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Biological machines

Zhiwei Zhou, Xiaotao Shen, Jia Tu, Zheng-Jiang Zhu
The rapid development of metabolomics has significantly advanced health and disease related research. However, metabolite identification remains a major analytical challenge for untargeted metabolomics. While the use of collision cross-section (CCS) values obtained in ion mobility - mass spectrometry (IM-MS) effectively increases identification confidence of metabolites, it is restricted by the limited number of available CCS values for metabolites. Here, we demonstrated the use of a machine-learning algorithm called support vector regression (SVR) to develop a prediction method that utilized 14 common molecular descriptors to predict CCS values for metabolites...
October 21, 2016: Analytical Chemistry
R D Astumian
Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy source vs. the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium...
October 21, 2016: Faraday Discussions
Fayyaz Ul Amir Afsar Minhas, Amina Asif, Muhammad Arif
: Feature selection and ranking is of great importance in the analysis of biomedical data. In addition to reducing the number of features used in classification or other machine learning tasks, it allows us to extract meaningful biological and medical information from a machine learning model. Most existing approaches in this domain do not directly model the fact that the relative importance of features can be different in different regions of the feature space. In this work, we present a context aware feature ranking algorithm called CAFÉ-Map...
October 11, 2016: Computers in Biology and Medicine
Kevin A McGoff, Xin Guo, Anastasia Deckard, Christina M Kelliher, Adam R Leman, Lauren J Francey, John B Hogenesch, Steven B Haase, John L Harer
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle...
October 19, 2016: Genome Biology
Carlo Luca Romanò, Delia Romanò, Ilaria Morelli, Lorenzo Drago
Biofilms have a tremendous impact on industrial machines working in moist environments, while in biological systems their effect is further complicated by the host's response.Implant-related infections are a complex process, starting with bacterial adhesion and biofilm formation, followed by the variable interaction between host, implant, microorganisms and their by-products. Depending on the balance of these factors, different clinical presentations are observed, which may eventually, at times, shift from one into the other...
October 19, 2016: Advances in Experimental Medicine and Biology
Chengcheng Yin, Yanjing Zhang, Qing Cai, Baosheng Li, Hua Yang, Heling Wang, Hua Qi, Yanmin Zhou, Weiyan Meng
In clinical applications, osseointegration is essential for the long-term stability of dental implants. Inspired by the hierarchical structure of natural bone, we applied the electrochemical etching (EC) technique to form a micro-nano structure on a titanium alloy (Ti6Al4V) substrate, called EC surface. Sand blasting and acid etching (SLA) and machined (M) methods were employed to generate micro and smooth textures, respectively, as the control groups. The surface topographies of the three substrates were characterized using scanning electron microscopy (SEM)...
October 18, 2016: Journal of Biomedical Materials Research. Part A
Michael R Loken, Andrew P Voigt, Lisa Eidenschink Brodersen, Wayne Fritschle, Andrew J Menssen, Soheil Meshinchi, Denise A Wells
Five reference populations in bone marrow specimens were identified by flow cytometry using specific combinations of reagents in order define the variation of gene product expression intensities both within and between individuals. Mature lymphocytes, uncommitted progenitor cells, promyelocytes, mature monocytes and mature neutrophils can be reproducibly identified as distinct clusters of events in heterogeneous, maturing bone marrow specimens. Support Vector Machines were used to identify the reference populations in order to reduce subjective bias in manually defining boundaries of these populations since they were not discretely separated from the remainder of the cells...
October 18, 2016: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Long Chen, Changan Di, Xuguang Chen, Zhengzhi Li, Jia Luo
Touch is produced by sensations that include approaching, sliding, pressing, and temperature. This concept has become a target of research in biotechnology, especially in the field of bionic biology. This study measured sliding and pressing with traditional tactile sensors in order to improve a machine operator's judgment of surface roughness. Based on the theory of acoustic emission, this study combined polyvinylidene fluoride (PVDF) with a sonic transducer to produce tactile sensors that can detect surface roughness...
October 18, 2016: Bioengineered
Shanshan Xu, Lanlan Dong, Yingying Shi, Liujun Chen, Peipei Yuan, Shuang Wang, Zhi Li, Yan Sun, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu
Human foamy virus (HFV) is a complex and unique retrovirus with the longest genomes among retroviruses used as vectors for gene therapy. Long non-coding RNAs (lncRNAs) are regarded as key regulators that involved in diverse biological processes during viral infection. However, the role of lncRNAs in HFV infection remains unknown. In this study, we utilized next-generation sequencing to first characterize lncRNAs in 293T cells after HFV infection, evaluating length distribution, exon number distribution, volcano picture and lncRNA class distribution...
October 18, 2016: AIDS Research and Human Retroviruses
Sourabh Boruah, Damien L Subit, Glenn R Paskoff, Barry S Shender, Jeff R Crandall, Robert S Salzar
The strength and compliance of the dense cortical layers of the human skull have been examined since the beginning of the 20th century with the wide range in the observed mechanical properties attributed to natural biological variance. Since this variance may be explained by the difference in structural arrangement of bone tissue, micro-computed tomography (µCT) was used in conjunction with mechanical testing to study the relationship between the microstructure of human skull cortical coupons and their mechanical response...
October 1, 2016: Journal of the Mechanical Behavior of Biomedical Materials
Runyu Guo, Jinke Gu, Meng Wu, Maojun Yang
Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang's group from Tsinghua University (Gu et al. Nature 237(7622):639-643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening...
October 14, 2016: Protein & Cell
Benedikt Wiestler, Anne Kluge, Mathias Lukas, Jens Gempt, Florian Ringel, Jürgen Schlegel, Bernhard Meyer, Claus Zimmer, Stefan Förster, Thomas Pyka, Christine Preibisch
Non-invasive, imaging-based examination of glioma biology has received increasing attention in the past couple of years. To this end, the development and refinement of novel MRI techniques, reflecting underlying oncogenic processes such as hypoxia or angiogenesis, has greatly benefitted this research area. We have recently established a novel BOLD (blood oxygenation level dependent) based MRI method for the measurement of relative oxygen extraction fraction (rOEF) in glioma patients. In a set of 37 patients with newly diagnosed glioma, we assessed the performance of a machine learning model based on multiple MRI modalities including rOEF and perfusion imaging to predict WHO grade...
October 14, 2016: Scientific Reports
Alexey Petrushin, Lorenzo Ferrara, Axel Blau
OBJECTIVE: In light of recent progress in mapping neural function to behavior, we briefly and selectively review past and present endeavors to reveal and reconstruct nervous system function in Caenorhabditis elegans through simulation. APPROACH: Rather than presenting an all-encompassing review on the mathematical modeling of C. elegans, this contribution collects snapshots of pathfinding key works and emerging technologies that recent single- and multi-center simulation initiatives are building on...
October 14, 2016: Journal of Neural Engineering
M J Paldino, F Golriz, M L Chapieski, W Zhang, Z D Chu
BACKGROUND AND PURPOSE: The biologic basis for intelligence rests to a large degree on the capacity for efficient integration of information across the cerebral network. We aimed to measure the relationship between network architecture and intelligence in the pediatric, epileptic brain. MATERIALS AND METHODS: Patients were retrospectively identified with the following: 1) focal epilepsy; 2) brain MR imaging at 3T, including resting-state functional MR imaging; and 3) full-scale intelligence quotient measured by a pediatric neuropsychologist...
October 13, 2016: AJNR. American Journal of Neuroradiology
Ji-Yong An, Zhu-Hong You, Xing Chen, De-Shuang Huang, Zheng-Wei Li, Gang Liu, Yin Wang
Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interaction proteins identification, developing an effective computational method based on protein sequence to detect SIPs is much important. In the study, we proposed a novel computational approach called RVMBIGP that combines the Relevance Vector Machine (RVM) model and Bi-gram probability (BIGP) to predict SIPs based on protein sequence...
October 8, 2016: Oncotarget
Rita Puglisi, Robert Yan, Salvatore Adinolfi, Annalisa Pastore
Iron sulfur clusters are essential universal prosthetic groups which can be formed inorganically but, in biology, are bound to proteins and produced enzymatically. Most of the components of the machine that produces the clusters are conserved throughout evolution. In bacteria, they are encoded in the isc operon. Previous reports provide information on the role of specific components but a clear picture of how the whole machine works is still missing. We have carried out a study of the effects of the co-chaperone HscB from the model system E...
2016: Frontiers in Molecular Biosciences
Robert J Gillies, Thomas Beyer
Over the past decades, imaging in oncology has been undergoing a "quiet" revolution to treat images as data, not as pictures. This revolution has been sparked by technological advances that enable capture of images that reflect not only anatomy, but also of tissue metabolism and physiology in situ Important advances along this path have been the increasing power of MRI, which can be used to measure spatially dependent differences in cell density, tissue organization, perfusion, and metabolism. In parallel, PET imaging allows quantitative assessment of the spatial localization of positron-emitting compounds, and it has also been constantly improving in the number of imageable tracers to measure metabolism and expression of macromolecules...
October 11, 2016: Cancer Research
Wei Chen, Pengmian Feng, Hui Ding, Hao Lin
The adenosine to inosine (A-to-I) editing is the most prevalent kind of RNA editing and involves in many biological processes. Accurate identification of A-to-I editing site is invaluable for better understanding its biological functions. Due to the limitations of experimental methods, in the present study, a support vector machine based-model, called PAI, is proposed to identify A-to-I editing site in D. melanogaster. In this model, RNA sequences are encoded by "pseudo dinucleotide composition" into which six RNA physiochemical properties were incorporated...
October 11, 2016: Scientific Reports
Gaurav Jerath, Prakash Kishore Hazam, Shashi Shekhar, Vibin Ramakrishnan
Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain...
2016: PloS One
Anouk S Lubbe, Jos C M Kistemaker, Esther J Smits, Ben L Feringa
As molecular machines move to exciting applications in various environments, the study of medium effects becomes increasingly relevant. It is difficult to predict how, for example, the large apolar structure of a light-driven rotary molecular motor is affected by a biological setting or surface proximity, while for future nanotechnology precise fine tuning and full understanding of the isomerization process are of the utmost importance. Previous investigations into solvent effects have mainly focused on the relatively large solvent-solute interaction of hydrogen bonding or polarization induced by the isomerization process...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
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