MI-NODES multiscale models of metabolic reactions, brain connectome, ecological, epidemic, world trade, and legal-social networks

[Abstract] Complex systems and networks appear in almost all areas of reality. We find then from proteins residue networks to Protein Interaction Networks (PINs). Chemical reactions form Metabolic Reactions Networks (MRNs) in living beings or Atmospheric reaction networks in planets and moons. Network of neurons appear in the worm C. elegans, in Human brain connectome, or in Artificial Neural Networks (ANNs). Infection spreading networks exist for contagious outbreaks networks in humans and in malware epidemiology for infection with viral software in internet or wireless networks. Social-legal networks with different rules evolved from swarm intelligence, to hunter-gathered societies, or citation networks of U.S. Supreme Court. In all these cases, we can see the same question. Can we predict the links based on structural information? We propose to solve the problem using Quantitative Structure-Property Relationship (QSPR) techniques commonly used in chemo-informatics. In so doing, we need software able to transform all types of networks/graphs like drug structure, drug-target interactions, protein structure, protein interactions, metabolic reactions, brain connectome, or social networks into numerical parameters. Consequently, we need to process in alignment-free mode multitarget, multiscale, and multiplexing, information. Later, we have to seek the QSPR model with Machine Learning techniques. MI-NODES is this type of software. Here we review the evolution of the software from chemoinformatics to bioinformatics and systems biology. This is an effort to develop a universal tool to study structure-property relationships in complex systems

Defending Our Public Biological Databases as a Global Critical Infrastructure

Progress in modern biology is being driven, in part, by the large amounts of freely available data in public resources such as the International Nucleotide Sequence Database Collaboration (INSDC), the world's primary database of biological sequence (and related) information. INSDC and similar databases have dramatically increased the pace of fundamental biological discovery and enabled a host of innovative therapeutic, diagnostic, and forensic applications. However, as high-value, openly shared resources with a high degree of assumed trust, these repositories share compelling similarities to the early days of the Internet. Consequently, as public biological databases continue to increase in size and importance, we expect that they will face the same threats as undefended cyberspace. There is a unique opportunity, before a significant breach and loss of trust occurs, to ensure they evolve with quality and security as a design philosophy rather than costly “retrofitted” mitigations. This Perspective surveys some potential quality assurance and security weaknesses in existing open genomic and proteomic repositories, describes methods to mitigate the likelihood of both intentional and unintentional errors, and offers recommendations for risk mitigation based on lessons learned from cybersecurity

2023 IMSAloquium

Welcome to IMSAloquium 2023. This is IMSA’s 36 th year of leading in educationalinnovation, and the 35th year of the IMSA Student Inquiry and Research (SIR) Program.https://digitalcommons.imsa.edu/archives_sir/1033/thumbnail.jp

Special oils for halal and safe cosmetics

Three types of non conventional oils were extracted, analyzed and tested for toxicity. Date palm kernel oil (DPKO), mango kernel oil (MKO) and Ramputan seed oil (RSO). Oil content for tow cultivars of dates Deglect Noor and Moshkan was 9.67% and 7.30%, respectively. The three varieties of mango were found to contain about 10% oil in average. The red yellow types of Ramputan were found to have 11 and 14% oil, respectively. The phenolic compounds in DPKO, MKO and RSO were 0.98, 0.88 and 0.78 mg/ml Gallic acid equivalent, respectively. Oils were analyzed for their fatty acid composition and they are rich in oleic acid C18:1 and showed the presence of (dodecanoic acid) lauric acid C12:0, which reported to appear some antimicrobial activities. All extracted oils, DPKO, MKO and RSO showed no toxic effect using prime shrimp bioassay. Since these oils are stable, melt at skin temperature, have good lubricity and are great source of essential fatty acids; they could be used as highly moisturizing, cleansing and nourishing oils because of high oleic acid content. They are ideal for use in such halal cosmetics such as Science, Engineering and Technology 75 skin care and massage, hair-care, soap and shampoo products

Machine-Learning Methods for Computational Science and Engineering

The re-kindled fascination in machine learning (ML), observed over the last few decades, has also percolated into natural sciences and engineering. ML algorithms are now used in scientific computing, as well as in data-mining and processing. In this paper, we provide a review of the state-of-the-art in ML for computational science and engineering. We discuss ways of using ML to speed up or improve the quality of simulation techniques such as computational fluid dynamics, molecular dynamics, and structural analysis. We explore the ability of ML to produce computationally efficient surrogate models of physical applications that circumvent the need for the more expensive simulation techniques entirely. We also discuss how ML can be used to process large amounts of data, using as examples many different scientific fields, such as engineering, medicine, astronomy and computing. Finally, we review how ML has been used to create more realistic and responsive virtual reality applications

Machine-Learning Methods for Computational Science and Engineering

The re-kindled fascination in machine learning (ML), observed over the last few decades, has also percolated into natural sciences and engineering. ML algorithms are now used in scientific computing, as well as in data-mining and processing. In this paper, we provide a review of the state-of-the-art in ML for computational science and engineering. We discuss ways of using ML to speed up or improve the quality of simulation techniques such as computational fluid dynamics, molecular dynamics, and structural analysis. We explore the ability of ML to produce computationally efficient surrogate models of physical applications that circumvent the need for the more expensive simulation techniques entirely. We also discuss how ML can be used to process large amounts of data, using as examples many different scientific fields, such as engineering, medicine, astronomy and computing. Finally, we review how ML has been used to create more realistic and responsive virtual reality applications

2015 Oklahoma Research Day Full Program

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University

Acetylcholine esterase as a possible marker for the detection of halal way of slaughtering

Introduction: Different methods of slaughtering are being practiced because of differences in religious guidelines and environmental issues (use of electricity) or convenience of handling etc. Variation in methods of slaughtering results in different conditions namely, release of varying amount of blood and different degree of movement of its body parts prior to death. These issues are related to the release of neurotransmitter (NT) at the neuro-muscular junction (NMJ) eventually is subject to be released from the body through the blood flow. Experimental design: Muscle samples from chicken in small pieces were collected immediately after slaughtering. Slaughtering was carried out using sharp knife. Two different conditions pertaining to the Islamic guidelines of slaughtering were investigated. such as whether the neck was severed (S+) or not (S-) from the body during slaughtering and whether the animal just after slaughtering was released (R+) or not (R-). The level of acetylecholine esterase mRNA involved in the degradation of acetylecholine, a NT at NMJ was investigated by RT-PCR. Results: The level of acetylecholine esterase mRNA was not detected in the sample obtained from the chicken slaughtered following Islamic guidelines i.e., neck should not be severed and body should be released just after the slaughtering (R+S-). Conclusions: Level of acetylcholine or acetylcholine esterase can be used as a biomarker to identify if the slaughtering is performed following Islamic guidelines

Calophyllum canum : antibacterial and anticancer plant

Human have used plants as a source of medicine throughout the world since time immemorial. Today there are at least 120 distinct chemical substances derived from plants that are considered as important drugs currently in use in one or more countries in the world. In particular, 60% drugs currently in clinical use for treatment of cancer were found to be of natural origin. Calophyllum canum is a large tree which grows in South East Asia and which is popular for its timber. This plant belongs to the family Guttiferae; a family that boasts species which are rich in bioactive phytochemicals. Some species are believed to having medicinal values and are used against several diseases including anti-inflammatory, anti infectious, astringent and antipyretic. We have successfully isolated two compounds from the methanol extract of Calophyllum canum stembarks that active inhibit the growth of Staphylococcus aureus (ATCC 29213 and ATCC 25923). The cytotoxic study on the extracts revealed that the n-hexane extract had the strongest antiproliferation activity, followed by the methanol extract. n-hexane strongly inhibited the growth of TE1 and MCF7 cell lines. IC50 for n-hexane and methanol extract activity on the A549 cell line was found to be 27.96 μg/mL and 78.9 μg/mL respectively.The compounds (CE0 - CE5) isolated from ethyl acetate extract of C. canum are active to inhibit cell proliferation of human cervix adenocarcinoma cells