris volume were associated with angle greater deepening by LPI. Conclusion: Eyes with a shallow anterior chamber and thinner irises are more likely to experience angle opening from an LPI