Multiple instance learning for sequence data with across bag dependencies

In Multiple Instance Learning (MIL) problem for sequence data, the instances inside the bags are sequences. In some real world applications such as bioinformatics, comparing a random couple of sequences makes no sense. In fact, each instance may have structural and/or functional relations with instances of other bags. Thus, the classification task should take into account this across bag relation. In this work, we present two novel MIL approaches for sequence data classification named ABClass and ABSim. ABClass extracts motifs from related instances and use them to encode sequences. A discriminative classifier is then applied to compute a partial classification result for each set of related sequences. ABSim uses a similarity measure to discriminate the related instances and to compute a scores matrix. For both approaches, an aggregation method is applied in order to generate the final classification result. We applied both approaches to solve the problem of bacterial Ionizing Radiation Resistance prediction. The experimental results of the presented approaches are satisfactory

Insights into Ionizing-Radiation-Resistant Bacteria S-Layer Proteins and Nanobiotechnology for Bioremediation of Hazardous and Radioactive Waste

S-layers are crystalline arrays formed by proteinaceous subunits that cover the outer surface of many different kinds of microorganisms. This “proteinaceous cover” is particularly important in the case of ionizing-radiation-resistant bacteria (IRRB) that might be used in bioremediating hazardous and radioactive wastes (HRW). Despite the exponential growth in the number of comparative studies and solved proteic crystal structures, the proteic networks, diversity, and bioremediation-useful structural properties of IRRB S-layers remain unknown. Here, aided by literature, a tentative model of Deinococcus radiodurans R1 S-layer proteins (SLPs) and the network of its main constituents were proposed. The domain analysis of this network was performed. Moreover, to show the diversity of IRRB S-layers, comparative genomics and computer modeling experiments were carried out. In addition, using in silico modeling, assisted by previously published data, the outermost exposed segments of D. radiodurans SlpA (surface layer protein A) that were predicted to interact with uranium were mapped. The combination of data and results pointed to various prospective applications of IRRB S-layers in nanobiotechnology for bioremediation of radioactive waste

Aerospace medicine and biology: A continuing bibliography with indexes

This bibliography lists 148 reports, articles and other documents introduced into the NASA scientific and technical information system in December 1984

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing-Review

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals

Aerospace Medicine and Biology: A continuing bibliography with indexes (supplement 291)

This bibliography lists 131 reports, articles and other documents introduced into the NASA scientific and technical information system in November 1986

Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization.

While many efforts have been made to pave the way toward human space colonization, little consideration has been given to the methods of protecting spacefarers against harsh cosmic and local radioactive environments and the high costs associated with protection from the deleterious physiological effects of exposure to high-Linear energy transfer (high-LET) radiation. Herein, we lay the foundations of a roadmap toward enhancing human radioresistance for the purposes of deep space colonization and exploration. We outline future research directions toward the goal of enhancing human radioresistance, including upregulation of endogenous repair and radioprotective mechanisms, possible leeways into gene therapy in order to enhance radioresistance via the translation of exogenous and engineered DNA repair and radioprotective mechanisms, the substitution of organic molecules with fortified isoforms, and methods of slowing metabolic activity while preserving cognitive function. We conclude by presenting the known associations between radioresistance and longevity, and articulating the position that enhancing human radioresistance is likely to extend the healthspan of human spacefarers as well

Evolution of Ionizing Radiation Research

The industrial and medical applications of radiation have been augmented and scientific insight into mechanisms for radiation action notably progressed. In addition, the public concern about radiation risk has also grown extensively. Today the importance of risk communication among stakeholders involved in radiation-related issues is emphasized much more than any time in the past. Thus, the circumstances of radiation research have drastically changed, and the demand for a novel approach to radiation-related issues is increasing. It is thought that the publication of the book Evolution of Ionizing Radiation Research at this time would have enormous impacts on the society. The editor believes that technical experts would find a variety of new ideas and hints in this book that would be helpful to them to tackle ionizing radiation

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 367)

This bibliography lists 205 reports, articles, and other documents introduced into the NASA Scientific and Technical Information System during Aug. 1992. Subject coverage includes the following: aerospace medicine and physiology, life support systems and man/system technology, protective clothing, exobiology and extraterrestrial life, planetary biology, and flight crew behavior and performance

Mechanisms of Resistance to Ionizing Radiation in Extremophiles

Extremophiles display an astonishing array of adaptations to harsh environmental conditions. We analyzed the mechanisms of ionizing radiation resistance from a diverse group of extremophilic archaea and bacteria. In Halobacterium salinarum IR resistance is conferred by antioxidant Mn2+-complexes, and protein-free cell extracts (ultrafiltrates, UFs) of super-resistant (IR+) isolates of H. salinarum had increased concentrations of Mn, PO4 and amino acids compared to the founder strain. Proteomic analysis determined that IR+ isolates with increased Mn had elevated protein expression for central carbon metabolism, suggesting a Mn-stimulated metabolic route to increased IR resistance. We examined the role of mannosylglycerate, di-myo-inositol phosphate, and trehalose in the IR resistance of various thermophiles; aerobic thermophiles had UFs which were radioprotective of enzyme activity under aerobic conditions, which is attributed to Mn, PO4 and trehalose accumulation. In contrast, anaerobic thermophile UFs did not contain significant amounts of Mn, and were radioprotective only under anaerobic conditions; we conclude the anaerobic environment confers their IR resistance