A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable

MTAP: The Motif Tool Assessment Platform

Background: In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with the best performance characteristics for specific problem domains. Identifying the correct tool is difficult because of the great variability in motif detection software. Consequently, many labs spend considerable effort testing methods to find one that works well in their problem of interest. Results: In this work, we propose a method (MTAP) that substantially reduces the effort required to assess de novo regulatory motif discovery software. MTAP differs from previous attempts at regulatory motif assessment in that it automates motif discovery tool pipelines (something that traditionally required many manual steps), automatically constructs orthologous upstream sequences, and provides automated benchmarks for many popular tools. As a proof of concept, we have run benchmarks over human, mouse, fly, yeast, E. coli and B. subtilis. Conclusion: MTAP presents a new approach to the challenging problem of assessing regulatory motif discovery methods. The most current version of MTAP can be downloaded from http:// biobase.ist.unomaha.edu

MTAP: The Motif Tool Assessment Platform

Background: In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with the best performance characteristics for specific problem domains. Identifying the correct tool is difficult because of the great variability in motif detection software. Consequently, many labs spend considerable effort testing methods to find one that works well in their problem of interest. Results: In this work, we propose a method (MTAP) that substantially reduces the effort required to assess de novo regulatory motif discovery software. MTAP differs from previous attempts at regulatory motif assessment in that it automates motif discovery tool pipelines (something that traditionally required many manual steps), automatically constructs orthologous upstream sequences, and provides automated benchmarks for many popular tools. As a proof of concept, we have run benchmarks over human, mouse, fly, yeast, E. coli and B. subtilis. Conclusion: MTAP presents a new approach to the challenging problem of assessing regulatory motif discovery methods. The most current version of MTAP can be downloaded from http://biobase.ist.unomaha.edu

Efficacy of N-Acetylcysteine, Glutathione, and Ascorbic Acid in Acute Toxicity of Paraoxon to Wistar Rats: Survival Study

There are a great number of reports with assertions that oxidative stress is produced by organophosphorus compound (OPC) poisoning and is a cofactor of mortality and morbidity in OPC toxicity. In addition, antioxidants have been suggested as adjuncts to standard therapy. However, there is no substantial evidence for the benefit of the use of antioxidants in survival after acute intoxication of OPCs. The present study was conducted to assess the effectiveness of three non-enzymatic antioxidants (NEAOs), N-acetylcysteine (NAC), glutathione (GSH), and ascorbic acid (AA), in acute intoxication of adult male Wister rats with paraoxon. The efficacy of the antioxidants was estimated as both a pretreatment and a concurrent application along with the standard oxime, pralidoxime (2-PAM). Relative risk of death after 48 hours of application was estimated by Cox regression analysis. The results revealed no benefit of either tested NEAO to the improvement in survival of experimental rats. The application of these antioxidants was found to be deleterious when administered along with pralidoxime compared to the treatment with pralidoxime alone. It has been concluded that the tested non-enzymatic antioxidants are not useful in acute toxicity for improving survival rates. However, the individual toxic dynamics of diversified OPCs should not be overlooked and further studies with different OPCs are suggested

Significance of storage on solar photovoltaic system : a residential load case study in Australia

Signing of History book "The Community's College: A History of Johnson County Community College (1969-1999)" by Charles C. Bishop in Carlsen Center on April 3rd, 200

Significance of storage on solar photovoltaic system : a residential load case study in Australia

Energy storage is an essential part in effective utilization of Renewable Energy (RE). Most RE sources cannot provide constant energy supply and introduce a potential unbalance in generation and demand, especially in off-peak periods when RE generates more energy and in peak period when load demand rises too high. Storage allows intermittent sources like solar Photovoltaic (PV) to address timely load demand and adds flexibility in load management. This paper analyses the significance of storage for residential load considering solar PV as RE generator. The significance of storage was evaluated in off-grid or stand alone and grid connected configurations. Moreover it outlined the significance of storage in terms of environment and economics by comparing the Renewable Fraction (RF), Greenhouse Gas (GHG) emission, Cost of Energy (COE) and Net Present Cost (NPC). Investigation showed that storage has positive influences on both (off-grid and grid connected) configurations by improving PV utilization. It was found that in grid connected configuration storage reduced 46.47% of GHG emission, reduced COE, NPC and improved RF compared to the system without storage

Synthesis of Nanostructured Silicon - Germanium Thermoelectric Materials by Mechanical Alloying

Silicon-germanium (SiGe) thermoelectric material is especially suited in power generation operating above 700 °C to 1000 °C to convert heat into electricity. Traditional bulk SiGe alloy thermoelectric materials has the value of dimensionless thermoelectric figure of merit (ZT) at maximum about 0.93 at 900 °C. It corresponds to 8% highest device efficiency to convert heat into electricity for commercial SiGe thermoelectric devices. Recently, many efforts have been made to increase the ZT value of SiGe thermoelectric materials. Among them, nanostructuring of SiGe alloy is an effective mechanism to enhance the ZT value of the thermoelectric material. In this approach, the ZT value increases due to the reduction of thermal conductivity caused by enhanced phonon scattering off the increased density of nanograin boundaries. There are different approaches to make nanostructured SiGe alloy bulk thermoelectric materials. Mechanical alloying of elemental Si and Ge powder is one of them. In this thesis work, different compositions of elemental Si and Ge micro powders have been mechanically alloyed using ball milling technique to produce SiGe alloy nanopowder and then were compacted and sintered by spark plasma sintering (SPS) method. Different characterization techniques have been used to see the effect of compositions, milling parameters and sintering conditions on the properties of the synthesized nanopowders and sintered compact samples

Internal Structure, Petrography and Mineralogy of Beryl in Bahr-e-Abad Area, East of Afghanistan

This paper deals with the study of beryl, its variety, petrographic, and gemological specifications in the Bahr-e-Abad area of Jalalabad city. Beryl is a relatively rare silicate mineral, cyclo-silicate, with a chemical composition of Be3Al2 (Si6O18) and a hexagonal crystal shape. It is found in igneous and metamorphic rocks in many parts of the world. In order to achieve the aim of this paper, three methods, namely; library work, fieldwork, and lab work, were conducted, and about 20 specimens were collected from the above-mentioned area and taken to the Afghanistan Geological Survey (AGS) for making the thin sections and spectrometry analysis. Bahr-e-Abad area is related to the tectonic zone of Jalalabad. Jalalabad zone is located in the eastern part of Afghanistan and southeast of the Nuristan zone. Correspondingly, this zone is related to the upper Cambrian or younger Cambrian. In this area, the age of rocks is related to Archean- Middle Proterozoic AR-PR2. Beryl mineral is mostly found in Europe, Norway, Austria, Germany, Sweden, Ireland, Russia, Brazil, the US, Colombia, and Pakistan. Afghanistan is counted as one of the world’s leading countries in having rare-metal pegmatites, which are present in Afghanistan’s pegmatite belts in Afghanistan. This mineral is widely available in the pegmatite veins of Nuristan, Sistan, Panjshir, and Laghman. All pegmatite groups of Afghanistan are related to intrusive rocks. This study found that the rocks which are situated within pegmatite veins, besides beryl mineral, generally have the same composition and contain plagioclase, feldspar alkali (sodium-potassium), and mica (phlogopite and biotite) minerals. This is a microcline – albite type

Exploring Teaching and Learning Experience during COVID-19 Pandemic in Engineering Education

The education system is continuously modernizing by accommodating the need due to the industrial revolution. Various teaching modes are also introduced including a diverse range of students, particularly in engineering education. The COVID-19 pandemic has disrupted normal education worldwide, forced to shut down campus activity for an extended period which forced Universities to adopt alternative approaches to continue student’s academic year. Engineering education faced significant challenges to find a realistic substitution for lab-based hands-on activity as well as group or team-based learning experiences. It is therefore very important to know the challenges and ways to address them. This paper evaluates the teaching and learning experiences observed in engineering education in Australia and abroad during the COVID-19 period compared to the pre-COVID period. The key motivation of this study is to identify key challenges arises due to COVID-19, develop Teaching & Learning (T & L) approaches to address these challenges and evaluate the effectiveness of the applied changes in the T & L approach, identify shortcomings, and find ways to improve them. The student feedback on selected engineering units have been collected from Deakin and Murdoch university in Australia to evaluate the performances of the applied changes. This data is considered as an authentic source of information to compare and identify the key challenges and effectiveness for students’ learning in pre-COVID and during COVID condition. This study later explored various literatures to gather experiences from other universities across the globe and by analysing all findings including academic experiences finally developed constructive recommendations for improvement. It is found that the current form of online mode of teaching has room to improve further as one segment of students finds it challenging and some others like a few approaches. It is also found that the online infrastructure, staff skills to innovate new unit designs, and motivating students are the other challenging areas. Therefore, a new teaching and learning framework is required to overcome all the challenges for future learning

Physiotherapy combined with dry needling among patients with chronic low back pain: Study protocol for a randomized controlled clinical trial

Background: Chronic low back pain (CLBP) is an extremely common public health concern responsible for pain-related disability. CLBP is challenging to manage despite having a plethora of treatment options. Physiotherapy is a guideline-recommended treatment for CLBP. Furthermore, some forms of complementary medicines, such as dry needling, spinal manipulation, Tai Chi, and yoga are also recommended for CLBP treatment. We hypothesized that the combined treatment would be more effective when managing CLBP. Therefore, this randomized clinical trial aims to examine the impact of combined therapy of dry needling and physiotherapy compared to the treatment effect of only physiotherapy among patients with CLBP. Methods: The study is a two-armed single-center, randomized controlled clinical superiority trial where participants are randomized to combined therapy of usual care physiotherapy and dry needling or only usual care physiotherapy (1:1). Individuals who are 18 years or older and experiencing LBP with or without leg pain for a minimum of three months will be considered eligible for the study. Pain severity, pain affective and physical interference, activity limitation, and insomnia symptoms of patients with CLBP will be measured at the baseline after four, 12 and 24-week treatment started. Conclusion: Finding a better management strategy for managing CLBP is an ongoing challenge. Most of the novel techniques that try to manage CLBP are limitedly tested. This study will allow testing of the combined effect of usual care physiotherapy and dry needling when managing CLBP in terms of clinical efficacy. If the combined therapy is proven significantly effective, compared to usual care physiotherapy alone will provide plausible evidence of an effective treatment option to manage CLBP. Trial registration: Clinical Trial Registry-India; trial registration number- CTRI/2022/09/045625