Rock ramp design guidelines

USGS Publications Warehouse

Mooney, David M.; Holmquist-Johnson, Christopher L.; Broderick, Susan

2007-01-01

Rock ramps or roughened channels consist of steep reaches stabilized by large immobile material (riprap). Primary objectives for rock ramps include: Create adequate head for diversionMaintain fish passage during low-flow conditionsMaintain hydraulic conveyance during high-flow conditionsSecondary objectives for rock ramp design include:Emulate natural systemsMinimize costsThe rock ramp consists of a low-flow channel designed to maintain biologically adequate depth and velocity conditions during periods of small discharges. The remainder of the ramp is designed to withstand and pass large flows with minimal structural damage. The following chapters outline a process for designing rock ramps.

Report of the Interagency biological methods workshop

USGS Publications Warehouse

Gurtz, Martin E.; Muir, Thomas A.

1994-01-01

The U.S. Geological Survey hosted the Interagency Biological Methods Workshop in Reston, Virginia, during June 22-23, 1993. The purposes of the workshop were to (1) promote better communication among Federal agencies that are using or developing biological methods in water-quality assessment programs for streams and rivers, and (2) facilitate the sharing of data and interagency collaboration. The workshop was attended by 45 biologists representing numerous Federal agencies and programs, and a few regional and State programs that were selected to provide additional perspectives. The focus of the workshop was community assessment methods for fish, invertebrates, and algae; physical habitat characterization; and chemical analyses of biological tissues. Charts comparing program objectives, design features, and sampling methods were compiled from materials that were provided by participating agencies prior to the workshop and formed the basis for small workgroup discussions. Participants noted that differences in methods among programs were often necessitated by differences in program objectives. However, participants agreed that where programs have identified similar data needs, the use of common methods is beneficial. Opportunities discussed for improving data compatibility and information sharing included (1) modifying existing methods, (2) adding parameters, (3) improving access to data through shared databases (potentially with common database structures), and (4) future collaborative efforts that range from research on selected protocol questions to followup meetings and continued discussions.

Cosmic-ray interaction data for designing biological experiments in space

NASA Astrophysics Data System (ADS)

Straume, T.; Slaba, T. C.; Bhattacharya, S.; Braby, L. A.

2017-05-01

There is growing interest in flying biological experiments beyond low-Earth orbit (LEO) to measure biological responses potentially relevant to those expected during a human mission to Mars. Such experiments could be payloads onboard precursor missions, including unmanned private-public partnerships, as well as small low-cost spacecraft (satellites) designed specifically for biosentinel-type missions. It is the purpose of this paper to provide physical cosmic-ray interaction data and related information useful to biologists who may be planning such experiments. It is not the objective here to actually design such experiments or provide radiobiological response functions, which would be specific for each experiment and biological endpoint. Nuclide-specific flux and dose rates were calculated using OLTARIS and these results were used to determine particle traversal rates and doses in hypothetical biological targets. Comparisons are provided between GCR in interplanetary space and inside the ISS. Calculated probabilistic estimates of dose from solar particle events are also presented. Although the focus here is on biological experiments, the information provided may be useful for designing other payloads as well if the space radiation environment is a factor to be considered.

Equivalency of general biology (for majors) across a state-system

NASA Astrophysics Data System (ADS)

Regier, Kimberly Fayette

General biology courses (for majors) are often transferred from one institution to another. These courses must prepare students for upper division courses in biology. A survey of U.S. college biology faculty was conducted and revealed that more 4-year faculty do not believe that all general biology courses are equivalent. An evaluation of course grades in two upper division biology courses at University of Colorado Denver (N = 2129) based upon course grades in general biology and the type of institution where general biology was taken (2-year school, 4-year, in-residence at UCD, AP credit, CLEP credit, or IB credit) was conducted. Students who transferred general biology credit received lower grades in upper division biology courses and withdrew from upper division biology courses more frequently. Syllabi from a small sample (N = 9) of general biology courses offered at Colorado 2- and 4-year schools show variation in course design. Only 30% of the courses had detailed learning objectives. Sample exams reveal a range in variation between 3-69% of questions requiring higher-order thinking according to Bloom's Taxonomy. Increasing communication between high school, 2-year and 4-year biology faculty is necessary if consistency is to be gained. Professional development for faculty to increase awareness about exam development, curriculum alignment, and curriculum mapping may reduce the disparities between the preparation of students in biology. Transfer student grade outcomes should be further investigated across the state.

Biological Investigation of the Stimulated Flapping Motions of the Moth, Manduca sexta

DTIC Science & Technology

2011-03-01

the sites of toxic chemical spills or damaged nuclear reactors (Alexander, 2002). Dr. Mark Reeder, Editor-in-Chief of the International Journal...Process The overall objective of research, using bio -inspired technology and techniques, is to develop clear scientific understanding about some of...it in a small container and submerging it in a bucket of ice for approximately 15 minutes, until the moth was unresponsive to stimulation.  Under

Research opportunities in human behavior and performances

NASA Technical Reports Server (NTRS)

Christensen, J. M.; Talbot, J. M.

1985-01-01

The NASA research program in the biological and medical aspects of space flight includes investigations of human behavior and performance. The research focuses on psychological and psychophysiological responses to operational and environmental stresses and demands of spaceflight, and encompasses problems in perception, cognition, motivation, psychological stability, small group dynamics, and performance. The primary objective is to acquire the knowledge and methodology to aid in achieving high productivity and essential psychological support of space and ground crews in the Space Shuttle and space station programs. The Life Sciences Research Office (LSRO) of the Federation of American Societies for Experimental Biology reviewed its program in psychology and identified its research for future program planning to be in line with NASA's goals.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

PubMed Central

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

Research on Objectives for High-School Biology

ERIC Educational Resources Information Center

Korgan, John J., Jr.; Wilson, John T.

1973-01-01

Describes procedures to develop instructional objectives for high school biology. Two kinds of objectives are identified as pre-objectives and performance objectives. Models to classify these in branches of biology and to ensure quality control are provided. (PS)

Advanced slow-magic angle spinning probe for magnetic resonance imaging and spectroscopy

DOEpatents

Wind, Robert A.; Hu, Jian Zhi; Minard, Kevin R.; Rommereim, Donald N.

2006-01-24

The present invention relates to a probe and processes useful for magnetic resonance imaging and spectroscopy instruments. More particularly, the invention relates to a MR probe and processes for obtaining resolution enhancements of fluid objects, including live specimens, using an ultra-slow (magic angle) spinning (MAS) of the specimen combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. Proton NMR spectra were measured of the torso and the top part of the belly of a female BALBc mouse in a 2T field, while spinning the animal at a speed of 1.5 Hz. Results show that even in this relatively low field with PHORMAT, an isotropic spectrum is obtained with line widths that are a factor 4.6 smaller than those obtained in a stationary mouse. Resolution of ¹H NMR metabolite spectra are thus significantly enhanced. Results indicate that PHORMAT has the potential to significantly increase the utility of ¹H NMR spectroscopy for in vivo biochemical, biomedical and/or medical applications involving large-sized biological objects such as mice, rats and even humans within a hospital setting. For small-sized objects, including biological objects, such as excised tissues, organs, live bacterial cells, and biofilms, use of PASS at a spinning rate of 30 Hz and above is preferred.

Advancing Biological Understanding and Therapeutics Discovery with Small Molecule Probes

PubMed Central

Schreiber, Stuart L.; Kotz, Joanne D.; Li, Min; Aubé, Jeffrey; Austin, Christopher P.; Reed, John C.; Rosen, Hugh; White, E. Lucile; Sklar, Larry A.; Lindsley, Craig W.; Alexander, Benjamin R.; Bittker, Joshua A.; Clemons, Paul A.; de Souza, Andrea; Foley, Michael A.; Palmer, Michelle; Shamji, Alykhan F.; Wawer, Mathias J.; McManus, Owen; Wu, Meng; Zou, Beiyan; Yu, Haibo; Golden, Jennifer E.; Schoenen, Frank J.; Simeonov, Anton; Jadhav, Ajit; Jackson, Michael R.; Pinkerton, Anthony B.; Chung, Thomas D.Y.; Griffin, Patrick R.; Cravatt, Benjamin F.; Hodder, Peter S.; Roush, William R.; Roberts, Edward; Chung, Dong-Hoon; Jonsson, Colleen B.; Noah, James W.; Severson, William E.; Ananthan, Subramaniam; Edwards, Bruce; Oprea, Tudor I.; Conn, P. Jeffrey; Hopkins, Corey R.; Wood, Michael R.; Stauffer, Shaun R.; Emmitte, Kyle A.

2015-01-01

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery. PMID:26046436

Exclusivity strategies and opportunities in view of the Biologics Price Competition and Innovation Act.

PubMed

Gaudry, Kate S

2011-01-01

Government-provided exclusivity periods provide pharmaceutical companies with incentives to invest in new drugs. Meanwhile, encouraging competition serves another worthy goal of improving the affordability of medications. Decades ago, the Hatch-Waxman Act set forth provisions attempting to balance these objectives in the context of small-molecule drugs. Recently, the Biologics Price Competition and Innovation Act was enacted to meet similar aims in the context of biologic drugs. This article presents a detailed comparison of these two Acts. While the Acts share many global similarities (e.g., providing exclusivity terms and abbreviated approval processes), many differences are also apparent when analyzing details of the provisions. One area of great departure between the Acts is the requirements of how a generic or follow-on applicant must address patents covering a reference product. After describing these differences, the article presents predictions of how reference product sponsors will adapt their patent-prosecution strategies in view of the new Biologics Act.

Marital quality and health: A meta-analytic review

PubMed Central

Robles, Theodore F.; Slatcher, Richard B.; Trombello, Joseph M.; McGinn, Meghan M.

2013-01-01

This meta-analysis reviewed 126 published empirical articles over the past 50 years describing associations between marital relationship quality and physical health in over 72,000 individuals. Health outcomes included clinical endpoints (objective assessments of function, disease severity, and mortality; subjective health assessments) and surrogate endpoints (biological markers that substitute for clinical endpoints, such as blood pressure). Biological mediators included cardiovascular reactivity and hypothalamic-pituitary-adrenal axis activity. Greater marital quality was related to better health, with mean effect sizes from r = .07 to .21, including lower risk of mortality, r = .11, and lower cardiovascular reactivity during marital conflict, r = −.13, but not daily cortisol slopes or cortisol reactivity during conflict. The small effect sizes were similar in magnitude to previously found associations between health behaviors (e.g., diet) and health outcomes. Effect sizes for a small subset of clinical outcomes were susceptible to publication bias. In some studies, effect sizes remained significant after accounting for confounds such as age and socioeconomic status. Studies with a higher proportion of women in the sample demonstrated larger effect sizes, but we found little evidence for gender differences in studies that explicitly tested gender moderation, with the exception of surrogate endpoint studies. Our conclusions are limited by small numbers of studies for specific health outcomes, unexplained heterogeneity, and designs that limit causal inferences. These findings highlight the need to explicitly test affective, health behavior, and biological mechanisms in future research, and focus on moderating factors that may alter the relationship between marital quality and health. PMID:23527470

Behavioral and biological interactions with confined microsocieties in a programmed environment

NASA Technical Reports Server (NTRS)

Emurian, H. H.; Brady, J. V.; Meyerhoff, J. L.; Mougey, E. H.

1981-01-01

This paper presents a summary of the background, objectives, and methodological approach of an ongoing research project devoted to the analysis of individual and small group performance effectiveness under conditions of isolation and confinement during extended residences in a continuously programmed environment. A more detailed description is provided of the results of a recent series of experiments designed and conducted to assess hormonal and behavioral effects of a change in group membership and size.

Exploring biology with small organic molecules

PubMed Central

Stockwell, Brent R.

2011-01-01

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore ‘biological-activity space’. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars — uncharted territory is explored using a system of coordinates that describes where each new feature lies. PMID:15602550

Photoacoustic tomography of foreign bodies in soft biological tissue.

PubMed

Cai, Xin; Kim, Chulhong; Pramanik, Manojit; Wang, Lihong V

2011-04-01

In detecting small foreign bodies in soft biological tissue, ultrasound imaging suffers from poor sensitivity (52.6%) and specificity (47.2%). Hence, alternative imaging methods are needed. Photoacoustic (PA) imaging takes advantage of strong optical absorption contrast and high ultrasonic resolution. A PA imaging system is employed to detect foreign bodies in biological tissues. To achieve deep penetration, we use near-infrared light ranging from 750 to 800 nm and a 5-MHz spherically focused ultrasonic transducer. PA images were obtained from various targets including glass, wood, cloth, plastic, and metal embedded more than 1 cm deep in chicken tissue. The locations and sizes of the targets from the PA images agreed well with those of the actual samples. Spectroscopic PA imaging was also performed on the objects. These results suggest that PA imaging can potentially be a useful intraoperative imaging tool to identify foreign bodies.

Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

NASA Astrophysics Data System (ADS)

Gao, Jun; Pan, Hongmiao; Yue, Haidong; Song, Tao; Zhao, Yong; Chen, Guanjun; Wu, Longfei; Xiao, Tian

2006-12-01

Magnetotactic bacteria have become a hot spot of research in microbiology attracting intensive interest of researchers in multiple disciplinary fields. However, the studies were limited in few fastidious bacteria. The objective of this study aims at isolating new marine magnetic bacteria and better comprehension of magnetotactic bacteria. In this study, an aerobic magnetotactic bacterium YSC-1 was isolated from sediments in the Yellow Sea Cold Water Mass (YSCWM). In TEM, magnetic cells have one or several circular magnetosomes in diameter of 100nm, and consist of Fe and Co shown on energy dispersive X-ray spectrum. The biological and physiological characteristics of this bacterium were also described. The colour of YSC-1 colony is white in small rod. The gram stain is negative. Results showed that Strain YSC-1 differs from microaerophile magnetotactic bacteria MS-1 and WD-1 in biology.

[Advances in Liquid Biopsy and its Clinical Application in the Diagnosis 
and Treatment of Non-small Cell Lung Cancer].

PubMed

Zheng, Difan; Chen, Haiquan

2016-06-20

With the advances of technology, great progresses have been made in liquid biopsy in recent years. Liquid biopsy is currently playing a more and more important role in early diagnosis and treatment of cancer. Compared with traditional tissue biopsy, liquid biopsy is more popular in clinical practice due to its non-invasiveness, convenience and high repeatability. It has huge potential in the future. This review introduces circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) as the most important objects in liquid biopsy, mainly focusing on their history, biological characteristics, detection technologies, limitations and applications in non-small cell lung cancer.

Cosmic-ray interaction data for designing biological experiments in space.

PubMed

Straume, T; Slaba, T C; Bhattacharya, S; Braby, L A

2017-05-01

There is growing interest in flying biological experiments beyond low-Earth orbit (LEO) to measure biological responses potentially relevant to those expected during a human mission to Mars. Such experiments could be payloads onboard precursor missions, including unmanned private-public partnerships, as well as small low-cost spacecraft (satellites) designed specifically for biosentinel-type missions. It is the purpose of this paper to provide physical cosmic-ray interaction data and related information useful to biologists who may be planning such experiments. It is not the objective here to actually design such experiments or provide radiobiological response functions, which would be specific for each experiment and biological endpoint. Nuclide-specific flux and dose rates were calculated using OLTARIS and these results were used to determine particle traversal rates and doses in hypothetical biological targets. Comparisons are provided between GCR in interplanetary space and inside the ISS. Calculated probabilistic estimates of dose from solar particle events are also presented. Although the focus here is on biological experiments, the information provided may be useful for designing other payloads as well if the space radiation environment is a factor to be considered. Published by Elsevier Ltd.

Construction of a cost effective optical tweezers for manipulation of birefringent materials using circularly polarized light

NASA Astrophysics Data System (ADS)

McMahon, Allison; Sauncy, Toni

2008-10-01

Light manipulation is a very powerful tool in physics, biology, and chemistry. There are several physical principles underlying the apparatus known as the ``optical tweezers,'' the term given to using focused light to manipulate and control small objects. By carefully controlling the orientation and position of a focused laser beam, dielectric particles can be effectively trapped and manipulated. We have designed a cost efficient and effective undergraduate optical tweezers apparatus by using standard ``off the shelf'' components and starting with a standard undergraduate laboratory microscope. Images are recorded using a small CCD camera interfaced to a computer and controlled by LabVIEW^TM software. By using wave plates to produce circular polarized light, rotational motion can be induced in small particles of birefringent materials such as calcite and mica.

Biologically inspired collision avoidance system for unmanned vehicles

NASA Astrophysics Data System (ADS)

Ortiz, Fernando E.; Graham, Brett; Spagnoli, Kyle; Kelmelis, Eric J.

2009-05-01

In this project, we collaborate with researchers in the neuroscience department at the University of Delaware to develop an Field Programmable Gate Array (FPGA)-based embedded computer, inspired by the brains of small vertebrates (fish). The mechanisms of object detection and avoidance in fish have been extensively studied by our Delaware collaborators. The midbrain optic tectum is a biological multimodal navigation controller capable of processing input from all senses that convey spatial information, including vision, audition, touch, and lateral-line (water current sensing in fish). Unfortunately, computational complexity makes these models too slow for use in real-time applications. These simulations are run offline on state-of-the-art desktop computers, presenting a gap between the application and the target platform: a low-power embedded device. EM Photonics has expertise in developing of high-performance computers based on commodity platforms such as graphic cards (GPUs) and FPGAs. FPGAs offer (1) high computational power, low power consumption and small footprint (in line with typical autonomous vehicle constraints), and (2) the ability to implement massively-parallel computational architectures, which can be leveraged to closely emulate biological systems. Combining UD's brain modeling algorithms and the power of FPGAs, this computer enables autonomous navigation in complex environments, and further types of onboard neural processing in future applications.

Automatic Segmentation of Granular Objects in Images: Combining Local Density Clustering and Gradient-Barrier Watershed

DTIC Science & Technology

2014-01-01

in applications, such as the recognition of biological cells [12,17], cell nuclei [8–10], colonies, and pollen [34,35], as well as nanoparticles [6... pollen image shown in Fig. 8, we see that two pollen grains on the upper-right are merged in the gradient-weighted distance trans- form watershed...10.1016/j.patcog.2013.11.004i images, pollen images, as well as physical nanoparticle images. This is only a small selection of this approach’s

Application of Temperature-Dependent Fluorescent Dyes to the Measurement of Millimeter Wave Absorption in Water Applied to Biomedical Experiments

PubMed Central

Popenko, Oleksandr

2014-01-01

Temperature sensitivity of the fluorescence intensity of the organic dyes solutions was used for noncontact measurement of the electromagnetic millimeter wave absorption in water. By using two different dyes with opposite temperature effects, local temperature increase in the capillary that is placed inside a rectangular waveguide in which millimeter waves propagate was defined. The application of this noncontact temperature sensing is a simple and novel method to detect temperature change in small biological objects. PMID:25435859

Application of temperature-dependent fluorescent dyes to the measurement of millimeter wave absorption in water applied to biomedical experiments.

PubMed

Kuzkova, Nataliia; Popenko, Oleksandr; Yakunov, Andrey

2014-01-01

Temperature sensitivity of the fluorescence intensity of the organic dyes solutions was used for noncontact measurement of the electromagnetic millimeter wave absorption in water. By using two different dyes with opposite temperature effects, local temperature increase in the capillary that is placed inside a rectangular waveguide in which millimeter waves propagate was defined. The application of this noncontact temperature sensing is a simple and novel method to detect temperature change in small biological objects.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

PubMed

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

Microsystem strategies for sample preparation in biological detection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

James, Conrad D.; Galambos, Paul C.; Bennett, Dawn Jonita

2005-03-01

The objective of this LDRD was to develop microdevice strategies for dealing with samples to be examined in biological detection systems. This includes three sub-components: namely, microdevice fabrication, sample delivery to the microdevice, and sample processing within the microdevice. The first component of this work focused on utilizing Sandia's surface micromachining technology to fabricate small volume (nanoliter) fluidic systems for processing small quantities of biological samples. The next component was to develop interfaces for the surface-micromachined silicon devices. We partnered with Micronics, a commercial company, to produce fluidic manifolds for sample delivery to our silicon devices. Pressure testing was completedmore » to examine the strength of the bond between the pressure-sensitive adhesive layer and the silicon chip. We are also pursuing several other methods, both in house and external, to develop polymer-based fluidic manifolds for packaging silicon-based microfluidic devices. The second component, sample processing, is divided into two sub-tasks: cell collection and cell lysis. Cell collection was achieved using dielectrophoresis, which employs AC fields to collect cells at energized microelectrodes, while rejecting non-cellular particles. Both live and dead Staph. aureus bacteria have been collected using RF frequency dielectrophoresis. Bacteria have been separated from polystyrene microspheres using frequency-shifting dielectrophoresis. Computational modeling was performed to optimize device separation performance, and to predict particle response to the dielectrophoretic traps. Cell lysis is continuing to be pursued using microactuators to mechanically disrupt cell membranes. Novel thermal actuators, which can generate larger forces than previously tested electrostatic actuators, have been incorporated with and tested with cell lysis devices. Significant cell membrane distortion has been observed, but more experiments need to be conducted to determine the effects of the observed distortion on membrane integrity and cell viability. Finally, we are using a commercial PCR DNA amplification system to determine the limits of detectable sample size, and to examine the amplification of DNA bound to microspheres. Our objective is to use microspheres as capture-and-carry chaperones for small molecules such as DNA and proteins, enabling the capture and concentration of the small molecules using dielectrophoresis. Current tests demonstrated amplification of DNA bound to micron-sized polystyrene microspheres using 20-50 microliter volume size reactions.« less

Prior knowledge guided active modules identification: an integrated multi-objective approach.

PubMed

Chen, Weiqi; Liu, Jing; He, Shan

2017-03-14

Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is correlated with cellular or disease states. A prior information guided active module identification approach is proposed to detect modules that are both active and enriched by prior knowledge. We formulate the active module identification problem as a multi-objective optimisation problem, which consists two conflicting objective functions of maximising the coverage of known biological pathways and the activity of the active module simultaneously. Network is constructed from protein-protein interaction database. A beta-uniform-mixture model is used to estimate the distribution of p-values and generate scores for activity measurement from microarray data. A multi-objective evolutionary algorithm is used to search for Pareto optimal solutions. We also incorporate a novel constraints based on algebraic connectivity to ensure the connectedness of the identified active modules. Application of proposed algorithm on a small yeast molecular network shows that it can identify modules with high activities and with more cross-talk nodes between related functional groups. The Pareto solutions generated by the algorithm provides solutions with different trade-off between prior knowledge and novel information from data. The approach is then applied on microarray data from diclofenac-treated yeast cells to build network and identify modules to elucidate the molecular mechanisms of diclofenac toxicity and resistance. Gene ontology analysis is applied to the identified modules for biological interpretation. Integrating knowledge of functional groups into the identification of active module is an effective method and provides a flexible control of balance between pure data-driven method and prior information guidance.

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions

PubMed Central

Yip, Kevin Y.; Gerstein, Mark

2009-01-01

Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While there are many computational techniques proposed for this network reconstruction task, their accuracy is consistently limited by the small number of high-confidence examples, and the uneven distribution of these examples across the potential interaction space, with some objects having many known interactions and others few. Results: To address this issue, we propose two computational methods based on the concept of training set expansion. They work particularly effectively in conjunction with kernel approaches, which are a popular class of approaches for fusing together many disparate types of features. Both our methods are based on semi-supervised learning and involve augmenting the limited number of gold-standard training instances with carefully chosen and highly confident auxiliary examples. The first method, prediction propagation, propagates highly confident predictions of one local model to another as the auxiliary examples, thus learning from information-rich regions of the training network to help predict the information-poor regions. The second method, kernel initialization, takes the most similar and most dissimilar objects of each object in a global kernel as the auxiliary examples. Using several sets of experimentally verified protein–protein interactions from yeast, we show that training set expansion gives a measurable performance gain over a number of representative, state-of-the-art network reconstruction methods, and it can correctly identify some interactions that are ranked low by other methods due to the lack of training examples of the involved proteins. Contact: mark.gerstein@yale.edu Availability: The datasets and additional materials can be found at http://networks.gersteinlab.org/tse. PMID:19015141

Brain activation related to the perception of minimal agency cues: the role of the mirror system.

PubMed

Stosic, Marina; Brass, Marcel; Van Hoeck, Nicole; Ma, Ning; Van Overwalle, Frank

2014-02-01

Recent fMRI studies indicate that the posterior superior temporal sulcus (pSTS) and the mirror system are involved in analyzing goal-directed actions performed by non-human objects. However, these studies have some limitations: the animations showed moving shapes that resemble humans and human movement, or showed the interaction of two moving shapes rather than one alone. This may have prompted participants to assume a human agent instead of an object. To avoid this potential confound, in this study, animations showed a small circular shape (agent) jumping toward a bigger circular shape (goal) with an obstacle separating them. We manipulated agency of the small circular shape by showing its movements as self-propelled (Agent condition) or as launched by a lever mechanism (Non-agent condition). The small shape succeeded in avoiding an obstacle and reaching the goal object or failed to do so. Our results showed that goal-directed actions performed by an agentic shape recruited the mirror system (the inferior parietal lobe and the premotor cortex) in comparison with shapes that were launched. Success or failure to avoid the obstacle had no effect on these areas. These results complement and further extend previous findings indicating that the mirror system does not appear to be selective for biological actions and their goals, nor does it require the presence of a human, human body parts or human-made objects. Instead, it seems to play a general role in representing goal-directed actions of agents regardless of their form. © 2013.

3D light scanning macrography.

PubMed

Huber, D; Keller, M; Robert, D

2001-08-01

The technique of 3D light scanning macrography permits the non-invasive surface scanning of small specimens at magnifications up to 200x. Obviating both the problem of limited depth of field inherent to conventional close-up macrophotography and the metallic coating required by scanning electron microscopy, 3D light scanning macrography provides three-dimensional digital images of intact specimens without the loss of colour, texture and transparency information. This newly developed technique offers a versatile, portable and cost-efficient method for the non-invasive digital and photographic documentation of small objects. Computer controlled device operation and digital image acquisition facilitate fast and accurate quantitative morphometric investigations, and the technique offers a broad field of research and educational applications in biological, medical and materials sciences.

Biased and unbiased strategies to identify biologically active small molecules.

PubMed

Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

2014-08-15

Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. Copyright © 2014. Published by Elsevier Ltd.

A review on plants extract mediated synthesis of silver nanoparticles for antimicrobial applications: A green expertise

PubMed Central

Ahmed, Shakeel; Ahmad, Mudasir; Swami, Babu Lal; Ikram, Saiqa

2015-01-01

Metallic nanoparticles are being utilized in every phase of science along with engineering including medical fields and are still charming the scientists to explore new dimensions for their respective worth which is generally attributed to their corresponding small sizes. The up-and-coming researches have proven their antimicrobial significance. Among several noble metal nanoparticles, silver nanoparticles have attained a special focus. Conventionally silver nanoparticles are synthesized by chemical method using chemicals as reducing agents which later on become accountable for various biological risks due to their general toxicity; engendering the serious concern to develop environment friendly processes. Thus, to solve the objective; biological approaches are coming up to fill the void; for instance green syntheses using biological molecules derived from plant sources in the form of extracts exhibiting superiority over chemical and/or biological methods. These plant based biological molecules undergo highly controlled assembly for making them suitable for the metal nanoparticle syntheses. The present review explores the huge plant diversity to be utilized towards rapid and single step protocol preparatory method with green principles over the conventional ones and describes the antimicrobial activities of silver nanoparticles. PMID:26843966

[Sample preparation and bioanalysis in mass spectrometry].

PubMed

Bourgogne, Emmanuel; Wagner, Michel

2015-01-01

The quantitative analysis of compounds of clinical interest of low molecular weight (<1000 Da) in biological fluids is currently in most cases performed by liquid chromatography-mass spectrometry (LC-MS). Analysis of these compounds in biological fluids (plasma, urine, saliva, hair...) is a difficult task requiring a sample preparation. Sample preparation is a crucial part of chemical/biological analysis and in a sense is considered the bottleneck of the whole analytical process. The main objectives of sample preparation are the removal of potential interferences, analyte preconcentration, and converting (if needed) the analyte into a more suitable form for detection or separation. Without chromatographic separation, endogenous compounds, co-eluted products may affect a quantitative method in mass spectrometry performance. This work focuses on three distinct parts. First, quantitative bioanalysis will be defined, different matrices and sample preparation techniques currently used in bioanalysis by mass spectrometry of/for small molecules of clinical interest in biological fluids. In a second step the goals of sample preparation will be described. Finally, in a third step, sample preparation strategies will be made either directly ("dilute and shoot") or after precipitation.

A Fuzzy Logic Approach to Marine Spatial Management

NASA Astrophysics Data System (ADS)

Teh, Lydia C. L.; Teh, Louise S. L.

2011-04-01

Marine spatial planning tends to prioritise biological conservation targets over socio-economic considerations, which may incur lower user compliance and ultimately compromise management success. We argue for more inclusion of human dimensions in spatial management, so that outcomes not only fulfill biodiversity and conservation objectives, but are also acceptable to resource users. We propose a fuzzy logic framework that will facilitate this task- The protected area suitability index (PASI) combines fishers' spatial preferences with biological criteria to assess site suitability for protection from fishing. We apply the PASI in a spatial evaluation of a small-scale reef fishery in Sabah, Malaysia. While our results pertain to fishers specifically, the PASI can also be customized to include the interests of other stakeholders and resource users, as well as incorporate varying levels of protection.

Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) Mission Concept

NASA Technical Reports Server (NTRS)

Ennico, K. A.; Sandford, S. A.; Allamandola, L.; Bregman, J.; Cohen, M.; Cruikshank, D.; Dumas, C.; Greene, T.; Hudgins, D.; Kwok, S.

2004-01-01

The AstroBiology Explorer (ABE) mission concept consists of a dedicated space observatory having a 60 cm class primary mirror cooled to T < 50 K equipped with medium resolution cross-dispersed spectrometers having cooled large format near- and mid-infrared detector arrays. Such a system would be capable of addressing outstanding problems in Astrochemistry and Astrophysics that are particularly relevant to Astrobiology and addressable via astronomical observation. The mission s observational program would make fundamental scientific progress in establishing the nature, distribution, formation and evolution of organic and other molecular materials in the following extra-terrestrial environments: 1) The Outflow of Dying Stars, 2) The Diffuse Interstellar Medium, 3) Dense Molecular Clouds, Star Formation Regions, and Young StellarPlanetary Systems, 4) Planets, Satellites, and Small Bodies within the Solar System, and 5 ) The Interstellar Media of Other Galaxies. ABE could make fundamental progress in all of these areas by conducting a 1 to 2 year mission to obtain a coordinated set of infrared spectroscopic observations over the 2.5-20 micron spectral range at a spectral resolution of R > 2000 of about 1500 objects including galaxies, stars, planetary nebulae, young stellar objects, and solar system objects. Keywords: Astrobiology, infrared, Explorers, interstellar organics, telescope, spectrometer, space, infrared detectors

Biologic disease-modifying anti-rheumatic drugs and the risk of non-vertebral osteoporotic fractures in patients with rheumatoid arthritis aged 50 years and over.

PubMed

Roussy, J-P; Bessette, L; Bernatsky, S; Rahme, E; Lachaine, J

2013-09-01

Prevention of bone mineral density loss in rheumatoid arthritis (RA) has been associated with use of biologic disease-modifying anti-rheumatic drugs (DMARDs). However, in this study, we could not demonstrate a reduction in the risk of non-vertebral fractures. Additional research is required to clarify the impact of biologic DMARDs on fracture risk in RA. Small studies have suggested biologic DMARDs preserve bone mineral density at 6-12 months. Our objective was to determine the association between biologic DMARD use and the risk of non-vertebral osteoporotic fractures in RA subjects aged ≥50 years. A nested case-control study was conducted using Quebec physician billing and hospital discharge data. RA subjects were identified from International Classification of Disease-9/10 codes in billing and hospitalisation data and followed from cohort entry until the earliest of non-vertebral osteoporotic fracture, death, or end of study period. Controls were matched to cases (4:1 ratio) on age, sex, and date of cohort entry. Biologic DMARD exposure was defined as being on treatment for ≥180 days pre-fracture (index). Conditional logistic regression was used, adjusting for indicators of RA severity, comorbidity, drugs influencing fracture risk, and measures of health care utilisation. Over the study period, 1,515 cases were identified (6,023 controls). The most frequent fracture site was hip/femur (42.3%). In total, 172 subjects (49 cases and 123 controls) were exposed to biologic DMARDs. The median duration of exposure was 735 (interquartile range (IQR), 564) and 645 (IQR, 903) days in cases and controls, respectively. We were unable to demonstrate an association between biologic DMARDs and fracture risk (odds ratio, 1.03; 95% confidence interval, 0.42-2.53). RA duration significantly increased the fracture risk. Despite the positive impact of biologic DMARDs on bone remodelling observed in small studies, we were unable to demonstrate a reduction in the risk of non-vertebral osteoporotic fractures in older adults with RA.

Magnetic separation: its application in mining, waste purification, medicine, biochemistry and chemistry.

PubMed

Iranmanesh, M; Hulliger, J

2017-10-02

The use of strong magnetic field gradients and high magnetic fields generated by permanent magnets or superconducting coils has found applications in many fields such as mining, solid state chemistry, biochemistry and medical research. Lab scale or industrial implementations involve separation of macro- and nanoparticles, cells, proteins, and macromolecules down to small molecules and ions. Most promising are those attempts where the object to be separated is attached to a strong magnetic nanoparticle. Here, all kinds of specific affinity interactions are used to attach magnetic carrier particles to mainly objects of biological interest. Other attempts use a strong paramagnetic suspension for the separation of purely diamagnetic objects, such as bio-macromolecules or heavy metals. The application of magnetic separation to superconducting inorganic phases is of particular interest in combination with ceramic combinatorial chemistry to generate a library of e.g. cuprate superconductors.

Auditory-visual object recognition time suggests specific processing for animal sounds.

PubMed

Suied, Clara; Viaud-Delmon, Isabelle

2009-01-01

Recognizing an object requires binding together several cues, which may be distributed across different sensory modalities, and ignoring competing information originating from other objects. In addition, knowledge of the semantic category of an object is fundamental to determine how we should react to it. Here we investigate the role of semantic categories in the processing of auditory-visual objects. We used an auditory-visual object-recognition task (go/no-go paradigm). We compared recognition times for two categories: a biologically relevant one (animals) and a non-biologically relevant one (means of transport). Participants were asked to react as fast as possible to target objects, presented in the visual and/or the auditory modality, and to withhold their response for distractor objects. A first main finding was that, when participants were presented with unimodal or bimodal congruent stimuli (an image and a sound from the same object), similar reaction times were observed for all object categories. Thus, there was no advantage in the speed of recognition for biologically relevant compared to non-biologically relevant objects. A second finding was that, in the presence of a biologically relevant auditory distractor, the processing of a target object was slowed down, whether or not it was itself biologically relevant. It seems impossible to effectively ignore an animal sound, even when it is irrelevant to the task. These results suggest a specific and mandatory processing of animal sounds, possibly due to phylogenetic memory and consistent with the idea that hearing is particularly efficient as an alerting sense. They also highlight the importance of taking into account the auditory modality when investigating the way object concepts of biologically relevant categories are stored and retrieved.

Handheld hyperspectral imager for standoff detection of chemical and biological aerosols

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele; Jensen, James O.; McAnally, Gerard

2004-08-01

Pacific Advanced Technology has developed a small hand held imaging spectrometer, Sherlock, for gas leak and aerosol detection and imaging. The system is based on a patented technique, (IMSS Image Multi-spectral Sensing), that uses diffractive optics and image processing algorithms to detect spectral information about objects in the scene of the camera. This cameras technology has been tested at Dugway Proving Ground and Dstl Porton Down facilities looking at Chemical and Biological agent simulants. In addition to Chemical and Biological detection, the camera has been used for environmental monitoring of green house gases and is currently undergoing extensive laboratory and field testing by the Gas Technology Institute, British Petroleum and Shell Oil for applications for gas leak detection and repair. In this paper we will present some of the results from the data collection at the TRE test at Dugway Proving Ground during the summer of 2002 and laboratory testing at the Dstl facility at Porton Down in the UK in the fall of 2002.

Rethinking Physics for Biologists: A design-based research approach

NASA Astrophysics Data System (ADS)

Sawtelle, Vashti

2015-03-01

Biology majors at the University of Maryland are required to take courses in biology, chemistry, and physics - but they often see these courses as disconnected. Over the past three years the NEXUS/Physics course has been working to develop an interdisciplinary learning environment that bridges the disciplinary domains of biology and physics. Across the three years we have gone from teaching in a small class with one instructor to teaching in a large lecture hall with multiple instructors. We have used a design-based research approach to support critical reflection of the course at multiple-time scales. In this presentation I will detail our process of collecting systematic data, listening to and valuing students' reasoning, and bridging diverse perspectives led. I will demonstrate how this process led to improved curricular design, refined assessment objectives, and new design heuristics. This work is supported by NSF-TUES DUE 11-22818, the HHMI NEXUS grant, and a NSF Graduate Research Fellowship (DGE 0750616).

Solid Phase Microextraction and Related Techniques for Drugs in Biological Samples

PubMed Central

Moein, Mohammad Mahdi; Said, Rana; Bassyouni, Fatma

2014-01-01

In drug discovery and development, the quantification of drugs in biological samples is an important task for the determination of the physiological performance of the investigated drugs. After sampling, the next step in the analytical process is sample preparation. Because of the low concentration levels of drug in plasma and the variety of the metabolites, the selected extraction technique should be virtually exhaustive. Recent developments of sample handling techniques are directed, from one side, toward automatization and online coupling of sample preparation units. The primary objective of this review is to present the recent developments in microextraction sample preparation methods for analysis of drugs in biological fluids. Microextraction techniques allow for less consumption of solvent, reagents, and packing materials, and small sample volumes can be used. In this review the use of solid phase microextraction (SPME), microextraction in packed sorbent (MEPS), and stir-bar sorbtive extraction (SBSE) in drug analysis will be discussed. In addition, the use of new sorbents such as monoliths and molecularly imprinted polymers will be presented. PMID:24688797

Applications of penetrating radiation for small animal imaging

NASA Astrophysics Data System (ADS)

Hasegawa, Bruce H.; Wu, Max C.; Iwata, Koji; Hwang, Andrew B.; Wong, Kenneth H.; Barber, William C.; Dae, Michael W.; Sakdinawat, Anne E.

2002-11-01

Researchers long have relied on research involving small animals to unravel scientific mysteries in the biological sciences, and to develop new diagnostic and therapeutic techniques in the medical and health sciences. Within the past 2 decades, new techniques have been developed to manipulate the genome of the mouse, allowing the development of transgenic and knockout models of mammalian and human disease, development, and physiology. Traditionally, much biological research involving small animals has relied on the use of invasive methods such as organ harvesting, tissue sampling, and autoradiography during which the animal was sacrificed to perform a single measurement. More recently, imaging techniques have been developed that assess anatomy and physiology in the intact animal, in a way that allows the investigator to follow the progression of disease, or to monitor the response to therapeutic interventions. Imaging techniques that use penetrating radiation at millimeter or submillimeter levels to image small animals include x-ray computed tomography (microCT), single-photon emission computed tomography (microSPECT), and imaging positron emission computed tomography (microPET). MicroCT generates cross-sectional slices which reveal the structure of the object with spatial resolution in the range of 50 to 100 microns. MicroSPECT and microPET are radionuclide imaging techniques in which a radiopharmaceutical is injected into the animal that is accumulated to metabolism, blood flow, bone remodeling, tumor growth, or other biological processes. Both microSPECT and microPET offer spatial resolutions in the range of 1-2 millimeters. However, microPET records annihilation photons produced by a positron-emitting radiopharmaceutical using electronic coincidence, and has a sensitivity approximately two orders of magnitude better than microSPECT, while microSPECT is compatible with gamma-ray emitting radiopharmaceuticals that are less expensive and more readily available than those used with microPET. High-resolution dual-modality imaging systems now are being developed that combine microPET or microSPECT with microCT in a way that facilitates more direct correlation of anatomy and physiology in the same animal. Small animal imaging allows researchers to perform experiments that are not possible with conventional invasive techniques, and thereby are becoming increasingly important tools for discovery of fundamental biological information, and development of new diagnostic and therapeutic techniques in the biomedical sciences.

Theoretical principles for biology: Variation.

PubMed

Montévil, Maël; Mossio, Matteo; Pocheville, Arnaud; Longo, Giuseppe

2016-10-01

Darwin introduced the concept that random variation generates new living forms. In this paper, we elaborate on Darwin's notion of random variation to propose that biological variation should be given the status of a fundamental theoretical principle in biology. We state that biological objects such as organisms are specific objects. Specific objects are special in that they are qualitatively different from each other. They can undergo unpredictable qualitative changes, some of which are not defined before they happen. We express the principle of variation in terms of symmetry changes, where symmetries underlie the theoretical determination of the object. We contrast the biological situation with the physical situation, where objects are generic (that is, different objects can be assumed to be identical) and evolve in well-defined state spaces. We derive several implications of the principle of variation, in particular, biological objects show randomness, historicity and contextuality. We elaborate on the articulation between this principle and the two other principles proposed in this special issue: the principle of default state and the principle of organization. Copyright © 2016 Elsevier Ltd. All rights reserved.

Near-infrared luminescent cubic silicon carbide nanocrystals for in vivo biomarker applications: an ab initio Study

NASA Astrophysics Data System (ADS)

Gali, Adam; Zólyomi, Viktor; Somogyi, Bálint

2013-03-01

Small molecule-sized fluorescent emitters are needed as probes to image and track the locations of targeted nano-sized objects with minimal perturbation, and are much sought-after to probe biomolecules in living cells. For in vivo biological imaging, fluorescent biomarkers have to meet the following stringent requirements: (i) they should be non-toxic and bioinert, (ii) their hydrodynamical size should be sufficiently small for clearance, (iii) they should be photo-stable. Furthermore, it is highly desirable that (iv) they have intense, stable emission in the near-infrared range, and (v) they can be produced in relatively large amount for biological studies. Here we report time-density functional calculations on SiC-based QDs in the aspect of in vivo biological imaging applications. We find that Si-vacancy, divacancy, as well as single metal dopants such as Vanadium (V), Molybdenum (Mo) and Tungsten (W) in molecule-sized (1-2 nm) SiC QDs emit light efficiently in the near-infrared range. Furthermore, their emission wavelength varies on the size of host SiC QDs at less extent than that of pristine SiC QDs, thus sharper emission spectrum is expected even in a disperse size distribution of these QDs. These fluorescent SiC QDs are paramagnetic in the ground state. EU FP7 DIAMANT (Grant No. 270197)

Computational systems chemical biology.

PubMed

Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

Computational Systems Chemical Biology

PubMed Central

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2013-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

StrateGene: object-oriented programming in molecular biology.

PubMed

Carhart, R E; Cash, H D; Moore, J F

1988-03-01

This paper describes some of the ways that object-oriented programming methodologies have been used to represent and manipulate biological information in a working application. When running on a Xerox 1100 series computer, StrateGene functions as a genetic engineering workstation for the management of information about cloning experiments. It represents biological molecules, enzymes, fragments, and methods as classes, subclasses, and members in a hierarchy of objects. These objects may have various attributes, which themselves can be defined and classified. The attributes and their values can be passed from the classes of objects down to the subclasses and members. The user can modify the objects and their attributes while using them. New knowledge and changes to the system can be incorporated relatively easily. The operations on the biological objects are associated with the objects themselves. This makes it easier to invoke them correctly and allows generic operations to be customized for the particular object.

Seasonal change in precipitation, snowpack, snowmelt, soil water and streamwater chemistry, northern Michigan

USGS Publications Warehouse

Stottlemyer, R.; Toczydlowski, D.

1999-01-01

We have studied weekly precipitation, snowpack, snowmelt, soil water and streamwater chemistry throughout winter for over a decade in a small (176 ha) northern Michigan watershed with high snowfall and vegetated by 60 to 80 year-old northern hardwoods. In this paper, we examine physical, chemical, and biological processes responsible for observed seasonal change in streamwater chemistry based upon intensive study during winter 1996-1997. The objective was to define the contributions made to winter and spring streamwater chemical concentration and flux by processes as snowmelt, over-winter forest floor and surface soil mineralization, immobilization, and exchange, and subsurface flowpath. The forest floor and soil were unfrozen beneath the snowpack which permitted most snowmelt to enter. Over-winter soil mineralization and other biological processes maintain shallow subsurface ion and dissolved organic carbon (DOC) reservoirs. Small, but steady, snowmelt throughout winter removed readily mobilized soil NO3- which resulted in high over-winter streamwater concentrations but little flux. Winter soil water levels and flowpaths were generally deep which increased soil water and streamwater base cation (C(B)), HCO3-, and Si concentrations. Spring snowmelt increased soil water levels and removal of ions and DOC from the biologically active forest floor and shallow soils. The snowpack solute content was a minor component in determining streamwater ion concentration or flux during and following peak snowmelt. Exchangeable ions, weakly adsorbed anions, and DOC in the forest floor and surface soils dominated the chemical concentration and flux in soil water and streamwater. Following peak snowmelt, soil microbial immobilization and rapidly increased plant uptake of limiting nutrients removed nearly all available nitrogen from soil water and streamwater. During the growing season high evapotranspiration increased subsurface flowpath depth which in turn removed weathering products, especially C(B), HCO3-, and Si, from deeper soils. Soil water was a major component in the hydrologic and chemical budgets.We have studied weekly precipitation, snowpack, snowmelt, soil water and streamwater chemistry throughout winter for over a decade in a small (176 ha) northern Michigan watershed with high snowfall and vegetated by 60 to 80 year-old northern hardwoods. In this paper, we examine physical, chemical, and biological processes responsible for observed seasonal change in streamwater chemistry based upon intensive study during winter 1996-1997. The objective was to define the contributions made to winter and spring streamwater chemical concentration and flux by processes as snowmelt, over-winter forest floor and surface soil mineralization, immobilization, and exchange, and subsurface flowpath. The forest floor and soils were unfrozen beneath the snowpack which permitted most snowmelt to enter. Over-winter soil mineralization and other biological processes maintain shallow subsurface ion and dissolved organic carbon (DOC) reservoirs. Small, but steady, snowmelt throughout winter removed readily mobilized soil NO3- which resulted in high over-winter streamwater concentrations but little flux. Winter soil water levels and flowpaths were generally deep which increased soil water and streamwater base cation (CB), HCO3-, and Si concentrations. Spring snowmelt increased soil water levels and removal of ions and DOC from the biologically active forest floor and shallow soils. The snowpack solute content was a minor component in determining streamwater ion concentration or flux during and following peak snowmelt. Exchangeable ions, weakly adsorbed anions, and DOC in the forest floor and surface soils dominated the chemical concentration and flux in soil water and streamwater. Following peak snowmelt, soil microbial immobilization and rapidly increased plant uptake of limiting nutrients removed nearly all available nitrogen from soil water and streamwater. D

Visually Inexperienced Chicks Exhibit Spontaneous Preference for Biological Motion Patterns

PubMed Central

Regolin, Lucia; Marconato, Fabio

2005-01-01

When only a small number of points of light attached to the torso and limbs of a moving organism are visible, the animation correctly conveys the animal's activity. Here we report that newly hatched chicks, reared and hatched in darkness, at their first exposure to point-light animation sequences, exhibit a spontaneous preference to approach biological motion patterns. Intriguingly, this predisposition is not specific for the motion of a hen, but extends to the pattern of motion of other vertebrates, even to that of a potential predator such as a cat. The predisposition seems to reflect the existence of a mechanism in the brain aimed at orienting the young animal towards objects that move semi-rigidly (as vertebrate animals do), thus facilitating learning, i.e., through imprinting, about their more specific features of motion. PMID:15934787

[Biolgical problems of a manmade small lake (author's transl)].

PubMed

Tiefenbrunner, F; Rott, E

1975-05-01

In connection with an intensive hygienic supervision of public bathing facilities and the attempts to draw up a law on bathing hygiene, the lack of contamination standards for small lakes available to the public for bathing was particularly conspicuous. In addition to the current chemical and bacteriological routine examinations, a small bathing lake with a surface area of 3000 square metres containing about 7000 m3 of water and which has been in existence for over 10 years was objected to extensive biological investigations during the months July to September. The results of the analysis show a relatively constant hydrogen ion concentration (pH 8.2), small variations in electrolytic conductivity and 8 German degrees of hardness. The mean phosphourus level was 60 mug/L. the orthophosphate levels ranged between 5.2 and 18.5 mug/L. Oxygen saturation during the entire summer months was more than 100%. Altogether, 49 different kinds of phytoplankton- and 12 kinds of zooplancton-organisms were identified. The total biological mass of phytoplancton organisms was between 8.5 and 16 mg fresh weight per litre, bacterial biomass varied between 4.5 and 9.5 mg/l. Particularly striking for summer conditions was the high proportion of Cyclotella- and Synedra species among the phytoplancton mass, while the algal-bloom producing Microcystis flos aquae attained a maximum proportion of 15%. In spite of the great variety of its forms, green algae were present in small numbers only. The comparison of the described findings with the trophic-systems of HUTCHINSON, NYGAARD and RAWSON indicated an eutrophic type of lake; classification according to the types of the various saprobic systems of NAUMANN, KOLKWITZ and LIEBMANN yielded a predominantly beta-mesosaprobic type of lake. The investigations described show, however, that this is probably a lake rich in nutrients, but that there is a relatively stable biological equilibrium and that, consequently, there is no further threat of progressive eutrophism. Special hygienic parameters, contamination due to visitors and phytoplancton production will be reported in a second communication.

Application of composite small calibration objects in traffic accident scene photogrammetry.

PubMed

Chen, Qiang; Xu, Hongguo; Tan, Lidong

2015-01-01

In order to address the difficulty of arranging large calibration objects and the low measurement accuracy of small calibration objects in traffic accident scene photogrammetry, a photogrammetric method based on a composite of small calibration objects is proposed. Several small calibration objects are placed around the traffic accident scene, and the coordinate system of the composite calibration object is given based on one of them. By maintaining the relative position and coplanar relationship of the small calibration objects, the local coordinate system of each small calibration object is transformed into the coordinate system of the composite calibration object. The two-dimensional direct linear transformation method is improved based on minimizing the reprojection error of the calibration points of all objects. A rectified image is obtained using the nonlinear optimization method. The increased accuracy of traffic accident scene photogrammetry using a composite small calibration object is demonstrated through the analysis of field experiments and case studies.

Decomposing the Apoptosis Pathway Into Biologically Interpretable Principal Components

PubMed Central

Wang, Min; Kornblau, Steven M; Coombes, Kevin R

2018-01-01

Principal component analysis (PCA) is one of the most common techniques in the analysis of biological data sets, but applying PCA raises 2 challenges. First, one must determine the number of significant principal components (PCs). Second, because each PC is a linear combination of genes, it rarely has a biological interpretation. Existing methods to determine the number of PCs are either subjective or computationally extensive. We review several methods and describe a new R package, PCDimension, that implements additional methods, the most important being an algorithm that extends and automates a graphical Bayesian method. Using simulations, we compared the methods. Our newly automated procedure is competitive with the best methods when considering both accuracy and speed and is the most accurate when the number of objects is small compared with the number of attributes. We applied the method to a proteomics data set from patients with acute myeloid leukemia. Proteins in the apoptosis pathway could be explained using 6 PCs. By clustering the proteins in PC space, we were able to replace the PCs by 6 “biological components,” 3 of which could be immediately interpreted from the current literature. We expect this approach combining PCA with clustering to be widely applicable. PMID:29881252

Spectral analysis of pair-correlation bandwidth: application to cell biology images.

PubMed

Binder, Benjamin J; Simpson, Matthew J

2015-02-01

Images from cell biology experiments often indicate the presence of cell clustering, which can provide insight into the mechanisms driving the collective cell behaviour. Pair-correlation functions provide quantitative information about the presence, or absence, of clustering in a spatial distribution of cells. This is because the pair-correlation function describes the ratio of the abundance of pairs of cells, separated by a particular distance, relative to a randomly distributed reference population. Pair-correlation functions are often presented as a kernel density estimate where the frequency of pairs of objects are grouped using a particular bandwidth (or bin width), Δ>0. The choice of bandwidth has a dramatic impact: choosing Δ too large produces a pair-correlation function that contains insufficient information, whereas choosing Δ too small produces a pair-correlation signal dominated by fluctuations. Presently, there is little guidance available regarding how to make an objective choice of Δ. We present a new technique to choose Δ by analysing the power spectrum of the discrete Fourier transform of the pair-correlation function. Using synthetic simulation data, we confirm that our approach allows us to objectively choose Δ such that the appropriately binned pair-correlation function captures known features in uniform and clustered synthetic images. We also apply our technique to images from two different cell biology assays. The first assay corresponds to an approximately uniform distribution of cells, while the second assay involves a time series of images of a cell population which forms aggregates over time. The appropriately binned pair-correlation function allows us to make quantitative inferences about the average aggregate size, as well as quantifying how the average aggregate size changes with time.

Fixture-abutment connection surface and micro-gap measurements by 3D micro-tomographic technique analysis.

PubMed

Meleo, Deborah; Baggi, Luigi; Di Girolamo, Michele; Di Carlo, Fabio; Pecci, Raffaella; Bedini, Rossella

2012-01-01

X-ray micro-tomography (micro-CT) is a miniaturized form of conventional computed axial tomography (CAT) able to investigate small radio-opaque objects at a-few-microns high resolution, in a non-destructive, non-invasive, and tri-dimensional way. Compared to traditional optical and electron microscopy techniques, which provide two-dimensional images, this innovative investigation technology enables a sample tri-dimensional analysis without cutting, coating or exposing the object to any particular chemical treatment. X-ray micro-tomography matches ideal 3D microscopy features: the possibility of investigating an object in natural conditions and without any preparation or alteration; non-invasive, non-destructive, and sufficiently magnified 3D reconstruction; reliable measurement of numeric data of the internal structure (morphology, structure and ultra-structure). Hence, this technique has multi-fold applications in a wide range of fields, not only in medical and odontostomatologic areas, but also in biomedical engineering, materials science, biology, electronics, geology, archaeology, oil industry, and semi-conductors industry. This study shows possible applications of micro-CT in dental implantology to analyze 3D micro-features of dental implant to abutment interface. Indeed, implant-abutment misfit is known to increase mechanical stress on connection structures and surrounding bone tissue. This condition may cause not only screw preload loss or screw fracture, but also biological issues in peri-implant tissues.

Chemogenomics: a discipline at the crossroad of high throughput technologies, biomarker research, combinatorial chemistry, genomics, cheminformatics, bioinformatics and artificial intelligence.

PubMed

Maréchal, Eric

2008-09-01

Chemogenomics is the study of the interaction of functional biological systems with exogenous small molecules, or in broader sense the study of the intersection of biological and chemical spaces. Chemogenomics requires expertises in biology, chemistry and computational sciences (bioinformatics, cheminformatics, large scale statistics and machine learning methods) but it is more than the simple apposition of each of these disciplines. Biological entities interacting with small molecules can be isolated proteins or more elaborate systems, from single cells to complete organisms. The biological space is therefore analyzed at various postgenomic levels (genomic, transcriptomic, proteomic or any phenotypic level). The space of small molecules is partially real, corresponding to commercial and academic collections of compounds, and partially virtual, corresponding to the chemical space possibly synthesizable. Synthetic chemistry has developed novel strategies allowing a physical exploration of this universe of possibilities. A major challenge of cheminformatics is to charter the virtual space of small molecules using realistic biological constraints (bioavailability, druggability, structural biological information). Chemogenomics is a descendent of conventional pharmaceutical approaches, since it involves the screening of chemolibraries for their effect on biological targets, and benefits from the advances in the corresponding enabling technologies and the introduction of new biological markers. Screening was originally motivated by the rigorous discovery of new drugs, neglecting and throwing away any molecule that would fail to meet the standards required for a therapeutic treatment. It is now the basis for the discovery of small molecules that might or might not be directly used as drugs, but which have an immense potential for basic research, as probes to explore an increasing number of biological phenomena. Concerns about the environmental impact of chemical industry open new fields of research for chemogenomics.

Low cost light-sheet microscopy for whole brain imaging

NASA Astrophysics Data System (ADS)

Kumar, Manish; Nasenbeny, Jordan; Kozorovitskiy, Yevgenia

2018-02-01

Light-sheet microscopy has evolved as an indispensable tool in imaging biological samples. It can image 3D samples at fast speed, with high-resolution optical sectioning, and with reduced photobleaching effects. These properties make light-sheet microscopy ideal for imaging fluorophores in a variety of biological samples and organisms, e.g. zebrafish, drosophila, cleared mouse brains, etc. While most commercial turnkey light-sheet systems are expensive, the existing lower cost implementations, e.g. OpenSPIM, are focused on achieving high-resolution imaging of small samples or organisms like zebrafish. In this work, we substantially reduce the cost of light-sheet microscope system while targeting to image much larger samples, i.e. cleared mouse brains, at single-cell resolution. The expensive components of a lightsheet system - excitation laser, water-immersion objectives, and translation stage - are replaced with an incoherent laser diode, dry objectives, and a custom-built Arduino-controlled translation stage. A low-cost CUBIC protocol is used to clear fixed mouse brain samples. The open-source platforms of μManager and Fiji support image acquisition, processing, and visualization. Our system can easily be extended to multi-color light-sheet microscopy.

Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) Mission Concept

NASA Technical Reports Server (NTRS)

Ennico, Kimberly; Sandford, S.; Allamandola, L.; Bregman, J.; Cohen, M.; Cruikshank, D.; Dumas, C.; Greene, T.; Hudgins, D.; Kwok, S.

2004-01-01

The AstroBiology Explorer (ABE) mission concept consists of a modest dedicated space observatory having a 60 cm class primary mirror cooled to T less than 50 K equipped with medium resolution cross-dispersed spectrometers having cooled large format near- and mid-infrared detector arrays. Such a system would be capable of addressing outstanding problems in Astrochemistry and Astrophysics that are particularly relevant to Astrobiology and addressable via astronomical observation. The mission's observaticxiai program woiild make fundamental scieztific: prngress in establishing the nature, distribution, formation and evolution of organic and other molecular materials in the following extra-terrestrial environments: 1) The Outflow of Dying Stars; 2) The Diffuse Interstellar Medium (DISM); 3) Dense Molecular Clouds, Star Formation Regions, and Young Stellar/Planetary Systems; 4) Planets, Satellites, and Small Bodies within the Solar System; and 5) The Interstellar Media of Other Galaxies ABE could make fundamental progress in all of these area by conducting a 1 to 2 year mission to obtain a coordinated set of infrared spectroscopic observations over the 2.5 - 20 micron spectral range at a spectral resolution of R greater than 2500 of about 1500 galaxies, stars, planetary nebulae, young stellar objects, and solar system objects.

[Fundamental biological model for trials of wound ballistics].

PubMed

Krajsa, J; Hirt, M

2006-10-01

The aim of our experiment was the testing of effects of common ammunition on usable and slightly accessible biological tissue thereby to create fundamental simple biological model for trials of wounded ballistic. Like objective tissue was elected biological material - pork and beef hind-limbs, pork head, pork bodily cavity. It was discovered that objective tissue is able to react to singles types of shots in all spectrum results namely simple smooth penetration wound as well as splintery fracture in dependence on kind of using ammunition. Pork hind-limb was evaluated like the most suitable biological material for given object.

BRC4Env, a network of Biological Resource Centres for research in environmental and agricultural sciences.

PubMed

Mougin, Christian; Artige, Emmanuelle; Marchand, Frédéric; Mondy, Samuel; Ratié, Céline; Sellier, Nadine; Castagnone-Sereno, Philippe; D'Acier, Armelle Cœur; Esmenjaud, Daniel; Faivre-Primot, Céline; Granjon, Laurent; Hamelet, Valérie; Lange, Frederic; Pagès, Sylvie; Rimet, Frédéric; Ris, Nicolas; Sallé, Guillaume

2018-04-19

The Biological Resource Centre for the Environment BRC4Env is a network of Biological Resource Centres (BRCs) and collections whose leading objectives are to improve the visibility of genetic and biological resources maintained by its BRCs and collections and to facilitate their use by a large research community, from agriculture research to life sciences and environmental sciences. Its added value relies on sharing skills, harmonizing practices, triggering projects in comparative biology, and ultimately proposing a single-entry portal to facilitate access to documented samples, taking into account the partnership policies of research institutions as well as the legal frame which varies with the biological nature of resources. BRC4Env currently includes three BRCs: the Centre for Soil Genetic Resources of the platform GenoSol, in partnership with the European Conservatory of Soil Samples; the Egg Parasitoids Collection (EP-Coll); and the collection of ichthyological samples, Colisa. BRC4Env is also associated to several biological collections: microbial consortia (entomopathogenic bacteria, freshwater microalgae…), terrestrial arthropods, nematodes (plant parasitic, entomopathogenic, animal parasitic...), and small mammals. The BRCs and collections of BRC4Env are involved in partnership with academic scientists, as well as private companies, in the fields of medicinal mining, biocontrol, sustainable agriculture, and additional sectors. Moreover, the staff of the BRCs is involved in many training courses for students from French licence degree to Ph.D, engineers, as well as ongoing training.

Multiple objects tracking in fluorescence microscopy.

PubMed

Kalaidzidis, Yannis

2009-01-01

Many processes in cell biology are connected to the movement of compact entities: intracellular vesicles and even single molecules. The tracking of individual objects is important for understanding cellular dynamics. Here we describe the tracking algorithms which have been developed in the non-biological fields and successfully applied to object detection and tracking in biological applications. The characteristics features of the different algorithms are compared.

Application of Composite Small Calibration Objects in Traffic Accident Scene Photogrammetry

PubMed Central

Chen, Qiang; Xu, Hongguo; Tan, Lidong

2015-01-01

In order to address the difficulty of arranging large calibration objects and the low measurement accuracy of small calibration objects in traffic accident scene photogrammetry, a photogrammetric method based on a composite of small calibration objects is proposed. Several small calibration objects are placed around the traffic accident scene, and the coordinate system of the composite calibration object is given based on one of them. By maintaining the relative position and coplanar relationship of the small calibration objects, the local coordinate system of each small calibration object is transformed into the coordinate system of the composite calibration object. The two-dimensional direct linear transformation method is improved based on minimizing the reprojection error of the calibration points of all objects. A rectified image is obtained using the nonlinear optimization method. The increased accuracy of traffic accident scene photogrammetry using a composite small calibration object is demonstrated through the analysis of field experiments and case studies. PMID:26011052

In Vivo Production of Entomopathogenic Nematodes.

PubMed

Shapiro-Ilan, David I; Morales-Ramos, Juan A; Rojas, M Guadalupe

2016-01-01

In nature, entomopathogenic nematodes in the genera Heterorhabditis and Steinernema are obligate parasites of insects. The nematodes are used widely as biopesticides for suppression of insect pests. More than a dozen entomopathogenic nematode species have been commercialized for use in biological control. Most nematodes intended for commercial application are produced in artificial media via solid or liquid fermentation. However, for laboratory research and small greenhouse or field trials, in vivo production of entomopathogenic nematodes is the common method of propagation. Additionally, small companies continue to produce nematodes using in vivo methods for application in niche markets. Advances in mechanization and alternative production routes (e.g., production geared toward application of nematodes in infected host cadavers) can improve efficiency and economy of scale. The objective of this chapter is to describe basic and advanced procedures for in vivo production of entomopathogenic nematodes.

Ordinary differential equations with applications in molecular biology.

PubMed

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances. Ordinary differential equations are used to model biological processes on various levels ranging from DNA molecules or biosynthesis phospholipids on the cellular level.

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Lewis, M. L.

1982-01-01

Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

Objectives and methodology of BIOBADASER phase iii.

PubMed

Sanchez-Piedra, Carlos; Hernández Miguel, M Victoria; Manero, Javier; Roselló, Rosa; Sánchez-Costa, Jesús Tomás; Rodríguez-Lozano, Carlos; Campos, Cristina; Cuende, Eduardo; Fernández-Lopez, Jesús Carlos; Bustabad, Sagrario; Martín Domenech, Raquel; Pérez-Pampín, Eva; Del Pino-Montes, Javier; Millan-Arcineas, Ana Milena; Díaz-González, Federico; Gómez-Reino, Juan Jesús

2017-09-18

Describe the objectives, methods and results of the first year of the new version of the Spanish registry of adverse events involving biological therapies and synthetic drugs with an identifiable target in rheumatic diseases (BIOBADASER III). Multicenter prospective registry of patients with rheumatic inflammatory diseases being treated with biological drugs or synthetic drugs with an identifiable target in rheumatology departments in Spain. The main objective of BIOBADASER Phase III is the registry and analysis of adverse events; moreover, a secondary objective was added consisting of assessing the effectiveness by means of the registry of activity indexes. Patients in the registry are evaluated at least once every year and whenever they experience an adverse event or a change in treatment. The collection of data for phase iii began on 17 December 2015. During the first year, 35 centers participated. The number of patients included in this new phase in December 2016 was 2,664. The mean age was 53.7 years and the median duration of treatment was 8.1 years. In all, 40.4% of the patients were diagnosed with rheumatoid arthritis. The most frequent adverse events were infections and infestations. BIOBADASER Phase III has been launched to adapt to a changing pharmacological environment, with the introduction of biosimilars and small molecules in the treatment of rheumatic diseases. This new stage is adapted to the changes in the reporting of adverse events and now includes information related to activity scores. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

Recent advances in superhydrophobic surfaces and their relevance to biology and medicine.

PubMed

Ciasca, G; Papi, M; Businaro, L; Campi, G; Ortolani, M; Palmieri, V; Cedola, A; De Ninno, A; Gerardino, A; Maulucci, G; De Spirito, M

2016-02-04

By mimicking naturally occurring superhydrophobic surfaces, scientists can now realize artificial surfaces on which droplets of a few microliters of water are forced to assume an almost spherical shape and an extremely high contact angle. In recent decades, these surfaces have attracted much attention due to their technological applications for anti-wetting and self-cleaning materials. Very recently, researchers have shifted their interest to investigate whether superhydrophobic surfaces can be exploited to study biological systems. This research effort has stimulated the design and realization of new devices that allow us to actively organize, visualize and manipulate matter at both the microscale and nanoscale levels. Such precise control opens up wide applications in biomedicine, as it allows us to directly manipulate objects at the typical length scale of cells and macromolecules. This progress report focuses on recent biological and medical applications of superhydrophobicity. Particular regard is paid to those applications that involve the detection, manipulation and study of extremely small quantities of molecules, and to those that allow high throughput cell and biomaterial screening.

Design principles of hair-like structures as biological machines

PubMed Central

2018-01-01

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas. PMID:29848593

The Benefits of Using Clickers in Small-Enrollment Seminar-Style Biology Courses

ERIC Educational Resources Information Center

Smith, Michelle K.; Trujillo, Caleb; Su, Tin Tin

2011-01-01

Although the use of clickers and peer discussion is becoming common in large-lecture undergraduate biology courses, their use is limited in small-enrollment seminar-style courses. To investigate whether facilitating peer discussion with clickers would add value to a small-enrollment seminar-style course, we evaluated their usefulness in an…

Dual-wavelength digital holographic imaging with phase background subtraction

NASA Astrophysics Data System (ADS)

Khmaladze, Alexander; Matz, Rebecca L.; Jasensky, Joshua; Seeley, Emily; Holl, Mark M. Banaszak; Chen, Zhan

2012-05-01

Three-dimensional digital holographic microscopic phase imaging of objects that are thicker than the wavelength of the imaging light is ambiguous and results in phase wrapping. In recent years, several unwrapping methods that employed two or more wavelengths were introduced. These methods compare the phase information obtained from each of the wavelengths and extend the range of unambiguous height measurements. A straightforward dual-wavelength phase imaging method is presented which allows for a flexible tradeoff between the maximum height of the sample and the amount of noise the method can tolerate. For highly accurate phase measurements, phase unwrapping of objects with heights higher than the beat (synthetic) wavelength (i.e. the product of the original two wavelengths divided by their difference), can be achieved. Consequently, three-dimensional measurements of a wide variety of biological systems and microstructures become technically feasible. Additionally, an effective method of removing phase background curvature based on slowly varying polynomial fitting is proposed. This method allows accurate volume measurements of several small objects with the same image frame.

Imaging with a small number of photons

PubMed Central

Morris, Peter A.; Aspden, Reuben S.; Bell, Jessica E. C.; Boyd, Robert W.; Padgett, Miles J.

2015-01-01

Low-light-level imaging techniques have application in many diverse fields, ranging from biological sciences to security. A high-quality digital camera based on a multi-megapixel array will typically record an image by collecting of order 105 photons per pixel, but by how much could this photon flux be reduced? In this work we demonstrate a single-photon imaging system based on a time-gated intensified camera from which the image of an object can be inferred from very few detected photons. We show that a ghost-imaging configuration, where the image is obtained from photons that have never interacted with the object, is a useful approach for obtaining images with high signal-to-noise ratios. The use of heralded single photons ensures that the background counts can be virtually eliminated from the recorded images. By applying principles of image compression and associated image reconstruction, we obtain high-quality images of objects from raw data formed from an average of fewer than one detected photon per image pixel. PMID:25557090

An efficient way of high-contrast, quasi-3D cellular imaging: off-axis illumination.

PubMed

Hostounský, Zdenĕk; Pelc, Radek

2006-07-31

An imaging system enabling a convenient visualisation of cells and other small objects is presented. It represents an adaptation of the optical microscope condenser, accommodating a built-in edge (relief) diaphragm brought close to the condenser iris diaphragm and enabling high-contrast pseudo-relief (quasi-3D) imaging. The device broadens the family of available apparatus based on the off-axis (or anaxial, asymmetric, inclined, oblique, schlieren-type, sideband) illumination. The simplicity of the design makes the condenser a user-friendly, dedicated device delivering high-contrast quasi-3D images of phase objects. Those are nearly invisible under the ordinary (axial) illumination. The phase contrast microscopy commonly used in visualisation of phase objects does not deliver the quasi-3D effect and introduces a disturbing 'halo' effect around the edges. The performance of the device presented here is demonstrated on living cells and tissue replicas. High-contrast quasi-3D images of cell-free preparations of biological origin (paper fibres and microcrystals) are shown as well.

Behavioral and biological interactions with small groups in confined microsocieties

NASA Technical Reports Server (NTRS)

Brady, J. V.; Emurian, H. H.

1982-01-01

Requirements for high levels of human performance in the unfamiliar and stressful environments associated with space missions necessitate the development of research-based technological procedures for maximizing the probability of effective functioning at all levels of personnel participation. Where the successful accomplishment of such missions requires the coordinated contributions of several individuals collectively identified with the achievement of a common objective, the conditions for characterizing a team, crew, or functional group are operationally defined. For the most part, studies of group performances under operational conditions which emphasize relatively long exposure to extended mission environments have been limited by the constraints imposed on experimental manipulations to identify critical effectiveness factors. On the other hand, laboratory studies involving relatively brief exposures to contrived task situations have been considered of questionable generality to operational settings requiring realistic group objectives.

The effects of small field dosimetry on the biological models used in evaluating IMRT dose distributions

NASA Astrophysics Data System (ADS)

Cardarelli, Gene A.

The primary goal in radiation oncology is to deliver lethal radiation doses to tumors, while minimizing dose to normal tissue. IMRT has the capability to increase the dose to the targets and decrease the dose to normal tissue, increasing local control, decrease toxicity and allow for effective dose escalation. This advanced technology does present complex dose distributions that are not easily verified. Furthermore, the dose inhomogeneity caused by non-uniform dose distributions seen in IMRT treatments has caused the development of biological models attempting to characterize the dose-volume effect in the response of organized tissues to radiation. Dosimetry of small fields can be quite challenging when measuring dose distributions for high-energy X-ray beams used in IMRT. The proper modeling of these small field distributions is essential in reproducing accurate dose for IMRT. This evaluation was conducted to quantify the effects of small field dosimetry on IMRT plan dose distributions and the effects on four biological model parameters. The four biological models evaluated were: (1) the generalized Equivalent Uniform Dose (gEUD), (2) the Tumor Control Probability (TCP), (3) the Normal Tissue Complication Probability (NTCP) and (4) the Probability of uncomplicated Tumor Control (P+). These models are used to estimate local control, survival, complications and uncomplicated tumor control. This investigation compares three distinct small field dose algorithms. Dose algorithms were created using film, small ion chamber, and a combination of ion chamber measurements and small field fitting parameters. Due to the nature of uncertainties in small field dosimetry and the dependence of biological models on dose volume information, this examination quantifies the effects of small field dosimetry techniques on radiobiological models and recommends pathways to reduce the errors in using these models to evaluate IMRT dose distributions. This study demonstrates the importance of valid physical dose modeling prior to the use of biological modeling. The success of using biological function data, such as hypoxia, in clinical IMRT planning will greatly benefit from the results of this study.

Philosophy of race meets population genetics.

PubMed

Spencer, Quayshawn

2015-08-01

In this paper, I respond to four common semantic and metaphysical objections that philosophers of race have launched at scholars who interpret recent human genetic clustering results in population genetics as evidence for biological racial realism. I call these objections 'the discreteness objection', 'the visibility objection', 'the very important objection', and 'the objectively real objection.' After motivating each objection, I show that each one stems from implausible philosophical assumptions about the relevant meaning of 'race' or the nature of biological racial realism. In order to be constructive, I end by offering some advice for how we can productively critique attempts to defend biological racial realism based on recent human genetic clustering results. I also offer a clarification of the relevant human-population genetic research. Copyright © 2015 Elsevier Ltd. All rights reserved.

A semantic web ontology for small molecules and their biological targets.

PubMed

Choi, Jooyoung; Davis, Melissa J; Newman, Andrew F; Ragan, Mark A

2010-05-24

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and UniProt, and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery.

Biostack: A study of the biological effects on HZE galactic cosmic radiation

NASA Technical Reports Server (NTRS)

Buecker, H.

1975-01-01

The Biostack experiment designed to study the effect of individual heavy nucleii of the cosmic radiation environment upon biological systems during actual space flight is described. In each Biostack, several thousand biological objects were hit by an HZE particle. The response of the biological objects was studied. Results are discussed in terms of sensitivity to the hit.

Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

PubMed

Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

2017-06-01

Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

Vasculitis Terms A to Z

MedlinePlus

... interleukins, and vaccines. Also called biologic agent and biological agent. Capillaries: The smallest blood vessel in the body. Capillaries connect arterioles (small arteries) with venules (small veins). Capillaries form an intricate network throughout the body for the interchange of various ...

Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.

PubMed

Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

2014-10-22

In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or natural product-inspired DOS.

Controlled biological and biomimetic systems for landmine detection.

PubMed

Habib, Maki K

2007-08-30

Humanitarian demining requires to accurately detect, locate and deactivate every single landmine and other buried mine-like objects as safely and as quickly as possible, and in the most non-invasive manner. The quality of landmine detection affects directly the efficiency and safety of this process. Most of the available methods to detect explosives and landmines are limited by their sensitivity and/or operational complexities. All landmines leak with time small amounts of their explosives that can be found on surrounding ground and plant life. Hence, explosive signatures represent the robust primary indicator of landmines. Accordingly, developing innovative technologies and efficient techniques to identify in real-time explosives residue in mined areas represents an attractive and promising approach. Biological and biologically inspired detection technology has the potential to compete with or be used in conjunction with other artificial technology to complement performance strengths. Biological systems are sensitive to many different scents concurrently, a property that has proven difficult to replicate artificially. Understanding biological systems presents unique opportunities for developing new capabilities through direct use of trained bio-systems, integration of living and non-living components, or inspiring new design by mimicking biological capabilities. It is expected that controlled bio-systems, biotechnology and microbial techniques will contribute to the advancement of mine detection and other application domains. This paper provides directions, evaluation and analysis on the progress of controlled biological and biomimetic systems for landmine detection. It introduces and discusses different approaches developed, underlining their relative advantages and limitations, and highlighting trends, safety and ecology concern, and possible future directions.

Diagnosis Applications of Non-Crystalline Diffraction of Collagen Fibres: Breast Cancer and Skin Diseases

NASA Astrophysics Data System (ADS)

Costa, M.; Benseny-Cases, N.; Cócera, M.; Teixeira, C. V.; Alsina, M.; Cladera, J.; López, O.; Fernández, M.; Sabés, M.

In previous chapters, the basis of SAXS for the study of biological systems like proteins in solution have been presented. The SAXS patterns of proteins in solution present, in general, broad dependences with the scattering vector, and the interpretation requires a huge component of modelling. In this chapter and in the following one, it is shown how SAXS technique can be used to study biological systems that are partially crystalline and with a large crystalline cells. This is done by analysing the diffraction obtained from these systems at small angles. In this chapter, a new approach to the application of small-angle X-ray scattering (SAXS) for diagnosis using the diffraction pattern of collagen is presented. This chapter shows the development of a new strategy in the preventive diagnosis of breast cancer following changes on collagen from breast connective tissue. SAXS profiles are related to different features in cutaneous preparations and to the supra-molecular arrangement of skin layers (stratum corneum, epidermis and dermis), in order to introduce objective values on the diagnosis of different skin pathologies. Working parameters (size, thickness) and methods (freezing, paraffin embedment) have been established. The results suggest that collagen diffraction patterns could be used as diagnostic indicators; especially for breast cancer and preliminary results obtained with skin collagen are promising too.

Ecology and ethnoecology of dusky grouper [garoupa, Epinephelus marginatus (Lowe, 1834)] along the coast of Brazil

PubMed Central

Begossi, Alpina; Silvano, Renato AM

2008-01-01

Dusky grouper (garoupa, Epinephelus marginatus) is an important catch for several artisanal small-scale fisheries along the Brazilian coast. It is a sedentary, monandric, and late maturing protogynous species, which makes it vulnerable to overharvesting even though it is mainly caught through hook and line or spear fishing through free diving. Lack of information on the ecology and biology of this species in Brazil is astonishing. Much of the information found in the literature concerns Mediterranean dusky groupers. Studies compiling local knowledge (ethnoecology) about fish species complement biological data, and have been fundamental for effective fisheries management. In this study, our objectives are to obtain data about dusky grouper through fish catches and analysis of stomach contents and gonad maturation (macroscopic analyses), along with interviews from fishermen from six small-scales communities from the southern (Pântano do Sul, Florianópolis, Santa Catarina State) to the northern Brazilian coast (Porto Sauípe, Bahia State). We conclude that precautionary approaches and 'data-less' management approaches are needed in the coast of Brazil. Research on this species and on the potential of aquaculture for its cultivation, are urgent, due to the apparent vulnerability and decrease of dusky grouper along the coast of Brazil. PMID:18793394

Insight into Bone-Derived Biological Apatite: Ultrastructure and Effect of Thermal Treatment

PubMed Central

Liu, Quan; Pan, Haobo; Chen, Zhuofan; Matinlinna, Jukka Pekka

2015-01-01

Objectives. This study aims at examining the ultrastructure of bone-derived biological apatite (BAp) from a series of small vertebrates and the effect of thermal treatment on its physiochemical properties. Materials and Methods. Femurs/fin rays and vertebral bodies of 5 kinds of small vertebrates were firstly analyzed with X-ray microtomography. Subsequently, BAp was obtained with thermal treatment and low power plasma ashing, respectively. The properties of BAp, including morphology, functional groups, and crystal characteristics were then analyzed. Results. The bones of grouper and hairtail were mainly composed of condensed bone. Spongy bone showed different distribution in the bones from frog, rat, and pigeon. No significant difference was found in bone mineral density of condensed bone and trabecular thickness of spongy bone. Only platelet-like crystals were observed for BAp obtained by plasma ashing, while rod-like and irregular crystals were both harvested from the bones treated by sintering. A much higher degree of crystallinity and larger crystal size but a lower content of carbonate were detected in the latter. Conclusion. Platelet-like BAp is the common inorganic component of vertebrate bones. BAp distributing in condensed and spongy bone may exhibit differing thermal reactivity. Thermal treatment may alter BAp's in vivo structure and composition. PMID:25695088

Small Brazilian wild fruits: Nutrients, bioactive compounds, health-promotion properties and commercial interest.

PubMed

Neri-Numa, Iramaia Angélica; Soriano Sancho, Renata A; Pereira, Ana Paula Aparecida; Pastore, Glaucia Maria

2018-01-01

Brazilian berries present great nutritional, functional and economic characteristics comparable to temperate berries. They constitute an important innovation domain for the food, pharmaceutical and cosmetic industries, due to their positive health effects and market potential. The main objective of this review was to describe the physicochemical, nutritional and biological aspects of six Brazilian small native wild fruits from the Arecaceae (açaí, buriti and pupunha), Mirtaceae (camu-camu and jaboticaba) and Malpighiaceae (murici) families, highlighting their antioxidant, anti-lipidaemic, anti-inflammatory, antiproliferative, and antigenotoxic potential among others. It also discussed some relevant topics for new studies that could be of benefit to industry and improve the local economy where these fruits are found. Thus, the dissemination of the works already carried out with these fruits strategically relevant can stimulate new lines of research to consolidate this new field for the food industries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design.

PubMed

Gurung, A B; Bhattacharjee, A; Ajmal Ali, M; Al-Hemaid, F; Lee, Joongku

2017-02-01

Protein-protein interaction is a vital process which drives many important physiological processes in the cell and has also been implicated in several diseases. Though the protein-protein interaction network is quite complex but understanding its interacting partners using both in silico as well as molecular biology techniques can provide better insights for targeting such interactions. Targeting protein-protein interaction with small molecules is a challenging task because of druggability issues. Nevertheless, several studies on the kinetics as well as thermodynamic properties of protein-protein interactions have immensely contributed toward better understanding of the affinity of these complexes. But, more recent studies on hot spots and interface residues have opened up new avenues in the drug discovery process. This approach has been used in the design of hot spot based modulators targeting protein-protein interaction with the objective of normalizing such interactions.

SCORPI and SCORPI-T: Neurophysiological experiments on animals in space

NASA Astrophysics Data System (ADS)

Serafini, L.; Ramacciotti, T.; Vigano, W.; Donati, A.; Porciani, M.; Zolesi, V.; Schulze-Varnholt, D.; Manieri, P.; El-Din Sallam, A.; Schmah, M.; Horn, E. R.

2005-08-01

The study of physiological adaptation to long-term space flights with special consideration of the internal clock systems of scorpions is the goal of the SCORPI and SCORPI-T experiments. SCORPI was selected for flight on the International Space Station (ISS) and will be mounted in the European facility BIOLAB, the ESA laboratory designed to support biological experiments on micro-organisms, cells, tissue, cultures, small plants and small invertebrates. SCORPI-T experiment, performed on the Russian FOTON-M2 satellite in May-June 2005, represents an important precursor for the success of the experiment SCORPI on BIOLAB. This paper outlines the main features of the hardware designed and developed in order to allow the analysis of critical aspects of experiment execution and the verification of experiment objectives. The capabilities of the hardware developed for SCORPI and SCORPI-T show its potential use for any future similar type of experiments in space.

Insomnia with Objective Short Sleep Duration: the Most Biologically Severe Phenotype of the Disorder

PubMed Central

Vgontzas, Alexandros N.; Fernandez-Mendoza, Julio; Liao, Duanping; Bixler, Edward O.

2013-01-01

Summary Until recently, the association of chronic insomnia with significant medical morbidity was not established and its diagnosis was based solely on subjective complaints. We present evidence that insomnia with objective short sleep duration is the most biologically severe phenotype of the disorder, as it is associated with cognitive-emotional and cortical arousal, activation of both limbs of the stress system, and a higher risk for hypertension, impaired heart rate variability, diabetes, neurocognitive impairment, and mortality. Also, it appears that objective short sleep duration is a biological marker of genetic predisposition to chronic insomnia. In contrast, insomnia with objective normal sleep duration is associated with cognitive-emotional and cortical arousal and sleep misperception but not with signs of activation of both limbs of the stress system or medical complications. Furthermore, the first phenotype is associated with unremitting course, whereas the latter is more likely to remit. We propose that short sleep duration in insomnia is a reliable marker of the biological severity and medical impact of the disorder. Objective measures of sleep obtained in the home environment of the patient would become part of the routine assessment of insomnia patients in a clinician’s office setting. We speculate that insomnia with objective short sleep duration has primarily biological roots and may respond better to biological treatments, whereas insomnia with objective normal sleep duration has primarily psychological roots and may respond better to psychological interventions alone. PMID:23419741

Insomnia with objective short sleep duration: the most biologically severe phenotype of the disorder.

PubMed

Vgontzas, Alexandros N; Fernandez-Mendoza, Julio; Liao, Duanping; Bixler, Edward O

2013-08-01

Until recently, the association of chronic insomnia with significant medical morbidity was not established and its diagnosis was based solely on subjective complaints. We present evidence that insomnia with objective short sleep duration is the most biologically severe phenotype of the disorder, as it is associated with cognitive-emotional and cortical arousal, activation of both limbs of the stress system, and a higher risk for hypertension, impaired heart rate variability, diabetes, neurocognitive impairment, and mortality. Also, it appears that objective short sleep duration is a biological marker of genetic predisposition to chronic insomnia. In contrast, insomnia with objective normal sleep duration is associated with cognitive-emotional and cortical arousal and sleep misperception but not with signs of activation of both limbs of the stress system or medical complications. Furthermore, the first phenotype is associated with unremitting course, whereas the latter is more likely to remit. We propose that short sleep duration in insomnia is a reliable marker of the biological severity and medical impact of the disorder. Objective measures of sleep obtained in the home environment of the patient would become part of the routine assessment of insomnia patients in a clinician's office setting. We speculate that insomnia with objective short sleep duration has primarily biological roots and may respond better to biological treatments, whereas insomnia with objective normal sleep duration has primarily psychological roots and may respond better to psychological interventions alone. Copyright © 2012 Elsevier Ltd. All rights reserved.

An overview of surface radiance and biology studies in FIFE

NASA Astrophysics Data System (ADS)

Blad, B. L.; Schimel, D. S.

1992-11-01

The use of satellite data to study and to understand energy and mass exchanges between the land surface and the atmosphere requires information about various biological processes and how various reflected or emitted spectral radiances are influenced by or manifested in these processes. To obtain such information, studies were conducted by the First ISLSCP Field Experiment (FIFE) surface radiances and biology (SRB) group using surface, near-surface, helicopter, and aircraft measurements. The two primary objectives of this group were to relate radiative fluxes to biophysical parameters and physiological processes and to assess how various management treatments affect important biological processes. This overview paper summarizes the results obtained by various SRB teams working in nine different areas: (1) measurement of bidirectional reflectance and estimation of hemispherical albedo; (2) evaluation of spatial and seasonal variability of spectral reflectance and vegetation indices; (3) determination of surface and radiational factors and their effects on vegetation indices and PAR relationships; (4) use of surface temperatures to estimate sensible heat flux; (5) controls over photosynthesis and respiration at small scales; (6) soil surface CO2 fluxes and grassland carbon budget; (7) landscape variations in controls over gas exchange and energy partitioning; (8) radiometric response of prairie to management and topography; and (9) determination of nitrogen gas exchanges in a tallgrass prairie.

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling

PubMed Central

Wagner, Bridget K.; Clemons, Paul A.

2009-01-01

Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene-expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe- and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of “virtual” profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe and drug discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections. PMID:19825513

Application of chemical biology in target identification and drug discovery.

PubMed

Zhu, Yue; Xiao, Ting; Lei, Saifei; Zhou, Fulai; Wang, Ming-Wei

2015-09-01

Drug discovery and development is vital to the well-being of mankind and sustainability of the pharmaceutical industry. Using chemical biology approaches to discover drug leads has become a widely accepted path partially because of the completion of the Human Genome Project. Chemical biology mainly solves biological problems through searching previously unknown targets for pharmacologically active small molecules or finding ligands for well-defined drug targets. It is a powerful tool to study how these small molecules interact with their respective targets, as well as their roles in signal transduction, molecular recognition and cell functions. There have been an increasing number of new therapeutic targets being identified and subsequently validated as a result of advances in functional genomics, which in turn led to the discovery of numerous active small molecules via a variety of high-throughput screening initiatives. In this review, we highlight some applications of chemical biology in the context of drug discovery.

Caenorhabditis elegans chemical biology: lessons from small molecules

USDA-ARS?s Scientific Manuscript database

How can we complement Caenorhabditis elegans genomics and proteomics with a comprehensive structural and functional annotation of its metabolome? Several lines of evidence indicate that small molecules of largely undetermined structure play important roles in C. elegans biology, including key pathw...

The biology of small, introduced populations, with special reference to biological control

PubMed Central

Fauvergue, Xavier; Vercken, Elodie; Malausa, Thibaut; Hufbauer, Ruth A

2012-01-01

Populations are introduced into novel environments in different contexts, one being the biological control of pests. Despite intense efforts, less than half introduced biological control agents establish. Among the possible approaches to improve biological control, one is to better understand the processes that underpin introductions and contribute to ecological and evolutionary success. In this perspective, we first review the demographic and genetic processes at play in small populations, be they stochastic or deterministic. We discuss the theoretical outcomes of these different processes with respect to individual fitness, population growth rate, and establishment probability. Predicted outcomes differ subtly in some cases, but enough so that the evaluating results of introductions have the potential to reveal which processes play important roles in introduced populations. Second, we attempt to link the theory we have discussed with empirical data from biological control introductions. A main result is that there are few available data, but we nonetheless report on an increasing number of well-designed, theory-driven, experimental approaches. Combining demography and genetics from both theoretical and empirical perspectives highlights novel and exciting avenues for research on the biology of small, introduced populations, and great potential for improving both our understanding and practice of biological control. PMID:22949919

A system to evaluate the scientific quality of biological and restoration objectives using National Wildlife Refuge Comprehensive Conservation Plans as a case study

USGS Publications Warehouse

Schroeder, R.L.

2006-01-01

It is widely accepted that plans for restoration projects should contain specific, measurable, and science-based objectives to guide restoration efforts. The United States Fish and Wildlife Service (USFWS) is in the process of developing Comprehensive Conservation Plans (CCPs) for more than 500 units in the National Wildlife Refuge System (NWRS). These plans contain objectives for biological and ecosystem restoration efforts on the refuges. Based on USFWS policy, a system was developed to evaluate the scientific quality of such objectives based on three critical factors: (1) Is the objective specific, measurable, achievable, results-oriented, and time-fixed? (2) What is the extent of the rationale that explains the assumptions, logic, and reasoning for the objective? (3) How well was available science used in the development of the objective? The evaluation system scores each factor on a scale of 1 (poor) to 4 (excellent) according to detailed criteria. The biological and restoration objectives from CCPs published as of September 2004 (60 total) were evaluated. The overall average score for all biological and restoration objectives was 1.73. Average scores for each factor were: Factor 1-1.97; Factor 2-1.86; Factor 3-1.38. The overall scores increased from 1997 to 2004. Future restoration efforts may benefit by using this evaluation system during the process of plan development, to ensure that biological and restoration objectives are of the highest scientific quality possible prior to the implementation of restoration plans, and to allow for improved monitoring and adaptive management.

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

NASA Astrophysics Data System (ADS)

Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

2016-10-01

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

The surface-to-volume ratio in thermal physics: from cheese cube physics to animal metabolism

NASA Astrophysics Data System (ADS)

Planinšič, Gorazd; Vollmer, Michael

2008-03-01

The surface-to-volume ratio is an important quantity in thermal physics. For example it governs the behaviour of heating or cooling of physical objects as a function of size like, e.g. cubes or spheres made of different material. The starting point in our paper is the simple physics problem of how cheese cubes of different sizes behave if heated either in a conventional oven or in a microwave oven. The outcome of these experiments depends on a balance between heating and cooling with the surface-to-volume ratio (S/V) as the key parameter. The role of (S/V) becomes most obvious in studying cooling curves of differently sized objects like cubes or spheres, alone. Besides problems in thermal physics, the surface-to-volume ratio has many important applications in biochemistry, chemistry and biology. It allows us to draw general conclusions concerning the thermal and mechanical properties of different-sized animals, in particular their metabolism. Hence, this topic offers rich contexts for interdisciplinary teaching. An example presented in this paper starts in physics while studying thermal properties of cheese cubes and ends up in biology by discussing the differences in food intake of animals from small mice to huge elephants.

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

PubMed Central

Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

2016-01-01

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification. PMID:27762292

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms.

PubMed

Mirkovic, Djordje; Stepanian, Phillip M; Kelly, Jeffrey F; Chilson, Phillip B

2016-10-20

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

Large-scale additive manufacturing with bioinspired cellulosic materials.

PubMed

Sanandiya, Naresh D; Vijay, Yadunund; Dimopoulou, Marina; Dritsas, Stylianos; Fernandez, Javier G

2018-06-05

Cellulose is the most abundant and broadly distributed organic compound and industrial by-product on Earth. However, despite decades of extensive research, the bottom-up use of cellulose to fabricate 3D objects is still plagued with problems that restrict its practical applications: derivatives with vast polluting effects, use in combination with plastics, lack of scalability and high production cost. Here we demonstrate the general use of cellulose to manufacture large 3D objects. Our approach diverges from the common association of cellulose with green plants and it is inspired by the wall of the fungus-like oomycetes, which is reproduced introducing small amounts of chitin between cellulose fibers. The resulting fungal-like adhesive material(s) (FLAM) are strong, lightweight and inexpensive, and can be molded or processed using woodworking techniques. We believe this first large-scale additive manufacture with ubiquitous biological polymers will be the catalyst for the transition to environmentally benign and circular manufacturing models.

Numerical study on trapping and guiding of nanoparticles in a flow using scattering field of laser light

NASA Astrophysics Data System (ADS)

Yokoi, Naomichi; Aizu, Yoshihisa

2018-01-01

Optical trapping and guiding using laser have been proven to be useful for non-contact and non-invasive manipulation of small objects such as biological cells, organelles within cells, and dielectric particles. We have numerically investigated so far the motion of a Brownian particle suspended in still water under the illumination of a speckle pattern generated by the interference of coherent light scattered by a rough object. In the present study, we investigate numerically the motion of a particle in a water flow under the illumination of a speckle pattern that is at rest or in motion. Trajectory of the particle is simulated in relation with its size, flow velocity, maximum irradiance, and moving velocity of the speckle pattern to confirm the feasibility of the present method for performing optical trapping and guiding of the particle in the flow.

Automatic analysis and quantification of fluorescently labeled synapses in microscope images

NASA Astrophysics Data System (ADS)

Yona, Shai; Katsman, Alex; Orenbuch, Ayelet; Gitler, Daniel; Yitzhaky, Yitzhak

2011-09-01

The purpose of this work is to classify and quantify synapses and their properties in the cultures of a mouse's hippocampus, from images acquired by a fluorescent microscope. Quantification features include the number of synapses, their intensity and their size characteristics. The images obtained by the microscope contain hundreds to several thousands of synapses with various elliptic-like shape features and intensities. These images also include other features such as glia cells and other biological objects beyond the focus plane; those features reduce the visibility of the synapses and interrupt the segmentation process. The proposed method comprises several steps, including background subtraction, identification of suspected centers of synapses as local maxima of small neighborhoods, evaluation of the tendency of objects to be synapses according to intensity properties at their larger neighborhoods, classification of detected synapses into categories as bulks or single synapses and finally, delimiting the borders of each synapse.

Numerical study on trapping and guiding of nanoparticles in a flow using scattering field of laser light

NASA Astrophysics Data System (ADS)

Yokoi, Naomichi; Aizu, Yoshihisa

2018-06-01

Optical trapping and guiding using laser have been proven to be useful for non-contact and non-invasive manipulation of small objects such as biological cells, organelles within cells, and dielectric particles. We have numerically investigated so far the motion of a Brownian particle suspended in still water under the illumination of a speckle pattern generated by the interference of coherent light scattered by a rough object. In the present study, we investigate numerically the motion of a particle in a water flow under the illumination of a speckle pattern that is at rest or in motion. Trajectory of the particle is simulated in relation with its size, flow velocity, maximum irradiance, and moving velocity of the speckle pattern to confirm the feasibility of the present method for performing optical trapping and guiding of the particle in the flow.

Negotiation of intracellular membrane barriers by TAT-modified gold nanoparticles.

PubMed

Krpetić, Zeljka; Saleemi, Samia; Prior, Ian A; Sée, Violaine; Qureshi, Rumana; Brust, Mathias

2011-06-28

This paper contributes to the debate on how nanosized objects negotiate membrane barriers inside biological cells. The uptake of peptide-modified gold nanoparticles by HeLa cells has been quantified using atomic emission spectroscopy. The TAT peptide from the HIV virus was singled out as a particularly effective promoter of cellular uptake. The evolution of the intracellular distribution of TAT-modified gold nanoparticles with time has been studied in detail by TEM and systematic image analysis. An unusual trend of particles disappearing from the cytosol and the nucleus and accumulating massively in vesicular bodies was observed. Subsequent release of the particles, both by membrane rupture and by direct transfer across the membrane boundary, was frequently found. Ultimately, near total clearing of particles from the cells occurred. This work provides support for the hypothesis that cell-penetrating peptides can enable small objects to negotiate membrane barriers also in the absence of dedicated transport mechanisms.

Control of fluxes in metabolic networks

PubMed Central

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-01-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. PMID:27197218

Physical, Hydrological, and Biological Characteristics of the Loxahatchee River Estuary, Florida

USGS Publications Warehouse

McPherson, Benjamin F.; Sabanskas, Maryann; Long, William A.

1982-01-01

The Loxahatchee River estuary empties into the Atlantic Ocean at Jupiter Inlet in southeastern Florida. Although relatively small, the estuary is important for its esthetic value and for its sport fishing, boating, recreation, tourism, and prime residential development. In recent years, the condition of the estuary has become of concern to many citizens and agencies of the State. In response to this concern, the U.S. Geological Survey planned and carried out an in-depth environmental investigation. The events that led to the investigation and the objectives of the investigation are outlined in a recent U.S. Geological Survey report by McPherson and Sabanskas (WRI 80-1109).

[Some aspects of animal-to-human approximation of low frequency electromagnetic field exposure conditions].

PubMed

Vasin, A L

2003-01-01

Appropriateness of representation of a biological object surface as an equipotential surface has been proved for conditions of a quasistatic exposure to EMF of frequencies lower than 1 MHz. The conditions, at which a self capacitance of a biological object is its basic electrical parameter, have been considered. A factor of animal-to-human approximation of low-frequency EMF exposure conditions was estimated on the basis of equal dose loading in biological objects of different geometric sizes.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2013-02-26

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2014-04-15

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

2015-11-24

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biologically plausible learning in neural networks: a lesson from bacterial chemotaxis.

PubMed

Shimansky, Yury P

2009-12-01

Learning processes in the brain are usually associated with plastic changes made to optimize the strength of connections between neurons. Although many details related to biophysical mechanisms of synaptic plasticity have been discovered, it is unclear how the concurrent performance of adaptive modifications in a huge number of spatial locations is organized to minimize a given objective function. Since direct experimental observation of even a relatively small subset of such changes is not feasible, computational modeling is an indispensable investigation tool for solving this problem. However, the conventional method of error back-propagation (EBP) employed for optimizing synaptic weights in artificial neural networks is not biologically plausible. This study based on computational experiments demonstrated that such optimization can be performed rather efficiently using the same general method that bacteria employ for moving closer to an attractant or away from a repellent. With regard to neural network optimization, this method consists of regulating the probability of an abrupt change in the direction of synaptic weight modification according to the temporal gradient of the objective function. Neural networks utilizing this method (regulation of modification probability, RMP) can be viewed as analogous to swimming in the multidimensional space of their parameters in the flow of biochemical agents carrying information about the optimality criterion. The efficiency of RMP is comparable to that of EBP, while RMP has several important advantages. Since the biological plausibility of RMP is beyond a reasonable doubt, the RMP concept provides a constructive framework for the experimental analysis of learning in natural neural networks.

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin.

PubMed

Ghanta, Sindhu; Jordan, Michael I; Kose, Kivanc; Brooks, Dana H; Rajadhyaksha, Milind; Dy, Jennifer G

2017-01-01

Segmenting objects of interest from 3D data sets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution, and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, the shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance, and unknown locations. The driving application that inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear, and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease, and cancer usually start. Detecting the DEJ is challenging, because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped "peaks and valleys." In addition, RCM imaging resolution, contrast, and intensity vary with depth. Thus, a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10- 20 μm .

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin

PubMed Central

Ghanta, Sindhu; Jordan, Michael I.; Kose, Kivanc; Brooks, Dana H.; Rajadhyaksha, Milind; Dy, Jennifer G.

2016-01-01

Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance and unknown locations. The driving application which inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease and cancer usually start. Detecting the DEJ is challenging because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped “peaks and valleys”. In addition, RCM imaging resolution, contrast and intensity vary with depth. Thus a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10 – 20µm. PMID:27723590

Simulating complex intracellular processes using object-oriented computational modelling.

PubMed

Johnson, Colin G; Goldman, Jacki P; Gullick, William J

2004-11-01

The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation.

Data Integration for Health and Stress Monitoring: Biological Metabolites, Wearables Data, and Self-Reporting

NASA Astrophysics Data System (ADS)

Dunn, Jocelyn T.

Integrative and unobtrusive approaches to monitoring health and stress can assist in preventative medicine and disease management, and provide capabilities for complex work environments, such as military deployments and long-duration human space exploration missions. With many data streams that could potentially provide critical information about the health, behavior, and psychosocial states of individuals or small groups, the central question of this research is how to reliably measure health and stress states over time. This integrative approach to health and stress monitoring has implemented biological metabolite profiling, wearables data analysis, and survey assessment for comparing biological, behavioral, and psychological perspectives. Health monitoring technologies aim to provide objective data about health status. Providing objective information can help mitigate biases or blind spots in an individual's perception. Consider an individual who is unwilling to openly admit to psychosocial distress and unhealthy habits, or an individual who has habituated to long-term stressors and is unable to recognize a chronic state of high stress. Both honesty and self-awareness are required for accurate self-reporting. Digital health technologies, such as wearable devices, provide objective data for health monitoring. Compared to surveys, wearables are less influenced by participant openness, and compared to biological samples, wearables require less equipment and less labor for analysis. However, inherent to every data stream are limitations due to uncertainty and sensitivity. This research has been conducted in collaboration with Hawaii Space Exploration Analog and Simulation (HI-SEAS), which is a Mars analog research site on the slopes on Mauna Loa volcano in Hawaii. During 8-month and 12-month HI-SEAS missions in the 2014-2016 timeframe, twelve individuals provided hair and urine samples for metabolite profiling, utilized consumer-grade wearables to monitor sleep and activity behaviors, and responded to surveys for recording perceived health and stress levels. This work has developed a self-report instrument for stress characterization, efficient protocols for metabolite profiling, novel measures of sleep quality and activity levels, and has evaluated performance differences of JawboneRTM and FitbitRTM wearable devices that were worn in tandem. There is considerable debate about the accuracy of data collected from wearable devices. Therefore, the success of next-generation wearable devices is hinging on the ability to reliably process wearables data into meaningful health information. By simultaneously quantifying biological metabolites, sleep and activity behaviors, and psychological perceptions of health, this research is evaluating possible predictors of health and stress, such as evaluating if activity and sleep behaviors recorded by wearables can be predictive of biological metabolites and perceived health. This research has developed data-driven insights for advancing the next-generation of biological, behavioral, and psychological health monitoring capabilities.

[Experience of the development special medical technical laboratory for studies of effects caused by potent electromagnetic radiation in biologic objects].

PubMed

Gorodetsky, B N; Kalyada, T V; Petrov, S V

2015-01-01

This article covers topics of creating special medical technical laboratory for medial and biologic studies concerning influence of potent high-frequency elecromagnetic radiation on various biologic objects. The authors gave example of such laboratory, described its construction features, purpose and main characteristics of the included devices.

Human papillomavirus molecular biology.

PubMed

Harden, Mallory E; Munger, Karl

Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Microfabricated Circuits for Terahertz Wave Amplification and Terahertz Biosensors

NASA Astrophysics Data System (ADS)

Fawole, Olutosin Charles

The terahertz frequency band extends from deep infrared (100 THz) down to millimeter waves (0.4 THz), and this band was mostly inaccessible due to the lack of appropriate sources and detectors. Those with access to this band had to endure the small-intensity pulsed signals (nanowatts to microwatts) that the terahertz sources of those times could provide. In recent years, however, sufficient development has led to the availability of terahertz sources with sufficient power (1-100 muW) and the ease of use these sources has in turn enabled researchers to develop newer sources, detectors, and application areas. The terahertz regime is interesting because a) many molecules have vibrational, rotation and transition absorption bands in this regime, b) the terahertz electromagnetic wavelength is sufficiently small to resolve centimeter to millimeter scale objects, and c) scattering and absorption in metals in the terahertz regime make it very challenging to devise terahertz signal processing circuits. Thus, performing terahertz reflection/transmission measurements may enable precise identification of chemicals in a sample. Furthermore, small wavelengths and strong scattering by metallic objects make imaging with terahertz waves quite attractive. Finally, the ability to devise terahertz communication circuits and links will provide access to a frequency domain that is restricted and not available to others. One of the main objectives of this work is to develop 0.75 - 1.1 terahertz (free space wavelength 272 mum - 400 ?mum) amplifiers. Another objective of this work is to explore the suitability of terahertz waves in biological imaging and sensing. The terahertz amplifiers developed in this work consisted of distributed components such as rectangular waveguides and cylindrical dielectric resonators. In contrast to discrete amplifiers, which are based on solid-state devices, distributed traveling wave amplifiers can potentially handle and produce larger powers. Three different distributed terahertz amplifier circuits were considered in this work. These were based on a) coupled dielectric resonators, b) dielectric waveguides with periodic slots, and c) metallic meandering waveguides. The result of the hot test of the last circuit on interaction with an electron beam energy source yielded an amplification of 12 dB of a -55 dBm, 0.9 terahertz signal over 1 gigahertz bandwidth. The electron beam acceleration voltage was 4.8 kV and its current was approximately 20 microamps. The terahertz biosensing system developed in this work was used to study the unique interaction of terahertz waves with the chemical and physical components of biological tissues, and the products of biochemical reactions. A terahertz near-field imaging system was also developed to image mouse brain slices, plants, and bug wings. In addition, this work also demonstrated the capabilities and limitations of terahertz waves for the real-time noninvasive monitoring of bioethanol production by yeast cells.

Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology.

PubMed

Zhou, Jie; Du, Xuewen; Xu, Bing

2015-01-01

Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine.

Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology

PubMed Central

Zhou, Jie; Du, Xuewen; Xu, Bing

2015-01-01

Abstract Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine. PMID:25738892

Nanobacteria-like calcite single crystals at the surface of the Tataouine meteorite

PubMed Central

Benzerara, Karim; Menguy, Nicolas; Guyot, François; Dominici, Christian; Gillet, Philippe

2003-01-01

Nanobacteria-like objects evidenced at the surface of the orthopyroxenes of the Tataouine meteorite in South Tunisia have been studied by scanning and transmission electron microscopies. A method of micromanipulation has been developed to ensure that exactly the same objects were studied by both methods. We have shown that the nanobacteria-like objects are spatially correlated with filaments of microorganisms that colonized the surface of the meteoritic pyroxene during its 70 years of residence in the aridic Tataouine soil. Depressions of a few micrometers in depth are observed in the pyroxene below the carbonates, indicating preferential dissolution of the pyroxene and calcite precipitation at these locations. The nanobacteria-like small rods that constitute calcium carbonate rosettes are well crystallized calcite single crystals surrounded by a thin amorphous layer of carbonate composition that smoothes the crystal edges and induces rounded shapes. Those morphologies are unusual for calcite single crystals observed in natural samples. A survey of recent literature suggests that the intervention of organic compounds derived from biological activity is likely in their formation. PMID:12792020

Nanobacteria-like calcite single crystals at the surface of the Tataouine meteorite.

PubMed

Benzerara, Karim; Menguy, Nicolas; Guyot, Francois; Dominici, Christian; Gillet, Philippe

2003-06-24

Nanobacteria-like objects evidenced at the surface of the orthopyroxenes of the Tataouine meteorite in South Tunisia have been studied by scanning and transmission electron microscopies. A method of micromanipulation has been developed to ensure that exactly the same objects were studied by both methods. We have shown that the nanobacteria-like objects are spatially correlated with filaments of microorganisms that colonized the surface of the meteoritic pyroxene during its 70 years of residence in the aridic Tataouine soil. Depressions of a few micrometers in depth are observed in the pyroxene below the carbonates, indicating preferential dissolution of the pyroxene and calcite precipitation at these locations. The nanobacteria-like small rods that constitute calcium carbonate rosettes are well crystallized calcite single crystals surrounded by a thin amorphous layer of carbonate composition that smoothes the crystal edges and induces rounded shapes. Those morphologies are unusual for calcite single crystals observed in natural samples. A survey of recent literature suggests that the intervention of organic compounds derived from biological activity is likely in their formation.

Nano-assembly of nanodiamonds by conjugation to actin filaments.

PubMed

Bradac, Carlo; Say, Jana M; Rastogi, Ishan D; Cordina, Nicole M; Volz, Thomas; Brown, Louise J

2016-03-01

Fluorescent nanodiamonds (NDs) are remarkable objects. They possess unique mechanical and optical properties combined with high surface areas and controllable surface reactivity. They are non-toxic and hence suited for use in biological environments. NDs are also readily available and commercially inexpensive. Here, the exceptional capability of controlling and tailoring their surface chemistry is demonstrated. Small, bright diamond nanocrystals (size ˜30 nm) are conjugated to protein filaments of actin (length ˜3-7 µm). The conjugation to actin filaments is extremely selective and highly target-specific. These unique features, together with the relative simplicity of the conjugation-targeting method, make functionalised nanodiamonds a powerful and versatile platform in biomedicine and quantum nanotechnologies. Applications ranging from using NDs as superior biological markers to, potentially, developing novel bottom-up approaches for the fabrication of hybrid quantum devices that would bridge across the bio/solid-state interface are presented and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical toolkits for in vivo deep tissue laser scanning microscopy: a primer

NASA Astrophysics Data System (ADS)

Lee, Woei Ming; McMenamin, Thomas; Li, Yongxiao

2018-06-01

Life at the microscale is animated and multifaceted. The impact of dynamic in vivo microscopy in small animals has opened up opportunities to peer into a multitude of biological processes at the cellular scale in their native microenvironments. Laser scanning microscopy (LSM) coupled with targeted fluorescent proteins has become an indispensable tool to enable dynamic imaging in vivo at high temporal and spatial resolutions. In the last few decades, the technique has been translated from imaging cells in thin samples to mapping cells in the thick biological tissue of living organisms. Here, we sought to provide a concise overview of the design considerations of a LSM that enables cellular and subcellular imaging in deep tissue. Individual components under review include: long working distance microscope objectives, laser scanning technologies, adaptive optics devices, beam shaping technologies and photon detectors, with an emphasis on more recent advances. The review will conclude with the latest innovations in automated optical microscopy, which would impact tracking and quantification of heterogeneous populations of cells in vivo.

SPED light sheet microscopy: fast mapping of biological system structure and function

PubMed Central

Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M.; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

2016-01-01

The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light-sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca2+ imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function. PMID:26687363

Intuitive biological thought: Developmental changes and effects of biology education in late adolescence.

PubMed

Coley, John D; Arenson, Melanie; Xu, Yian; Tanner, Kimberly D

2017-02-01

A large body of cognitive research has shown that people intuitively and effortlessly reason about the biological world in complex and systematic ways. We addressed two questions about the nature of intuitive biological reasoning: How does intuitive biological thinking change during adolescence and early adulthood? How does increasing biology education influence intuitive biological thinking? To do so, we developed a battery of measures to systematically test three components of intuitive biological thought: anthropocentric thinking, teleological thinking and essentialist thinking, and tested 8th graders and university students (both biology majors, and non-biology majors). Results reveal clear evidence of persistent intuitive reasoning among all populations studied, consistent but surprisingly small differences between 8th graders and college students on measures of intuitive biological thought, and consistent but again surprisingly small influence of increasing biology education on intuitive biological reasoning. Results speak to the persistence of intuitive reasoning, the importance of taking intuitive knowledge into account in science classrooms, and the necessity of interdisciplinary research to advance biology education. Further studies are necessary to investigate how cultural context and continued acquisition of expertise impact intuitive biology thinking. Copyright © 2016 Elsevier Inc. All rights reserved.

A subcontinental view of forest plant invasions

Treesearch

Christopher M. Oswalt; Songlin Fei; Qinfeng Guo; Basil V. Iannone III; Sonja N. Oswalt; Bryan C. Pijanowski; Kevin M. Potter

2015-01-01

Over the last few decades, considerable attention has focused on small-scale studies of invasive plants and invaded systems. Unfortunately, small scale studies rarely provide comprehensive insight into the complexities of biological invasions at macroscales. Systematic and repeated monitoring of biological invasions at broad scales are rare. In this report, we...

Biological control of saltcedar (Tamarix spp.) by saltcedar leaf beetles (Diorhabda spp.): effects on small mammals

USDA-ARS?s Scientific Manuscript database

The spread of introduced saltcedar (Tamarix spp.) throughout many riparian systems across the western United States motivated the introduction of biological control agents that are specific to saltcedar, saltcedar leaf beetles (Diorhabda carinulata, D. elongata; Chrysomelidae). I monitored small mam...

Biomedical Research Experiences for Biology Majors at a Small College

ERIC Educational Resources Information Center

Stover, Shawn K.; Mabry, Michelle L.

2010-01-01

A program-level assessment of the biology curriculum at a small liberal arts college validates a previous study demonstrating success in achieving learning outcomes related to content knowledge and communication skills. Furthermore, research opportunities have been provided to complement pedagogical strategies and give students a more complete…

Efficient and equitable design of marine protected areas in Fiji through inclusion of stakeholder-specific objectives in conservation planning.

PubMed

Gurney, Georgina G; Pressey, Robert L; Ban, Natalie C; Álvarez-Romero, Jorge G; Jupiter, Stacy; Adams, Vanessa M

2015-10-01

The efficacy of protected areas varies, partly because socioeconomic factors are not sufficiently considered in planning and management. Although integrating socioeconomic factors into systematic conservation planning is increasingly advocated, research is needed to progress from recognition of these factors to incorporating them effectively in spatial prioritization of protected areas. We evaluated 2 key aspects of incorporating socioeconomic factors into spatial prioritization: treatment of socioeconomic factors as costs or objectives and treatment of stakeholders as a single group or multiple groups. Using as a case study the design of a system of no-take marine protected areas (MPAs) in Kubulau, Fiji, we assessed how these aspects affected the configuration of no-take MPAs in terms of trade-offs between biodiversity objectives, fisheries objectives, and equity in catch losses among fisher stakeholder groups. The achievement of fisheries objectives and equity tended to trade-off concavely with increasing biodiversity objectives, indicating that it is possible to achieve low to mid-range biodiversity objectives with relatively small losses to fisheries and equity. Importantly, the extent of trade-offs depended on the method used to incorporate socioeconomic data and was least severe when objectives were set for each fisher stakeholder group explicitly. We found that using different methods to incorporate socioeconomic factors that require similar data and expertise can result in plans with very different impacts on local stakeholders. © 2015 Society for Conservation Biology.

The 'right' size in nanobiotechnology.

PubMed

Whitesides, George M

2003-10-01

The biological and physical sciences share a common interest in small structures (the definition of 'small' depends on the application, but can range from 1 nm to 1 mm). A vigorous trade across the borders of these areas of science is developing around new materials and tools (largely from the physical sciences) and new phenomena (largely from the biological sciences). The physical sciences offer tools for synthesis and fabrication of devices for measuring the characteristics of cells and sub-cellular components, and of materials useful in cell and molecular biology; biology offers a window into the most sophisticated collection of functional nanostructures that exists.

Protocol Development for the NASA-JSC Lunar-Mars Life Support Test Project (LMLSTP) Phase 3 Project: A Report on Baseline Studies at KSC for Continuous Salad Production

NASA Technical Reports Server (NTRS)

Goins, G. D.; Yorio, N. C.; Vivenzio, H. R.

1998-01-01

The Phase 3 Lunar-Mars Life Support Test Project (LMLSTP) was conducted in a 20-foot chamber at Johnson Space Center. The overall objective of the Phase 3 project was to conduct a 90-day regenerative life support system test involving 4 human subjects to demonstrate an integrated biological and physicochemical life support system. A secondary objective of the Phase 3 LMLSTP was to demonstrate the ability to produce salad-type vegetable by integration of a small benchtop growth chamber located within the crew habitat area. This small chamber, commercially manufactured as the Controlled Environment Research Ecosystem (CERES 2010(TM)), functioned as a means to continuously provide fresh lettuce crops for crew members. The CERES 2010(TM) growth chamber utilized hardware components developed for effective plant biomass production in spaceflight applications. These components included: (1) LED lighting; (2) Astroculture(TM) Root Trays; and (3) Zeoponic media. In planning for the LMLSTP Phase 3, a request was put forward for KSC scientists to generate a protocol for successful continuous planting, culturing, and harvesting of the salad-crop, lettuce. By conducting baseline tests with components of the CERES 2010(TM), a protocol was developed.

Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Teacher's Guide.

ERIC Educational Resources Information Center

Alberta Environment, Edmonton. Environmental Education Resources Branch.

The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Student Manual.

ERIC Educational Resources Information Center

Alberta Environment, Edmonton. Environmental Education Resources Branch.

The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

Small object transporter. [Patent: for objects 0. 01 to 2. 00 mm dia

DOEpatents

Winkler, M.A.

1980-05-21

The disclosure relates to a small object transporter. Gas is passed through a conduit having a venturi. Small objects are picked up at a first location by a pickup tube in communication with the venturi and are forced out one end of the conduit at a desired second location.

LASER BIOLOGY AND MEDICINE: Optoacoustic laser monitoring of cooling and freezing of tissues

NASA Astrophysics Data System (ADS)

Larin, Kirill V.; Larina, I. V.; Motamedi, M.; Esenaliev, R. O.

2002-11-01

Real-time monitoring of cooling and freezing of tissues, cells, and other biological objects with a high spatial and time resolution, which is necessary for selective destruction of cancer and benign tumours during cryotherapy, as well as for preventing any damage to the structure and functioning of biological objects in cryobiology, is considered. The optoacoustic method, based on the measurement and analysis of acoustic waves induced by short laser pulses, is proposed for monitoring the cooling and freezing of the tissue. The effect of cooling and freezing on the amplitude and time profile of acoustic signals generated in real tissues and in a model object is studied. The experimental results indicate that the optoacoustic laser technique can be used for real-time monitoring of cooling and freezing of biological objects with a submillimeter spatial resolution and a high contrast.

Multi-energy method of digital radiography for imaging of biological objects

NASA Astrophysics Data System (ADS)

Ryzhikov, V. D.; Naydenov, S. V.; Opolonin, O. D.; Volkov, V. G.; Smith, C. F.

2016-03-01

This work has been dedicated to the search for a new possibility to use multi-energy digital radiography (MER) for medical applications. Our work has included both theoretical and experimental investigations of 2-energy (2E) and 3- energy (3D) radiography for imaging the structure of biological objects. Using special simulation methods and digital analysis based on the X-ray interaction energy dependence for each element of importance to medical applications in the X-ray range of energy up to 150 keV, we have implemented a quasi-linear approximation for the energy dependence of the X-ray linear mass absorption coefficient μm (E) that permits us to determine the intrinsic structure of the biological objects. Our measurements utilize multiple X-ray tube voltages (50, 100, and 150 kV) with Al and Cu filters of different thicknesses to achieve 3-energy X-ray examination of objects. By doing so, we are able to achieve significantly improved imaging quality of the structure of the subject biological objects. To reconstruct and visualize the final images, we use both two-dimensional (2D) and three-dimensional (3D) palettes of identification. The result is a 2E and/or 3E representation of the object with color coding of each pixel according to the data outputs. Following the experimental measurements and post-processing, we produce a 3D image of the biological object - in the case of our trials, fragments or parts of chicken and turkey.

Mid-level perceptual features distinguish objects of different real-world sizes.

PubMed

Long, Bria; Konkle, Talia; Cohen, Michael A; Alvarez, George A

2016-01-01

Understanding how perceptual and conceptual representations are connected is a fundamental goal of cognitive science. Here, we focus on a broad conceptual distinction that constrains how we interact with objects--real-world size. Although there appear to be clear perceptual correlates for basic-level categories (apples look like other apples, oranges look like other oranges), the perceptual correlates of broader categorical distinctions are largely unexplored, i.e., do small objects look like other small objects? Because there are many kinds of small objects (e.g., cups, keys), there may be no reliable perceptual features that distinguish them from big objects (e.g., cars, tables). Contrary to this intuition, we demonstrated that big and small objects have reliable perceptual differences that can be extracted by early stages of visual processing. In a series of visual search studies, participants found target objects faster when the distractor objects differed in real-world size. These results held when we broadly sampled big and small objects, when we controlled for low-level features and image statistics, and when we reduced objects to texforms--unrecognizable textures that loosely preserve an object's form. However, this effect was absent when we used more basic textures. These results demonstrate that big and small objects have reliably different mid-level perceptual features, and suggest that early perceptual information about broad-category membership may influence downstream object perception, recognition, and categorization processes. (c) 2015 APA, all rights reserved).

M1.3 - a small scaffold for DNA origami

NASA Astrophysics Data System (ADS)

Said, Hassan; Schüller, Verena J.; Eber, Fabian J.; Wege, Christina; Liedl, Tim; Richert, Clemens

2012-12-01

The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed ``M1.3'' as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed ``M1.3'' as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments. Electronic supplementary information (ESI) available: Materials, full sequence of M1.3, alternative restriction reactions, sequences and origami designs, ALEX data, estimated cost of producing M13, additional melting data for origami, and MALDI spectra of individual capped oligonucleotides. See DOI: 10.1039/c2nr32393a

Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution

DTIC Science & Technology

2010-09-30

1 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. Physical and Biological Controls of Copepod Aggregation...distribution. OBJECTIVES The objectives of this study are to • Elucidate the mechanisms of copepod aggregation in the Great South Channel, a...Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

Dark field differential dynamic microscopy enables accurate characterization of the roto-translational dynamics of bacteria and colloidal clusters

NASA Astrophysics Data System (ADS)

Cerbino, Roberto; Piotti, Davide; Buscaglia, Marco; Giavazzi, Fabio

2018-01-01

Micro- and nanoscale objects with anisotropic shape are key components of a variety of biological systems and inert complex materials, and represent fundamental building blocks of novel self-assembly strategies. The time scale of their thermal motion is set by their translational and rotational diffusion coefficients, whose measurement may become difficult for relatively large particles with small optical contrast. Here we show that dark field differential dynamic microscopy is the ideal tool for probing the roto-translational Brownian motion of anisotropic shaped particles. We demonstrate our approach by successful application to aqueous dispersions of non-motile bacteria and of colloidal aggregates of spherical particles.

Mining for Micropeptides.

PubMed

Makarewich, Catherine A; Olson, Eric N

2017-09-01

Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kant on biological teleology: Towards a two-level interpretation.

PubMed

Quarfood, Marcel

2006-12-01

According to Kant's Critique of the power of judgment, teleological considerations are unavoidable for conceptualizing organisms. Does this mean that teleology is more than merely heuristic? Kant stresses the regulative status of teleological attributions, but sometimes he seems to treat teleology as a constitutive condition for biology. To clarify this issue, the concept of natural purpose and its role for biology are examined. I suggest that the concept serves an identificatory function: it singles out objects as natural purposes, whereby the special science of biology is constituted. This relative constitutivity of teleology is explicated by means of a distinction of levels: on the object level of biological science, teleology is taken as constitutive, though it is merely regulative on the philosophical meta level. This distinction also concerns the place of Aristotelian teleology in Kant: on the object level, the Aristotelian view is accepted, whereas on the meta level, an agnostic stance is taken concerning teleology.

Antibody-enabled small-molecule drug discovery.

PubMed

Lawson, Alastair D G

2012-06-29

Although antibody-based therapeutics have become firmly established as medicines for serious diseases, the value of antibodies as tools in the early stages of small-molecule drug discovery is only beginning to be realized. In particular, antibodies may provide information to reduce risk in small-molecule drug discovery by enabling the validation of targets and by providing insights into the design of small-molecule screening assays. Moreover, antibodies can act as guides in the quest for small molecules that have the ability to modulate protein-protein interactions, which have traditionally only been considered to be tractable targets for biological drugs. The development of small molecules that have similar therapeutic effects to current biologics has the potential to benefit a broader range of patients at earlier stages of disease.

Popularity and user diversity of online objects

NASA Astrophysics Data System (ADS)

Wang, Jia-Hua; Guo, Qiang; Yang, Kai; Zhang, Yi-Lu; Han, Jingti; Liu, Jian-Guo

2016-11-01

The popularity has been widely used to describe the object property of online user-object bipartite networks regardless of the user characteristics. In this paper, we introduce a measurement namely user diversity to measure diversity of users who select or rate one type of objects by using the information entropy. We empirically calculate the user diversity of objects with specific degree for both MovieLens and Diggs data sets. The results indicate that more types of users select normal-degree objects than those who select large-degree and small-degree objects. Furthermore, small-degree objects are usually selected by large-degree users while large-degree objects are usually selected by small-degree users. Moreover, we define 15% objects of smallest degrees as unpopular objects and 10% ones of largest degrees as popular objects. The timestamp is introduced to help further analyze the evolution of user diversity of popular objects and unpopular objects. The dynamic analysis shows that as objects become popular gradually, they are more likely accepted by small-degree users but lose attention among the large-degree users.

Investigation of small solar system objects with the space telescope

NASA Technical Reports Server (NTRS)

Morrison, D.

1979-01-01

The application of the space telescope (ST) to study small objects in the solar system in order to understand the birth and the early evolution of the solar system is discussed. The upper size limit of the small bodies is defined as approximately 5000 km and includes planetary satellites, planetary rings, asteroids, and comets.The use of the astronomical instruments aboard the ST, such as the faint object camera, ultraviolet and infrared spectrometers, and spectrophotometers, to study the small solar system objects is discussed.

Bringing the Real World into the Biology Curriculum

ERIC Educational Resources Information Center

Lewis, Jenny

2006-01-01

This study followed a small but diverse group of biology teachers through the first two years of the pilot for a new Advanced Level Biology course--Salters-Nuffield Advanced Biology. SNAB aims to modernise A-level Biology using real world contexts and examples as the starting point, promoting conceptual understanding rather than factual recall,…

Consideration of Experimental Approaches in the Physical and Biological Sciences in Designing Long-Term Watershed Studies in Forested Landscapes

NASA Astrophysics Data System (ADS)

Stallard, R. F.

2011-12-01

The importance of biological processes in controlling weathering, erosion, stream-water composition, soil formation, and overall landscape development is generally accepted. The U.S. Geological Survey (USGS) Water, Energy, and Biogeochemical Budgets (WEBB) Project in eastern Puerto Rico and Panama and the Smithsonian Tropical Research Institute (STRI) Panama Canal Watershed Experiment (PCWE) are landscape-scale studies based in the humid tropics where the warm temperatures, moist conditions, and luxuriant vegetation promote especially rapid biological and chemical processes - photosynthesis, respiration, decay, and chemical weathering. In both studies features of small-watershed, large-watershed, and landscape-scale-biology experiments are blended to satisfy the research needs of the physical and biological sciences. The WEBB Project has successfully synthesized its first fifteen years of data, and has addressed the influence of land cover, geologic, topographic, and hydrologic variability, including huge storms on a wide range of hydrologic, physical, and biogeochemical processes. The ongoing PCWE should provide a similar synthesis of a moderate-sized humid tropical watershed. The PCWE and the Agua Salud Project (ASP) within the PCWE are now addressing the role of land cover (mature forests, pasture, invasive-grass dominated, secondary succession, native species plantation, and teak) at scales ranging from small watersheds to the whole Panama Canal watershed. Biologists have participated in the experimental design at both watershed scales, and small (0.1 ha) to large (50 ha) forest-dynamic plots have a central role in interfacing between physical scientists and biologists. In these plots, repeated, high-resolution mapping of all woody plants greater than 1-cm diameter provides a description of population changes through time presumably reflecting individual life histories, interactions with other organisms and the influence of landscape processes and climate, thereby bridging the research needs and conceptual scales of hydrologists and biogeochemists with those of biologists. Both experiments are embedded in larger data-collection networks: the WEBB within the hydrological and meteorological monitoring programs of the USGS and other federal agencies, and the PCWE in the long-term monitoring conducted by the Panama Canal Authority (ACP), its antecedents, and STRI. Examination of landscape-scale processes in a changing world requires the development of detailed landscape-scale data sets, including a formulation of reference states that can act as surrogate experimental controls. For example, the concept of a landscape steady state provides a convenient reference in which present-day observations can be interpreted. Extreme hydrological states must also be described, and both WEBB and PCWE have successfully examined the role of droughts and large storms and their impact on geomorphology, biogeochemistry, and biology. These experiments also have provided platforms for research endeavors never contemplated in the original objectives, a testament to the importance of developing approaches that consider the needs of physical and biological sciences.

A system and methodology for high-content visual screening of individual intact living cells in suspension

NASA Astrophysics Data System (ADS)

Renaud, Olivier; Heintzmann, Rainer; Sáez-Cirión, Asier; Schnelle, Thomas; Mueller, Torsten; Shorte, Spencer

2007-02-01

Three dimensional imaging provides high-content information from living intact biology, and can serve as a visual screening cue. In the case of single cell imaging the current state of the art uses so-called "axial through-stacking". However, three-dimensional axial through-stacking requires that the object (i.e. a living cell) be adherently stabilized on an optically transparent surface, usually glass; evidently precluding use of cells in suspension. Aiming to overcome this limitation we present here the utility of dielectric field trapping of single cells in three-dimensional electrode cages. Our approach allows gentle and precise spatial orientation and vectored rotation of living, non-adherent cells in fluid suspension. Using various modes of widefield, and confocal microscope imaging we show how so-called "microrotation" can provide a unique and powerful method for multiple point-of-view (three-dimensional) interrogation of intact living biological micro-objects (e.g. single-cells, cell aggregates, and embryos). Further, we show how visual screening by micro-rotation imaging can be combined with micro-fluidic sorting, allowing selection of rare phenotype targets from small populations of cells in suspension, and subsequent one-step single cell cloning (with high-viability). Our methodology combining high-content 3D visual screening with one-step single cell cloning, will impact diverse paradigms, for example cytological and cytogenetic analysis on haematopoietic stem cells, blood cells including lymphocytes, and cancer cells.

Optimal fire histories for biodiversity conservation.

PubMed

Kelly, Luke T; Bennett, Andrew F; Clarke, Michael F; McCarthy, Michael A

2015-04-01

Fire is used as a management tool for biodiversity conservation worldwide. A common objective is to avoid population extinctions due to inappropriate fire regimes. However, in many ecosystems, it is unclear what mix of fire histories will achieve this goal. We determined the optimal fire history of a given area for biological conservation with a method that links tools from 3 fields of research: species distribution modeling, composite indices of biodiversity, and decision science. We based our case study on extensive field surveys of birds, reptiles, and mammals in fire-prone semi-arid Australia. First, we developed statistical models of species' responses to fire history. Second, we determined the optimal allocation of successional states in a given area, based on the geometric mean of species relative abundance. Finally, we showed how conservation targets based on this index can be incorporated into a decision-making framework for fire management. Pyrodiversity per se did not necessarily promote vertebrate biodiversity. Maximizing pyrodiversity by having an even allocation of successional states did not maximize the geometric mean abundance of bird species. Older vegetation was disproportionately important for the conservation of birds, reptiles, and small mammals. Because our method defines fire management objectives based on the habitat requirements of multiple species in the community, it could be used widely to maximize biodiversity in fire-prone ecosystems. © 2014 Society for Conservation Biology.

Small Molecule Signaling Agents: The Integrated Chemistry and Biochemistry of Nitrogen Oxides, Oxides of Carbon, Dioxygen, Hydrogen Sulfide, and Their Derived Species

PubMed Central

Fukuto, Jon M.; Carrington, Samantha J.; Tantillo, Dean J.; Harrison, Jason G.; Ignarro, Louis J.; Freeman, Bruce A.; Chen, Andrew; Wink, David A.

2014-01-01

Several small molecule species formally known primarily as toxic gases have, over the past 20 years, been shown to be endogenously generated signaling molecules. The biological signaling associated with the small molecules NO, CO, H2S (and the nonendogenously generated O2), and their derived species have become a topic of extreme interest. It has become increasingly clear that these small molecule signaling agents form an integrated signaling web that affects/regulates numerous physiological processes. The chemical interactions between these species and each other or biological targets is an important factor in their roles as signaling agents. Thus, a fundamental understanding of the chemistry of these molecules is essential to understanding their biological/physiological utility. This review focuses on this chemistry and attempts to establish the chemical basis for their signaling functions. PMID:22263838

Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution

DTIC Science & Technology

2011-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Physical and Biological Controls of Copepod Aggregation and...DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution...OBJECTIVES The objectives of this study are to: • Elucidate the mechanisms of copepod aggregation in the Great South Channel, a major

Equal-magnitude size-weight illusions experienced within and between object categories.

PubMed

Buckingham, Gavin; Goodale, Melvyn A; White, Justin A; Westwood, David A

2016-01-01

In the size-weight illusion (SWI), small objects feel heavier than larger objects of the same mass. This effect is typically thought to be a consequence of the lifter's expectation that the large object will outweigh the small object, because objects of the same type typically get heavier as they get larger. Here, we show that this perceptual effect can occur across object category, where there are no strong expectations about the correspondence between size and mass. One group of participants lifted same-colored large and small cubes with the same mass as one another, while another group lifted differently-colored large and small cubes with the same mass as one another. The group who lifted the same-colored cubes experienced a robust SWI and initially lifted the large object with more force than the small object. By contrast, the group who lifted the different-colored objects did so with equal initial forces on the first trial, but experienced just as strong an illusion as those who lifted the same-colored objects. These results demonstrate that color cues can selectively influence the application of fingertip force rates while not impacting at all upon the lifter's perception of object weight, highlighting a stark dissociation in how prior information affects perception and action.

Small-Molecule “BRCA1-Mimetics” Are Antagonists of Estrogen Receptor-α

PubMed Central

Ma, Yongxian; Tomita, York; Preet, Anju; Clarke, Robert; Englund, Erikah; Grindrod, Scott; Nathan, Shyam; De Oliveira, Eliseu; Brown, Milton L.

2014-01-01

Context: Resistance to conventional antiestrogens is a major cause of treatment failure and, ultimately, death in breast cancer. Objective: The objective of the study was to identify small-molecule estrogen receptor (ER)-α antagonists that work differently from tamoxifen and other selective estrogen receptor modulators. Design: Based on in silico screening of a pharmacophore database using a computed model of the BRCA1-ER-α complex (with ER-α liganded to 17β-estradiol), we identified a candidate group of small-molecule compounds predicted to bind to a BRCA1-binding interface separate from the ligand-binding pocket and the coactivator binding site of ER-α. Among 40 candidate compounds, six inhibited estradiol-stimulated ER-α activity by at least 50% in breast carcinoma cells, with IC50 values ranging between 3 and 50 μM. These ER-α inhibitory compounds were further studied by molecular and cell biological techniques. Results: The compounds strongly inhibited ER-α activity at concentrations that yielded little or no nonspecific toxicity, but they produced only a modest inhibition of progesterone receptor activity. Importantly, the compounds blocked proliferation and inhibited ER-α activity about equally well in antiestrogen-sensitive and antiestrogen-resistant breast cancer cells. Representative compounds disrupted the interaction of BRCA1 and ER-α in the cultured cells and blocked the interaction of ER-α with the estrogen response element. However, the compounds had no effect on the total cellular ER-α levels. Conclusions: These findings suggest that we have identified a new class of ER-α antagonists that work differently from conventional antiestrogens (eg, tamoxifen and fulvestrant). PMID:25264941

Secondary school biology teaching, 1983--2004: Objectives as stated in periodical literature

NASA Astrophysics Data System (ADS)

Russell, James W., Sr.

Purpose of the study. The major purpose of this study was to identify and to classify objectives for teaching biology in secondary school in the United States during the period 1983-2004. These objectives were identified by objective statements in articles from selected professional periodicals. Procedure. The 1983-2004 period was divided into four subperiods on the basis of major historical events. Selected professional periodicals were searched for statements of objectives of secondary school biology teaching. These statements were catalogued into Knowledge, Process, Product, Attitude and Interest, or Cultural Awareness categories. The resulting data were classified within and across the four subperiods according to frequency of occurrence, category, authorship, and year. Findings. The major findings of this investigation included the following: (1) Authorships in Higher Education produced the most articles and the most statements in each subperiod. Miscellaneous authors produced the least articles and statements. (2) Statements in the Attitude and Interest category were the most frequent in the four subperiods. (3) The "most important" objectives for secondary school biology teaching were Presents major facts, principles, or fundamentals (from the Knowledge category), Expresses scientific attitudes and appreciation, Identifies the nature of science and scientists, and Identifies scientific interest and career development (from the Attitude and Interest category), and Develops scientific method of thinking (from the Process category). Conclusions. Based on the findings of this investigation, the following conclusions were made: (1) The objectives for teaching secondary school biology were influenced by historical events, especially the publication of A Nation at Risk: The Imperative for Educational Reform in 1983, America 2000 in 1988, Goals 2000 in 1994, No Child Left Behind in 2000. The rapid growth and expansion of technology and the World Wide Web during the time span of the study also influenced the number of objectives. (2) Authors in Higher Education wrote more articles about the objectives for the teaching of secondary school biology than those in Secondary Education or other categories. This was probably a reflection of the "publish or perish" environment in many colleges and universities.

[Comprehension of emotions accompanied by everyday actions: comparison of biological-motion pictures with real-person pictures].

PubMed

Higashiyama, Atsuki; Imoto, Hisato; Tsuinashi, Seiichi

2005-12-01

Forty participants viewed and interpreted videotapes that were composed of displays representing different human actions (e.g., running and washing hands) and emotions (pleasant, neutral, and unpleasant). Half the videotapes were usual movies of real persons and the other videotapes were biological motions as produced by 22 light points on a human body in otherwise total darkness. In each display, an expert or a novice played a series of large or small body actions under each emotion. We found that (1) pleasant-unpleasant feeling was well discriminated in the real-person displays and in the biological motion display of large body actions, but it was less discriminated in the biological-motion displays of small body actions, (2) actions by experts were rated to be pleasant, and (3) actions were successfully identified for the real displays of large actions by experts, but they were poorly identified for the biological-motion displays of small body actions by novices. These results suggested that the observers correctly judged the emotion of players that was represented through suitable actions.

Minireview: The Roles of Small RNA Pathways in Reproductive Medicine

PubMed Central

Buchold, Gregory M.

2011-01-01

The discovery of small noncoding RNA, including P-element-induced wimpy testis-interacting RNA, small interfering RNA, and microRNA, has energized research in reproductive medicine. In the two decades since the identification of small RNA, first in Caenorhabditis elegans and then in other animals, scientists in many disciplines have made significant progress in elucidating their biology. A powerful battery of tools, including knockout mice and small RNA mimics and antagonists, has facilitated investigation into the functional roles and therapeutic potential of these small RNA pathways. Current data indicate that small RNA play significant roles in normal development and physiology and pathological conditions of the reproductive tracts of females and males. Biologically plausible mRNA targets for these microRNA are aggressively being discovered. The next phase of research will focus on elucidating the clinical utility of small RNA-selective agonists and antagonists. PMID:21546411

Using GEO Optical Observations to Infer Orbit Populations

NASA Technical Reports Server (NTRS)

Matney, Mark; Africano, John

2002-01-01

NASA's Orbital Debris measurements program has a goal to characterize the small debris environment in the geosynchronous Earth-orbit (GEO) region using optical telescopes ("small" refers to objects too small to catalog and track with current systems). Traditionally, observations of GEO and near-GEO objects involve following the object with the telescope long enough to obtain an orbit. When observing very dim objects with small field-of-view telescopes, though, the observations are generally too short to obtain accurate orbital elements. However, it is possible to use such observations to statistically characterize the small object environment. A telescope pointed at a particular spot could potentially see objects in a number of different orbits. Inevitably, when looking at one region for certain types of orbits, there are objects in other types of orbits that cannot be seen. Observation campaigns are designed with these limitations in mind and are set up to span a number of regions of the sky, making it possible to sample all potential orbits under consideration. Each orbit is not seen with the same probability, however, so there are observation biases intrinsic to any observation campaign. Fortunately, it is possible to remove such biases and reconstruct a meaningful estimate of the statistical orbit populations of small objects in GEO. This information, in turn, can be used to investigate the nature of debris sources and to characterize the risk to GEO spacecraft. This paper describes these statistical tools and presents estimates of small object GEO populations.

A knowledge discovery object model API for Java

PubMed Central

Zuyderduyn, Scott D; Jones, Steven JM

2003-01-01

Background Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at . PMID:14583100

Discovery of novel small molecule inhibitors of cardiac hypertrophy using high throughput, high content imaging

PubMed Central

Reid, Brian G.; Stratton, Matthew S.; Bowers, Samantha; Cavasin, Maria A.; Demos-Davies, Kimberley M.; Susano, Isidro; McKinsey, Timothy A.

2016-01-01

Chronic cardiac hypertrophy is maladaptive and contributes to the pathogenesis of heart failure. The objective of this study was to identify small molecule inhibitors of pathological cardiomyocyte hypertrophy. High content screening was performed with primary neonatal rat ventricular myocytes (NRVMs) cultured on 96-well plates and treated with a library of 3241 distinct small molecules. Non-toxic hit compounds that blocked hypertrophy in response to phenylephrine (PE) and phorbol myristate acetate (PMA) were identified based on their ability to reduce cell size and inhibit expression of atrial natriuretic factor (ANF), which is a biomarker of pathological cardiac hypertrophy. Many of the hit compounds are existing drugs that have not previously been evaluated for benefit in the setting of cardiovascular disease. One such compound, the anti-malarial drug artesunate, blocked left ventricular hypertrophy (LVH) and improved cardiac function in adult mice subjected to transverse aortic constriction (TAC). These findings demonstrate that phenotypic screening with primary cardiomyocytes can be used to discover anti-hypertrophic lead compounds for heart failure drug discovery. Using annotated libraries of compounds with known selectivity profiles, this screening methodology also facilitates chemical biological dissection of signaling networks that control pathological growth of the heart. PMID:27130278

Did A Galactic Gamma-Ray Burst Kill the Dinosaurs?

NASA Astrophysics Data System (ADS)

Brecher, K.

1997-12-01

Gamma-ray bursts now appear to be primarily of extragalactic origin. Statistically, assuming isotropic emission, the observed event rates and fluxes imply that one event occurs per 10(4) \\ - 10(6) \\ years per galaxy, with about 10(51) \\ - 10(53) \\ ergs in gamma-rays emitted per event. Unless the Milky Way is unusual, a gamma-ray burst should occur within 10(2) \\ - 10(3) \\ pc of the Sun in a time span of order 10(8) \\ years. Independent of the underlying cause of the event, it would irradiate the solar system with a brief flash of MeV gamma-rays with a fluence as large as 10(9) - 10(11) \\ erg cm(-2) . What is the effect of such an event on the Earth and objects nearby? Ruderman (\\underbar{Science}, 184, 1079, 1974) and subsequent authors have considered a number of effects of a flash of gamma-rays from a nearby supernova explosion on the Earth's atmosphere, and on its biota. However, with regard to the demise of the dinosaurs, it appears that there was a marked increase in the deposition rate of the rare earth iridium coincident with their extinction. For this reason, an asteroid-Earth impact has been considered the leading contender for the death of the dinosaurs. Here we consider a new mechanism for mass biological extinctions, caused by small comets nudged into the inner solar system by nearby gamma-ray bursts. If comets populate the Oort cloud with a wide distribution of masses, radii and orbital eccentricities, we find that small (< 1 km), low density (10(-2) \\ gm cm(-3) ) objects in highly eccentric orbits can be injected into the inner solar system by a nearby gamma-ray burst. For a relatively brief period of time, the near Earth comet population would increase dramatically. The consequent increased probability of comet-Earth impacts of appropriate energy and material content could account for many of the characteristics of the Cretaceous-Tertiary or other terrestrial mass biological extinctions.

Real-time bio-sensors for enhanced C2ISR operator performance

NASA Astrophysics Data System (ADS)

Miller, James C.

2005-05-01

The objectives of two Air Force Small Business research topics were to develop a real-time, unobtrusive, biological sensing and monitoring technology for evaluating cognitive readiness in command and control environments (i.e., console operators). We sought an individualized status monitoring system for command and control operators and teams. The system was to consist of a collection of bio-sensing technologies and processing and feedback algorithms that could eventually guide the effective incorporation of fatigue-adaptive workload interventions into weapon systems to mitigate episodes of cognitive overload and lapses in operator attention that often result in missed signals and catastrophic failures. Contractors set about determining what electro-physiological and other indicators of compromised operator states are most amenable for unobtrusive monitoring of psychophysiological and warfighter performance data. They proposed multi-sensor platforms of bio-sensing technologies for development. The sensors will be continuously-wearable or off-body and will not require complicated or uncomfortable preparation. A general overview of the proposed approaches and of progress toward the objective is presented.

Optical tweezers for the measurement of binding forces: system description and application for the study of E. coli adhesion

NASA Astrophysics Data System (ADS)

Fallman, Erik G.; Schedin, Staffan; Andersson, Magnus J.; Jass, Jana; Axner, Ove

2003-06-01

Optical tweezers together with a position sensitive detection system allows measurements of forces in the pN range between micro-sized biological objects. A prototype force measurement system has been constructed around in inverted microscope with an argon-ion pumped Ti:sapphire laser as light source for optical trapping. A trapped particle in the focus of the high numerical aperture microscope-objective behaves like an omni-directional mechanical spring if an external force displaces it. The displacement from the equilibrium position is a measure of the exerted force. For position detection of the trapped particle (polystyrene beads), a He-Ne laser beam is focused a small distance below the trapping focus. An image of the bead appears as a distinct spot in the far field, monitored by a photosensitive detector. The position data is converted to a force measurement by a calibration procedure. The system has been used for measuring the binding forces between E-coli bacterial adhesin and their receptor sugars.

Control of fluxes in metabolic networks.

PubMed

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-07-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. © 2016 Basler et al.; Published by Cold Spring Harbor Laboratory Press.

Two-Photon Excitation in Biological Material for Conventional and Long Working-Distance Objectives.

NASA Astrophysics Data System (ADS)

Keeler, W. J.; McGhee, P.

2000-03-01

The application of laser two-photon excitation or nonlinear second-harmonic generation to imaging, spectroscopy, and light activated medical therapies, is an expanding field of research. When small feature sizes such as cells and their components are to be studied, high numerical aperture (NA) lenses are required to obtain the necessary lateral and axial resolutions. If one wishes to increase the depth of sample penetration, factors such as scattering and absorption quickly degrade the quality of the focused beam. The problem is further exacerbated by the short working distance of conventional high NA microscope objectives if they are used for light delivery and pickup. These lenses and their accompanying eyepieces, are designed to produce an exit pupil that can be accomodated by the human eye. Such a design will underfil detectors such as large CCD arrays. To simultaneously increase the working distance at the sample and the system exit pupil, larger scale objectives can be used. We will report the results of two-photon excitation and fluorescence investigations of several feature sizes as a function of penetration depth in homogeneous media and tissue samples, for conventional and long working distance objectives. The possible implications of these results to imaging and therapeutic dose delivery will also be presented.

Electric field tomography for contactless imaging of resistivity in biomedical applications.

PubMed

Korjenevsky, A V

2004-02-01

The technique of contactless imaging of resistivity distribution inside conductive objects, which can be applied in medical diagnostics, has been suggested and analyzed. The method exploits the interaction of a high-frequency electric field with a conductive medium. Unlike electrical impedance tomography, no electric current is injected into the medium from outside. The interaction is accompanied with excitation of high-frequency currents and redistribution of free charges inside the medium leading to strong and irregular perturbation of the field's magnitude outside and inside the object. Along with this the considered interaction also leads to small and regular phase shifts of the field in the area surrounding the object. Measuring these phase shifts using a set of electrodes placed around the object enables us to reconstruct the internal structure of the medium. The basics of this technique, which we name electric field tomography (EFT), are described, simple analytical estimations are made and requirements for measuring equipment are formulated. The realizability of the technique is verified by numerical simulations based on the finite elements method. Results of simulation have confirmed initial estimations and show that in the case of EFT even a comparatively simple filtered backprojection algorithm can be used for reconstructing the static resistivity distribution in biological tissues.

[Bio-objects and biological methods of space radiation effects evaluation].

PubMed

Kaminskaia, E V; Nevzgodina, L V; Platova, N G

2009-01-01

The unique conditions of space experiments place austere requirements to bio-objects and biological methods of radiation effects evaluation. The paper discusses suitability of a number of bio-objects varying in stage of evolution and metabolism for space researches aimed to state common patterns of the radiation damage caused by heavy ions (HI), and character of HI-cell interaction. Physical detectors in space experiments of the BIOBLOCK series make it possible to identify bio-objects hit by space HI and to set correlation between HI track topography and biological effect. The paper provides an all-round description of the bio-objects chosen for two BIOBLOCK experiments (population of hydrophyte Wolffia arrhiza (fam. duckweed) and Lactuca sativa seeds) and the method of evaluating effects from single space radiation HI. Direct effects of heavy ions on cells can be determined by the criteria of chromosomal aberrations and delayed morphologic abnormalities. The evaluation results are compared with the data about human blood lymphocytes. Consideration is being given to the procedures of test-objects' treatment and investigation.

Biological organization of the extraocular muscles.

PubMed

Spencer, Robert F; Porter, John D

2006-01-01

Extraocular muscle is fundamentally distinct from other skeletal muscles. Here, we review the biological organization of the extraocular muscles with the intent of understanding this novel muscle group in the context of oculomotor system function. The specific objectives of this review are threefold. The first objective is to understand the anatomic arrangement of the extraocular muscles and their compartmental or layered organization in the context of a new concept of orbital mechanics, the active pulley hypothesis. The second objective is to present an integrated view of the morphologic, cellular, and molecular differences between extraocular and the more traditional skeletal muscles. The third objective is to relate recent data from functional and molecular biology studies to the established extraocular muscle fiber types. Developmental mechanisms that may be responsible for the divergence of the eye muscles from a skeletal muscle prototype also are considered. Taken together, a multidisciplinary understanding of extraocular muscle biology in health and disease provides insights into oculomotor system function and malfunction. Moreover, because the eye muscles are selectively involved or spared in a variety of neuromuscular diseases, knowledge of their biology may improve current pathogenic models of and treatments for devastating systemic diseases.

Opportunities for Merging Chemical and Biological Synthesis

PubMed Central

Wallace, Stephen; Balskus, Emily P.

2014-01-01

Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecule production. We highlight recent advances in combining enzymatic and non-enzymatic catalysis in vitro, discuss the application of design principles from organic chemistry for engineering non-biological reactivity into enzymes, and describe the development of biocompatible chemistry that can be interfaced with microbial metabolism. PMID:24747284

Nuclear Magnetic Resonance Spectroscopy Applications: Proton NMR In Biological Objects Subjected To Magic Angle Spinning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wind, Robert A.; Hu, Jian Zhi

2005-01-01

Proton NMR in Biological Objects Submitted to Magic Angle Spinning, In Encyclopedia of Analytical Science, Second Edition (Paul J. Worsfold, Alan Townshend and Colin F. Poole, eds.), Elsevier, Oxford 6:333-342. Published January 1, 2005. Proposal Number 10896.

A plea for a global natural history collection - online

USDA-ARS?s Scientific Manuscript database

Species are the currency of comparative biology: scientists from many biological disciplines, including community ecology, conservation biology, pest management, and biological control rely on scientifically sound, objective species data. However, large-scale species identifications are often not fe...

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

ABRF-MARG RESEARCH STUDY: EVALUATION OF SMALL SAMPLE NUCLEIC ACID AMPLIFICATION TECHNOLOGIES FOR GENE EXPRESSION PROFILING

EPA Science Inventory

Microarrays have had a significant impact on many areas of biology. However, there are still many fertile research areas that would benefit from microarray analysis but are limited by the amount of biological material that can be obtained (e.g. samples obtained by small biopsy, f...

Students' Knowledge Construction in Small Groups in the Seventh Grade Biology Laboratory: Verbal Communication and Physical Engagement.

ERIC Educational Resources Information Center

She, Hsiao-Ching

1999-01-01

Reports on a study of seventh-grade students' interactions in small groups during a biology laboratory activity. Finds that girls have the potential to perform equally as well as do boys in the science laboratory and that both individual and gender differences contribute to students' differential verbal communication and laboratory engagement.…

A new species of Gadirtha Walker (Nolidae: Collomeninae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States

USDA-ARS?s Scientific Manuscript database

Gadirtha fusca, new species, is described from Hong Kong. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker. Species is a possible biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the ...

Applications of optical manipulation in plant biology

NASA Astrophysics Data System (ADS)

Buer, Charles S.

Measuring small forces in biology is important for determining basic physiological parameters of a cell. The plant cell wall provides a primary defense and presents a barrier to research. Magnitudes of small forces are impossible to measure with mechanical transducers, glass needles, atomic force microscopy, or micropipet-based force transduction due to the cell wall. Therefore, a noninvasive method of breaching the plant cell wall to access the symplastic region of the cell is required. Laser light provides sub-micrometer positioning, particle manipulation without mechanical contact, and piconewton force determination. Consequently, the extension of laser microsurgery to expand an experimental tool for plant biology encompassed the overall objective. A protocol was developed for precisely inserting microscopic objects into the periplasmic region of plant callus cells using laser microsurgery. Ginkgo biloba and Agrobacterium rhizogenes were used as the model system for developing the optical tweezers and scalpel techniques. Better than 95% survival was achieved after plasmolyzing G. biloba cells, ablating a 2-4 μm hole through the cell wall using a pulsed UV laser beam, trapping and manipulating bacteria into the periplasmic region, and deplasmolyzing the cells. Optical trapping experiments implied a difference existed between the bacteria models. Determining the optical trapping efficiency of Agrobacterium rhizogenes and A. tumefaciens strains indicated the A. rhizogenes strain, ATCC 11325, was significantly less efficiently trapped than strains A4 and ATCC 15834 and the A. tumefaciens strain LBA4404. Differences were also found in capsule generation, growth media viscosity, and transmission electron microscopy negative staining implying that a difference in surface structure exists. Calcofluor fluorescence suggests the difference involves an exopolysaccharide. Callus cell plasmolysis revealed Hechtian strands interconnecting the plasma membrane and the cell wall. The spring tension of these strands was measured in normal and cold-hardened G. biloba and N. tabacum callus cells. There was little change in flexibility between the groups of cultured cells in either species studied. Microspheres were attached to Hechtian strands in normal cultured Nicotiana tabacum and the cells were deplasmolyzed and replasmolyzed to determine the fate of Hechtian strands. The microspheres either moved to the plasma membrane and adhered or moved to the cell wall and adhered. The attached microspheres occasionally moved independently on the same strand. Inserted microspheres provided a visual probe to follow physiological events within a plant cell.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

Towards Routine Uncued Surveillance of Small Objects at and near Geostationary Orbit with Small Telescopes

NASA Astrophysics Data System (ADS)

Zimmer, P.; McGraw, J. T.; Ackermann, M. R.

There is considerable interest in the capability to discover and monitor small objects (d 20cm) in geosynchronous (GEO) and near-GEO orbital regimes using small, ground-based optical telescopes (D < 0.5m). The threat of such objects is clear. Small telescopes have an unrivaled cost advantage and, under ideal lighting and sky conditions, have the capability of detecting faint objects. This combination of conditions, however, is relatively rare, making routine and persistent surveillance more challenging. In a truly geostationary orbit, a small object is easy to detect because its apparent rate of motion is nearly zero for a ground-based observer, and signal accumulation occurs as it would for more traditional sidereal-tracked astronomical observations. In this regime, though, small objects are not expected to be in controlled or predictable orbits, thus a range of inclinations and eccentricities is possible. This results in a range of apparent angular rates and directions that must be surveilled. This firmly establishes this task as uncued or blind surveillance. Detections in this case are subject to what is commonly called “trailing loss,” where the signal from the object does not accumulate in a fixed detection element, resulting in far lower sensitivity than for a similar object optimally tracked. We review some of the limits of detecting these objects under less than ideal observing conditions, subject further to the current limitations based on technological and operational realities. We demonstrate progress towards this goal using telescopes much smaller than normally considered viable for this task using novel detection and analysis techniques.

A structural biology perspective on bioactive small molecules and their plant targets.

PubMed

Kumari, Selva; van der Hoorn, Renier A L

2011-10-01

Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Acoustic detection of absorption of millimeter-band electromagnetic waves in biological objects].

PubMed

Polnikov, I G; Putvinskiĭ, A V

1988-01-01

Principles of photoacoustic spectroscopy were applied to elaborate a new method for controlling millimeter electromagnetic waves absorption in biological objects. The method was used in investigations of frequency dependence of millimeter wave power absorption in vitro and in vivo in the commonly used experimental irradiation systems.

Laser desorption/ionization mass spectrometry for direct profiling and imaging of small molecules from raw biological materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cha, Sangwon

2008-01-01

Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternativemore » assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for the first time by graphite-assisted LDI(GALDI) IMS.« less

Zero curvature-surface driven small objects

NASA Astrophysics Data System (ADS)

Dou, Xiaoxiao; Li, Shanpeng; Liu, Jianlin

2017-08-01

In this study, we investigate the spontaneous migration of small objects driven by surface tension on a catenoid, formed by a layer of soap constrained by two rings. Although the average curvature of the catenoid is zero at each point, the small objects always migrate to the position near the ring. The force and energy analyses have been performed to uncover the mechanism, and it is found that the small objects distort the local shape of the liquid film, thus making the whole system energetically favorable. These findings provide some inspiration to design microfluidics, aquatic robotics, and miniature boats.

Challenges and opportunities in absorption, distribution, metabolism, and excretion studies of therapeutic biologics.

PubMed

Xu, Xin; Vugmeyster, Yulia

2012-12-01

With the advancement of biotechnology in the last two decades, optimized and novel modalities and platforms of biologic moieties have emerged rapidly in drug discovery pipelines. In addition, new technologies for delivering therapeutic biologics (e.g., needle-free devices, nanoparticle complexes), as well as novel approaches for disease treatments (e.g., stem cell therapy, individualized medicine), continue to be developed. While pharmacokinetic studies are routinely carried out for therapeutic biologics, experiments that elucidate underlying mechanisms for clearance and biodistribution or identify key factors that govern absorption, distribution, metabolism, and excretion (ADME) of biologics often are not thoroughly conducted. Realizing the importance of biologics as therapeutic agents, pharmaceutical industry has recently begun to move the research focus from small molecules only to a blended portfolio consisting of both small molecules and biologics. This trend brings many opportunities for scientists working in the drug disposition research field. In anticipation of these opportunities and associated challenges, this review highlights impact of ADME studies on clinical and commercial success of biologics, with a particular focus on emerging applications and technologies and linkage with mechanistic pharmacokinetic/pharmacodynamic modeling and biomarker research.

Rapid Evaluation of Platelet Function With T2 Magnetic Resonance

PubMed Central

Cuker, Adam; Husseinzadeh, Holleh; Lebedeva, Tatiana; Marturano, Joseph E.; Massefski, Walter; Lowery, Thomas J.; Lambert, Michele P.; Abrams, Charles S.; Weisel, John W.

2016-01-01

Objectives: The clinical diagnosis of qualitative platelet disorders (QPDs) based on light transmission aggregometry (LTA) requires significant blood volume, time, and expertise, all of which can be barriers to utilization in some populations and settings. Our objective was to develop a more rapid assay of platelet function by measuring platelet-mediated clot contraction in small volumes (35 µL) of whole blood using T2 magnetic resonance (T2MR). Methods: We established normal ranges for platelet-mediated clot contraction using T2MR, used these ranges to study patients with known platelet dysfunction, and then evaluated agreement between T2MR and LTA with arachidonic acid, adenosine diphosphate, epinephrine, and thrombin receptor activator peptide. Results: Blood from 21 healthy donors was studied. T2MR showed 100% agreement with LTA with each of the four agonists and their cognate inhibitors tested. T2MR successfully detected abnormalities in each of seven patients with known QPDs, with the exception of one patient with a novel mutation leading to Hermansky-Pudlak syndrome. T2MR appeared to detect platelet function at similar or lower platelet counts than LTA. Conclusions: T2MR may provide a clinically useful approach to diagnose QPDs using small volumes of whole blood, while also providing new insight into platelet biology not evident using plasma-based platelet aggregation tests. PMID:28028118

Noninvasive in situ observation of the crystallization kinetics of biological macromolecules by confocal laser scanning microscopy.

PubMed

Mühlig, P; Klupsch, Th; Kaulmann, U; Hilgenfeld, R

2003-04-01

High-resolution confocal laser scanning microscopy (CLSM) is a powerful tool for in situ observation and analysis of protein crystal growth kinetics. Because the resolution of CLSM is not diffraction-limited by the object, it is possible to visualize, under certain conditions, objects in molecular dimensions. A modified batch technique is applied which allows the growth kinetics of sufficiently small crystallites fixed at the lower side of a cover glass, within a hanging drop, to be studied in reflected light near the total reflection angle. A gap, or cavity, filled with solution is formed between the cover glass and the upper crystal face, which acts to fix small crystallites by hydrodynamic friction forces. The cavity height enables the propagation of molecular steps across the upper crystal face without constraint, so that the propagation velocity and geometrical parameters can be measured by CLSM. The layer growth kinetics of monoclinic crystallites of a long-acting insulin derivative (Insulin Glargine) is investigated. For a twofold supersaturation of the solution, the growth is governed by 2D nucleation at the edges of the crystallites followed by a spreading of molecular steps. The layer growth kinetics are well fitted by the simple cubic kinetic lattice model. We find that only about one of a thousand solute (protein) molecules which push a kink place due to their Brownian motion becomes really incorporated into the growing crystal.

Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

PubMed Central

2005-01-01

The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of Gagne's Conditions of Learning instructional design theory. This theory, although first published in the early 1970s, is still fundamental in instructional design and instructional technology. First, top-level as well as prerequisite learning objectives for a microarray analysis workshop and a primer design workshop were defined. Then a hierarchy of objectives for each workshop was created. Hands-on tutorials were designed to meet these objectives. Finally, events of learning proposed by Gagne's theory were incorporated into the hands-on tutorials. The resultant manuals were tested on a small number of trainees, revised, and applied in 1-day bioinformatics workshops. Based on this experience and on observations made during the workshops, we conclude that Gagne's Conditions of Learning instructional design theory provides a useful framework for developing bioinformatics training, but may not be optimal as a method for teaching it. PMID:16220141

Biomarkers for Alzheimer's disease: academic, industry and regulatory perspectives.

PubMed

Hampel, Harald; Frank, Richard; Broich, Karl; Teipel, Stefan J; Katz, Russell G; Hardy, John; Herholz, Karl; Bokde, Arun L W; Jessen, Frank; Hoessler, Yvonne C; Sanhai, Wendy R; Zetterberg, Henrik; Woodcock, Janet; Blennow, Kaj

2010-07-01

Advances in therapeutic strategies for Alzheimer's disease that lead to even small delays in onset and progression of the condition would significantly reduce the global burden of the disease. To effectively test compounds for Alzheimer's disease and bring therapy to individuals as early as possible there is an urgent need for collaboration between academic institutions, industry and regulatory organizations for the establishment of standards and networks for the identification and qualification of biological marker candidates. Biomarkers are needed to monitor drug safety, to identify individuals who are most likely to respond to specific treatments, to stratify presymptomatic patients and to quantify the benefits of treatments. Biomarkers that achieve these characteristics should enable objective business decisions in portfolio management and facilitate regulatory approval of new therapies.

Pulse-coupled neural network implementation in FPGA

NASA Astrophysics Data System (ADS)

Waldemark, Joakim T. A.; Lindblad, Thomas; Lindsey, Clark S.; Waldemark, Karina E.; Oberg, Johnny; Millberg, Mikael

1998-03-01

Pulse Coupled Neural Networks (PCNN) are biologically inspired neural networks, mainly based on studies of the visual cortex of small mammals. The PCNN is very well suited as a pre- processor for image processing, particularly in connection with object isolation, edge detection and segmentation. Several implementations of PCNN on von Neumann computers, as well as on special parallel processing hardware devices (e.g. SIMD), exist. However, these implementations are not as flexible as required for many applications. Here we present an implementation in Field Programmable Gate Arrays (FPGA) together with a performance analysis. The FPGA hardware implementation may be considered a platform for further, extended implementations and easily expanded into various applications. The latter may include advanced on-line image analysis with close to real-time performance.

[Surgical peculiarities of gunshot injuries to arteries of the extremities caused by modern small arms and light weapons].

PubMed

Samokhvalov, I M; Reva, V A; Denisov, A V; Ozeretskovskiĭ, L B; Pronchenko, A A

2014-10-01

The aim of the given study was development of surgical tactics in case of femoral artery injury, caused by medium-calibre bullet, on the basis acute experiment on large biological objects. Experimental animals were shot into mid third of the femora by a rifle cartridge in 7,62-mm calibre (AK-47 made in 1943). The analysis of microstructure, made in 5 cross-sections performed every 1-centimetre way from the wound canal, showed that there were no any damages of arterial wall. Authors came to conclusion that the surgical debridement of the gunshot wound, made by a rifle cartridge in 7,62-mm calibre of AK-47, should consist of exsection of devitalized section of artery.

Resolving future fire management conflicts using multicriteria decision making.

PubMed

Driscoll, Don A; Bode, Michael; Bradstock, Ross A; Keith, David A; Penman, Trent D; Price, Owen F

2016-02-01

Management strategies to reduce the risks to human life and property from wildfire commonly involve burning native vegetation. However, planned burning can conflict with other societal objectives such as human health and biodiversity conservation. These conflicts are likely to intensify as fire regimes change under future climates and as growing human populations encroach farther into fire-prone ecosystems. Decisions about managing fire risks are therefore complex and warrant more sophisticated approaches than are typically used. We applied a multicriteria decision making approach (MCDA) with the potential to improve fire management outcomes to the case of a highly populated, biodiverse, and flammable wildland-urban interface. We considered the effects of 22 planned burning options on 8 objectives: house protection, maximizing water quality, minimizing carbon emissions and impacts on human health, and minimizing declines of 5 distinct species types. The MCDA identified a small number of management options (burning forest adjacent to houses) that performed well for most objectives, but not for one species type (arboreal mammal) or for water quality. Although MCDA made the conflict between objectives explicit, resolution of the problem depended on the weighting assigned to each objective. Additive weighting of criteria traded off the arboreal mammal and water quality objectives for other objectives. Multiplicative weighting identified scenarios that avoided poor outcomes for any objective, which is important for avoiding potentially irreversible biodiversity losses. To distinguish reliably among management options, future work should focus on reducing uncertainty in outcomes across a range of objectives. Considering management actions that have more predictable outcomes than landscape fuel management will be important. We found that, where data were adequate, an MCDA can support decision making in the complex and often conflicted area of fire management. © 2015 Society for Conservation Biology.

Implementation of Multi-Agent Object Attention System Based on Biologically Inspired Attractor Selection

NASA Astrophysics Data System (ADS)

Hashimoto, Ryoji; Matsumura, Tomoya; Nozato, Yoshihiro; Watanabe, Kenji; Onoye, Takao

A multi-agent object attention system is proposed, which is based on biologically inspired attractor selection model. Object attention is facilitated by using a video sequence and a depth map obtained through a compound-eye image sensor TOMBO. Robustness of the multi-agent system over environmental changes is enhanced by utilizing the biological model of adaptive response by attractor selection. To implement the proposed system, an efficient VLSI architecture is employed with reducing enormous computational costs and memory accesses required for depth map processing and multi-agent attractor selection process. According to the FPGA implementation result of the proposed object attention system, which is accomplished by using 7,063 slices, 640×512 pixel input images can be processed in real-time with three agents at a rate of 9fps in 48MHz operation.

Deciphering principles of transcription regulation in eukaryotic genomes

PubMed Central

Nguyen, Dat H; D'haeseleer, Patrik

2006-01-01

Transcription regulation has been responsible for organismal complexity and diversity in the course of biological evolution and adaptation, and it is determined largely by the context-dependent behavior of cis-regulatory elements (CREs). Therefore, understanding principles underlying CRE behavior in regulating transcription constitutes a fundamental objective of quantitative biology, yet these remain poorly understood. Here we present a deterministic mathematical strategy, the motif expression decomposition (MED) method, for deriving principles of transcription regulation at the single-gene resolution level. MED operates on all genes in a genome without requiring any a priori knowledge of gene cluster membership, or manual tuning of parameters. Applying MED to Saccharomyces cerevisiae transcriptional networks, we identified four functions describing four different ways that CREs can quantitatively affect gene expression levels. These functions, three of which have extrema in different positions in the gene promoter (short-, mid-, and long-range) whereas the other depends on the motif orientation, are validated by expression data. We illustrate how nature could use these principles as an additional dimension to amplify the combinatorial power of a small set of CREs in regulating transcription. PMID:16738557

Critical issues for engineering cord blood stem cells to produce insulin.

PubMed

Denner, Larry; Urban, Randall J

2008-09-01

The objectives of using cord blood stem cells for treating type 1 diabetes are simple in principle yet complex in biological and molecular mechanisms. These are defined by the complexity of the insulin-producing unit of the pancreas, the islet. Islets are composed of various cell types that arise from diverse lineages and communicate by hormones, growth factors and small-molecule mediators. These processes are regulated by integration of signal transduction pathways. While advances have been made to engineer umbilical cord blood stem cells to produce insulin, these studies only illuminate the potential of such cells to fulfil a necessary, but not sufficient, requirement for transplantation. The challenges ahead demand detailed understanding of molecular mechanisms to move from an opportunistic, phenotypic approach to transplantation and amelioration of blood glucose, to an orderly and logical approach to a biologically and medically meaningful solution. The issues include expansion to generate large numbers of cells, self-renewal to regulate the destiny of cord blood stem cells to repopulate the hematopoietic system, and multipotency of stem cells to generate the distinct cell types of an islet.

Kyiv Small Rivers in Metropolis Water Objects System

NASA Astrophysics Data System (ADS)

Krelshteyn, P.; Dubnytska, M.

2017-12-01

The article answers the question, what really are the small underground rivers with artificial watercourses: water bodies or city engineering infrastructure objects? The place of such rivers in metropolis water objects system is identified. The ecological state and the degree of urbanization of small rivers, as well as the dynamics of change in these indicators are analysed on the Kiev city example with the help of water objects cadastre. It was found that the registration of small rivers in Kyiv city is not conducted, and the summary information on such water objects is absent and is not taken into account when making managerial decisions at the urban level. To solve this problem, we propose to create some water bodies accounting system (water cadastre).

BATMAV: a 2-DOF bio-inspired flapping flight platform

NASA Astrophysics Data System (ADS)

Bunget, Gheorghe; Seelecke, Stefan

2010-04-01

Due to the availability of small sensors, Micro-Aerial Vehicles (MAVs) can be used for detection missions of biological, chemical and nuclear agents. Traditionally these devices used fixed or rotary wings, actuated with electric DC motortransmission, a system which brings the disadvantage of a heavier platform. The overall objective of the BATMAV project is to develop a biologically inspired bat-like MAV with flexible and foldable wings for flapping flight. This paper presents a flight platform that features bat-inspired wings which are able to actively fold their elbow joints. A previous analysis of the flight physics for small birds, bats and large insects, revealed that the mammalian flight anatomy represents a suitable flight platform that can be actuated efficiently using Shape Memory Alloy (SMA) artificial-muscles. A previous study of the flight styles in bats based on the data collected by Norberg [1] helped to identify the required joint angles as relevant degrees of freedom for wing actuation. Using the engineering theory of robotic manipulators, engineering kinematic models of wings with 2 and 3-DOFs were designed to mimic the wing trajectories of the natural flier Plecotus auritus. Solid models of the bat-like skeleton were designed based on the linear and angular dimensions resulted from the kinematic models. This structure of the flight platform was fabricated using rapid prototyping technologies and assembled to form a desktop prototype with 2-DOFs wings. Preliminary flapping test showed suitable trajectories for wrist and wingtip that mimic the flapping cycle of the natural flyer.

Surface desensitization of polarimetric waveguide interferometers

NASA Astrophysics Data System (ADS)

Worth, Colin

Non-specific binding of small molecules to the surface of waveguide biosensors presents a major obstacle to surface-sensing techniques that attempt to detect very low concentrations (<1 g/mm2) of large (500 nm to 3 mum) biological objects. Interferometric waveguide biosensors use the interaction of an evanescent light field outside of the guiding layer with a biological sample to detect a particular type of cell or bacteria at some distance from the sensor surface. In such experiments, binding of small proteins close to the surface can be a significant source of noise. It is possible to significantly improve the signal-to-noise ratio by varying the properties of the biosensor, in order to reduce or eliminate the biosensor's response to a thin protein layer at the waveguide surface, without significantly reducing the response to larger target particles. In many biosensing applications, specifically bound particles, such as bacteria, are much larger than non-specifically bound particles such as proteins. In addition, due to laminar flow conditions at the sensor surface, the latter smaller particles tend to accumulate on the sensor surface. By varying the waveguide parameters, it is possible to vary the sensitivity of the detector response as a function of sample distance from the detector, by changing the properties of the TE0 and TM0 guided modes. This results in a signal reduction of more than 85%, for thin (30 nm or less) layers adjacent to the waveguide surface.

Regenerative Chemical Biology: Current Challenges and Future Potential

PubMed Central

Ao, Ada; Hao, Jijun; Hong, Charles C.

2011-01-01

The enthusiasm surrounding the clinical potential of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) is tempered by the fact that key issues regarding their safety, efficacy, and long-term benefits have thus far been suboptimal. Small molecules can potentially relieve these problems at major junctions of stem cell biology and regenerative therapy. In this review, we will introduce recent advances in these important areas and the first-generation of small molecules used in the regenerative context. Current chemical biology studies will provide the archetype for future interdisciplinary collaborations, and improve clinical benefits of cell-based therapies. PMID:21513877

Objectives | Office of Cancer Clinical Proteomics Research

Cancer.gov

The overall objective of CPTAC is to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand the molecular basis of cancer that is not fully elucidated or not possible through genomics and to accelerate the translation of molecular findings into the clinic.  This is to be achieved through enhancing our understanding of cancer genome biology by adding a complementary functional layer of protein biology (a “proteogenome” approach) that refines/prioritizes driver genes, enhances understanding of pathogenesis

Teachers' Journal Club: Bridging between the Dynamics of Biological Discoveries and Biology Teachers

ERIC Educational Resources Information Center

Brill, Gilat; Falk, Hedda; Yarden, Anat

2003-01-01

Since biology is one of the most dynamic research fields within the natural sciences, the gap between the accumulated knowledge in biology and the knowledge that is taught in schools, increases rapidly with time. Our long-term objective is to develop means to bridge between the dynamics of biological discoveries and the biology teachers and…

Application of shift-and-add algorithms for imaging objects within biological media

NASA Astrophysics Data System (ADS)

Aizert, Avishai; Moshe, Tomer; Abookasis, David

2017-01-01

The Shift-and-Add (SAA) technique is a simple mathematical operation developed to reconstruct, at high spatial resolution, atmospherically degraded solar images obtained from stellar speckle interferometry systems. This method shifts and assembles individual degraded short-exposure images into a single average image with significantly improved contrast and detail. Since the inhomogeneous refractive indices of biological tissue causes light scattering similar to that induced by optical turbulence in the atmospheric layers, we assume that SAA methods can be successfully implemented to reconstruct the image of an object within a scattering biological medium. To test this hypothesis, five SAA algorithms were evaluated for reconstructing images acquired from multiple viewpoints. After successfully retrieving the hidden object's shape, quantitative image quality metrics were derived, enabling comparison of imaging error across a spectrum of layer thicknesses, demonstrating the relative efficacy of each SAA algorithm for biological imaging.

On the mechanisms of interaction of low-intensity millimeter waves with biological objects

NASA Astrophysics Data System (ADS)

Betskii, O. V.

1994-01-01

The interaction of low-intensity millimeter-band electromagnetic waves with biological objects is examined. These waves are widely used in medical practice as a means of physiotherapy for the treatment of various human disorders. Principal attention is given to the mechanisms through which millimeter waves act on the human organism.

INSTRUCTIONAL PERFORMANCE OBJECTIVES FOR A COURSE IN GENERAL BIOLOGY.

ERIC Educational Resources Information Center

MAFFETT, JAMES E.

THE INSTRUCTIONAL OBJECTIVES OF A FRESHMAN COURSE IN GENERAL BIOLOGY ARE ORGANIZED FOR THE STUDENT'S EASE OF REFERENCE. THE COURSE IS OUTLINED, BY DEGREE OF COMPLEXITY, AS FOLLOWS--(1) ORIENTATION AND INTRODUCTION, (2) ORIGIN AND ORGANIZATION OF LIFE, (3) CYTOLOGY, (4) METABOLISM AND BIOCHEMISTRY, (5) PLANT LIFE (VASCULAR AND NON-VASCULAR), (6)…

Advanced Rotating Biological Surface Operation. Training Module 2.122.4.77.

ERIC Educational Resources Information Center

Paulson, W. L.

This document is an instructional module package prepared in objective form for use by an instructor familiar with operation and maintenance of a rotating biological surface (RBS) wastewater treatment system. Included are objectives, instructor guides, student handouts, and transparency masters. This is the third level of a three module series and…

On the Limits of Infants' Quantification of Small Object Arrays

ERIC Educational Resources Information Center

Feigenson, Lisa; Carey, Susan

2005-01-01

Recent work suggests that infants rely on mechanisms of object-based attention and short-term memory to represent small numbers of objects. Such work shows that infants discriminate arrays containing 1, 2, or 3 objects, but fail with arrays greater than 3 [Feigenson, L., & Carey, S. (2003). Tracking individuals via object-files: Evidence from…

Modeling Protein Evolution

NASA Astrophysics Data System (ADS)

Goldstein, Richard; Pollock, David

The study of biology is fundamentally different from many other scientific pursuits, such as geology or astrophysics. This difference stems from the ubiquitous questions that arise about function and purpose. These are questions concerning why biological objects operate the way they do: what is the function of a polymerase? What is the role of the immune system? No one, aside from the most dedicated anthropist or interventionist theist, would attempt to determine the purpose of the earth's mantle or the function of a binary star. Among the sciences, it is only biology in which the details of what an object does can be said to be part of the reason for its existence. This is because the process of evolution is capable of improving an object to better carry out a function; that is, it adapts an object within the constraints of mechanics and history (i.e., what has come before). Thus, the ultimate basis of these biological questions is the process of evolution; generally, the function of an enzyme, cell type, organ, system, or trait is the thing that it does that contributes to the fitness (i.e., reproductive success) of the organism of which it is a part or characteristic. Our investigations cannot escape the simple fact that all things in biology (including ourselves) are, ultimately, the result of an evolutionary process.

Looking for scaling laws, or physics with nuts and shells

NASA Astrophysics Data System (ADS)

Sheets, H. David; Lauffenburger, James C.

1999-09-01

Scaling laws relating the volume of a class of objects to a characteristic dimension of the object appear commonly in physics, chemistry, and biology. In this laboratory exercise for an introductory physics course scaling laws are derived for machine nuts and clam shells. In addition to covering a standard problem in physics, determining volume of the object by measuring the buoyant force on it, the biologically interesting idea of scaling laws are incorporated into the same lab.

Current advances in screening for bioactive components from medicinal plants by affinity ultrafiltration mass spectrometry.

PubMed

Chen, Guilin; Huang, Bill X; Guo, Mingquan

2018-05-21

Medicinal plants have played an important role in maintaining human health for thousands of years. However, the interactions between the active components in medicinal plants and some certain biological targets during a disease are still unclear in most cases. To conduct the high-throughput screening for small active molecules that can interact with biological targets, which is of great theoretical significance and practical value. The ultrafiltration mass spectrometry (UF-LC/MS) is a powerful bio-analytical method by combining affinity ultrafiltration and liquid chromatography-mass spectrometry (LC/MS), which could rapidly screen and identify small active molecules that bind to biological targets of interest at the same time. Compared with other analytical methods, affinity UF-LC/MS has the characteristics of fast, sensitive and high throughput, and is especially suitable for the complicated extracts of medicinal plants. In this review, the basic principle, characteristics and some most recent challenges in UF-LC/MS have been demonstrated. Meanwhile, the progress and applications of affinity UF-LC/MS in the discovery of the active components from natural medicinal plants and the interactions between small molecules and biological target proteins are also briefly summarised. In addition, the future directions for UF-LC/MS are also prospected. Affinity UF-LC/MS is a powerful tool in studies on the interactions between small active molecules and biological protein targets, especially in the high-throughput screening of active components from the natural medicinal plants. Copyright © 2018 John Wiley & Sons, Ltd.

Bayesian integration of position and orientation cues in perception of biological and non-biological forms.

PubMed

Thurman, Steven M; Lu, Hongjing

2014-01-01

Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares) comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic form analysis.

Discerning the Chemistry in Individual Organelles with Small-Molecule Fluorescent Probes.

PubMed

Xu, Wang; Zeng, Zebing; Jiang, Jian-Hui; Chang, Young-Tae; Yuan, Lin

2016-10-24

Principle has it that even the most advanced super-resolution microscope would be futile in providing biological insight into subcellular matrices without well-designed fluorescent tags/probes. Developments in biology have increasingly been boosted by advances of chemistry, with one prominent example being small-molecule fluorescent probes that not only allow cellular-level imaging, but also subcellular imaging. A majority, if not all, of the chemical/biological events take place inside cellular organelles, and researchers have been shifting their attention towards these substructures with the help of fluorescence techniques. This Review summarizes the existing fluorescent probes that target chemical/biological events within a single organelle. More importantly, organelle-anchoring strategies are described and emphasized to inspire the design of new generations of fluorescent probes, before concluding with future prospects on the possible further development of chemical biology. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ground-facilities at the DLR Institute of Aerospace Medicine for preparation of flight experiments

NASA Astrophysics Data System (ADS)

Hemmersbach, Ruth; Hendrik Anken, Ralf; Hauslage, Jens; von der Wiesche, Melanie; Baerwalde, Sven; Schuber, Marianne

In order to investigate the influence of altered gravity on biological systems and to identify gravisensitive processes, various experimental platforms have been developed, which are useful to simulate weightlessness or are able to produce hypergravity. At the Institute of Aerospace Medicine, DLR Cologne, a broad spectrum of applications is offered to scientists: clinostats with one rotation axis and variable rotation speeds for cultivation of small objects (including aquatic organisms) in simulated weightlessness conditions, for online microscopic observations and for online kinetic measurements. Own research concentrates on comparative studies with other kinds of methods to simulate weightlessness, also available at the institute: Rotating Wall Vessel (RWV) for aquatic studies, Random Positioning Machine (RPM; manufactured by Dutch Space, Leiden, The Netherlands). Correspondingly, various centrifuge devices are available to study different test objects under hypergravity conditions -such as NIZEMI, a slow rotating centrifuge microscope, and MUSIC, a multi-sample centrifuge. Mainly for experiments with human test subjects (artificial gravity), but also for biological systems or for testing various kinds of (flight-) hardware, the SAHC, a short arm human centrifuge -loaned by ESA -was installed in Cologne and completes our experimental scenario. Furthermore, due to our specific tasks such as providing laboratories during the German Parabolic Flight Experiments starting from Cologne and being the Facility Responsible Center for BIOLAB, a science rack in the Columbus module aboard the ISS, scientists have the possibility for an optimal preparation of their flight experiments.

ABCG5 gene responses to treadmill running with or without administration of Pistachio atlantica in female rats

PubMed Central

Ghanbari-Niaki, Abbass; Zare-Kookandeh, Navabeh; Zare-Kookandeh, Asghar

2014-01-01

Objective(s): ABC transporters comprise a large family of transmembrane proteins that use the energy provided by ATP hydrolysis to translocate a variety of substrates across biological membranes. All members of the human ABCG subfamily, except for ABCG2, are cholesterol-transporter. The aim of this study was to determine the liver, the small intestine and kidney ABCG5 relative gene expression in response to treadmill-running training in female rats. Materials and Methods: Twenty Wistar rats (6-8 weeks old and 125-135 g weight) were used. Animals were randomly assigned to saline-control (SC), saline-training (ST), and Baneh-control (BC), and Baneh-training (BT) groups. Training groups did the exercise on a motor-driven treadmill at 25 m/min (0% grade) for 60 min/day for eight weeks (5 days/week). Rats were fed orally, with Baneh extraction and saline for six weeks. The two-way ANOVA was employed for statistical analysis. ABCG5 relative gene expression was detected by Real-time PCR method. Results: The current findings indicate that the Baneh-treated tissues had significantly lower levels of ABCG5 gene expression in the liver, small intestine, and kidneys (P< 0.001, P< 0.003, P< 0.001, respectively), when compared with saline-treated tissues. However, a higher level of gene expression was observed in exercise groups. A lower level of HDL-c but not triglyceride (TG) and total cholesterol (TC) levels were found in Baneh-treated animals at rest. Conclusion: Exercise training increases ABCG5 relative gene expression in the liver, small intestine and kidney tissues; therefore exercise training may adjust the reduction of ABCG5 relative gene expression in Baneh-training group. PMID:24847418

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Biological Small Angle Scattering: Techniques, Strategies and Tips

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaudhuri, Barnali; Muñoz, Inés G.; Urban, Volker S.

This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins,more » and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications.The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS.The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for exploring the diversity of solution SAS methods and applications.« less

Bio-medical telemetry: Sensing and transmitting biological information from animals to man

NASA Technical Reports Server (NTRS)

Mackay, S.

1971-01-01

The application of small radio transmitters for monitoring biological activity in animals and humans is discussed. The microminiaturization of the electronic transmitters makes it possible for them to be swallowed and to operate within the body with no external connections. The small size also makes it possible for the transmitters to be surgically implanted or carried externally to monitor specific bodily functions. The use of satellites to monitor the activity of birds and animals carrying small transmitters is described. Photographs of birds, fish, and reptiles which were equipped with miniature electronic monitors are provided.

The Biostack Experiments I and II aboard Apollo 16 and 17.

PubMed

Bucker, H

1974-01-01

The concept of the Biostack experiment has become practicable through European scientific collaboration and with help of NASA. The objectives of this experiment flown aboard Apollo 16 and 17 are to study the biological effects of individual heavy cosmic particles of high-energy loss (HZE) not available on earth; to study the influence of additional spaceflight factors; to get some knowledge on the mechanism by which HZE particles damage biological materials; to get information on the spectrum of charge and energy of the cosmic ions in the spacecraft; to estimate the radiation hazards for man in space. For this purpose the Biostack experiment comprises a widespread spectrum of biological objects, and various radiobiological end-points are under investigation. Bacterial spores, protozoa cysts, plant seeds, shrimp eggs, and insect eggs were included in the Biostack experiment packages together with different physical radiation detectors (nuclear emulsions, plastics, AgCl crystals, and LiF thermoluminescence dosimeters). By using special arrangements of biological objects and physical track detectors, individual evaluation of tracks was obtained allowing the identification of each penetrating particle in relation to the possible biological effects on its path. The response of the different biological objects to space flight and HZE ions bombardment was of different degree, presumably depending on the ability of the organism to replace the cells damaged by a hit. The results help to estimate the radiation hazard for astronauts during space missions of long duration.

The Implementation of Research-based Learning on Biology Seminar Course in Biology Education Study Program of FKIP UMRAH

NASA Astrophysics Data System (ADS)

Amelia, T.

2018-04-01

Biology Seminar is a course in Biology Education Study Program of Faculty of Teacher Training and Education University of Maritim Raja Ali Haji (FKIP UMRAH) that requires students to have the ability to apply scientific attitudes, perform scientific writing and undertake scientific publications on a small scale. One of the learning strategies that can drive the achievement of learning outcomes in this course is Research-Based Learning. Research-Based Learning principles are considered in accordance with learning outcomes in Biology Seminar courses and generally in accordance with the purpose of higher education. On this basis, this article which is derived from a qualitative research aims at describing Research-based Learning on Biology Seminar course. Based on a case study research, it was known that Research-Based Learning on Biology Seminar courses is applied through: designing learning activities around contemporary research issues; teaching research methods, techniques and skills explicitly within program; drawing on personal research in designing and teaching courses; building small-scale research activities into undergraduate assignment; and infusing teaching with the values of researchers.

Local x-ray structure analysis of optically manipulated biological micro-objects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cojoc, Dan; Ferrari, Enrico; Santucci, Silvia C.

2010-12-13

X-ray diffraction using micro- and nanofocused beams is well suited for nanostructure analysis at different sites of a biological micro-object. To conduct in vitro studies without mechanical contact, we developed object manipulation by optical tweezers in a microfluidic cell. Here we report x-ray microdiffraction analysis of a micro-object optically trapped in three dimensions. We revealed the nanostructure of a single starch granule at different points and investigated local radiation damage induced by repeated x-ray exposures at the same position, demonstrating high stability and full control of the granule orientation by multiple optical traps.

Standardized Curriculum for Small Engine Repair.

ERIC Educational Resources Information Center

Mississippi State Dept. of Education, Jackson. Office of Vocational, Technical and Adult Education.

This curriculum guide for small engine repair was developed by the state of Mississippi to standardize vocational education course titles and core contents. The objectives contained in this document are common to all small engine repair programs in the state. The guide contains objectives for small engine repair I and II courses. Units in course I…

Characterizing protein domain associations by Small-molecule ligand binding

PubMed Central

Li, Qingliang; Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

2012-01-01

Background Protein domains are evolutionarily conserved building blocks for protein structure and function, which are conventionally identified based on protein sequence or structure similarity. Small molecule binding domains are of great importance for the recognition of small molecules in biological systems and drug development. Many small molecules, including drugs, have been increasingly identified to bind to multiple targets, leading to promiscuous interactions with protein domains. Thus, a large scale characterization of the protein domains and their associations with respect to small-molecule binding is of particular interest to system biology research, drug target identification, as well as drug repurposing. Methods We compiled a collection of 13,822 physical interactions of small molecules and protein domains derived from the Protein Data Bank (PDB) structures. Based on the chemical similarity of these small molecules, we characterized pairwise associations of the protein domains and further investigated their global associations from a network point of view. Results We found that protein domains, despite lack of similarity in sequence and structure, were comprehensively associated through binding the same or similar small-molecule ligands. Moreover, we identified modules in the domain network that consisted of closely related protein domains by sharing similar biochemical mechanisms, being involved in relevant biological pathways, or being regulated by the same cognate cofactors. Conclusions A novel protein domain relationship was identified in the context of small-molecule binding, which is complementary to those identified by traditional sequence-based or structure-based approaches. The protein domain network constructed in the present study provides a novel perspective for chemogenomic study and network pharmacology, as well as target identification for drug repurposing. PMID:23745168

Associated impairment of the categories of conspecifics and biological entities: cognitive and neuroanatomical aspects of a new case.

PubMed

Capitani, Erminio; Chieppa, Francesca; Laiacona, Marcella

2010-05-01

Case A.C.A. presented an associated impairment of visual recognition and semantic knowledge for celebrities and biological objects. This case was relevant for (a) the neuroanatomical correlations, and (b) the relationship between visual recognition and semantics within the biological domain and the conspecifics domain. A.C.A. was not affected by anterior temporal damage. Her bilateral vascular lesions were localized on the medial and inferior temporal gyrus on the right and on the intermediate fusiform gyrus on the left, without concomitant lesions of the parahippocampal gyrus or posterior fusiform. Data analysis was based on a novel methodology developed to estimate the rate of stored items in the visual structural description system (SDS) or in the face recognition unit. For each biological object, no particular correlation was found between the visual information accessed through the semantic system and that tapped by the picture reality judgement. Findings are discussed with reference to whether a putative resource commonality is likely between biological objects and conspecifics, and whether or not either category may depend on an exclusive neural substrate.

Discord of Biological and Psychological Measures in a Group of Depressed African American and White Cancer Patients

PubMed Central

Zhang, Amy Y

2011-01-01

Objective: This study examined racial differences in the self-report of depressive symptoms by reference to biological states. Methods: The study used a convenience sample of 20 depressed cancer patients (CES-D ≥16) (15 African Americans and 5 Whites). Subjects completed depression assessment on a battery of psychological measures and provided blood and saliva samples. Laboratory tests were performed on biomarkers (serotonin, cortisol and IL-6). T-test was computed to examine racial differences on biological and psychological measures. Results: Depressed Whites had a significantly higher cortisol level than depressed African Americans, but no significant group difference was found on any self-reported psychological measures of depression. There was a trend that African Americans reported fewer depressive symptoms on psychological measures but exceeded Whites on the domain of somatization; however, such group differences did not approach statistic significance in this small sample. Conclusion: African Americans did not appear to underreport depression in consideration of their biological states, but had a tendency to report more somatic symptoms than Whites; this may be attributable to non-depression diseases or reporting behavior rather than somatic sensitivity. African Americans exhibited more mistrust in the health care system, which could affect the self-report of depression. There is a discord between biological and psychological measures of depression. Biomarkers prove to be useful for evaluating racial difference in the self-report of depression. Implication for Nursing: Nurses should be cautious of somatic complaints when assessing African American cancer patient’s depression. Establishing trust is essential for an accurate assessment of depression in African American cancer patients. PMID:22135714

Feature-fused SSD: fast detection for small objects

NASA Astrophysics Data System (ADS)

Cao, Guimei; Xie, Xuemei; Yang, Wenzhe; Liao, Quan; Shi, Guangming; Wu, Jinjian

2018-04-01

Small objects detection is a challenging task in computer vision due to its limited resolution and information. In order to solve this problem, the majority of existing methods sacrifice speed for improvement in accuracy. In this paper, we aim to detect small objects at a fast speed, using the best object detector Single Shot Multibox Detector (SSD) with respect to accuracy-vs-speed trade-off as base architecture. We propose a multi-level feature fusion method for introducing contextual information in SSD, in order to improve the accuracy for small objects. In detailed fusion operation, we design two feature fusion modules, concatenation module and element-sum module, different in the way of adding contextual information. Experimental results show that these two fusion modules obtain higher mAP on PASCAL VOC2007 than baseline SSD by 1.6 and 1.7 points respectively, especially with 2-3 points improvement on some small objects categories. The testing speed of them is 43 and 40 FPS respectively, superior to the state of the art Deconvolutional single shot detector (DSSD) by 29.4 and 26.4 FPS.

[The determination of the natural content of chemical elements in human biological objects (liver, kidney, stomach) by mass spectrometry with inductively coupled plasma].

PubMed

Luzanova, I S; Svetlolobov, D Iu; Zorin, Iu V

2014-01-01

The objective of the present work was to continue the studies of the sites of concentration of the chemical elements corresponding to normal homeostasis in human biological objects by mass spectrometry with inductively coupled plasma. The study yielded the data on the natural content of 27 elements in the cadaveric liver, kidney, and stomach. It is recommended to use these findings as the reference parameters corresponding to normal homeostasis.

A Comparison of the Effects of an Advanced Organizer and/or Behavioral Objectives on the Achievement of Disadvantaged Biology Students.

ERIC Educational Resources Information Center

Kahle, Jane Butler

The use of an advanced organizer (a generalizable, encompassing concept) prior to an individualized instructional sequence in a self-paced, audiotutorial learning format was accompanied by gains in individual unit achievement and in retention by disadvantaged biology students. Although behavioral objectives generally were shown to make no…

The Feasibility of Systems Thinking in Biology Education

ERIC Educational Resources Information Center

Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

2011-01-01

Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

Method for high resolution magnetic resonance analysis using magic angle technique

DOEpatents

Wind, Robert A.; Hu, Jian Zhi

2003-11-25

A method of performing a magnetic resonance analysis of a biological object that includes placing the biological object in a main magnetic field and in a radio frequency field, the main magnetic field having a static field direction; rotating the biological object at a rotational frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. According to another embodiment, the radio frequency is pulsed to provide a sequence capable of producing a spectrum that is substantially free of spinning sideband peaks.

Bioinspired spring origami

NASA Astrophysics Data System (ADS)

Faber, Jakob A.; Arrieta, Andres F.; Studart, André R.

2018-03-01

Origami enables folding of objects into a variety of shapes in arts, engineering, and biological systems. In contrast to well-known paper-folded objects, the wing of the earwig has an exquisite natural folding system that cannot be sufficiently described by current origami models. Such an unusual biological system displays incompatible folding patterns, remains open by a bistable locking mechanism during flight, and self-folds rapidly without muscular actuation. We show that these notable functionalities arise from the protein-rich joints of the earwig wing, which work as extensional and rotational springs between facets. Inspired by this biological wing, we establish a spring origami model that broadens the folding design space of traditional origami and allows for the fabrication of precisely tunable, four-dimensional–printed objects with programmable bioinspired morphing functionalities.

Nanoparticle PEBBLE sensors in live cells and in vivo

PubMed Central

Smith, Ron

2009-01-01

Nanoparticle sensors have been developed for imaging and dynamic monitoring, in live cells and in vivo, of the molecular or ionic components, constructs, forces and dynamics, all in real time, during biological/chemical/physical processes. With their biocompatible small size and inert matrix, nanoparticle sensors have been successfully applied for non-invasive real-time measurements of analytes and fields in cells and rodents, with spatial, temporal, physical and chemical resolution. This review describes the diverse designs of nanoparticle sensors for ions and small molecules, physical fields and biological features, as well as the characterization, properties, and applications of these nanosensors to in vitro and in vivo measurements. Their floating as well as localization ability in biological media is captured by the acronym PEBBLE: photonic explorer for bioanalysis with biologically localized embedding. PMID:20098636

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Population maintenance among tropical reef fishes: Inferences from small-island endemics

PubMed Central

Robertson, D. Ross

2001-01-01

To what extent do local populations of tropical reef fishes persist through the recruitment of pelagic larvae to their natal reef? Endemics from small, isolated islands can help answer that question by indicating whether special biological attributes are needed for long-term survival under enforced localization in high-risk situations. Taxonomically and biologically, the endemics from seven such islands are broadly representative of their regional faunas. As natal-site recruitment occurs among reef fishes in much less isolated situations, these characteristics of island endemics indicate that a wide range of reef fishes could have persistent self-sustaining local populations. Because small islands regularly support substantial reef fish faunas, regional systems of small reserves could preserve much of the diversity of these fishes. PMID:11331752

[Small compounds libraries: a research tool for chemical biology].

PubMed

Florent, Jean-Claude

2013-01-01

Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction. © Société de Biologie, 2013.

The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology

USDA-ARS?s Scientific Manuscript database

It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (P...

Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction

NASA Astrophysics Data System (ADS)

Kim, Jonghoon; Jung, Jinjoo; Koo, Jaeyoung; Cho, Wansang; Lee, Won Seok; Kim, Chanwoo; Park, Wonwoo; Park, Seung Bum

2016-10-01

Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.

CEBS object model for systems biology data, SysBio-OM.

PubMed

Xirasagar, Sandhya; Gustafson, Scott; Merrick, B Alex; Tomer, Kenneth B; Stasiewicz, Stanley; Chan, Denny D; Yost, Kenneth J; Yates, John R; Sumner, Susan; Xiao, Nianqing; Waters, Michael D

2004-09-01

To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

[Biogeography: geography or biology?].

PubMed

Kafanov, A I

2009-01-01

General biogeography is an interdisciplinary science, which combines geographic and biological aspects constituting two distinct research fields: biological geography and geographic biology. These fields differ in the nature of their objects of study, employ different methods and represent Earth sciences and biological sciences, respectively. It is suggested therefore that the classification codes for research fields and the state professional education standard should be revised.

On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry

PubMed Central

2016-01-01

Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is “tethering”—a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein–protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: “multifunctional scaffolding” versus “on-demand targeting”. By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms. PMID:26907082

On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry.

PubMed

Long, Marcus J C; Poganik, Jesse R; Aye, Yimon

2016-03-23

Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.

Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

PubMed

Mellis, Ian A; Raj, Arjun

2015-10-01

Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines. © 2015 Mellis and Raj; Published by Cold Spring Harbor Laboratory Press.

Multidisciplinary study of Wyoming test sites. [hydrology, biology, geology, lithology, geothermal, and land use

NASA Technical Reports Server (NTRS)

Houston, R. S. (Principal Investigator); Marrs, R. W.; Agard, S. S.; Downing, K. G.; Earle, J. L.; Froman, N. L.; Gordon, R.; Kolm, K. E.; Tomes, B.; Vietti, J.

1974-01-01

The author has identified the following significant results. Investigation of a variety of applications of EREP photographic data demonstrated that EREP S-190 data offer a unique combination of synoptic coverage and image detail. The broad coverage is ideal for regional geologic mapping and tectonic analysis while the detail is adequate for mapping of crops, mines, urban areas, and other relatively small features. The investigative team at the University of Wyoming has applied the EREP S-190 data to: (1) analysis of photolinear elements of the Powder River Basin, southern Montana, and the Wind River Mountains; (2) drainage analysis of the Powder River Basin and Beartooth Mountains; (3) lithologic and geologic mapping in the Powder River Basin, Black Hills, Green River Basin, Bighorn Basin and Southern Bighorn Mountains; (4) location of possible mineralization in the Absaroka Range; and (5) land use mapping near Riverton and Gillette. All of these applications were successful to some degree. Image enhancement procedures were useful in some efforts requiring distinction of small objects or subtle contrasts.

Evaluating thermoregulation in reptiles: the fallacy of the inappropriately applied method.

PubMed

Seebacher, Frank; Shine, Richard

2004-01-01

Given the importance of heat in most biological processes, studies on thermoregulation have played a major role in understanding the ecology of ectothermic vertebrates. It is, however, difficult to assess whether body temperature is actually regulated, and several techniques have been developed that allow an objective assessment of thermoregulation. Almost all recent studies on reptiles follow a single methodology that, when used correctly, facilitates comparisons between species, climates, and so on. However, the use of operative temperatures in this methodology assumes zero heat capacity of the study animals and is, therefore, appropriate for small animals only. Operative temperatures represent potentially available body temperatures accurately for small animals but can substantially overestimate the ranges of body temperature available to larger animals whose slower rates of heating and cooling mean that they cannot reach equilibrium if they encounter operative temperatures that change rapidly through either space or time. This error may lead to serious misinterpretations of field data. We derive correction factors specific for body mass and rate of movement that can be used to estimate body temperature null distributions of larger reptiles, thereby overcoming this methodological problem.

Gas-Grain Simulation Facility: Fundamental studies of particle formation and interactions. Volume 2: Abstracts, candidate experiments and feasibility study

NASA Technical Reports Server (NTRS)

Fogleman, Guy (Editor); Huntington, Judith L. (Editor); Schwartz, Deborah E. (Editor); Fonda, Mark L. (Editor)

1989-01-01

An overview of the Gas-Grain Simulation Facility (GGSF) project and its current status is provided. The proceedings of the Gas-Grain Simulation Facility Experiments Workshop are recorded. The goal of the workshop was to define experiments for the GGSF--a small particle microgravity research facility. The workshop addressed the opportunity for performing, in Earth orbit, a wide variety of experiments that involve single small particles (grains) or clouds of particles. Twenty experiments from the fields of exobiology, planetary science, astrophysics, atmospheric science, biology, physics, and chemistry were described at the workshop and are outlined in Volume 2. Each experiment description included specific scientific objectives, an outline of the experimental procedure, and the anticipated GGSF performance requirements. Since these experiments represent the types of studies that will ultimately be proposed for the facility, they will be used to define the general science requirements of the GGSF. Also included in the second volume is a physics feasibility study and abstracts of example Gas-Grain Simulation Facility experiments and related experiments in progress.

Cell biology perspectives in phage biology.

PubMed

Ansaldi, Mireille

2012-01-01

Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

Handheld hyperspectral imager for standoff detection of chemical and biological aerosols

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele; Jensen, James O.; McAnally, Gerard

2004-02-01

Pacific Advanced Technology has developed a small hand held imaging spectrometer, Sherlock, for gas leak and aerosol detection and imaging. The system is based on a patent technique that uses diffractive optics and image processing algorithms to detect spectral information about objects in the scene of the camera (IMSS Image Multi-spectral Sensing). This camera has been tested at Dugway Proving Ground and Dstl Porton Down facility looking at Chemical and Biological agent simulants. The camera has been used to investigate surfaces contaminated with chemical agent simulants. In addition to Chemical and Biological detection the camera has been used for environmental monitoring of green house gases and is currently undergoing extensive laboratory and field testing by the Gas Technology Institute, British Petroleum and Shell Oil for applications for gas leak detection and repair. The camera contains an embedded Power PC and a real time image processor for performing image processing algorithms to assist in the detection and identification of gas phase species in real time. In this paper we will present an over view of the technology and show how it has performed for different applications, such as gas leak detection, surface contamination, remote sensing and surveillance applications. In addition a sampling of the results form TRE field testing at Dugway in July of 2002 and Dstl at Porton Down in September of 2002 will be given.

Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

ERIC Educational Resources Information Center

Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

2008-01-01

The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

Exploring Visuomotor Priming Following Biological and Non-Biological Stimuli

ERIC Educational Resources Information Center

Gowen, E.; Bradshaw, C.; Galpin, A.; Lawrence, A.; Poliakoff, E.

2010-01-01

Observation of human actions influences the observer's own motor system, termed visuomotor priming, and is believed to be caused by automatic activation of mirror neurons. Evidence suggests that priming effects are larger for biological (human) as opposed to non-biological (object) stimuli and enhanced when viewing stimuli in mirror compared to…

Characterization of Pathogenic Human MSH2 Missense Mutations Using Yeast as a Model System: A Laboratory Course in Molecular Biology

ERIC Educational Resources Information Center

Gammie, Alison E.; Erdeniz, Naz

2004-01-01

This work describes the project for an advanced undergraduate laboratory course in cell and molecular biology. One objective of the course is to teach students a variety of cellular and molecular techniques while conducting original research. A second objective is to provide instruction in science writing and data presentation by requiring…

Science K-12, Living Things Are Products of Their Heredity and Their Environment. Utica City School District Articulated Curriculum: Project SEARCH, 1975.

ERIC Educational Resources Information Center

Utica City School District, NY.

Two-column objectives are listed for an integrated science curriculum (grades K-12), often subheaded according to science area (biology, health, general science, physical science) and grade level. Concepts regarding characteristics of living things are stressed in objectives for the primary grades (K-5), and reproductive biology is covered…

How to Generate Understanding of the Scientific Process in Introductory Biology: A Student-Designed Laboratory Exercise on Yeast Fermentation

ERIC Educational Resources Information Center

Collins, Linda T.; Bell, Rebekah P.

2004-01-01

Heavy faculty teaching loads and limited funds biology teachers designed certain objectives in order to increase the understandability of the subject matter of the laboratory exercises they write. In relation to these objectives an old "cookbook" laboratory exercise on yeast fermentation is introduced which involve students asking questions,…

Clinical history and biologic age predicted falls better than objective functional tests.

PubMed

Gerdhem, Paul; Ringsberg, Karin A M; Akesson, Kristina; Obrant, Karl J

2005-03-01

Fall risk assessment is important because the consequences, such as a fracture, may be devastating. The objective of this study was to find the test or tests that best predicted falls in a population-based sample of elderly women. The fall-predictive ability of a questionnaire, a subjective estimate of biologic age and objective functional tests (gait, balance [Romberg and sway test], thigh muscle strength, and visual acuity) were compared in 984 randomly selected women, all 75 years of age. A recalled fall was the most important predictor for future falls. Only recalled falls and intake of psycho-active drugs independently predicted future falls. Women with at least five of the most important fall predictors (previous falls, conditions affecting the balance, tendency to fall, intake of psychoactive medication, inability to stand on one leg, high biologic age) had an odds ratio of 11.27 (95% confidence interval 4.61-27.60) for a fall (sensitivity 70%, specificity 79%). The more time-consuming objective functional tests were of limited importance for fall prediction. A simple clinical history, the inability to stand on one leg, and a subjective estimate of biologic age were more important as part of the fall risk assessment.

A light-driven artificial flytrap

PubMed Central

Wani, Owies M.; Zeng, Hao; Priimagi, Arri

2017-01-01

The sophistication, complexity and intelligence of biological systems is a continuous source of inspiration for mankind. Mimicking the natural intelligence to devise tiny systems that are capable of self-regulated, autonomous action to, for example, distinguish different targets, remains among the grand challenges in biomimetic micro-robotics. Herein, we demonstrate an autonomous soft device, a light-driven flytrap, that uses optical feedback to trigger photomechanical actuation. The design is based on light-responsive liquid-crystal elastomer, fabricated onto the tip of an optical fibre, which acts as a power source and serves as a contactless probe that senses the environment. Mimicking natural flytraps, this artificial flytrap is capable of autonomous closure and object recognition. It enables self-regulated actuation within the fibre-sized architecture, thus opening up avenues towards soft, autonomous small-scale devices. PMID:28534872

Heterogeneous Deformable Modeling of Bio-Tissues and Haptic Force Rendering for Bio-Object Modeling

NASA Astrophysics Data System (ADS)

Lin, Shiyong; Lee, Yuan-Shin; Narayan, Roger J.

This paper presents a novel technique for modeling soft biological tissues as well as the development of an innovative interface for bio-manufacturing and medical applications. Heterogeneous deformable models may be used to represent the actual internal structures of deformable biological objects, which possess multiple components and nonuniform material properties. Both heterogeneous deformable object modeling and accurate haptic rendering can greatly enhance the realism and fidelity of virtual reality environments. In this paper, a tri-ray node snapping algorithm is proposed to generate a volumetric heterogeneous deformable model from a set of object interface surfaces between different materials. A constrained local static integration method is presented for simulating deformation and accurate force feedback based on the material properties of a heterogeneous structure. Biological soft tissue modeling is used as an example to demonstrate the proposed techniques. By integrating the heterogeneous deformable model into a virtual environment, users can both observe different materials inside a deformable object as well as interact with it by touching the deformable object using a haptic device. The presented techniques can be used for surgical simulation, bio-product design, bio-manufacturing, and medical applications.

Optical micromanipulation methods for controlled rotation, transportation, and microinjection of biological objects.

PubMed

Mohanty, S K; Gupta, P K

2007-01-01

The use of laser microtools for rotation and controlled transport of microscopic biological objects and for microinjection of exogenous material in cells is discussed. We first provide a brief overview of the laser tweezers-based methods for rotation or orientation of microscopic objects. Particular emphasis is placed on the methods that are more suitable for the manipulation of biological objects, and the use of these for two-dimensional (2D) and 3D rotations/orientations of intracellular objects is discussed. We also discuss how a change in the shape of a red blood cell (RBC) suspended in hypertonic buffer leads to its rotation when it is optically tweezed. The potential use of this approach for the diagnosis of malaria is also illustrated. The use of a line tweezers having an asymmetric intensity distribution about the center of its major axis for simultaneous transport of microscopic objects, and the successful use of this approach for induction, enhancement, and guidance of neuronal growth cones is presented next. Finally, we describe laser microbeam-assisted microinjection of impermeable drugs into cells and also briefly discuss possible adverse effects of the laser trap or microbeams on cells.

False-Positive Rate of AKI Using Consensus Creatinine–Based Criteria

PubMed Central

Lin, Jennie; Fernandez, Hilda; Shashaty, Michael G.S.; Negoianu, Dan; Testani, Jeffrey M.; Berns, Jeffrey S.; Parikh, Chirag R.

2015-01-01

Background and objectives Use of small changes in serum creatinine to diagnose AKI allows for earlier detection but may increase diagnostic false–positive rates because of inherent laboratory and biologic variabilities of creatinine. Design, setting, participants, & measurements We examined serum creatinine measurement characteristics in a prospective observational clinical reference cohort of 2267 adult patients with AKI by Kidney Disease Improving Global Outcomes creatinine criteria and used these data to create a simulation cohort to model AKI false–positive rates. We simulated up to seven successive blood draws on an equal population of hypothetical patients with unchanging true serum creatinine values. Error terms generated from laboratory and biologic variabilities were added to each simulated patient’s true serum creatinine value to obtain the simulated measured serum creatinine for each blood draw. We determined the proportion of patients who would be erroneously diagnosed with AKI by Kidney Disease Improving Global Outcomes creatinine criteria. Results Within the clinical cohort, 75.0% of patients received four serum creatinine draws within at least one 48-hour period during hospitalization. After four simulated creatinine measurements that accounted for laboratory variability calculated from assay characteristics and 4.4% of biologic variability determined from the clinical cohort and publicly available data, the overall false–positive rate for AKI diagnosis was 8.0% (interquartile range =7.9%–8.1%), whereas patients with true serum creatinine ≥1.5 mg/dl (representing 21% of the clinical cohort) had a false–positive AKI diagnosis rate of 30.5% (interquartile range =30.1%–30.9%) versus 2.0% (interquartile range =1.9%–2.1%) in patients with true serum creatinine values <1.5 mg/dl (P<0.001). Conclusions Use of small serum creatinine changes to diagnose AKI is limited by high false–positive rates caused by inherent variability of serum creatinine at higher baseline values, potentially misclassifying patients with CKD in AKI studies. PMID:26336912

PPARα siRNA–Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy

PubMed Central

Dai, Xudong; Souza, Angus T. De; Dai, Hongyue; Lewis, David L; Lee, Chang-kyu; Spencer, Andy G; Herweijer, Hans; Hagstrom, Jim E; Linsley, Peter S; Bassett, Douglas E; Ulrich, Roger G; He, Yudong D

2007-01-01

Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi) phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs) against the gene for peroxisome proliferator-activated receptor α (Ppara), our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARα-induced liver hypertrophy is supported by their ability to predict non-PPARα–induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005). Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug-induced toxicity from siRNA-treated expression profiles. When combined with phenotypic evaluation, our approach should help to unleash the full potential of siRNAs in systematically unveiling the molecular mechanism of biological events. PMID:17335344

Low-gravity Orbiting Research Laboratory Environment Potential Impact on Space Biology Research

NASA Technical Reports Server (NTRS)

Jules, Kenol

2006-01-01

One of the major objectives of any orbital space research platform is to provide a quiescent low gravity, preferably a zero gravity environment, to perform fundamental as well as applied research. However, small disturbances exist onboard any low earth orbital research platform. The impact of these disturbances must be taken into account by space research scientists during their research planning, design and data analysis in order to avoid confounding factors in their science results. The reduced gravity environment of an orbiting research platform in low earth orbit is a complex phenomenon. Many factors, among others, such as experiment operations, equipment operation, life support systems and crew activity (if it is a crewed platform), aerodynamic drag, gravity gradient, rotational effects as well as the vehicle structural resonance frequencies (structural modes) contribute to form the overall reduced gravity environment in which space research is performed. The contribution of these small disturbances or accelerations is precisely why the environment is NOT a zero gravity environment, but a reduced acceleration environment. This paper does not discuss other factors such as radiation, electromagnetic interference, thermal and pressure gradient changes, acoustic and CO2 build-up to name a few that affect the space research environment as well, but it focuses solely on the magnitude of the acceleration level found on orbiting research laboratory used by research scientists to conduct space research. For ease of analysis this paper divides the frequency spectrum relevant to most of the space research disciplines into three regimes: a) quasi-steady, b) vibratory and c) transient. The International Space Station is used as an example to illustrate the point. The paper discusses the impact of these three regimes on space biology research and results from space flown experiments are used to illustrate the potential negative impact of these disturbances (accelerations) on space biology research.

A comparison of form processing involved in the perception of biological and nonbiological movements

PubMed Central

Thurman, Steven M.; Lu, Hongjing

2016-01-01

Although there is evidence for specialization in the human brain for processing biological motion per se, few studies have directly examined the specialization of form processing in biological motion perception. The current study was designed to systematically compare form processing in perception of biological (human walkers) to nonbiological (rotating squares) stimuli. Dynamic form-based stimuli were constructed with conflicting form cues (position and orientation), such that the objects were perceived to be moving ambiguously in two directions at once. In Experiment 1, we used the classification image technique to examine how local form cues are integrated across space and time in a bottom-up manner. By comparing with a Bayesian observer model that embodies generic principles of form analysis (e.g., template matching) and integrates form information according to cue reliability, we found that human observers employ domain-general processes to recognize both human actions and nonbiological object movements. Experiments 2 and 3 found differential top-down effects of spatial context on perception of biological and nonbiological forms. When a background does not involve social information, observers are biased to perceive foreground object movements in the direction opposite to surrounding motion. However, when a background involves social cues, such as a crowd of similar objects, perception is biased toward the same direction as the crowd for biological walking stimuli, but not for rotating nonbiological stimuli. The model provided an accurate account of top-down modulations by adjusting the prior probabilities associated with the internal templates, demonstrating the power and flexibility of the Bayesian approach for visual form perception. PMID:26746875

Identification of Direct Protein Targets of Small Molecules

PubMed Central

2010-01-01

Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area. PMID:21077692

How to build a course in mathematical-biological modeling: content and processes for knowledge and skill.

PubMed

Hoskinson, Anne-Marie

2010-01-01

Biological problems in the twenty-first century are complex and require mathematical insight, often resulting in mathematical models of biological systems. Building mathematical-biological models requires cooperation among biologists and mathematicians, and mastery of building models. A new course in mathematical modeling presented the opportunity to build both content and process learning of mathematical models, the modeling process, and the cooperative process. There was little guidance from the literature on how to build such a course. Here, I describe the iterative process of developing such a course, beginning with objectives and choosing content and process competencies to fulfill the objectives. I include some inductive heuristics for instructors seeking guidance in planning and developing their own courses, and I illustrate with a description of one instructional model cycle. Students completing this class reported gains in learning of modeling content, the modeling process, and cooperative skills. Student content and process mastery increased, as assessed on several objective-driven metrics in many types of assessments.

How to Build a Course in Mathematical–Biological Modeling: Content and Processes for Knowledge and Skill

PubMed Central

2010-01-01

Biological problems in the twenty-first century are complex and require mathematical insight, often resulting in mathematical models of biological systems. Building mathematical–biological models requires cooperation among biologists and mathematicians, and mastery of building models. A new course in mathematical modeling presented the opportunity to build both content and process learning of mathematical models, the modeling process, and the cooperative process. There was little guidance from the literature on how to build such a course. Here, I describe the iterative process of developing such a course, beginning with objectives and choosing content and process competencies to fulfill the objectives. I include some inductive heuristics for instructors seeking guidance in planning and developing their own courses, and I illustrate with a description of one instructional model cycle. Students completing this class reported gains in learning of modeling content, the modeling process, and cooperative skills. Student content and process mastery increased, as assessed on several objective-driven metrics in many types of assessments. PMID:20810966

A semi-automated image analysis procedure for in situ plankton imaging systems.

PubMed

Bi, Hongsheng; Guo, Zhenhua; Benfield, Mark C; Fan, Chunlei; Ford, Michael; Shahrestani, Suzan; Sieracki, Jeffery M

2015-01-01

Plankton imaging systems are capable of providing fine-scale observations that enhance our understanding of key physical and biological processes. However, processing the large volumes of data collected by imaging systems remains a major obstacle for their employment, and existing approaches are designed either for images acquired under laboratory controlled conditions or within clear waters. In the present study, we developed a semi-automated approach to analyze plankton taxa from images acquired by the ZOOplankton VISualization (ZOOVIS) system within turbid estuarine waters, in Chesapeake Bay. When compared to images under laboratory controlled conditions or clear waters, images from highly turbid waters are often of relatively low quality and more variable, due to the large amount of objects and nonlinear illumination within each image. We first customized a segmentation procedure to locate objects within each image and extracted them for classification. A maximally stable extremal regions algorithm was applied to segment large gelatinous zooplankton and an adaptive threshold approach was developed to segment small organisms, such as copepods. Unlike the existing approaches for images acquired from laboratory, controlled conditions or clear waters, the target objects are often the majority class, and the classification can be treated as a multi-class classification problem. We customized a two-level hierarchical classification procedure using support vector machines to classify the target objects (< 5%), and remove the non-target objects (> 95%). First, histograms of oriented gradients feature descriptors were constructed for the segmented objects. In the first step all non-target and target objects were classified into different groups: arrow-like, copepod-like, and gelatinous zooplankton. Each object was passed to a group-specific classifier to remove most non-target objects. After the object was classified, an expert or non-expert then manually removed the non-target objects that could not be removed by the procedure. The procedure was tested on 89,419 images collected in Chesapeake Bay, and results were consistent with visual counts with >80% accuracy for all three groups.

A Semi-Automated Image Analysis Procedure for In Situ Plankton Imaging Systems

PubMed Central

Bi, Hongsheng; Guo, Zhenhua; Benfield, Mark C.; Fan, Chunlei; Ford, Michael; Shahrestani, Suzan; Sieracki, Jeffery M.

2015-01-01

Plankton imaging systems are capable of providing fine-scale observations that enhance our understanding of key physical and biological processes. However, processing the large volumes of data collected by imaging systems remains a major obstacle for their employment, and existing approaches are designed either for images acquired under laboratory controlled conditions or within clear waters. In the present study, we developed a semi-automated approach to analyze plankton taxa from images acquired by the ZOOplankton VISualization (ZOOVIS) system within turbid estuarine waters, in Chesapeake Bay. When compared to images under laboratory controlled conditions or clear waters, images from highly turbid waters are often of relatively low quality and more variable, due to the large amount of objects and nonlinear illumination within each image. We first customized a segmentation procedure to locate objects within each image and extracted them for classification. A maximally stable extremal regions algorithm was applied to segment large gelatinous zooplankton and an adaptive threshold approach was developed to segment small organisms, such as copepods. Unlike the existing approaches for images acquired from laboratory, controlled conditions or clear waters, the target objects are often the majority class, and the classification can be treated as a multi-class classification problem. We customized a two-level hierarchical classification procedure using support vector machines to classify the target objects (< 5%), and remove the non-target objects (> 95%). First, histograms of oriented gradients feature descriptors were constructed for the segmented objects. In the first step all non-target and target objects were classified into different groups: arrow-like, copepod-like, and gelatinous zooplankton. Each object was passed to a group-specific classifier to remove most non-target objects. After the object was classified, an expert or non-expert then manually removed the non-target objects that could not be removed by the procedure. The procedure was tested on 89,419 images collected in Chesapeake Bay, and results were consistent with visual counts with >80% accuracy for all three groups. PMID:26010260

Acoustic suspension system

NASA Technical Reports Server (NTRS)

Lee, M. C.; Wang, T. G. (Inventor)

1983-01-01

An acoustic levitation system is described, with single acoustic source and a small reflector to stably levitate a small object while the object is processed as by coating or heating it. The system includes a concave acoustic source which has locations on opposite sides of its axis that vibrate towards and away from a focal point to generate a converging acoustic field. A small reflector is located near the focal point, and preferably slightly beyond it, to create an intense acoustic field that stably supports a small object near the reflector. The reflector is located about one-half wavelength from the focal point and is concavely curved to a radius of curvature (L) of about one-half the wavelength, to stably support an object one-quarter wavelength (N) from the reflector.

Adding small differences can increase similarity and choice.

PubMed

Kim, Jongmin; Novemsky, Nathan; Dhar, Ravi

2013-02-01

Similarity plays a critical role in many judgments and choices. Traditional models of similarity posit that increasing the number of differences between objects cannot increase judged similarity between them. In contrast to these previous models, the present research shows that introducing a small difference in an attribute that previously was identical across objects can increase perceived similarity between those objects. We propose an explanation based on the idea that small differences draw more attention than identical attributes do and that people's perceptions of similarity involve averaging attributes that are salient. We provide evidence that introducing small differences between objects increases perceived similarity. We also show that an increase in similarity decreases the difficulty of choice and the likelihood that a choice will be deferred.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

PubMed Central

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

Observing and understanding the ultrafast photochemistry in small molecules: applications to sunscreens.

PubMed

Baker, Lewis A; Stavros, Vasilios G

2016-09-01

In this review, we discuss the importance of biological and artificial photoprotection against overexposure to harmful ultraviolet radiation. Transient electronic and transient vibrational absorption spectroscopies are highlighted as important tools in understanding the energy transfer in small molecules, with a focus on the application to commercial sunscreens with representative examples given. Oxybenzone, a common ingredient in commercial sunscreens and sinapoyl malate, a biological sunscreen in plant leaves are presented as case studies.

Along the Central Dogma-Controlling Gene Expression with Small Molecules.

PubMed

Schneider-Poetsch, Tilman; Yoshida, Minoru

2018-05-04

The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Radar system components to detect small and fast objects

NASA Astrophysics Data System (ADS)

Hülsmann, Axel; Zech, Christian; Klenner, Mathias; Tessmann, Axel; Leuther, Arnulf; Lopez-Diaz, Daniel; Schlechtweg, Michael; Ambacher, Oliver

2015-05-01

Small and fast objects, for example bullets of caliber 5 to 10 mm, fired from guns like AK-47, can cause serious problems to aircrafts in asymmetric warfare. Especially slow and big aircrafts, like heavy transport helicopters are an easy mark of small caliber hand fire weapons. These aircrafts produce so much noise, that the crew is not able to recognize an attack unless serious problems occur and important systems of the aircraft fail. This is just one of many scenarios, where the detection of fast and small objects is desirable. Another scenario is the collision of space debris particles with satellites.

Integrated Chemistry and Biology for First-Year College Students

ERIC Educational Resources Information Center

Abdella, Beth R. J.; Walczak, Mary M.; Kandl, Kim A.; Schwinefus, Jeffrey J.

2011-01-01

A three-course sequence for first-year students that integrates beginning concepts in biology and chemistry has been designed. The first two courses that emphasize chemistry and its capacity to inform biological applications are described here. The content of the first course moves from small to large particles with an emphasis on membrane…

Outdoor Biology Instructional Strategies Trial Edition, Set IV.

ERIC Educational Resources Information Center

Throgmorton, Larry, Ed.; And Others

Eight games are included in the 24 activities in the Outdoor Biology Instructional Strategies (OBIS) Trial Edition Set IV. There are also simulations, crafts, biological techniques, and organism investigations focusing on animal and plant life in the forest, desert, and snow. Designed for small groups of children ages 10 to 15 from schools and…

Finding Clarity by Fostering Confusion: Reflections on Teaching an Undergraduate Integrated Biological Systems Course

ERIC Educational Resources Information Center

Martin, Kirsten H.

2015-01-01

Undergraduate biology programs in smaller liberal arts colleges are increasingly becoming focused on health science fields. This narrowing of focus potentially decreases opportunities for these students to explore other sub-fields of biology. This perspectives article highlights how one small university in Connecticut decided to institute a…

Outdoor Education, Junior Biology Field Studies.

ERIC Educational Resources Information Center

Aikman, John H.; And Others

Field studies for grade nine and ten biology students are developed in this teacher and student guide for outdoor education. A small section is devoted to teacher pre-planning and final sections are concerned with equipment, audio-visual resources, and a large booklist. Twenty-three investigations related to earth science and biology topics are…

Biopharmaceuticals: From peptide to drug

NASA Astrophysics Data System (ADS)

Hannappel, Margarete

2017-08-01

Biologics are therapeutic proteins or peptides that are produced by means of biological processes within living organisms and cells. They are highly specific molecules and play a crucial role as therapeutics for the treatment of severe and chronic diseases (e.g. cancer, rheumatoid arthritis, diabetes, autoimmune disorders). The development of new biologics and biologics-based drugs gains more and more importance in the fight against various diseases. A short overview on biotherapeutical drug development is given. Cone snails are a large group of poisonous, predatory sea snails with more than 700 species. They use a very powerful venom which rapidly inactivates and paralyzes their prey. Most bioactive venom components are small peptides (conotoxins, conopeptides) which are precisely directed towards a specific target (e.g. ion channel, receptors). Due to their small size, their precision and speed of action, naturally occurring cone snail venom peptides represent an attractive source for the identification and design of novel biological drug entities. The Jagna cone snail project is an encouraging initiative to map the ecological variety of cone snails around the island of Bohol (Philippines) and to conserve the biological information for potential future application.

Insights from Small-"N" Studies

ERIC Educational Resources Information Center

Gouvea, Julia

2017-01-01

Small-"N" studies have been relatively uncommon in biology education research and are likely less familiar to instructors and administrators than large-"N" studies. Nevertheless, many scholars in the social sciences have argued for the value of small-"N" studies in informing research and practice (e.g., Flyvbjerg…

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

PubMed Central

Sterling, Catherine H.; Veksler-Lublinsky, Isana; Ambros, Victor

2015-01-01

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate that the method provides a significant improvement in sensitivity compared to previous cloning methods while maintaining reproducible identification of diverse small RNA species. This method should have widespread applications in a variety of contexts, including biomarker discovery from scarce samples of human tissue or body fluids. PMID:25056322

Physical activity, subjective sleep quality and time in bed do not vary by moon phase in German adolescents.

PubMed

Smith, Maia P; Standl, Marie; Schulz, Holger; Heinrich, Joachim

2017-06-01

Lunar periodicity in human biology and behaviour, particularly sleep, has been reported. However, estimated relationships vary in direction (more or less sleep with full moon) if they exist at all, and studies tend to be so small that there is potential for confounding by weekly or monthly cycles. Lunar variation in physical activity has been posited as a driver of this relationship, but is likewise not well studied. We explore the association between lunar cycle, sleep and physical activity in a population-based sample of 1411 Germans age 14-17 years (46% male). Physical activity (daily minutes moderate-to-vigorous activity) was objectively assessed by accelerometry for a total of 8832 days between 2011 and 2014. At the same time, time in bed (h) and subjective sleep quality (1-6) were diaried each morning. In models corrected for confounding, we found that lunar phase was not significantly associated with physical activity, subjective sleep quality or time in bed in either sex, regardless of season. Observed relationships varied randomly in direction between models, suggesting artefact. Thus, this large, objectively-measured and well-controlled population of adolescents displayed no lunar periodicity in objective physical activity, subjective sleep quality or time in bed. © 2016 European Sleep Research Society.

[Prospects for Application of Gases and Gas Hydrates to Cryopreservation].

PubMed

Shishova, N V; Fesenko, E E

2015-01-01

In the present review, we tried to evaluate the known properties of gas hydrates and gases participating in the formation of gas hydrates from the point of view of the mechanisms of cryoinjury and cryoprotection, to consider the papers on freezing biological materials in the presence of inert gases, and to analyze the perspectives for the development of this direction. For the purpose, we searched for the information on the physical properties of gases and gas hydrates, compared processes occured during the formation of gas hydrates and water ice, analyzed the influence of the formation and growth of gas hydrates on the structure of biological objects. We prepared a short review on the biological effects of xenon, krypton, argon, carbon dioxide, hydrogen sulfide, and carbon monoxide especially on hypothermal conditions and probable application of these properties in cryopreservation technologies. The description of the existing experiments on cryopreservation of biological objects with the use of gases was analyzed. On the basis of the information we found, the most perspective directions of work in the field of cryopreservation of biological objects with the use of gases were outlined. An attempt was made to forecast the potential problems in this field.

Reaction-based small-molecule fluorescent probes for chemoselective bioimaging

PubMed Central

Chan, Jefferson; Dodani, Sheel C.; Chang, Christopher J.

2014-01-01

The dynamic chemical diversity of elements, ions and molecules that form the basis of life offers both a challenge and an opportunity for study. Small-molecule fluorescent probes can make use of selective, bioorthogonal chemistries to report on specific analytes in cells and in more complex biological specimens. These probes offer powerful reagents to interrogate the physiology and pathology of reactive chemical species in their native environments with minimal perturbation to living systems. This Review presents a survey of tools and tactics for using such probes to detect biologically important chemical analytes. We highlight design criteria for effective chemical tools for use in biological applications as well as gaps for future exploration. PMID:23174976

How chemistry supports cell biology: the chemical toolbox at your service.

PubMed

Wijdeven, Ruud H; Neefjes, Jacques; Ovaa, Huib

2014-12-01

Chemical biology is a young and rapidly developing scientific field. In this field, chemistry is inspired by biology to create various tools to monitor and modulate biochemical and cell biological processes. Chemical contributions such as small-molecule inhibitors and activity-based probes (ABPs) can provide new and unique insights into previously unexplored cellular processes. This review provides an overview of recent breakthroughs in chemical biology that are likely to have a significant impact on cell biology. We also discuss the application of several chemical tools in cell biology research. Copyright © 2014 Elsevier Ltd. All rights reserved.

AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

PubMed Central

Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2016-01-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

Method for detection of long-lived radioisotopes in small biochemical samples

DOEpatents

Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.; Davis, J.C.

1994-11-22

Disclosed is a method for detection of long-lived radioisotopes in small biochemical samples, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering the chemical specie to the biologist host in doses sufficiently low to avoid significant overt damage to the biological system, d. allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host, e. isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources, f. converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in the material by means of direct isotopic counting. 5 figs.

An overview of computational life science databases & exchange formats of relevance to chemical biology research.

PubMed

Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2013-03-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

Method for detection of long-lived radioisotopes in small biochemical samples

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.

1994-01-01

Disclosed is a method for detection of long-lived radioisotopes in small bio-chemical samples, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biologist host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Deep Residual Network Predicts Cortical Representation and Organization of Visual Features for Rapid Categorization.

PubMed

Wen, Haiguang; Shi, Junxing; Chen, Wei; Liu, Zhongming

2018-02-28

The brain represents visual objects with topographic cortical patterns. To address how distributed visual representations enable object categorization, we established predictive encoding models based on a deep residual network, and trained them to predict cortical responses to natural movies. Using this predictive model, we mapped human cortical representations to 64,000 visual objects from 80 categories with high throughput and accuracy. Such representations covered both the ventral and dorsal pathways, reflected multiple levels of object features, and preserved semantic relationships between categories. In the entire visual cortex, object representations were organized into three clusters of categories: biological objects, non-biological objects, and background scenes. In a finer scale specific to each cluster, object representations revealed sub-clusters for further categorization. Such hierarchical clustering of category representations was mostly contributed by cortical representations of object features from middle to high levels. In summary, this study demonstrates a useful computational strategy to characterize the cortical organization and representations of visual features for rapid categorization.

Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yubin; Yuan, Zhen, E-mail: zhenyuan@umac.mo

Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects withmore » different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular, their methods are able to resolve the intrinsic difficulties that occur when quantitative PAT is conducted by combining conventional PAT with the diffusion approximation or with radiation transport modeling.« less

Evaluation of post-authorization safety studies in the first cohort of EU Risk Management Plans at time of regulatory approval.

PubMed

Giezen, Thijs J; Mantel-Teeuwisse, Aukje K; Straus, Sabine M J M; Egberts, Toine C G; Blackburn, Stella; Persson, Ingemar; Leufkens, Hubert G M

2009-01-01

Since November 2005, an EU Risk Management Plan (EU-RMP) has had to be submitted as part of a marketing application for all new chemical entities in the EU. In the EU-RMP, the safety profile of the medicine has to be described and pharmacovigilance activities should be proposed to study further safety concerns during use of the drug in the real-world setting. These activities include, for example, collection of spontaneously reported adverse events and post-authorization safety studies (PASS). Since the submission of an EU-RMP is a relatively new requirement, there is limited knowledge on the quality and completeness of the study protocols of PASS at the time of approval and there are no data on the influence of certain drug characteristics on the proposed pharmacovigilance activities. To examine the types of proposed pharmacovigilance activities in a sample of EU-RMPs, describe and evaluate the methodology of PASS, identify problems and propose remedies, and compare characteristics between biologicals and small molecules. Eighteen EU-RMPs (nine for biologicals, nine for small molecules) given a positive decision regarding the marketing application by the Committee for Medicinal Products for Human Use between November 2005 and May 2007 were included in this descriptive cohort study. The EU-RMPs were selected over time and different therapeutic areas. Classification of the safety concerns ('important identified risks', 'important potential risks', 'important missing information' within the EU-RMP was studied. For PASS, data source (registry, population-based database, sponsor-owned clinical trial database), source of study population to be included in PASS and comprehensiveness of study protocol (full protocol, limited protocol, study synopsis, short description, commitment without further information) were studied. Compared to small molecules, safety concerns for biologicals were less frequently classified as important identified risks (relative risk [RR] 0.6; 95% CI 0.3, 1.0) and more frequently as important missing information (RR 1.6; 95% CI 1.0, 2.7). Forty-seven PASS were proposed; 31 for biologicals and 16 for small molecules. Compared with studies proposed in population-based databases (4 for biologicals, 8 for small molecules), studies in registries (18 for biologicals, 4 for small molecules) were more frequently proposed for biologicals than for small molecules (RR 2.5; 95% CI 1.1, 5.7). About 60% of the proposed PASS will include EU inhabitants. No full study protocols were submitted; 26% involved a limited study protocol, 33% a study synopsis, 37% a short description and 4% a commitment without further information. Approximately 40% of the study proposals for PASS were classified as a short description or a commitment to perform a study without further information, precluding an adequate scientific assessment. Studying non-EU populations may give rise to difficulties with generalizability of the results to the EU due to differences in patient characteristics, differences in the indication for the medicine and different healthcare systems. This study emphasizes the need for more complete study proposals to be submitted earlier on in the evaluation period and for the inclusion of EU inhabitants in PASS. In addition, differences in the characteristics between biologicals and small molecules, e.g. in the data source proposed, support the need for individualized tailored PASS depending on the type of drug.

Mathematical and numerical challenges in living biological materials

NASA Astrophysics Data System (ADS)

Forest, M. Gregory; Vasquez, Paula A.

2013-10-01

The proclaimed Century of Biology is rapidly leading to the realization of how starkly different and more complex biological materials are than the materials that underpinned the industrial and technological revolution. These differences arise, in part, because biological matter exhibits both viscous and elastic behavior. Moreover, this behavior varies across the frequency, wavelength and amplitude spectrum of forcing. This broadclass of responsesin biological matter requires multiple frequency-dependent functions to specify material behavior, instead of a discrete set of parameters that relate to either viscosity or elasticity. This complexity prevails even if the biological matter is assumed to be spatially homogeneous, which is rarely true. However, very little progress has been made on the characterization of heterogeneity and how to build that information into constitutive laws and predictive models. In addition, most biological matter is non-stationary, which motivates the term "living". Biomaterials typically are in an active state in order to perform certain functions, and they often are modified or replenished on the basis of external stimuli. It has become popular in materials engineering to try to duplicate some of the functionality of biomaterials, e.g., a lot of effort has gone into the design of self-assembling, self-healing and shape shifting materials. These distinguishing features of biomaterials require significantly more degrees of freedom than traditional composites and many of the molecular species and their roles in functionality have yet to be determined. A typical biological material includes small molecule biochemical species that react and diffuse within larger species. These large molecular weightspecies provide the primary structural and biophysical properties of the material. The small molecule binding and unbinding kinetics serves to modulate material properties, and typical small molecule production and release are governed by external stimuli (e.g., stress). The bottom line is that the mathematical and numerical tools of 20th Century materials science are often insufficient for describing biological materials and for predicting their behavior both in vitro and in vivo.

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism.

PubMed

Korecka, Agata; Dona, Anthony; Lahiri, Shawon; Tett, Adrian James; Al-Asmakh, Maha; Braniste, Viorica; D'Arienzo, Rossana; Abbaspour, Afrouz; Reichardt, Nicole; Fujii-Kuriyama, Yoshiaki; Rafter, Joseph; Narbad, Arjan; Holmes, Elaine; Nicholson, Jeremy; Arulampalam, Velmurugesan; Pettersson, Sven

2016-01-01

The ligand-induced transcription factor, aryl hydrocarbon receptor (AhR) is known for its capacity to tune adaptive immunity and xenobiotic metabolism-biological properties subject to regulation by the indigenous microbiome. The objective of this study was to probe the postulated microbiome-AhR crosstalk and whether such an axis could influence metabolic homeostasis of the host. Utilising a systems-biology approach combining in-depth 1 H-NMR-based metabonomics (plasma, liver and skeletal muscle) with microbiome profiling (small intestine, colon and faeces) of AhR knockout (AhR -/- ) and wild-type (AhR +/+ ) mice, we assessed AhR function in host metabolism. Microbiome metabolites such as short-chain fatty acids were found to regulate AhR and its target genes in liver and intestine. The AhR signalling pathway, in turn, was able to influence microbiome composition in the small intestine as evident from microbiota profiling of the AhR +/+ and AhR -/- mice fed with diet enriched with a specific AhR ligand or diet depleted of any known AhR ligands. The AhR -/- mice also displayed increased levels of corticosterol and alanine in serum. In addition, activation of gluconeogenic genes in the AhR -/- mice was indicative of on-going metabolic stress. Reduced levels of ketone bodies and reduced expression of genes involved in fatty acid metabolism in the liver further underscored this observation. Interestingly, exposing AhR -/- mice to a high-fat diet showed resilience to glucose intolerance. Our data suggest the existence of a bidirectional AhR-microbiome axis, which influences host metabolic pathways.

Detection of small number of Giardia in biological materials prepared from stray dogs.

PubMed

Esmailikia, Leila; Ebrahimzade, Elahe; Shayan, Parviz; Amininia, Narges

2017-12-20

Giardia lamblia is an intestinal protozoa with intermittent and low shedding especially in dogs, and the detection of Giardia is accompanied with problems such as sampling and diagnostic method. The objective of this study was to detection of Giardia in biological materials with low number of parasite using parasitological and molecular methods, and also to determine whether the examined stray dogs harbor known zoonotic genotype of Giardia. For this aim 85 fecal and duodenal samples were studied from which 1 was positive by Trichrome staining of stool, 4 were positive by staining of duodenal samples. The nested PCR analysis with primers derived from 18 SrRNA showed that the specific PCR product could be amplified in 4 stool and 4 duodenal samples. All positive samples in staining analysis were also positive in nested PCR. No amplification could be observed by nested PCR with primers derived from β giardin gene due to the single copy of gene. Interestingly, the extracted DNA from old fixed stained Giardia positive smears could be also amplified with primers derived from 18SrRNA gene. The sequence analysis of nested PCR products showed that they belong to the genotype D. In conclusion, it is to denote that the Trichrome or Giemsa methods were not suitable for the detection of small number of this parasite in stool and the nested PCR with primers derived from 18S rRNA gene can replace the traditional methods successfully. For detection of Giardia in stool, primers derived from β giardin will not be recommended.

Kinematic measurement from panned cinematography.

PubMed

Gervais, P; Bedingfield, E W; Wronko, C; Kollias, I; Marchiori, G; Kuntz, J; Way, N; Kuiper, D

1989-06-01

Traditional 2-D cinematography has used a stationary camera with its optical axis perpendicular to the plane of motion. This method has constrained the size of the object plane or has introduced potential errors from a small subject image size with large object field widths. The purpose of this study was to assess a panning technique that could overcome the inherent limitations of small object field widths, small object image sizes and limited movement samples. The proposed technique used a series of reference targets in the object field that provided the necessary scales and origin translations. A 102 m object field was panned. Comparisons between criterion distances and film measured distances for field widths of 46 m and 22 m resulted in absolute mean differences that were comparable to that of the traditional method.

Market uptake of biologic and small-molecule--targeted oncology drugs in Europe.

PubMed

Obradovic, Marko; Mrhar, Ales; Kos, Mitja

2009-12-01

The aim of this study was to investigate the market uptake of biologic and small-molecule-targeted oncology drugs in Europe. Targeted oncology drugs that were used in one of the selected European countries before the end of 2007 were eligible for inclusion in the analysis. The following European countries were included: Austria, Croatia, France, Germany, Hungary, Italy, Slovenia, and the United Kingdom. Monetary market uptake of targeted oncology drugs was assessed by using sales data (in euros) obtained from 2 large data- bases for the period 1997-2007. Market uptake was assessed in terms of expenditures for specific drugs in euros per capita and in market shares. The monetary market uptake of targeted oncology drugs had an exponential growth from 1997 to 2007 in all comparison countries and reached 40% of the total oncology drug market in 2007. Although the various European countries allocate substantially different amounts of resources per capita for oncology drugs, the share of expenditures attributed to targeted oncology drugs did not differ substantially among the countries. Biologic molecules were used in clinical practice before the small-molecule-targeted oncology drugs. Targeted oncology drugs that were introduced first to clinical practice in most of the comparison countries (ie, rituximab, trastuzumab, imatinib mesylate) maintained the leading positions on the market throughout the period of the analysis. In 2007, approximately 25% of all expenditures for oncology drugs were attributed to biologic oncology drugs, and approximately 15% were spent on small-molecule-targeted oncology drugs. Expenditures on targeted oncology drugs have been increasing exponentially in Europe throughout the past decade and have reached a 40% share of the oncology drug market. As of 2007, the market share of biologic oncology drugs was higher than the market share of small-molecule-targeted oncology drugs. Copyright 2009 Excerpta Medica Inc. All rights reserved.

Going wild: what a global small-animal tracking system could do for experimental biologists.

PubMed

Wikelski, Martin; Kays, Roland W; Kasdin, N Jeremy; Thorup, Kasper; Smith, James A; Swenson, George W

2007-01-01

Tracking animals over large temporal and spatial scales has revealed invaluable and spectacular biological information, particularly when the paths and fates of individuals can be monitored on a global scale. However, only large animals (greater than approximately 300 g) currently can be followed globally because of power and size constraints on the tracking devices. And yet the vast majority of animals is small. Tracking small animals is important because they are often part of evolutionary and ecological experiments, they provide important ecosystem services and they are of conservation concern or pose harm to human health. Here, we propose a small-animal satellite tracking system that would enable the global monitoring of animals down to the size of the smallest birds, mammals (bats), marine life and eventually large insects. To create the scientific framework necessary for such a global project, we formed the ICARUS initiative (www.IcarusInitiative.org), the International Cooperation for Animal Research Using Space. ICARUS also highlights how small-animal tracking could address some of the ;Grand Challenges in Environmental Sciences' identified by the US National Academy of Sciences, such as the spread of infectious diseases or the relationship between biological diversity and ecosystem functioning. Small-animal tracking would allow the quantitative assessment of dispersal and migration in natural populations and thus help solve enigmas regarding population dynamics, extinctions and invasions. Experimental biologists may find a global small-animal tracking system helpful in testing, validating and expanding laboratory-derived discoveries in wild, natural populations. We suggest that the relatively modest investment into a global small-animal tracking system will pay off by providing unprecedented insights into both basic and applied nature. Tracking small animals over large spatial and temporal scales could prove to be one of the most powerful techniques of the early 21st century, offering potential solutions to a wide range of biological and societal questions that date back two millennia to the Greek philosopher Aristotle's enigma about songbird migration. Several of the more recent Grand Challenges in Environmental Sciences, such as the regulation and functional consequences of biological diversity or the surveillance of the population ecology of zoonotic hosts, pathogens or vectors, could also be addressed by a global small-animal tracking system. Our discussion is intended to contribute to an emerging groundswell of scientific support to make such a new technological system happen.

Mind the gap: the minimal detectable separation distance between two objects during active electrolocation.

PubMed

Fechler, K; Holtkamp, D; Neusel, G; Sanguinetti-Scheck, J I; Budelli, R; von der Emde, G

2012-12-01

In a food-rewarded two-alternative forced-choice procedure, it was determined how well the weakly electric elephantnose fish Gnathonemus petersii can sense gaps between two objects, some of which were placed in front of complex backgrounds. The results show that at close distances, G. petersii is able to detect gaps between two small metal cubes (2 cm × 2 cm × 2 cm) down to a width of c. 1·5 mm. When larger objects (3 cm × 3 cm × 3 cm) were used, gaps with a width of 2-3 mm could still be detected. Discrimination performance was better (c. 1 mm gap size) when the objects were placed in front of a moving background consisting of plastic stripes or plant leaves, indicating that movement in the environment plays an important role for object identification. In addition, the smallest gap size that could be detected at increasing distances was determined. A linear relationship between object distance and gap size existed. Minimal detectable gap sizes increased from c. 1·5 mm at a distance of 1 cm, to 20 mm at a distance of 7 cm. Measurements and simulations of the electric stimuli occurring during gap detection revealed that the electric images of two close objects influence each other and superimpose. A large gap of 20 mm between two objects induced two clearly separated peaks in the electric image, while a 2 mm gap caused just a slight indentation in the image. Therefore, the fusion of electric images limits spatial resolution during active electrolocation. Relative movements either between the fish and the objects or between object and background might improve spatial resolution by accentuating the fine details of the electric images. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms.

PubMed

Schmidt, Markus; Pei, Lei; Budisa, Nediljko

The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.

NASA space biology accomplishments, 1982

NASA Technical Reports Server (NTRS)

Halstead, T. W.; Pleasant, L. G.

1983-01-01

Summaries of NASA's Space Biology Program projects are provided. The goals, objectives, accomplishments, and future plans of each project are described in this publication as individual technical summaries.

Individual wealth rank, community wealth inequality, and self-reported adult poor health: a test of hypotheses with panel data (2002-2006) from native Amazonians, Bolivia.

PubMed

Undurraga, Eduardo A; Nyberg, Colleen; Eisenberg, Dan T A; Magvanjav, Oyunbileg; Reyes-García, Victoria; Huanca, Tomás; Leonard, William R; McDade, Thomas W; Tanner, Susan; Vadez, Vincent; Godoy, Ricardo

2010-12-01

Growing evidence suggests that economic inequality in a community harms the health of a person. Using panel data from a small-scale, preindustrial rural society, we test whether individual wealth rank and village wealth inequality affects self-reported poor health in a foraging-farming native Amazonian society. A person's wealth rank was negatively but weakly associated with self-reported morbidity. Each step up/year in the village wealth hierarchy reduced total self-reported days ill by 0.4 percent. The Gini coefficient of village wealth inequality bore a positive association with self-reported poor health that was large in size, but not statistically significant. We found small village wealth inequality, and evidence that individual economic rank did not change. The modest effects may have to do with having used subjective rather than objective measures of health, having small village wealth inequality, and with the possibly true modest effect of a person's wealth rank on health in a small-scale, kin-based society. Finally, we also found that an increase in mean individual wealth by village was related to worse self-reported health. As the Tsimane' integrate into the market economy, their possibilities of wealth accumulation rise, which may affect their well-being. Our work contributes to recent efforts in biocultural anthropology to link the study of social inequalities, human biology, and human-environment interactions.

Objectives and Contents of the Educational Activity Oriented Toward the Small Child.

ERIC Educational Resources Information Center

Walczyna, Jadwiga

This paper emphasizes the importance of educational activities for small children and discusses the issues and problems associated with choice of educational objectives and activity content. Three factors which influence the formation of educational objectives are identified: (1) tradition, (2) specific character of socio-economic conditions in…

Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics.

PubMed

Yang, Chuanping; Wei, Hairong

2015-02-01

Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment. Contemporarily, most genomics experiments have two objectives: (1) to generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental conditions; (2) to build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest. Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discusses the major issues that researchers commonly face when embarking on microarray or RNA-seq experiments and summarizes important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but with more interaction to facilitate novel biological discoveries in modern plant genomics. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Collective dynamics of 'small-world' networks.

PubMed

Watts, D J; Strogatz, S H

1998-06-04

Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

EUD-based biological optimization for carbon ion therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brüningk, Sarah C., E-mail: sarah.brueningk@icr.ac.uk; Kamp, Florian; Wilkens, Jan J.

2015-11-15

Purpose: Treatment planning for carbon ion therapy requires an accurate modeling of the biological response of each tissue to estimate the clinical outcome of a treatment. The relative biological effectiveness (RBE) accounts for this biological response on a cellular level but does not refer to the actual impact on the organ as a whole. For photon therapy, the concept of equivalent uniform dose (EUD) represents a simple model to take the organ response into account, yet so far no formulation of EUD has been reported that is suitable to carbon ion therapy. The authors introduce the concept of an equivalentmore » uniform effect (EUE) that is directly applicable to both ion and photon therapies and exemplarily implemented it as a basis for biological treatment plan optimization for carbon ion therapy. Methods: In addition to a classical EUD concept, which calculates a generalized mean over the RBE-weighted dose distribution, the authors propose the EUE to simplify the optimization process of carbon ion therapy plans. The EUE is defined as the biologically equivalent uniform effect that yields the same probability of injury as the inhomogeneous effect distribution in an organ. Its mathematical formulation is based on the generalized mean effect using an effect-volume parameter to account for different organ architectures and is thus independent of a reference radiation. For both EUD concepts, quadratic and logistic objective functions are implemented into a research treatment planning system. A flexible implementation allows choosing for each structure between biological effect constraints per voxel and EUD constraints per structure. Exemplary treatment plans are calculated for a head-and-neck patient for multiple combinations of objective functions and optimization parameters. Results: Treatment plans optimized using an EUE-based objective function were comparable to those optimized with an RBE-weighted EUD-based approach. In agreement with previous results from photon therapy, the optimization by biological objective functions resulted in slightly superior treatment plans in terms of final EUD for the organs at risk (OARs) compared to voxel-based optimization approaches. This observation was made independent of the underlying objective function metric. An absolute gain in OAR sparing was observed for quadratic objective functions, whereas intersecting DVHs were found for logistic approaches. Even for considerable under- or overestimations of the used effect- or dose–volume parameters during the optimization, treatment plans were obtained that were of similar quality as the results of a voxel-based optimization. Conclusions: EUD-based optimization with either of the presented concepts can successfully be applied to treatment plan optimization. This makes EUE-based optimization for carbon ion therapy a useful tool to optimize more specifically in the sense of biological outcome while voxel-to-voxel variations of the biological effectiveness are still properly accounted for. This may be advantageous in terms of computational cost during treatment plan optimization but also enables a straight forward comparison of different fractionation schemes or treatment modalities.« less

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

PubMed

Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

2015-02-21

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Recent advances in the biology and treatment of brain metastases of non-small cell lung cancer: summary of a multidisciplinary roundtable discussion

PubMed Central

Preusser, Matthias; Winkler, Frank; Valiente, Manuel; Manegold, Christian; Moyal, Elizabeth; Widhalm, Georg; Tonn, Jörg-Christian; Zielinski, Christoph

2018-01-01

This article is the result of a round table discussion held at the European Lung Cancer Conference (ELCC) in Geneva in May 2017. Its purpose is to explore and discuss the advances in the knowledge about the biology and treatment of brain metastases originating from non-small cell lung cancer. The authors propose a series of recommendations for research and treatment within the discussed context. PMID:29387475

Incorporating Biological Knowledge into Evaluation of Casual Regulatory Hypothesis

NASA Technical Reports Server (NTRS)

Chrisman, Lonnie; Langley, Pat; Bay, Stephen; Pohorille, Andrew; DeVincenzi, D. (Technical Monitor)

2002-01-01

Biological data can be scarce and costly to obtain. The small number of samples available typically limits statistical power and makes reliable inference of causal relations extremely difficult. However, we argue that statistical power can be increased substantially by incorporating prior knowledge and data from diverse sources. We present a Bayesian framework that combines information from different sources and we show empirically that this lets one make correct causal inferences with small sample sizes that otherwise would be impossible.

A Novel and Non-Cytotoxic Self-Healing Supramolecular Elastomer Synthesized with Small Molecular Biological Acids.

PubMed

Liu, Ling; Pan, Cheng; Zhang, Liqun; Guo, Baochun

2016-10-01

A novel and non-cytotoxic self-healing supramolecular elastomer (SE) is synthesized with small-molecular biological acids by hydrogen-bonding interactions. The synthesized SEs behave as rubber at room temperature without additional plasticizers or crosslinkers, which is attributed to the phase-separated structure. The SE material exhibits outstanding self-healing capability at room temperature and essential non-cytotoxicity, which makes it a potential candidate for biomedical applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis.

PubMed

Sekiguchi, Yuki; Oroguchi, Tomotaka; Nakasako, Masayoshi

2016-01-01

Coherent X-ray diffraction imaging (CXDI) is one of the techniques used to visualize structures of non-crystalline particles of micrometer to submicrometer size from materials and biological science. In the structural analysis of CXDI, the electron density map of a sample particle can theoretically be reconstructed from a diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction is difficult because diffraction patterns are affected by Poisson noise and miss data in small-angle regions due to the beam stop and the saturation of detector pixels. In contrast to X-ray protein crystallography, in which the phases of diffracted waves are experimentally estimated, phase retrieval in CXDI relies entirely on the computational procedure driven by the PR algorithms. Thus, objective criteria and methods to assess the accuracy of retrieved electron density maps are necessary in addition to conventional parameters monitoring the convergence of PR calculations. Here, a data analysis scheme, named ASURA, is proposed which selects the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a diffraction pattern. Each electron density map composed of J pixels is expressed as a point in a J-dimensional space. Principal component analysis is applied to describe characteristics in the distribution of the maps in the J-dimensional space. When the distribution is characterized by a small number of principal components, the distribution is classified using the k-means clustering method. The classified maps are evaluated by several parameters to assess the quality of the maps. Using the proposed scheme, structure analysis of a diffraction pattern from a non-crystalline particle is conducted in two stages: estimation of the overall shape and determination of the fine structure inside the support shape. In each stage, the most accurate and probable density maps are objectively selected. The validity of the proposed scheme is examined by application to diffraction data that were obtained from an aggregate of metal particles and a biological specimen at the XFEL facility SACLA using custom-made diffraction apparatus.

Small target detection using objectness and saliency

NASA Astrophysics Data System (ADS)

Zhang, Naiwen; Xiao, Yang; Fang, Zhiwen; Yang, Jian; Wang, Li; Li, Tao

2017-10-01

We are motived by the need for generic object detection algorithm which achieves high recall for small targets in complex scenes with acceptable computational efficiency. We propose a novel object detection algorithm, which has high localization quality with acceptable computational cost. Firstly, we obtain the objectness map as in BING[1] and use NMS to get the top N points. Then, k-means algorithm is used to cluster them into K classes according to their location. We set the center points of the K classes as seed points. For each seed point, an object potential region is extracted. Finally, a fast salient object detection algorithm[2] is applied to the object potential regions to highlight objectlike pixels, and a series of efficient post-processing operations are proposed to locate the targets. Our method runs at 5 FPS on 1000*1000 images, and significantly outperforms previous methods on small targets in cluttered background.

Synthetic biology and the technicity of biofuels.

PubMed

Mackenzie, Adrian

2013-06-01

The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Performance evaluation of the bioreactor landfill in treatment and stabilisation of mechanically biologically treated municipal solid waste.

PubMed

Lakshmikanthan, P; Sivakumar Babu, G L

2017-03-01

The potential of bioreactor landfills to treat mechanically biologically treated municipal solid waste is analysed in this study. Developing countries like India and China have begun to investigate bioreactor landfills for municipal solid waste management. This article describes the impacts of leachate recirculation on waste stabilisation, landfill gas generation, leachate characteristics and long-term waste settlement. A small-scale and large-scale anaerobic cell were filled with mechanically biologically treated municipal solid waste collected from a landfill site at the outskirts of Bangalore, India. Leachate collected from the same landfill site was recirculated at the rate of 2-5 times a month on a regular basis for 370 days. The total quantity of gas generated was around 416 L in the large-scale reactor and 21 L in the small-scale reactor, respectively. Differential settlements ranging from 20%-26% were observed at two different locations in the large reactor, whereas 30% of settlement was observed in the small reactor. The biological oxygen demand/chemical oxygen demand (COD) ratio indicated that the waste in the large reactor was stabilised at the end of 1 year. The performance of the bioreactor with respect to the reactor size, temperature, landfill gas and leachate quality was analysed and it was found that the bioreactor landfill is efficient in the treatment and stabilising of mechanically biologically treated municipal solid waste.

Multifunctional and biologically active matrices from multicomponent polymeric solutions

NASA Technical Reports Server (NTRS)

Kiick, Kristi L. (Inventor); Yamaguchi, Nori (Inventor); Rabolt, John (Inventor); Casper, Cheryl (Inventor)

2012-01-01

A functionalized electrospun matrix for the controlled-release of biologically active agents, such as growth factors, is presented. The functionalized matrix comprises a matrix polymer, a compatibilizing polymer and a biomolecule or other small functioning molecule. In certain aspects the electrospun polymer fibers comprise at least one biologically active molecule functionalized with low molecular weight heparin.

Simulations of population dynamics of hemlock woolly adelgid and potential impact of biological control agents

Treesearch

Joseph S. Elkinton; Robert T. Trotter; Ann F. Paradis

2011-01-01

The hemlock woolly adelgid (Adelges tsugae) is a small invasive Hemipteran herbivore that threatens the continued presence and abundance of hemlock in eastern North America. Efforts to control the adelgid have focused on the introduction of classical biological control agents. These biological controls include six different species of predatory...

Public Understanding of Plant Biology: Voices from the Bottom of the Garden

ERIC Educational Resources Information Center

Watts, Mike

2015-01-01

Many household gardeners accumulate considerable knowledge of plant biology through a range of informal learning sources. This knowledge seldom relates to school biology and is driven by interest, keen motivation and what is termed here "vital relevance." A small opportunity sample of 12 gardeners (6 M, 6 F) is interviewed in terms of…

Summary Report: Pilot Study of an Innovative Biological Treatment Process for the Removal of Ammonia from a Small Drinking Water System

EPA Science Inventory

The use of biologically active filtration to oxidize ammonia as a full-scale drinking water treatment process has not been thoroughly considered in the United States. A number of concerns with biological water treatment exist including the potential release of excessive numbers o...

Getting a Grip on Complexes

PubMed Central

Nie, Yan; Viola, Cristina; Bieniossek, Christoph; Trowitzsch, Simon; Vijay-achandran, Lakshmi Sumitra; Chaillet, Maxime; Garzoni, Frederic; Berger, Imre

2009-01-01

We are witnessing tremendous advances in our understanding of the organization of life. Complete genomes are being deciphered with ever increasing speed and accuracy, thereby setting the stage for addressing the entire gene product repertoire of cells, towards understanding whole biological systems. Advances in bioinformatics and mass spectrometric techniques have revealed the multitude of interactions present in the proteome. Multiprotein complexes are emerging as a paramount cornerstone of biological activity, as many proteins appear to participate, stably or transiently, in large multisubunit assemblies. Analysis of the architecture of these assemblies and their manifold interactions is imperative for understanding their function at the molecular level. Structural genomics efforts have fostered the development of many technologies towards achieving the throughput required for studying system-wide single proteins and small interaction motifs at high resolution. The present shift in focus towards large multiprotein complexes, in particular in eukaryotes, now calls for a likewise concerted effort to develop and provide new technologies that are urgently required to produce in quality and quantity the plethora of multiprotein assemblies that form the complexome, and to routinely study their structure and function at the molecular level. Current efforts towards this objective are summarized and reviewed in this contribution. PMID:20514218

Variability of hydrologic regimes and morphology in constructed open-ditch channels

USGS Publications Warehouse

Strock, J.S.; Magner, J.A.; Richardson, W.B.; Sadowsky, M.J.; Sands, G.R.; Venterea, R.T.; ,

2004-01-01

Open-ditch ecosystems are potential transporters of considerable loads of nutrients, sediment, pathogens and pesticides from direct inflow from agricultural land to small streams and larger rivers. Our objective was to compare hydrology and channel morphology between two experimental open-ditch channels. An open-ditch research facility incorporating a paired design was constructed during 2002 near Lamberton, MN. A200-m reach of existing drainage channel was converted into a system of four parallel channels. The facility was equipped with water level control devices and instrumentation for flow monitoring and water sample collection on upstream and downstream ends of the system. Hydrographs from simulated flow during year one indicated that paired open-ditch channels responded similarly to changes in inflow. Variability in hydrologic response between open-ditches was attributed to differences in open-ditch channel bottom elevation and vegetation density. No chemical, biological, or atmospheric measurements were made during 2003. Potential future benefits of this research include improved biological diversity and integrity of open-ditch ecosystems, reduce flood peaks and increased flow during critical low-flow periods, improved and more efficient nitrogen retention within the open-ditch ecosystem, and decreased maintenance cost associated with reduced frequency of open-ditch maintenance.

A regulatory perspective of clinical trial applications for biological products with particular emphasis on Advanced Therapy Medicinal Products (ATMPs)

PubMed Central

Jones, David R; McBlane, James W; McNaughton, Graham; Rajakumaraswamy, Nishanthan; Wydenbach, Kirsty

2013-01-01

The safety of trial subjects is the tenet that guides the regulatory assessment of a Clinical Trial Authorization application and applies equally to trials involving small molecules and those with biological/biotechnological products, including Advanced Therapy Medicinal Products. The objective of a regulator is to ensure that the potential risk faced by a trial subject is outweighed by the potential benefit to them from taking part in the trial. The focus of the application review is to assess whether risks have been identified and appropriate steps taken to alleviate these as much as possible. Other factors are also taken into account during a review, such as regulatory requirements, and emerging non-clinical and clinical data from other trials on the same or similar products. This paper examines the regulatory review process of a Clinical Trial Authorization application from the perspectives of Quality, Non-Clinical and Clinical Regulatory Assessors at the Medicines and Healthcare products Regulatory Agency. It should be noted that each perspective has highlighted specific issues from their individual competence and that these can be different between the disciplines. PMID:23216470

DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes

NASA Astrophysics Data System (ADS)

Witham, Shawn; Boylen, Brett; Owesen, Barr; Rocchia, Walter; Alexov, Emil

2011-03-01

Electrostatic forces and energies are two of the major components that contribute to the stability, function and interaction of biological macromolecules. The calculations of the electrostatic potential distribution in such systems, which are comprised of irregularly shaped objects immersed in a water phase, is not a trivial task. In addition, an accurate model requires any missing hydrogen atoms of the corresponding structural files (Protein Data Bank, or, PDB files) to be generated in silico and, if necessary, missing atoms or residues to be predicted as well. Here we report a comprehensive suite, an academic DelPhi webserver, which allows the users to upload their structural file, calculate the components of the electrostatic energy, generate the corresponding potential (and/or concentration/dielectric constant) distribution map, and choose the appropriate force field. The webserver utilizes modern technology to take user input and construct an algorithm that suits the users specific needs. The webserver uses Clemson University's Palmetto Supercomputer Cluster to handle the DelPhi calculations, which can range anywhere from small and short computation times, to extensive and computationally demanding runtimes. The work was supported by a grant from NIGMS, NIH, grant number 1R01GM093937-01.

Making literature reviews more reliable through application of lessons from systematic reviews.

PubMed

Haddaway, N R; Woodcock, P; Macura, B; Collins, A

2015-12-01

Review articles can provide valuable summaries of the ever-increasing volume of primary research in conservation biology. Where findings may influence important resource-allocation decisions in policy or practice, there is a need for a high degree of reliability when reviewing evidence. However, traditional literature reviews are susceptible to a number of biases during the identification, selection, and synthesis of included studies (e.g., publication bias, selection bias, and vote counting). Systematic reviews, pioneered in medicine and translated into conservation in 2006, address these issues through a strict methodology that aims to maximize transparency, objectivity, and repeatability. Systematic reviews will always be the gold standard for reliable synthesis of evidence. However, traditional literature reviews remain popular and will continue to be valuable where systematic reviews are not feasible. Where traditional reviews are used, lessons can be taken from systematic reviews and applied to traditional reviews in order to increase their reliability. Certain key aspects of systematic review methods that can be used in a context-specific manner in traditional reviews include focusing on mitigating bias; increasing transparency, consistency, and objectivity, and critically appraising the evidence and avoiding vote counting. In situations where conducting a full systematic review is not feasible, the proposed approach to reviewing evidence in a more systematic way can substantially improve the reliability of review findings, providing a time- and resource-efficient means of maximizing the value of traditional reviews. These methods are aimed particularly at those conducting literature reviews where systematic review is not feasible, for example, for graduate students, single reviewers, or small organizations. © 2015 Society for Conservation Biology.

Application of fluorescent dyes for some problems of bioelectromagnetics

NASA Astrophysics Data System (ADS)

Babich, Danylo; Kylsky, Alexandr; Pobiedina, Valentina; Yakunov, Andrey

2016-04-01

Fluorescent organic dyes solutions are used for non-contact measurement of the millimeter wave absorption in liquids simulating biological tissue. There is still not any certain idea of the physical mechanism describing this process despite the widespread technology of microwave radiation in the food industry, biotechnology and medicine. For creating adequate physical model one requires an accurate command of knowledge concerning to the relation between millimeter waves and irradiated object. There were three H-bonded liquids selected as the samples with different coefficients of absorption in the millimeter range like water (strong absorption), glycerol (medium absorption) and ethylene glycol (light absorption). The measurements showed that the greatest response to the action of microwaves occurs for glycerol solutions: R6G (building-up luminescence) and RC (fading luminescence). For aqueous solutions the signal is lower due to lower quantum efficiency of luminescence, and for ethylene glycol — due to the low absorption of microwaves. In the area of exposure a local increase of temperature was estimated. For aqueous solutions of both dyes the maximum temperature increase is about 7° C caused with millimeter waves absorption, which coincides with the direct radio physical measurements and confirmed by theoretical calculations. However, for glycerol solution R6G temperature equivalent for building-up luminescence is around 9° C, and for the solution of ethylene glycol it's about 15°. It is assumed the possibility of non-thermal effect of microwaves on the different processes and substances. The application of this non-contact temperature sensing is a simple and novel method to detect temperature change in small biological objects.

Longitudinal Multiplexed Measurement of Quantitative Proteomic Signatures in Mouse Lymphoma Models Using Magneto-Nanosensors

PubMed Central

Lee, Jung-Rok; Appelmann, Iris; Miething, Cornelius; Shultz, Tyler O.; Ruderman, Daniel; Kim, Dokyoon; Mallick, Parag; Lowe, Scott W.; Wang, Shan X.

2018-01-01

Cancer proteomics is the manifestation of relevant biological processes in cancer development. Thus, it reflects the activities of tumor cells, host-tumor interactions, and systemic responses to cancer therapy. To understand the causal effects of tumorigenesis or therapeutic intervention, longitudinal studies are greatly needed. However, most of the conventional mouse experiments are unlikely to accommodate frequent collection of serum samples with a large enough volume for multiple protein assays towards single-object analysis. Here, we present a technique based on magneto-nanosensors to longitudinally monitor the protein profiles in individual mice of lymphoma models using a small volume of a sample for multiplex assays. Methods: Drug-sensitive and -resistant cancer cell lines were used to develop the mouse models that render different outcomes upon the drug treatment. Two groups of mice were inoculated with each cell line, and treated with either cyclophosphamide or vehicle solution. Serum samples taken longitudinally from each mouse in the groups were measured with 6-plex magneto-nanosensor cytokine assays. To find the origin of IL-6, experiments were performed using IL-6 knock-out mice. Results: The differences in serum IL-6 and GCSF levels between the drug-treated and untreated groups were revealed by the magneto-nanosensor measurement on individual mice. Using the multiplex assays and mouse models, we found that IL-6 is secreted by the host in the presence of tumor cells upon the drug treatment. Conclusion: The multiplex magneto-nanosensor assays enable longitudinal proteomic studies on mouse tumor models to understand tumor development and therapy mechanisms more precisely within a single biological object. PMID:29507628

Longitudinal Multiplexed Measurement of Quantitative Proteomic Signatures in Mouse Lymphoma Models Using Magneto-Nanosensors.

PubMed

Lee, Jung-Rok; Appelmann, Iris; Miething, Cornelius; Shultz, Tyler O; Ruderman, Daniel; Kim, Dokyoon; Mallick, Parag; Lowe, Scott W; Wang, Shan X

2018-01-01

Cancer proteomics is the manifestation of relevant biological processes in cancer development. Thus, it reflects the activities of tumor cells, host-tumor interactions, and systemic responses to cancer therapy. To understand the causal effects of tumorigenesis or therapeutic intervention, longitudinal studies are greatly needed. However, most of the conventional mouse experiments are unlikely to accommodate frequent collection of serum samples with a large enough volume for multiple protein assays towards single-object analysis. Here, we present a technique based on magneto-nanosensors to longitudinally monitor the protein profiles in individual mice of lymphoma models using a small volume of a sample for multiplex assays. Methods: Drug-sensitive and -resistant cancer cell lines were used to develop the mouse models that render different outcomes upon the drug treatment. Two groups of mice were inoculated with each cell line, and treated with either cyclophosphamide or vehicle solution. Serum samples taken longitudinally from each mouse in the groups were measured with 6-plex magneto-nanosensor cytokine assays. To find the origin of IL-6, experiments were performed using IL-6 knock-out mice. Results: The differences in serum IL-6 and GCSF levels between the drug-treated and untreated groups were revealed by the magneto-nanosensor measurement on individual mice. Using the multiplex assays and mouse models, we found that IL-6 is secreted by the host in the presence of tumor cells upon the drug treatment. Conclusion: The multiplex magneto-nanosensor assays enable longitudinal proteomic studies on mouse tumor models to understand tumor development and therapy mechanisms more precisely within a single biological object.

Modeling small cell lung cancer (SCLC) biology through deterministic and stochastic mathematical models.

PubMed

Salgia, Ravi; Mambetsariev, Isa; Hewelt, Blake; Achuthan, Srisairam; Li, Haiqing; Poroyko, Valeriy; Wang, Yingyu; Sattler, Martin

2018-05-25

Mathematical cancer models are immensely powerful tools that are based in part on the fractal nature of biological structures, such as the geometry of the lung. Cancers of the lung provide an opportune model to develop and apply algorithms that capture changes and disease phenotypes. We reviewed mathematical models that have been developed for biological sciences and applied them in the context of small cell lung cancer (SCLC) growth, mutational heterogeneity, and mechanisms of metastasis. The ultimate goal is to develop the stochastic and deterministic nature of this disease, to link this comprehensive set of tools back to its fractalness and to provide a platform for accurate biomarker development. These techniques may be particularly useful in the context of drug development research, such as combination with existing omics approaches. The integration of these tools will be important to further understand the biology of SCLC and ultimately develop novel therapeutics.

Ensemble of sparse classifiers for high-dimensional biological data.

PubMed

Kim, Sunghan; Scalzo, Fabien; Telesca, Donatello; Hu, Xiao

2015-01-01

Biological data are often high in dimension while the number of samples is small. In such cases, the performance of classification can be improved by reducing the dimension of data, which is referred to as feature selection. Recently, a novel feature selection method has been proposed utilising the sparsity of high-dimensional biological data where a small subset of features accounts for most variance of the dataset. In this study we propose a new classification method for high-dimensional biological data, which performs both feature selection and classification within a single framework. Our proposed method utilises a sparse linear solution technique and the bootstrap aggregating algorithm. We tested its performance on four public mass spectrometry cancer datasets along with two other conventional classification techniques such as Support Vector Machines and Adaptive Boosting. The results demonstrate that our proposed method performs more accurate classification across various cancer datasets than those conventional classification techniques.

110 Years of the Meyer–Overton Rule: Predicting Membrane Permeability of Gases and Other Small Compounds

PubMed Central

Missner, Andreas; Pohl, Peter

2010-01-01

The transport of gaseous compounds across biological membranes is essential in all forms of life. Although it was generally accepted that gases freely penetrate the lipid matrix of biological membranes, a number of studies challenged this doctrine as they found biological membranes to have extremely low gas-permeability values. These observations led to the identification of several membrane-embedded “gas” channels, which facilitate the transport of biological active gases, such as carbon dioxide, nitric oxide, and ammonia. However, some of these findings are in contrast to the well-established solubility–diffusion model (also known as the Meyer–Overton rule), which predicts membrane permeabilities from the molecule's oil–water partition coefficient. Herein, we discuss recently reported violations of the Meyer–Overton rule for small molecules, including carboxylic acids and gases, and show that Meyer and Overton continue to rule. PMID:19514034

Why do we need theories?

PubMed Central

Longo, Giuseppe; Soto, Ana M.

2017-01-01

Theories organize knowledge and construct objectivity by framing observations and experiments. The elaboration of theoretical principles is examined in the light of the rich interactions between physics and mathematics. These two disciplines share common principles of construction of concepts and of the proper objects of inquiry. Theory construction in physics relies on mathematical symmetries that preserve the key invariants observed and proposed by such theory; these invariants buttress the idea that the objects of physics are generic and thus interchangeable and they move along specific trajectories which are uniquely determined, in classical and relativistic physics. In contrast to physics, biology is a historical science that centers on the changes that organisms experience while undergoing ontogenesis and phylogenesis. Biological objects, namely organisms, are not generic but specific; they are individuals. The incessant changes they undergo represent the breaking of symmetries, and thus the opposite of symmetry conservation, a central component of physical theories. This instability corresponds to the changes of the environment and the phenotypes. Inspired by Galileo’s principle of inertia, the “default state” of inert matter, we propose a “default state” for biological dynamics following Darwin’s first principle, “descent with modification” that we transform into “proliferation with variation and motility” as a property that spans life, including cells in an organism. These dissimilarities between theories of the inert and of biology also apply to causality: biological causality is to be understood in relation to the distinctive role that constraints assume in this discipline. Consequently, the notion of cause will be reframed in a context where constraints to activity are seen as the core component of biological analyses. Finally, we assert that the radical materiality of life rules out distinctions such as “software vs. hardware.” PMID:27390105

Why do we need theories?

PubMed

Longo, Giuseppe; Soto, Ana M

2016-10-01

Theories organize knowledge and construct objectivity by framing observations and experiments. The elaboration of theoretical principles is examined in the light of the rich interactions between physics and mathematics. These two disciplines share common principles of construction of concepts and of the proper objects of inquiry. Theory construction in physics relies on mathematical symmetries that preserve the key invariants observed and proposed by such theory; these invariants buttress the idea that the objects of physics are generic and thus interchangeable and they move along specific trajectories which are uniquely determined, in classical and relativistic physics. In contrast to physics, biology is a historical science that centers on the changes that organisms experience while undergoing ontogenesis and phylogenesis. Biological objects, namely organisms, are not generic but specific; they are individuals. The incessant changes they undergo represent the breaking of symmetries, and thus the opposite of symmetry conservation, a central component of physical theories. This instability corresponds to the changes of the environment and the phenotypes. Inspired by Galileo's principle of inertia, the "default state" of inert matter, we propose a "default state" for biological dynamics following Darwin's first principle, "descent with modification" that we transform into "proliferation with variation and motility" as a property that spans life, including cells in an organism. These dissimilarities between theories of the inert and of biology also apply to causality: biological causality is to be understood in relation to the distinctive role that constraints assume in this discipline. Consequently, the notion of cause will be reframed in a context where constraints to activity are seen as the core component of biological analyses. Finally, we assert that the radical materiality of life rules out distinctions such as "software vs. hardware." Copyright © 2016 Elsevier Ltd. All rights reserved.

Small Schools Health Curriculum, K-3: Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

McInerney, Mike, Ed.; Destito, Therese, Ed.

The K-3 health curriculum developed during 1975-77 by teachers in small school districts working with district and state health education specialists presents student learning objectives and suggested activities, monitoring procedures and resources which are correlated to the 10 Goals for Washington Common Schools and the nine Small Schools Health…

Implementing goals for non-cognitive outcomes within a basic science course.

PubMed

Derstine, Pamela L

2002-09-01

An essential principle of competency-based education (CBE) is use of observable outcomes with assessments as judgments of competence based on defined criteria. Faculty are accustomed to using learning objectives as the defining criteria for knowledge, assessing students using written exams. Faculty are less familiar with how the principles of CBE are applied to other competencies. We recently adopted school-wide goals and objectives, modeled after the ACGME Outcomes Project. The present objective was to give faculty first-hand experience in CBE within a basic science course, including both cognitive and non-cognitive outcomes. The format for the learner-centered, first-year Cell and Molecular Biology course was previously described.(1) Course goals were that students: (1) gain an understanding of the principles and concepts of cell and molecular biology, (2) develop an appreciation for how these principles and concepts are important to medicine, (3) demonstrate an ability to think critically using these principles and concepts. Goal 1 was measured by written exams. We assumed goals 2 and 3 were met through small-group problem-solving sessions, and outcomes were not assessed. The revised 2001 course goals were to prepare students for medical knowledge and lifelong learning and communication and professionalism. The goals for medical knowledge and lifelong learning were to: (1) demonstrate ability to use principles and concepts of cell biology, molecular biology, and genetics to analyze medically relevant data, solve problems, make predictions, and determine a course of action; (2) effectively use information technology to search, evaluate, and critically review scientific evidence related to principles and concepts covered in the course; (3) use appropriate techniques to teach peers in a conference setting. The goals for communication and professionalism were to: (1) use appropriate skills and attitudes to collaborate effectively with peers and faculty to accomplish learning goals; (2) maintain a personal learning portfolio to develop habits of reflective learning, broaden understanding of content beyond recall, and enhance communication with faculty; (3) demonstrate personal integrity in meeting course requirements and in interactions with peers and faculty throughout the course. Goals for medical knowledge and lifelong learning were assessed by written exams and by separate tools utilizing four-point Likert scales (novice, advanced beginner, proficient, distinguished) with specific observable criteria for a written research paper and a group PowerPoint presentation. Faculty and student assessments generated a number that was combined with exam grades for a lettered competency grade. A 19-item, five-point Likert scale was used by students to self- and peer-assess goals for communication and professionalism. Small-group faculty facilitators used the tool to give formative feedback midcourse, summative feedback at course conclusion, and competency grades. The tools may be viewed at: . Faculty achieved enhanced understanding of students, assisted by descriptive criteria, while suggesting improvements in forms. Better agreement on criteria definitions and consistency in form use is needed. Students developed understanding and improved communication/professionalism skills, based on repeated exposures to criteria and feedback. It remains to be seen whether the skills are used/developed in other courses. A majority of students did not use the learning portfolio as envisioned. Better design and implementation of school-wide rather than course-specific reflective portfolios may increase use and integrate learning in all courses with all six competencies.

PERMANENCE OF BIOLOGICAL AND CHEMICAL WARFARE AGENTS IN MUNICIPAL SOLID WASTE LANDFILL LEACHATES

EPA Science Inventory

The objective of this work is to permit EPA/ORD's National Homeland Security Research Center (NHSRC) and Edgewood Chemical Biological Center to collaborate together to test the permanence of biological and chemical warfare agents in municipal solid waste landfills. Research into ...

Biological control of Botrytis cinerea: interactions with native vineyard yeasts from Washington State

USDA-ARS?s Scientific Manuscript database

Native fermentations are of increasing interest to Washington and US winemakers and consumers. This, and environmental impact concerns, warrant the exploration of biological control as an alternative to chemical fungicides. The objective of this study was to characterize the biological control activ...

3D Object Recognition: Symmetry and Virtual Views

DTIC Science & Technology

1992-12-01

NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATIONI Artificial Intelligence Laboratory REPORT NUMBER 545 Technology Square AIM 1409 Cambridge... ARTIFICIAL INTELLIGENCE LABORATORY and CENTER FOR BIOLOGICAL AND COMPUTATIONAL LEARNING A.I. Memo No. 1409 December 1992 C.B.C.L. Paper No. 76 3D Object...research done within the Center for Biological and Computational Learning in the Department of Brain and Cognitive Sciences, and at the Artificial

Conceptual Model-Based Systems Biology: Mapping Knowledge and Discovering Gaps in the mRNA Transcription Cycle

PubMed Central

Somekh, Judith; Choder, Mordechai; Dori, Dov

2012-01-01

We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure—the objects that comprise the system, and behavior—how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point—the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model. PMID:23308089

Fixed-focus camera objective for small remote sensing satellites

NASA Astrophysics Data System (ADS)

Topaz, Jeremy M.; Braun, Ofer; Freiman, Dov

1993-09-01

An athermalized objective has been designed for a compact, lightweight push-broom camera which is under development at El-Op Ltd. for use in small remote-sensing satellites. The high performance objective has a fixed focus setting, but maintains focus passively over the full range of temperatures encountered in small satellites. The lens is an F/5.0, 320 mm focal length Tessar type, operating over the range 0.5 - 0.9 micrometers . It has a 16 degree(s) field of view and accommodates various state-of-the-art silicon detector arrays. The design and performance of the objective is described in this paper.

Expedient construction of small molecule macroarrays via sequential palladium- and copper-mediated reactions and their ex situ biological testing.

PubMed

Frei, Reto; Breitbach, Anthony S; Blackwell, Helen E

2012-05-01

We report the highly efficient syntheses of a series of focused libraries in the small molecule macroarray format using Suzuki-Miyaura and copper-catalyzed azide-alkyne cycloaddition (or "click") reactions. The libraries were based on stilbene and triazole scaffolds, which are known to have a broad range of biological activities, including quorum-sensing (QS) modulation in bacteria. The library products were generated in parallel on the macroarray in extremely short reaction times (~10-20 min) and isolated in excellent purities. Biological testing of one macroarray library post-cleavage (ex situ) revealed several potent agonists of the QS receptor, LuxR, in Vibrio fischeri. These synthetic agonists, in contrast to others that we have reported, were only active in the presence of the native QS signal in V. fischeri, which is suggestive of a different mode of activity. Notably, the results presented herein showcase the ready compatibility of the macroarray platform with chemical reactions that are commonly utilized in small molecule probe and drug discovery today. As such, this work serves to expand the utility of the small molecule macroarray as a rapid and operationally straightforward approach toward the synthesis and screening of bioactive agents.

76 FR 35450 - Draft Guidance for Industry on Clinical Trial Endpoints for the Approval of Non-Small Cell Lung...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-17

...] Draft Guidance for Industry on Clinical Trial Endpoints for the Approval of Non-Small Cell Lung Cancer... entitled ``Clinical Trial Endpoints for the Approval of Non-Small Cell Lung Cancer Drugs and Biologics... draft guidance for industry entitled ``Clinical Trial Endpoints for the Approval of Non-Small Cell Lung...

Small Schools Student Learning Objectives, K-3: Reading, Language Arts, Mathematics, Science, Social Studies.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Developed by primary teachers and elementary principals from small districts in Snohomish and Island counties in Washington, this handbook contains sequenced student learning objectives for grades K-3 in the curriculum areas of reading, language arts, mathematics, science, and social studies. Each student learning objective is correlated to the…

Small Schools Mathematics Curriculum, 9-12: Scope Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Nelson, JoAnne, Ed.; And Others

The grade 9-12 mathematics curriculum learning objectives, activities, monitoring procedures and resources for small schools were developed during 1978-79 through the cooperative efforts of 10 Snohomish and Island County school districts, Educational Service District 189 and the Washington State Office of Public Instruction. The objectives were…

Small vs. Large Convective Cloud Objects from CERES Aqua Observations: Where are the Intraseasonal Variation Signals?

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man

2016-01-01

During inactive phases of Madden-Julian oscillation (MJO), there are plenty of deep but small convective systems and far fewer deep and large ones. During active phases of MJO, a manifestation of an increase in the occurrence of large and deep cloud clusters results from an amplification of large-scale motions by stronger convective heating. This study is designed to quantitatively examine the roles of small and large cloud clusters during the MJO life cycle. We analyze the cloud object data from Aqua CERES observations for tropical deep convective (DC) and cirrostratus (CS) cloud object types according to the real-time multivariate MJO index. The cloud object is a contiguous region of the earth with a single dominant cloud-system type. The size distributions, defined as the footprint numbers as a function of cloud object diameters, for particular MJO phases depart greatly from the combined (8-phase) distribution at large cloud-object diameters due to the reduced/increased numbers of cloud objects related to changes in the large-scale environments. The medium diameter corresponding to the combined distribution is determined and used to partition all cloud objects into "small" and "large" groups of a particular phase. The two groups corresponding to the combined distribution have nearly equal numbers of footprints. The medium diameters are 502 km for DC and 310 km for cirrostratus. The range of the variation between two extreme phases (typically, the most active and depressed phases) for the small group is 6-11% in terms of the numbers of cloud objects and the total footprint numbers. The corresponding range for the large group is 19-44%. In terms of the probability density functions of radiative and cloud physical properties, there are virtually no differences between the MJO phases for the small group, but there are significant differences for the large groups for both DC and CS types. These results suggest that the intreseasonal variation signals reside at the large cloud clusters while the small cloud clusters represent the background noises resulting from various types of the tropical waves with different wavenumbers and propagation directions/speeds.

An assessment of inservice training on the applications in biology/chemistry curriculum from the Center of Occupational Research and Development

NASA Astrophysics Data System (ADS)

Jobe, Robert Dale

Scope and method of study. The scope of the study consisted of respondents to a survey sent to all the participants of the inservice workshops for the Applied Biology/Chemistry curriculum from CORD. One hundred and six surveys were sent to teachers trained for Applied Biology/Chemistry classes for high school credit as a laboratory science requirement. Sixty-two people returned the questionnaire who were present or past teachers of Applied Biology/Chemistry classes for high school credit. The study assessed the participants' expectations and satisfaction with inservice training provided for certification in Oklahoma over the past five years. A common set of objectives that participants rated for importance to philosophy and strategies needed to successfully teach Applications in Biology/Chemistry using the curriculum written by the Center for Occupational Research and Development was evaluated for significance. Findings and conclusions. The analysis of the data revealed that the respondents' expectations and satisfaction were both above average for the workshop they attended. Therefore, it was concluded that the first seventeen objectives of this study should be the mainstay of any workshop used to train future teachers of Applications of Biology/Chemistry for high school credit. Eleven of the first seventeen questions (objectives) were found to be statistically significant at the alpha =.05 level. Therefore it was concluded that an increased emphasis on instruction in the guideline (objectives) areas that were statistically significant should be provided in future workshops. The respondents' answers to the survey questions provided insight on the time line configuration and structure of future workshops for teachers of Application in Biology/Chemistry for high school credit. Therefore it was concluded that workshops should be ten days in length, 6-8 hours a day of instruction, with follow-up sessions offered, college credit given and a stipend awarded. The days, months and structure of meetings should be arranged to facilitate attendance by participants.

Subattomole sensitivity in biological accelerator mass spectrometry.

PubMed

Salehpour, Mehran; Possnert, Göran; Bryhni, Helge

2008-05-15

The Uppsala University 5 MV Pelletron tandem accelerator has been used to study (14)C-labeled biological samples utilizing accelerator mass spectrometry (AMS) technology. We have adapted a sample preparation method for small biological samples down to a few tens of micrograms of carbon, involving among others, miniaturizing of the graphitization reactor. Standard AMS requires about 1 mg of carbon with a limit of quantitation of about 10 amol. Results are presented for a range of small sample sizes with concentrations down to below 1 pM of a pharmaceutical substance in human blood. It is shown that (14)C-labeled molecular markers can be routinely measured from the femtomole range down to a few hundred zeptomole (10 (-21) mol), without the use of any additional separation methods.

The opportunities of mining historical and collective data in drug discovery.

PubMed

Wassermann, Anne Mai; Lounkine, Eugen; Davies, John W; Glick, Meir; Camargo, L Miguel

2015-04-01

Vast amounts of bioactivity data have been generated for small molecules across public and corporate domains. Biological signatures, either derived from systematic profiling efforts or from existing historical assay data, have been successfully employed for small molecule mechanism-of-action elucidation, drug repositioning, hit expansion and screening subset design. This article reviews different types of biological descriptors and applications, and we demonstrate how biological data can outlive the original purpose or project for which it was generated. By comparing 150 HTS campaigns run at Novartis over the past decade on the basis of their active and inactive chemical matter, we highlight the opportunities and challenges associated with cross-project learning in drug discovery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Asian Network for Biological Sciences (ANBS).

ERIC Educational Resources Information Center

Asian Network for Biological Sciences.

The Asian Network for Biological Sciences (ANBS) is a group of institutions, laboratories, research centers, and scholars who are willing to cooperate in programs and activities aimed at improving teaching and research in the biological sciences. This publication: (1) outlines ANBS aims and objectives; (2) describes major activities in the past;…

Reinvigorating Introductory Biology: A Theme-based, Investigative Approach To Teaching Biology Majors.

ERIC Educational Resources Information Center

Norton, Cynthia G.; Gildensoph, Lynne H.; Phillips, Martha M.; Wygal, Deborah D.; Olson, Kurt H.; Pellegrini, John J.; Tweeten, Kathleen A.

1997-01-01

Describes the reform of an introductory biology curriculum to reverse high attrition rates. Objectives include fostering self-directed learning, emphasizing process over content, and offering laboratory experiences that model the way to acquire scientific knowledge. Teaching methods include discussion, group mentoring, laboratory sections, and…

Innovative Biological Water Treatment for the Removal of Elevated Ammonia

EPA Science Inventory

The objective of this work was to demonstrate the effectiveness of an innovative and simple biological water treatment approach for removing 3.3 mg N/L ammonia and iron from water using a pilot study conducted at a utility in Iowa. Biological water treatment can be an effective a...

Fixable or Fate? Perceptions of the Biology of Depression

ERIC Educational Resources Information Center

Lebowitz, Matthew S.; Ahn, Woo-Kyoung; Nolen-Hoeksema, Susan

2013-01-01

Objective: Previous research has shown that biological (e.g., genetic, biochemical) accounts of depression--currently in ascendancy--are linked to the general public's pessimism about the syndrome's prognosis. This research examined for the first time whether people with depressive symptoms would associate biological accounts of depression with…

Impaired Perception of Biological Motion in Parkinson’s Disease

PubMed Central

Jaywant, Abhishek; Shiffrar, Maggie; Roy, Serge; Cronin-Golomb, Alice

2016-01-01

Objective We examined biological motion perception in Parkinson’s disease (PD). Biological motion perception is related to one’s own motor function and depends on the integrity of brain areas affected in PD, including posterior superior temporal sulcus. If deficits in biological motion perception exist, they may be specific to perceiving natural/fast walking patterns that individuals with PD can no longer perform, and may correlate with disease-related motor dysfunction. Method 26 non-demented individuals with PD and 24 control participants viewed videos of point-light walkers and scrambled versions that served as foils, and indicated whether each video depicted a human walking. Point-light walkers varied by gait type (natural, parkinsonian) and speed (0.5, 1.0, 1.5 m/s). Participants also completed control tasks (object motion, coherent motion perception), a contrast sensitivity assessment, and a walking assessment. Results The PD group demonstrated significantly less sensitivity to biological motion than the control group (p<.001, Cohen’s d=1.22), regardless of stimulus gait type or speed, with a less substantial deficit in object motion perception (p=.02, Cohen’s d=.68). There was no group difference in coherent motion perception. Although individuals with PD had slower walking speed and shorter stride length than control participants, gait parameters did not correlate with biological motion perception. Contrast sensitivity and coherent motion perception also did not correlate with biological motion perception. Conclusion PD leads to a deficit in perceiving biological motion, which is independent of gait dysfunction and low-level vision changes, and may therefore arise from difficulty perceptually integrating form and motion cues in posterior superior temporal sulcus. PMID:26949927

Microfluidic technology platforms for synthesizing, labeling and measuring the kinetics of transport and biochemical reactions for developing molecular imaging probes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phelps, Michael E.

2009-09-01

Radiotracer techniques are used in environmental sciences, geology, biology and medicine. Radiotracers with Positron Emission Tomography (PET) provided biological examinations of ~3 million patients 2008. Despite the success of positron labeled tracers in many sciences, there is limited access in an affordable and convenient manner to develop and use new tracers. Integrated microfluidic chips are a new technology well matched to the concentrations of tracers. Our goal is to develop microfluidic chips and new synthesis approaches to enable wide dissemination of diverse types of tracers at low cost, and to produce new generations of radiochemists for which there are manymore » unfilled jobs. The program objectives are to: 1. Develop an integrated microfluidic platform technology for synthesizing and 18F-labeling diverse arrays of different classes of molecules. 2. Incorporate microfluidic chips into small PC controlled devices (“Synthesizer”) with a platform interfaced to PC for electronic and fluid input/out control. 3. Establish a de-centralized model with Synthesizers for discovering and producing molecular imaging probes, only requiring delivery of inexpensive [18F]fluoride ion from commercial PET radiopharmacies vs the centralized approach of cyclotron facilities synthesizing and shipping a few different types of 18F-probes. 4. Develop a position sensitive avalanche photo diode (PSAPD) camera for beta particles embedded in a microfluidic chip for imaging and measuring transport and biochemical reaction rates to valid new 18F-labeled probes in an array of cell cultures. These objectives are met within a research and educational program integrating radio-chemistry, synthetic chemistry, biochemistry, engineering and biology in the Crump Institute for Molecular Imaging. The Radiochemistry Training Program exposes PhD and post doctoral students to molecular imaging in vitro in cells and microorganisms in microfluidic chips and in vivo with PET, from new technologies for radiochemistry (macro to micro levels), biochemistry and biology to imaging principles, tracer kinetics, pharmacokinetics and biochemical assays. New generations of radiochemists will be immersed in the biochemistry and biology for which their labeled probes are being developed for assays of these processes. In this program engineers and radio-chemists integrate the principles of microfluidics and radiolabeling along with proper system design and chemistry rule sets to yield Synthesizers enabling biological and pharmaceutical scientists to develop diverse arrays of probes to pursue their interests. This progression would allow also radiochemists to focus on the further evolution of rapid, high yield synthetic reactions with new enabling technologies, rather than everyday production of radiotracers that should be done by technologists. The invention of integrated circuits in electronics established a platform technology that allowed an evolution of ideas and applications far beyond what could have been imagined at the beginning. Rather than provide a technology for the solution to a single problem, it is hoped that microfluidic radiochemistry will be an enabling platform technology for others to solve many problems. As part of this objective, another program goal is to commercialize the technologies that come from this work so that they can be provided to others who wish to use it.« less

X-Pinch And Its Applications In X-ray Radiograph

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zou Xiaobing; Wang Xinxin; Liu Rui

2009-07-07

An X-pinch device and the related diagnostics of x-ray emission from X-pinch were briefly described. The time-resolved x-ray measurements with photoconducting diodes show that the x-ray pulse usually consists of two subnanosecond peaks with a time interval of about 0.5 ns. Being consistent with these two peaks of the x-ray pulse, two point x-ray sources of size ranging from 100 mum to 5 mum and depending on cut-off x-ray photon energy were usually observed on the pinhole pictures. The x-pinch was used as x-ray source for backlighting of the electrical explosion of single wire and the evolution of X-pinch, andmore » for phase-contrast imaging of soft biological objects such as a small shrimp and a mosquito.« less

Surface growth kinematics via local curve evolution.

PubMed

Moulton, Derek E; Goriely, Alain

2014-01-01

A mathematical framework is developed to model the kinematics of surface growth for objects that can be generated by evolving a curve in space, such as seashells and horns. Growth is dictated by a growth velocity vector field defined at every point on a generating curve. A local orthonormal basis is attached to each point of the generating curve and the velocity field is given in terms of the local coordinate directions, leading to a fully local and elegant mathematical structure. Several examples of increasing complexity are provided, and we demonstrate how biologically relevant structures such as logarithmic shells and horns emerge as analytical solutions of the kinematics equations with a small number of parameters that can be linked to the underlying growth process. Direct access to cell tracks and local orientation enables for connections to be made to the underlying growth process.

Nanonewton optical force trap employing anti-reflection coated, high-refractive-index titania microspheres

NASA Astrophysics Data System (ADS)

Jannasch, Anita; Demirörs, Ahmet F.; van Oostrum, Peter D. J.; van Blaaderen, Alfons; Schäffer, Erik

2012-07-01

Optical tweezers are exquisite position and force transducers and are widely used for high-resolution measurements in fields as varied as physics, biology and materials science. Typically, small dielectric particles are trapped in a tightly focused laser and are often used as handles for sensitive force measurements. Improvement to the technique has largely focused on improving the instrument and shaping the light beam, and there has been little work exploring the benefit of customizing the trapped object. Here, we describe how anti-reflection coated, high-refractive-index core-shell particles composed of titania enable single-beam optical trapping with an optical force greater than a nanonewton. The increased force range broadens the scope of feasible optical trapping experiments and will pave the way towards more efficient light-powered miniature machines, tools and applications.

Cell and Particle Interactions and Aggregation During Electrophoretic Motion

NASA Technical Reports Server (NTRS)

Davis, Robert H.

2000-01-01

The objectives of this research were (i) to perform experiments for observing and quantifying electrophoretic aggregation, (ii) to develop a theoretical description to appropriately analyze and compare with the experimental results, (iii) to study the combined effects of electrophoretic and gravitational aggregation of large particles, and the combined effects of electrophoretic and Brownian aggregation of small particles, and (iv) to perform a preliminary design of a potential future flight experiment involving electrophoretic aggregation. Electrophoresis refers to the motion of charged particles, droplets or molecules in response to an applied electric field. Electrophoresis is commonly used for analysis and separation of biological particles or molecules. When particles have different surface charge densities or potentials, they will migrate at different velocities in an electric field. This differential migration leads to the possibility that they will collide and aggregate, thereby preventing separation.

Inertial effects of a small Brownian particle cause a colored power spectral density of thermal noise.

PubMed

Jannasch, Anita; Mahamdeh, Mohammed; Schäffer, Erik

2011-11-25

The random thermal force acting on Brownian particles is often approximated in Langevin models by a "white-noise" process. However, fluid entrainment results in a frequency dependence of this thermal force giving it a "color." While theoretically well understood, direct experimental evidence for this colored nature of the noise term and how it is influenced by a nearby wall is lacking. Here, we directly measured the color of the thermal noise intensity by tracking a particle strongly confined in an ultrastable optical trap. All our measurements are in quantitative agreement with the theoretical predictions. Since Brownian motion is important for microscopic, in particular, biological systems, the colored nature of the noise and its distance dependence to nearby objects need to be accounted for and may even be utilized for advanced sensor applications.

Importing super-resolution imaging into nanoscale puzzles of materials dynamics

NASA Astrophysics Data System (ADS)

King, John; Tsang, Chi Hang Boyce; Wilson, William; Granick, Steve

2014-03-01

A limitation of the exciting recent advances in sub-diffraction microscopy is that they focus on imaging rather than dynamical changes. We are engaged in extending this technique beyond the usual biological applications to address materials problems instead. To this end, we employ stimulated emission depletion (STED) microscopy, which relies on selectively turning off fluorescence emitters through stimulated emission, allowing only a small subset of emitters to be detected, such that the excitation spot size can be downsized to tens of nanometers. By coupling the STED excitation scheme to fluorescence correlation spectroscopy (FCS), diffusive processes are studied with nanoscale resolution. Here, we demonstrate the benefits of such experimental capabilities in a diverse range of complex systems, ranging from the diffusion of nano-objects in crowded 3D environments to the study of polymer diffusion on 2D surfaces.

Improved catalyzed reporter deposition, iCARD.

PubMed

Lohse, Jesper; Petersen, Kenneth Heesche; Woller, Nina Claire; Pedersen, Hans Christian; Skladtchikova, Galina; Jørgensen, Rikke Malene

2014-06-18

Novel reporters have been synthesized with extended hydrophilic linkers that in combination with polymerizing cross-linkers result in very efficient reporter deposition. By utilizing antibodies to stain HER2 proteins in a cell line model it is demonstrated that the method is highly specific and sensitive with virtually no background. The detection of HER2 proteins in tissue was used to visualize individual antigens as small dots visible in a microscope. Image analysis-assisted counting of fluorescent or colored dots allowed assessment of relative protein levels in tissue. Taken together, we have developed novel reporters that improve the CARD method allowing highly sensitive in situ detection of proteins in tissue. Our findings suggest that in situ protein quantification in biological samples can be performed by object recognition and enumeration of dots, rather than intensity-based fluorescent or colorimetric assays.

Novel graphene-oxide-coated SPR interfaces for biosensing applications

NASA Astrophysics Data System (ADS)

Volkov, V. S.; Stebunov, Yu. V.; Yakubovsky, D. I.; Fedyanin, D. Yu.; Arsenin, A. V.

2017-09-01

Carbon allotropes-based nanomaterials possess unique physical and chemical properties including high surface area, the possibility of pi-stacking interaction with a wide range of biological objects, rich availability of oxygen-containing functional groups in graphene-oxide (GO), and excellent optical properties, which make them an ideal candidate for use as a universal immobilization platform in SPR biosensing. Here, we propose a new surface plasmon resonance (SPR) biosensing interface for sensitive and selective detection of small molecules. This interface is based on the GO linking layers deposited on the gold/copper surface of SPR sensor chips. To estimate the binding capacity of GO layers, modification of carboxyl groups to N-Hydroxysuccinimide esters was performed in the flow cell of SPR instrument. For comparison, the same procedure was applied to commercial sensor chips based on linking layers of carboxymethylated dextran.

Normal form from biological motion despite impaired ventral stream function.

PubMed

Gilaie-Dotan, S; Bentin, S; Harel, M; Rees, G; Saygin, A P

2011-04-01

We explored the extent to which biological motion perception depends on ventral stream integration by studying LG, an unusual case of developmental visual agnosia. LG has significant ventral stream processing deficits but no discernable structural cortical abnormality. LG's intermediate visual areas and object-sensitive regions exhibit abnormal activation during visual object perception, in contrast to area V5/MT+ which responds normally to visual motion (Gilaie-Dotan, Perry, Bonneh, Malach, & Bentin, 2009). Here, in three studies we used point light displays, which require visual integration, in adaptive threshold experiments to examine LG's ability to detect form from biological and non-biological motion cues. LG's ability to detect and discriminate form from biological motion was similar to healthy controls. In contrast, he was significantly deficient in processing form from non-biological motion. Thus, LG can rely on biological motion cues to perceive human forms, but is considerably impaired in extracting form from non-biological motion. Finally, we found that while LG viewed biological motion, activity in a network of brain regions associated with processing biological motion was functionally correlated with his V5/MT+ activity, indicating that normal inputs from V5/MT+ might suffice to activate his action perception system. These results indicate that processing of biologically moving form can dissociate from other form processing in the ventral pathway. Furthermore, the present results indicate that integrative ventral stream processing is necessary for uncompromised processing of non-biological form from motion. Copyright © 2011 Elsevier Ltd. All rights reserved.

Long-Range Capture and Delivery of Water-Dispersed Nano-objects by Microbubbles Generated on 3D Plasmonic Surfaces.

PubMed

Tantussi, Francesco; Messina, Gabriele C; Capozza, Rosario; Dipalo, Michele; Lovato, Laura; De Angelis, Francesco

2018-05-22

The possibility of investigating small amounts of molecules, moieties, or nano-objects dispersed in solution constitutes a central step for various application areas in which high sensitivity is necessary. Here, we show that the rapid expansion of a water bubble can act as a fast-moving net for molecules or nano-objects, collecting the floating objects in the surrounding medium in a range up to 100 μm. Thanks to an engineered 3D patterning of the substrate, the collapse of the bubble could be guided toward a designed area of the surface with micrometric precision. Thus, a locally confined high density of particles is obtained, ready for evaluation by most optical/spectroscopic detection schemes. One of the main relevant strengths of the long-range capture and delivery method is the ability to increase, by a few orders of magnitude, the local density of particles with no changes in their physiological environment. The bubble is generated by an ultrafast IR laser pulse train focused on a resonant plasmonic antenna; due to the excitation process, the technique is trustworthy and applicable to biological samples. We have tested the reliabilities of the process by concentrating highly dispersed fluorescence molecules and fluorescent beads. Lastly, as an ultimate test, we have applied the bubble clustering method on nanosized exosome vesicles dispersed in water; due to the clustering effect, we were able to effectively perform Raman spectroscopy on specimens that were otherwise extremely difficult to measure.

Inspection and analysis of the walls of fluid filled tubes by active electrolocation: a biomimetic approach

NASA Astrophysics Data System (ADS)

Gottwald, Martin; Mayekar, Kavita; Reiswich, Vladislav; Bousack, Herbert; Damalla, Deepak; Biswas, Shubham; Metzen, Michael G.; von der Emde, Gerhard

2011-04-01

During their nocturnal activity period, weakly electric fish employ a process called "active electrolocation" for navigation and object detection. They discharge an electric organ in their tail, which emits electrical current pulses, called electric organ discharges (EOD). Local EODs are sensed by arrays of electroreceptors in the fish's skin, which respond to modulations of the signal caused by nearby objects. Fish thus gain information about the size, shape, complex impedance and distance of objects. Inspired by these remarkable capabilities, we have designed technical sensor systems which employ active electrolocation to detect and analyse the walls of small, fluid filled pipes. Our sensor systems emit pulsed electrical signals into the conducting medium and simultaneously sense local current densities with an array of electrodes. Sensors can be designed which (i) analyse the tube wall, (ii) detect and localize material faults, (iii) identify wall inclusions or objects blocking the tube (iv) and find leakages. Here, we present first experiments and FEM simulations on the optimal sensor arrangement for different types of sensor systems and different types of tubes. In addition, different methods for sensor read-out and signal processing are compared. Our biomimetic sensor systems promise to be relatively insensitive to environmental disturbances such as heat, pressure, turbidity or muddiness. They could be used in a wide range of tubes and pipes including water pipes, hydraulic systems, and biological systems. Medical applications include catheter based sensors which inspect blood vessels, urethras and similar ducts in the human body.

Biology-driven library design for probe discovery.

PubMed

Inglese, James; Hasson, Samuel A

2011-10-28

Libraries of diverse small molecules are important to probe and drug discovery. The current trend toward building massive screening collections to support drug development, a special application of chemical biology, can limit their broader potential. Biology-driven construction methods (Wallace et al., 2011) are rapidly emerging to bring chemical libraries back on a viable path. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Economics of Biosimilars

PubMed Central

Blackstone, Erwin A.; Joseph, P. Fuhr

2013-01-01

Background The high cost of pharmaceuticals, especially biologics, has become an important issue in the battle to control healthcare costs. The Hatch-Waxman Act encourages generic competition but still provides incentives for pioneers to develop new drugs. The Biologics Price Competition and Innovation Act is intended to do the same for biologics and biosimilars. Objective To examine information related to biosimilars to determine their potential impact on competition in the biologic market. Method Using information concerning the European Union (EU) and the pharmaceutical industry, this article reviews and analyzes the experience of biosimilars in the EU, as well as the obstacles and opportunities that biosimilars face in the United States. Much of the analysis is based on examining current trends in biologic drugs and the potential implications on the future of biosimilars. Discussion This article reviews the mixed success of biosimilars in the EU and the implications for the United States. Because biologics are produced from living organisms, manufacturing issues are more important than in the chemical drug market. The barriers to biosimilar entry into the marketplace are much more difficult to overcome than challenges generic manufacturers typically face and are similar to obstacles specialty injectable producers encounter. The competitive responses by pioneers are also likely to be more important. The capital costs and risk issues with biosimilars make alliances and partnering arrangements very likely. Biosimilars often enter emerging markets, where the barriers to entry are easier to overcome. Nevertheless, the United States represents the greatest opportunity for biosimilar producers, in part because it is the largest biologics market and has high prices for biologics. As the United States enters the biosimilar market, the pharmaceutical industry is likely to grow at an accelerated pace. Automatic substitution is likely to be slow to develop, because of safety and quality concerns. The beneficial impact of biosimilars is likely to take a long time to be realized and to be fraught with more difficulties than was the case for small-molecule generics. Conclusion Various factors, such as safety, pricing, manufacturing, entry barriers, physician acceptance, and marketing, will make the biosimilar market develop different from the generic market. The high cost to enter the market and the size of the biologic drug market make entry attractive but risky. PMID:24991376

Can a brief biologically-based psychoeducational intervention reduce stigma and increase help-seeking intentions for depression in young people? A randomised controlled trial.

PubMed

Howard, Kerry A; Griffiths, Kathleen M; McKetin, Rebecca; Ma, Jennifer

2018-05-01

There is disagreement in the literature as to whether biological attribution increases or decreases stigma. This study investigated the effect of an online biological intervention on stigma and help-seeking intentions for depression among adolescents. A three-arm, pre-post test, double-blind randomised controlled trial (RCT) was used to compare the effects of a biological and a psychosocial intervention delivered online. Participants comprised secondary school students (N = 327) aged 16-19 years. Outcome measures included anticipated self-stigma for depression (primary), personal stigma, help-seeking intention for depression, and biological and psychosocial attribution. Neither the biological nor the psychosocial educational intervention significantly reduced anticipated self-stigma or personal stigma for depression relative to the control. However, a small increase in help-seeking intention for depression relative to the control was found for the biological educational condition. The study was undertaken over a single session and it is unknown whether the intervention effect on help-seeking intentions was sustained or would translate into help-seeking behaviour. A brief online biological education intervention did not alter stigma, but did promote a small increase in help-seeking intentions for depression among adolescents. This type of intervention may be a practical means for facilitating help-seeking among adolescents with current or future depression treatment needs.

Combinational pixel-by-pixel and object-level classifying, segmenting, and agglomerating in performing quantitative image analysis that distinguishes between healthy non-cancerous and cancerous cell nuclei and delineates nuclear, cytoplasm, and stromal material objects from stained biological tissue materials

DOEpatents

Boucheron, Laura E

2013-07-16

Quantitative object and spatial arrangement-level analysis of tissue are detailed using expert (pathologist) input to guide the classification process. A two-step method is disclosed for imaging tissue, by classifying one or more biological materials, e.g. nuclei, cytoplasm, and stroma, in the tissue into one or more identified classes on a pixel-by-pixel basis, and segmenting the identified classes to agglomerate one or more sets of identified pixels into segmented regions. Typically, the one or more biological materials comprises nuclear material, cytoplasm material, and stromal material. The method further allows a user to markup the image subsequent to the classification to re-classify said materials. The markup is performed via a graphic user interface to edit designated regions in the image.

Bioinspired spring origami.

PubMed

Faber, Jakob A; Arrieta, Andres F; Studart, André R

2018-03-23

Origami enables folding of objects into a variety of shapes in arts, engineering, and biological systems. In contrast to well-known paper-folded objects, the wing of the earwig has an exquisite natural folding system that cannot be sufficiently described by current origami models. Such an unusual biological system displays incompatible folding patterns, remains open by a bistable locking mechanism during flight, and self-folds rapidly without muscular actuation. We show that these notable functionalities arise from the protein-rich joints of the earwig wing, which work as extensional and rotational springs between facets. Inspired by this biological wing, we establish a spring origami model that broadens the folding design space of traditional origami and allows for the fabrication of precisely tunable, four-dimensional-printed objects with programmable bioinspired morphing functionalities. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Biopathways representation and simulation on hybrid functional petri net.

PubMed

Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru

2011-01-01

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering aremore » now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."« less

Small Schools Student Learning Objectives, 9-12: Mathematics, Reading, Reading in the Content Areas, Language Arts.

ERIC Educational Resources Information Center

Nelson, JoAnne, Ed.; Hartl, David, Ed.

Designed by Washington curriculum specialists and secondary teachers to assist teachers in small schools with the improvement of curriculum and instruction and to aid smaller districts lacking curriculum personnel to comply with Washington's Student Learning Objectives Law, this handbook contains learning objectives in the areas of language arts,…

Small Schools Language Arts Curriculum, K-3: Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts that do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains language arts curriculum materials for grades K-3. Learning objectives are correlated to the Goals…

Disappearance of the inversion effect during memory-guided tracking of scrambled biological motion.

PubMed

Jiang, Changhao; Yue, Guang H; Chen, Tingting; Ding, Jinhong

2016-08-01

The human visual system is highly sensitive to biological motion. Even when a point-light walker is temporarily occluded from view by other objects, our eyes are still able to maintain tracking continuity. To investigate how the visual system establishes a correspondence between the biological-motion stimuli visible before and after the disruption, we used the occlusion paradigm with biological-motion stimuli that were intact or scrambled. The results showed that during visually guided tracking, both the observers' predicted times and predictive smooth pursuit were more accurate for upright biological motion (intact and scrambled) than for inverted biological motion. During memory-guided tracking, however, the processing advantage for upright as compared with inverted biological motion was not found in the scrambled condition, but in the intact condition only. This suggests that spatial location information alone is not sufficient to build and maintain the representational continuity of the biological motion across the occlusion, and that the object identity may act as an important information source in visual tracking. The inversion effect disappeared when the scrambled biological motion was occluded, which indicates that when biological motion is temporarily occluded and there is a complete absence of visual feedback signals, an oculomotor prediction is executed to maintain the tracking continuity, which is established not only by updating the target's spatial location, but also by the retrieval of identity information stored in long-term memory.

Using LabView for real-time monitoring and tracking of multiple biological objects

NASA Astrophysics Data System (ADS)

Nikolskyy, Aleksandr I.; Krasilenko, Vladimir G.; Bilynsky, Yosyp Y.; Starovier, Anzhelika

2017-04-01

Today real-time studying and tracking of movement dynamics of various biological objects is important and widely researched. Features of objects, conditions of their visualization and model parameters strongly influence the choice of optimal methods and algorithms for a specific task. Therefore, to automate the processes of adaptation of recognition tracking algorithms, several Labview project trackers are considered in the article. Projects allow changing templates for training and retraining the system quickly. They adapt to the speed of objects and statistical characteristics of noise in images. New functions of comparison of images or their features, descriptors and pre-processing methods will be discussed. The experiments carried out to test the trackers on real video files will be presented and analyzed.

TH-A-BRD-01: Radiation Biology for Radiation Therapy Physicists

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orton, C; Borras, C; Carlson, D

Mechanisms by which radiation kills cells and ways cell damage can be repaired will be reviewed. The radiobiological parameters of dose, fractionation, delivery time, dose rate, and LET will be discussed. The linear-quadratic model for cell survival for high and low dose rate treatments and the effect of repopulation will be presented and discussed. The rationale for various radiotherapy techniques such as conventional fractionation, hyperfractionation, hypofractionation, and low and high dose rate brachytherapy, including permanent implants, will be presented. The radiobiological principles underlying radiation protection guidelines and the different radiation dosimetry terms used in radiation biology and in radiation protectionmore » will be reviewed. Human data on radiation induced cancer, including increases in the risk of second cancers following radiation therapy, as well as data on radiation induced tissue reactions, such as cardiovascular effects, for follow up times up to 20–40 years, published by ICRP, NCRP and BEIR Committees, will be examined. The latest risk estimates per unit dose will be presented. Their adoption in recent radiation protection standards and guidelines and their impact on patient and workers safety in radiotherapy will be discussed. Biologically-guided radiotherapy (BGRT) provides a systematic method to derive prescription doses that integrate patient-specific information about tumor and normal tissue biology. Treatment individualization based on patient-specific biology requires the identification of biological objective functions to facilitate the design and comparison of competing treatment modalities. Biological objectives provide a more direct approach to plan optimization instead of relying solely on dose-based surrogates and can incorporate factors that alter radiation response, such as DNA repair, tumor hypoxia, and relative biological effectiveness. We review concepts motivating biological objectives and provide examples of how they might be used to address clinically relevant problems. Underlying assumptions and limitations of existing models and their proper application will be discussed. This multidisciplinary educational session combines the fundamentals of radiobiology for radiation therapy and radiation protection with the practical application of biophysical models for treatment planning and evaluation. Learning Objectives: To understand fractionation in teletherapy and dose rate techniques in brachytherapy. To understand how the linear-quadratic models the effect of radiobiological parameters for radiotherapy. To understand the radiobiological basis of radiation protection standards applied to radiotherapy. To distinguish between stochastic effects and tissue reactions. To learn how to apply concepts of biological effective dose and RBE-weighted dose and to incorporate biological factors that alter radiation response. To discuss clinical strategies to increase therapeutic ratio, i.e., maximize local control while minimizing the risk of acute and late normal tissue effects.« less

Alectinib for the treatment of ALK-positive stage IV non-small cell lung cancer.

PubMed

Wong, K M; Noonan, S; O'Bryant, C; Jimeno, A

2015-03-01

Our increased understanding of the molecular subsets of non-small cell lung cancer (NSCLC) has led to the development of highly effective targeted therapies. In particular, the outcomes of patients with advanced NSCLC driven by the EML4-ALK fusion protein, which comprise 3-5% of cases, have remarkably improved with the use of crizotinib, an oral multi-tyrosine kinase inhibitor that targets ALK. However, patients inevitably develop progression while on crizotinib due to various mechanisms of resistance. Alectinib is a novel oral small molecule that inhibits ALK with high potency and selectivity, and demonstrates promising antitumor effects in NSCLC. Preclinical studies have shown that it is also active against several mutant forms of ALK that confer resistance to crizotinib, including the gatekeeper mutation L1196M. Moreover, an objective response rate of over 90% was observed in a phase I trial. Due to the impressive results of early phase studies, alectinib was approved for the treatment of advanced ALK-positive NSCLC in Japan, while it has been granted a breakthrough therapy designation by the FDA. A phase III trial is currently ongoing. This review will describe the biology and significance of ALK rearrangements in NSCLC, ALK inhibition by crizotinib and mechanisms of resistance, as well as the preclinical and clinical evidence for the novel ALK inhibitor alectinib. Copyright 2015 Prous Science, S.A.U. or its licensors. All rights reserved.

How small business health exchanges can offer value to their future customers--and why they must.

PubMed

Kingsdale, Jon

2012-02-01

The success of the Small Business Health Options Program (SHOP)-health insurance exchanges targeted at the small-group market and opening for business in January 2014-will depend in large part on persuading small employers and qualified health plans to participate. The most important objective will be offering employers lower-cost health plans than they have now. Other critical objectives will be offering small firms administrative efficiencies and access to choices among high-value plans that are not offered elsewhere. This article frames the challenges that exchanges will encounter in meeting these objectives. In particular, it discusses the advisability of small-business exchanges' offering an "employee choice" model (which the article describes in detail); of combining the small-business and individual exchanges to broaden product offerings and gain operational efficiencies; and of encouraging low-cost plans to enter the exchange market, perhaps by enabling Medicaid managed care plans to offer comparable commercial products, and in turn affording health plans access to a uniquely motivated market of small firms and their workers who want affordable coverage.

Biological and dosimetric characterisation of spatially fractionated proton minibeams

NASA Astrophysics Data System (ADS)

Meyer, Juergen; Stewart, Robert D.; Smith, Daniel; Eagle, James; Lee, Eunsin; Cao, Ning; Ford, Eric; Hashemian, Reza; Schuemann, Jan; Saini, Jatinder; Marsh, Steve; Emery, Robert; Dorman, Eric; Schwartz, Jeff; Sandison, George

2017-12-01

The biological effectiveness of proton beams varies with depth, spot size and lateral distance from the beam central axis. The aim of this work is to incorporate proton relative biological effectiveness (RBE) and equivalent uniform dose (EUD) considerations into comparisons of broad beam and highly modulated proton minibeams. A Monte Carlo model of a small animal proton beamline is presented. Dose and variable RBE is calculated on a per-voxel basis for a range of energies (30-109 MeV). For an open beam, the RBE values at the beam entrance ranged from 1.02-1.04, at the Bragg peak (BP) from 1.3 to 1.6, and at the distal end of the BP from 1.4 to 2.0. For a 50 MeV proton beam, a minibeam collimator designed to produce uniform dose at the depth of the BP peak, had minimal impact on the open beam RBE values at depth. RBE changes were observed near the surface when the collimator was placed flush with the irradiated object, due to a higher neutron contribution derived from proton interactions with the collimator. For proton minibeams, the relative mean RBE weighted entrance dose (RWD) was ~25% lower than the physical mean dose. A strong dependency of the EUD with fraction size was observed. For 20 Gy fractions, the EUD varied widely depending on the radiosensitivity of the cells. For radiosensitive cells, the difference was up to ~50% in mean dose and ~40% in mean RWD and the EUD trended towards the valley dose rather than the mean dose. For comparative studies of uniform dose with spatially fractionated proton minibeams, EUD derived from a per-voxel RWD distribution is recommended for biological assessments of reproductive cell survival and related endpoints.

Biological and dosimetric characterisation of spatially fractionated proton minibeams.

PubMed

Meyer, Juergen; Stewart, Robert D; Smith, Daniel; Eagle, James; Lee, Eunsin; Cao, Ning; Ford, Eric; Hashemian, Reza; Schuemann, Jan; Saini, Jatinder; Marsh, Steve; Emery, Robert; Dorman, Eric; Schwartz, Jeff; Sandison, George

2017-11-21

The biological effectiveness of proton beams varies with depth, spot size and lateral distance from the beam central axis. The aim of this work is to incorporate proton relative biological effectiveness (RBE) and equivalent uniform dose (EUD) considerations into comparisons of broad beam and highly modulated proton minibeams. A Monte Carlo model of a small animal proton beamline is presented. Dose and variable RBE is calculated on a per-voxel basis for a range of energies (30-109 MeV). For an open beam, the RBE values at the beam entrance ranged from 1.02-1.04, at the Bragg peak (BP) from 1.3 to 1.6, and at the distal end of the BP from 1.4 to 2.0. For a 50 MeV proton beam, a minibeam collimator designed to produce uniform dose at the depth of the BP peak, had minimal impact on the open beam RBE values at depth. RBE changes were observed near the surface when the collimator was placed flush with the irradiated object, due to a higher neutron contribution derived from proton interactions with the collimator. For proton minibeams, the relative mean RBE weighted entrance dose (RWD) was ~25% lower than the physical mean dose. A strong dependency of the EUD with fraction size was observed. For 20 Gy fractions, the EUD varied widely depending on the radiosensitivity of the cells. For radiosensitive cells, the difference was up to ~50% in mean dose and ~40% in mean RWD and the EUD trended towards the valley dose rather than the mean dose. For comparative studies of uniform dose with spatially fractionated proton minibeams, EUD derived from a per-voxel RWD distribution is recommended for biological assessments of reproductive cell survival and related endpoints.

An Evaluative Review of Simulated Dynamic Smart 3d Objects

NASA Astrophysics Data System (ADS)

Romeijn, H.; Sheth, F.; Pettit, C. J.

2012-07-01

Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.

LBL Whole Frog Project

Science.gov Websites

specimens), X-ray CT imaging (industrial imaging of non-biological objects), and direct generation from experimental study unit for biology was developed with the assistance of several high school teachers, and

A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures.

PubMed

Kentzoglanakis, Kyriakos; Poole, Matthew

2012-01-01

In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.

Metabolomic Analysis in Brain Research: Opportunities and Challenges

PubMed Central

Vasilopoulou, Catherine G.; Margarity, Marigoula; Klapa, Maria I.

2016-01-01

Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and understanding the underlying mechanisms of its dysfunction(s). Therefore, quantifying an accurate metabolic network activity map under various physiological conditions is among the major objectives of systems biology in the context of many biological applications. Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading to the design of effective therapeutic treatments. Metabolomics has emerged as the high-throughput quantitative analysis of the concentration profile of small molecular weight metabolites, which act as reactants and products in metabolic reactions and as regulatory molecules of proteins participating in many biological processes. Thus, the metabolic profile provides a metabolic activity fingerprint, through the simultaneous analysis of tens to hundreds of molecules of pathophysiological and pharmacological interest. The application of metabolomics is at its standardization phase in general, and the challenges for paving a standardized procedure are even more pronounced in brain studies. In this review, we support the value of metabolomics in brain research. Moreover, we demonstrate the challenges of designing and setting up a reliable brain metabolomic study, which, among other parameters, has to take into consideration the sex differentiation and the complexity of brain physiology manifested in its regional variation. We finally propose ways to overcome these challenges and design a study that produces reproducible and consistent results. PMID:27252656

Self-Organization Processes at the Intracellular Level

NASA Astrophysics Data System (ADS)

Ponce Dawson, Silvina

2003-03-01

In spite of their relatively small sizes, cells are incredibly complex objects in which various sorts of self-organizing processes occur. Cell division is an example of a process that nearly all cells undergo in which a concerted sequence of events takes place. What are the signals that tell the cell to move along this sequence? Clearly, this is a self-organized process. Microtubules (long polymers that are part of the cytoskeleton) and calcium signals play a major role during cell division. In this course we will focus on some features of microtubule dynamics and calcium signals that are amenable to modeling. In both of these biological systems, behaviors at a single molecule level are key determinants of the self-organized dynamics that is observed at larger scales. Thus, the modeling of these systems presents interesting challenges which require novel strategies. Their study may not only provide answers for biologically motivated questions, but is also a natural setting in which the transition between particle-like and mean-field models can be explored. In this course we will first give a brief biological introduction on the structure of eukaryotic cells, microtubule dynamics and intracellular calcium signals. We will then describe some of the models that have been presented in the literature and discuss the spatio-temporal dynamics that they predict, comparing them with observed behaviors in vitro or in vivo. We will end with a discussion on the virtues and limitations of the various modeling strategies described.

Molecular PET imaging for biology-guided adaptive radiotherapy of head and neck cancer.

PubMed

Hoeben, Bianca A W; Bussink, Johan; Troost, Esther G C; Oyen, Wim J G; Kaanders, Johannes H A M

2013-10-01

Integration of molecular imaging PET techniques into therapy selection strategies and radiation treatment planning for head and neck squamous cell carcinoma (HNSCC) can serve several purposes. First, pre-treatment assessments can steer decisions about radiotherapy modifications or combinations with other modalities. Second, biology-based objective functions can be introduced to the radiation treatment planning process by co-registration of molecular imaging with planning computed tomography (CT) scans. Thus, customized heterogeneous dose distributions can be generated with escalated doses to tumor areas where radiotherapy resistance mechanisms are most prevalent. Third, monitoring of temporal and spatial variations in these radiotherapy resistance mechanisms early during the course of treatment can discriminate responders from non-responders. With such information available shortly after the start of treatment, modifications can be implemented or the radiation treatment plan can be adapted tailing the biological response pattern. Currently, these strategies are in various phases of clinical testing, mostly in single-center studies. Further validation in multicenter set-up is needed. Ultimately, this should result in availability for routine clinical practice requiring stable production and accessibility of tracers, reproducibility and standardization of imaging and analysis methods, as well as general availability of knowledge and expertise. Small studies employing adaptive radiotherapy based on functional dynamics and early response mechanisms demonstrate promising results. In this context, we focus this review on the widely used PET tracer (18)F-FDG and PET tracers depicting hypoxia and proliferation; two well-known radiation resistance mechanisms.

A new species of Gadirtha Walker (Nolidae, Eligminae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States

PubMed Central

Pogue, Michael G.

2014-01-01

Abstract Gadirtha fusca sp. n., is described from Guangxi Province, China. Gadirtha fusca differs in forewing color and pattern, male and female genitalia, and in larval pattern from all other species of Gadirtha. Gadirtha fusca has been evaluated as a potential biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the southeastern United States. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker. PMID:24624017

A new species of Gadirtha Walker (Nolidae, Eligminae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States.

PubMed

Pogue, Michael G

2014-01-01

Gadirtha fusca sp. n., is described from Guangxi Province, China. Gadirtha fusca differs in forewing color and pattern, male and female genitalia, and in larval pattern from all other species of Gadirtha. Gadirtha fusca has been evaluated as a potential biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the southeastern United States. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

The Optical Gravitational Lensing Experiment. Additional Planetary and Low-Luminosity Object Transits from the OGLE 2001 and 2002 Observational Campaigns

NASA Astrophysics Data System (ADS)

Udalski, A.; Pietrzynski, G.; Szymanski, M.; Kubiak, M.; Zebrun, K.; Soszynski, I.; Szewczyk, O.; Wyrzykowski, L.

2003-06-01

The photometric data collected by OGLE-III during the 2001 and 2002 observational campaigns aiming at detection of planetary or low-luminosity object transits were corrected for small scale systematic effects using the data pipeline by Kruszewski and Semeniuk and searched again for low amplitude transits. Sixteen new objects with small transiting companions, additional to previously found samples, were discovered. Most of them are small amplitude cases which remained undetected in the original data. Several new objects seem to be very promising candidates for systems containing substellar objects: extrasolar planets or brown dwarfs. Those include OGLE-TR-122, OGLE-TR-125, OGLE-TR-130, OGLE-TR-131 and a few others. Those objects are particularly worth spectroscopic follow-up observations for radial velocity measurements and mass determination. With well known photometric orbit only a few RV measurements should allow to confirm their actual status. All photometric data of presented objects are available to the astronomical community from the OGLE Internet archive.

Examining the intersection between splicing, nuclear export and small RNA pathways.

PubMed

Nabih, Amena; Sobotka, Julia A; Wu, Monica Z; Wedeles, Christopher J; Claycomb, Julie M

2017-11-01

Nuclear Argonaute/small RNA pathways in a variety of eukaryotic species are generally known to regulate gene expression via chromatin modulation and transcription attenuation in a process known as transcriptional gene silencing (TGS). However, recent data, including genetic screens, phylogenetic profiling, and molecular mechanistic studies, also point to a novel and emerging intersection between the splicing and nuclear export machinery with nuclear Argonaute/small RNA pathways in many organisms. In this review, we summarize the field's current understanding regarding the relationship between splicing, export and small RNA pathways, and consider the biological implications for coordinated regulation of transcripts by these pathways. We also address the importance and available approaches for understanding the RNA regulatory logic generated by the intersection of these particular pathways in the context of synthetic biology. The interactions between various eukaryotic RNA regulatory pathways, particularly splicing, nuclear export and small RNA pathways provide a type of combinatorial code that informs the identity ("self" versus "non-self") and dictates the fate of each transcript in a cell. Although the molecular mechanisms for how splicing and nuclear export impact small RNA pathways are not entirely clear at this early stage, the links between these pathways are widespread across eukaryotic phyla. The link between splicing, nuclear export, and small RNA pathways is emerging and establishes a new frontier for understanding the combinatorial logic of gene regulation across species that could someday be harnessed for therapeutic, biotechnology and agricultural applications. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Small Schools Mathematics Curriculum, Grades 7-8: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Developed during the 1976-77 school year to assist Washington grade 7-8 teachers in small school districts with the improvement of curriculum and instruction, this learning-objective-based curriculum suggests activities, monitoring procedures and resources for mathematics. Introductory materials describe the organization of Small School materials,…

The American Cowboy: Developing Small Group Social Studies Interaction Experiences in the Elementary Classroom.

ERIC Educational Resources Information Center

Holmes, Edward, Jr.

Appropriate for elementary school students, this resource unit on the American cowboy provides four activities for small group work. The unit also lists objectives and discusses the organization and dynamics of small groups. The general objective is for the student to learn how to work within groups and how to resolve group conflict. The…

Fock space, symbolic algebra, and analytical solutions for small stochastic systems.

PubMed

Santos, Fernando A N; Gadêlha, Hermes; Gaffney, Eamonn A

2015-12-01

Randomness is ubiquitous in nature. From single-molecule biochemical reactions to macroscale biological systems, stochasticity permeates individual interactions and often regulates emergent properties of the system. While such systems are regularly studied from a modeling viewpoint using stochastic simulation algorithms, numerous potential analytical tools can be inherited from statistical and quantum physics, replacing randomness due to quantum fluctuations with low-copy-number stochasticity. Nevertheless, classical studies remained limited to the abstract level, demonstrating a more general applicability and equivalence between systems in physics and biology rather than exploiting the physics tools to study biological systems. Here the Fock space representation, used in quantum mechanics, is combined with the symbolic algebra of creation and annihilation operators to consider explicit solutions for the chemical master equations describing small, well-mixed, biochemical, or biological systems. This is illustrated with an exact solution for a Michaelis-Menten single enzyme interacting with limited substrate, including a consideration of very short time scales, which emphasizes when stiffness is present even for small copy numbers. Furthermore, we present a general matrix representation for Michaelis-Menten kinetics with an arbitrary number of enzymes and substrates that, following diagonalization, leads to the solution of this ubiquitous, nonlinear enzyme kinetics problem. For this, a flexible symbolic maple code is provided, demonstrating the prospective advantages of this framework compared to stochastic simulation algorithms. This further highlights the possibilities for analytically based studies of stochastic systems in biology and chemistry using tools from theoretical quantum physics.

[Understanding the symbolic values of Japanese onomatopoeia: comparison of Japanese and Chinese speakers].

PubMed

Haryu, Etsuko; Zhao, Lihua

2007-10-01

Do non-native speakers of the Japanese language understand the symbolic values of Japanese onomatopoeia matching a voiced/unvoiced consonant with a big/small sound made by a big/small object? In three experiments, participants who were native speakers of Japanese, Japanese-learning Chinese, or Chinese without knowledge of the Japanese language were shown two pictures. One picture was of a small object making a small sound, such as a small vase being broken, and the other was of a big object making a big sound, such as a big vase being broken. Participants were presented with two novel onomatopoetic words with voicing contrasts, e.g.,/dachan/vs./tachan/, and were told that each word corresponded to one of the two pictures. They were then asked to match the words to the corresponding pictures. Chinese without knowledge of Japanese performed only at chance level, whereas Japanese and Japanese-learning Chinese successfully matched a voiced/unvoiced consonant with a big/small object respectively. The results suggest that the key to understanding the symbolic values of voicing contrasts in Japanese onomatopoeia is some basic knowledge that is intrinsic to the Japanese language.

A Neural Systems-Based Neurobiology and Neuropsychiatry Course: Integrating Biology, Psychodynamics, and Psychology in the Psychiatric Curriculum

ERIC Educational Resources Information Center

Lacy, Timothy; Hughes, John D.

2006-01-01

Objective: Psychotherapy and biological psychiatry remain divided in psychiatry residency curricula. Behavioral neurobiology and neuropsychiatry provide a systems-level framework that allows teachers to integrate biology, psychodynamics, and psychology. Method: The authors detail the underlying assumptions and outline of a neural systems-based…

Developing Information Fluency in Introductory Biology Students in the Context of an Investigative Laboratory

ERIC Educational Resources Information Center

Lindquester, Gary J.; Burks, Romi L.; Jaslow, Carolyn R.

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100…

Effects of cover crops on soil quality: Selected chemical and biological parameters

USDA-ARS?s Scientific Manuscript database

Cover crops may improve soil physical, chemical, and biological properties and thus help improve land productivity. The objective of this study was to evaluate short-term changes (6, 9, and 12 weeks) in soil chemical and biological properties as influenced by cover crops for two different soils and...

Directions in biomedical research: a plea for ideological pluralism.

PubMed

Malone, P Colm; Agutter, Paul S

2003-08-01

Feinstein [A.R. Feinstein, Am. J. Med. 107 (1999) 461] complained that 'basic medical science' has overwhelmed 'pathophysiological medical science' during the past half century, and 'destroyed the bridge between bedside and bench'. We agree that a 'drastic reorientation' will be necessary to correct the overemphasis and imbalance. Re-examining the roots of his problem, we believe that a plea to restore a balance between the 'status' (esteem) of 'large research' and 'small research' in medical science brings back into question the decision of academic physiologists to invoke the framework of Physics in/of 1847 [P.F. Cranefield, J. Hist. Med. Allied Sci. 12 (1957) 407] (together with an absolutist 'Prime Mover'/Metaphysic which Einstein would delete from Physics in 1905). The current 'imbalance' arose when that Cartesian 'Prime Mover' was NOT deleted from the Biological frame. Feinstein felt that the 'privileged status' (esteem) in which fund-giving bodies hold 'Small' researches compared to 'Large' should be cancelled. Once Biology replaces its Cartesian absolutism with a relativist framework, redress will follow naturally when living-material has regained the status of cause as well as effect. Descartes' 'Great Watchmaker' is a Dead God in Biology: a non-metaphysical Biological Perspective would restore balance between 'large' and 'small' investigations. ('Pluralism' implies that no scientific perspective would be second-rate in a relativist framework.)

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.

PubMed

Yang, Haixiu; Shang, Desi; Xu, Yanjun; Zhang, Chunlong; Feng, Li; Sun, Zeguo; Shi, Xinrui; Zhang, Yunpeng; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

2017-07-27

Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.

From boundary‐work to boundary object: how biology left and re‐entered the social sciences

PubMed Central

Meloni, Maurizio

2016-01-01

Abstract In an archaeological spirit this paper comes back to a founding event in the construction of the twentieth‐century episteme, the moment at which the life‐ and the social sciences parted ways and intense boundary‐work was carried out on the biology/society border, with significant benefits for both sides. Galton and Weismann for biology, and Alfred Kroeber for anthropology delimit this founding moment and I argue, expanding on an existing body of historical scholarship, for an implicit convergence of their views. After this excavation, I look at recent developments in the life sciences, which I have named the ‘social turn’ in biology (Meloni, 2014), and in particular at epigenetics with its promise to destabilize the social/biological border. I claim here that today a different account of ‘the biological’ to that established during the Galton–Kroeber period is emerging. Rather than being used to support a form of boundary‐work, biology has become a boundary object that crosses previously erected barriers, allowing different research communities to draw from it. PMID:27818538

Object-oriented parsing of biological databases with Python.

PubMed

Ramu, C; Gemünd, C; Gibson, T J

2000-07-01

While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.

Noun and knowledge retrieval for biological and non-biological entities following right occipitotemporal lesions.

PubMed

Bruffaerts, Rose; De Weer, An-Sofie; De Grauwe, Sophie; Thys, Miek; Dries, Eva; Thijs, Vincent; Sunaert, Stefan; Vandenbulcke, Mathieu; De Deyne, Simon; Storms, Gerrit; Vandenberghe, Rik

2014-09-01

We investigated the critical contribution of right ventral occipitotemporal cortex to knowledge of visual and functional-associative attributes of biological and non-biological entities and how this relates to category-specificity during confrontation naming. In a consecutive series of 7 patients with lesions confined to right ventral occipitotemporal cortex, we conducted an extensive assessment of oral generation of visual-sensory and functional-associative features in response to the names of biological and nonbiological entities. Subjects also performed a confrontation naming task for these categories. Our main novel finding related to a unique case with a small lesion confined to right medial fusiform gyrus who showed disproportionate naming impairment for nonbiological versus biological entities, specifically for tools. Generation of visual and functional-associative features was preserved for biological and non-biological entities. In two other cases, who had a relatively small posterior lesion restricted to primary visual and posterior fusiform cortex, retrieval of visual attributes was disproportionately impaired compared to functional-associative attributes, in particular for biological entities. However, these cases did not show a category-specific naming deficit. Two final cases with the largest lesions showed a classical dissociation between biological versus nonbiological entities during naming, with normal feature generation performance. This is the first lesion-based evidence of a critical contribution of the right medial fusiform cortex to tool naming. Second, dissociations along the dimension of attribute type during feature generation do not co-occur with category-specificity during naming in the current patient sample. Copyright © 2014 Elsevier Ltd. All rights reserved.

QEEN Workshop: "Quantifying Exposure to Engineered Nano ...

EPA Pesticide Factsheets

The measurement and characterization of nanomaterials in biological tissues is complicated by a number of factors including: the sensitivity of the assay to small sized particles or low concentrations of materials; the ability to distinguish different forms and transformations of the materials related to the biological matrix; distinguishing exogenous nanomaterials, which may be composed of biologically common elements such as carbon,from normal biological tissues; differentiating particle from ionic phases for materials that dissolve; localization of sparsely distributed materials in a complex substrate (the

Effects of saltcedar invasion and biological control on small mammals

USDA-ARS?s Scientific Manuscript database

Effects of invasive saltcedars (Tamarix spp.) on bird populations and communities have received considerable interest, but impacts on other vertebrate taxa have received less attention. Moreover, only one published study examined effects on vertebrates of biological control efforts directed at saltc...

Bringing Life Processes to Life

ERIC Educational Resources Information Center

Souders, Hannah

2018-01-01

Protein synthesis, involving such abstract concepts as "DNA," "RNA," "transcription," and "translation," is one of many biological processes too small to be seen by the naked eye. This combination of scientific jargon and sub-microscopic elements can make biology seem overwhelming to any student--but…

Mass spectrometry in systems biology an introduction.

PubMed

Dunn, Warwick B

2011-01-01

The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of proteins and metabolites. Here, the role of mass spectrometry in systems biology will be assessed, the advantages and disadvantages discussed, and the instrument configurations available described. Finally, general applications will be briefly reviewed. Copyright © 2011 Elsevier Inc. All rights reserved.

Small Schools Reading Curriculum, 7-8: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades 7 and 8. The objectives listed are correlated to the…

Small Schools Reading Curriculum, 4-6: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades 4-6. The objectives listed are correlated to the Goals…

Small Schools Social Studies Curriculum, K-3: Reading, Language Arts, Mathematics, Science, Social Studies. Scope Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Small schools will find this social studies curriculum guide for grades K-3 helpful in complying with Washington state education laws that require districts to identify student learning objectives and evaluate each student's performance relative to the attainment of the objectives. This curriculum, developed during 1975 and 1976 by teachers and…

Small Schools Reading Curriculum, K-3: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades K-3. The objectives listed are correlated to the Goals…

Archimedes Revisited: A Faster, Better, Cheaper Method of Accurately Measuring the Volume of Small Objects

ERIC Educational Resources Information Center

Hughes, Stephen W.

2005-01-01

A little-known method of measuring the volume of small objects based on Archimedes' principle is described, which involves suspending an object in a water-filled container placed on electronic scales. The suspension technique is a variation on the hydrostatic weighing technique used for measuring volume. The suspension method was compared with two…

Colloidal Bandpass and Bandgap Filters

NASA Astrophysics Data System (ADS)

Yellen, Benjamin; Tahir, Mukarram; Ouyang, Yuyu; Nori, Franco

2013-03-01

Thermally or deterministically-driven transport of objects through asymmetric potential energy landscapes (ratchet-based motion) is of considerable interest as models for biological transport and as methods for controlling the flow of information, material, and energy. Here, we provide a general framework for implementing a colloidal bandpass filter, in which particles of a specific size range can be selectively transported through a periodic lattice, whereas larger or smaller particles are dynamically trapped in closed-orbits. Our approach is based on quasi-static (adiabatic) transition in a tunable potential energy landscape composed of a multi-frequency magnetic field input signal with the static field of a spatially-periodic magnetization. By tuning the phase shifts between the input signal and the relative forcing coefficients, large-sized particles may experience no local energy barriers, medium-sized particles experience only one local energy barrier, and small-sized particles experience two local energy barriers. The odd symmetry present in this system can be used to nudge the medium-sized particles along an open pathway, whereas the large or small beads remain trapped in a closed-orbit, leading to a bandpass filter, and vice versa for a bandgap filter. NSF CMMI - 0800173, Youth 100 Scholars Fund

Improvement of small dairy producers in the central coast of Peru.

PubMed

Gomez, C; Fernandez, M; Salazar, I; Saldaña, I; Heredia, H

2007-12-01

The objective of this study was to characterize a group of small dairy producers in the central coast of Peru and determine the most important limiting factors that affect animal productivity, using Participatory Rural Appraisal methodologies. The information collected during a year included biological and socio-economic characteristics. Inappropriate nutrition, management, health and reproduction were observed in most farms. The average number of animals per family was 17.3, of which 40% were bulls and growing calves. Milk production and net cash income were reduced in the summer. The feeding programme for lactating and growing females of forage exchanged for labour and purchased concentrates did not theoretically or practically meet the cows' needs. All water was carried to the site on donkeys from one kilometre distance. All cows were negative for a number of potential infectious diseases. By California Mastitis Test of routine samples 7.1% of cows had clinical mastitis and 66.1% subclinical. Taking notional labour and forage costs into account, milk production was at a loss but the farmers considered neither and were satisfied with a net cash income from milk sales three times the average agricultural wage.

[New methodological approaches to the detection and quantitative registration of Salmonella in the study of water objects].

PubMed

Aleshnia, V V; Panasovets, O P; Zhuravlev, P V; Sukhanova, S M; Golubenko, I A; Nedachin, A E; Talaeva, Iu G; Artemova, T Z; Gipp, E K; Butorina, N N; Zagaĭnova, A V; Shvager, M M; Mitrofanova, T V

2011-01-01

The paper gives data on the use of techniques to detect and register Salmonella in the water objects, by applying a new liquid nutrient medium. Experimental and field studies have shown its advantage over the accumulation media widely used in practical healthcare. It has been ascertained that the nutrient medium not only accumulates biomass, but also provides the restoration of the biological properties of uncultivated Salmonella species. The use of the nutrient medium at practical laboratories makes it possible to unify guidelines for the examination of water objects with varying degrees of biological pollution and to obtain the comparable results of analyses.

The Biology of Linguistic Expression Impacts Neural Correlates for Spatial Language

PubMed Central

Emmorey, Karen; McCullough, Stephen; Mehta, Sonya; Ponto, Laura L. B.; Grabowski, Thomas J.

2013-01-01

Biological differences between signed and spoken languages may be most evident in the expression of spatial information. PET was used to investigate the neural substrates supporting the production of spatial language in American Sign Language as expressed by classifier constructions, in which handshape indicates object type and the location/motion of the hand iconically depicts the location/motion of a referent object. Deaf native signers performed a picture description task in which they overtly named objects or produced classifier constructions that varied in location, motion, or object type. In contrast to the expression of location and motion, the production of both lexical signs and object type classifier morphemes engaged left inferior frontal cortex and left inferior temporal cortex, supporting the hypothesis that unlike the location and motion components of a classifier construction, classifier handshapes are categorical morphemes that are retrieved via left hemisphere language regions. In addition, lexical signs engaged the anterior temporal lobes to a greater extent than classifier constructions, which we suggest reflects increased semantic processing required to name individual objects compared with simply indicating the type of object. Both location and motion classifier constructions engaged bilateral superior parietal cortex, with some evidence that the expression of static locations differentially engaged the left intraparietal sulcus. We argue that bilateral parietal activation reflects the biological underpinnings of sign language. To express spatial information, signers must transform visual–spatial representations into a body-centered reference frame and reach toward target locations within signing space. PMID:23249348

Development and Assessment of a Horizontally Integrated Biological Sciences Course Sequence for Pharmacy Education

PubMed Central

Wright, Nicholas J.D.; Alston, Gregory L.

2015-01-01

Objective. To design and assess a horizontally integrated biological sciences course sequence and to determine its effectiveness in imparting the foundational science knowledge necessary to successfully progress through the pharmacy school curriculum and produce competent pharmacy school graduates. Design. A 2-semester course sequence integrated principles from several basic science disciplines: biochemistry, molecular biology, cellular biology, anatomy, physiology, and pathophysiology. Each is a 5-credit course taught 5 days per week, with 50-minute class periods. Assessment. Achievement of outcomes was determined with course examinations, student lecture, and an annual skills mastery assessment. The North American Pharmacist Licensure Examination (NAPLEX) results were used as an indicator of competency to practice pharmacy. Conclusion. Students achieved course objectives and program level outcomes. The biological sciences integrated course sequence was successful in providing students with foundational basic science knowledge required to progress through the pharmacy program and to pass the NAPLEX. The percentage of the school’s students who passed the NAPLEX was not statistically different from the national percentage. PMID:26430276

Small-scale laser based electron accelerators for biology and medicine: a comparative study of the biological effectiveness

NASA Astrophysics Data System (ADS)

Labate, Luca; Andreassi, Maria Grazia; Baffigi, Federica; Basta, Giuseppina; Bizzarri, Ranieri; Borghini, Andrea; Candiano, Giuliana C.; Casarino, Carlo; Cresci, Monica; Di Martino, Fabio; Fulgentini, Lorenzo; Ghetti, Francesco; Gilardi, Maria Carla; Giulietti, Antonio; Köster, Petra; Lenci, Francesco; Levato, Tadzio; Oishi, Yuji; Russo, Giorgio; Sgarbossa, Antonella; Traino, Claudio; Gizzi, Leonida A.

2013-05-01

Laser-driven electron accelerators based on the Laser Wakefield Acceleration process has entered a mature phase to be considered as alternative devices to conventional radiofrequency linear accelerators used in medical applications. Before entering the medical practice, however, deep studies of the radiobiological effects of such short bunches as the ones produced by laser-driven accelerators have to be performed. Here we report on the setup, characterization and first test of a small-scale laser accelerator for radiobiology experiments. A brief description of the experimental setup will be given at first, followed by an overview of the electron bunch characterization, in particular in terms of dose delivered to the samples. Finally, the first results from the irradiation of biological samples will be briefly discussed.

Small wastewater treatment plants in mountain areas: combination of septic tank and biological filter.

PubMed

Maunoir, S; Philip, H; Rambaud, A

2007-01-01

Research work has been carried out for more than 20 years by Eparco and the University of Montpellier (France) on the application of biological wastewater treatment processes for small communities. This research has led to a new process which is particularly suitable for remote populations, taking into account several specificities such as as the seasonal fluctuations in the population, the accessibility of the site, the absence of a power supply on site, the reduced area of land available and the low maintenance. Thus, the process, which combines a septic tank operating under anaerobic conditions and a biological aerobic filter, is a solution for wastewater treatment in mountain areas. This paper presents the process and three full-scale applications in the region of the Alps.

The Future is Now – Biologics for Non-Infectious Pediatric Anterior Uveitis

PubMed Central

Lerman, Melissa A.; Rabinovich, C. Egla

2015-01-01

Anterior uveitis (AU), inflammation of the iris, choroid, or ciliary body, can cause significant eye morbidity, including visual loss. In the pediatric age group, the most common underlying diagnosis for AU is juvenile idiopathic associated uveitis and idiopathic AU, which are the focus of this paper. AU is often resistant to medications such as topical corticosteroids and methotrexate. In the past 15 years, biologic agents (biologics) have transformed treatment. In this review, we discuss those in widespread use and those with more theoretical applications for anterior uveitis. Tumor Necrosis Factor alpha inhibitors (anti-TNFα) have been available the longest and are used widely to treat pediatric uveitis. The effects of anti-TNFα in children are described mostly in small retrospective case series. Together, the literature suggests that the majority of children treated with anti-TNFα achieve decreased uveitis activity and reduce corticosteroid burden. However, many will have disease flares even on treatment. Only a few small studies directly compare outcomes between alternate anti-TNFα (infliximab and adalimumab). The use of different uveitis grading systems, inclusion criteria, and outcome measures, makes cross-study comparisons difficult. Whether the achievement and maintenance of inactive disease occurs more frequently with certain anti-TNFα remains controversial. Newer biologics that modulate the immune system differently (e.g., interfere with TH17 activation through IL-17a and IL-6 blockade, limit T lymphocyte costimulation, and deplete B lymphocytes), have shown promise for uveitis. Studies of these agents are small and include mostly adults. Additional biologics are also being explored to treat uveitis. With their advent, we are hopeful that outcomes will ultimately be improved for children with AU. With many biologics available, much work remains to identify the optimal inflammatory pathway to target in AU. PMID:25893479

The Future Is Now: Biologics for Non-Infectious Pediatric Anterior Uveitis.

PubMed

Lerman, Melissa A; Rabinovich, C Egla

2015-08-01

Anterior uveitis (AU), inflammation of the iris, choroid or ciliary body, can cause significant eye morbidity, including visual loss. In the pediatric age group, the most common underlying diagnosis for AU is juvenile idiopathic associated uveitis and idiopathic AU, which are the focus of this paper. AU is often resistant to medications such as topical corticosteroids and methotrexate. In the past 15 years, biologic agents (biologics) have transformed treatment. In this review, we discuss those in widespread use and those with more theoretical applications for anterior uveitis. Tumor necrosis factor alpha inhibitors (anti-TNFα) have been available the longest and are used widely to treat pediatric uveitis. The effects of anti-TNFα in children are described mostly in small retrospective case series. Together, the literature suggests that the majority of children treated with anti-TNFα achieve decreased uveitis activity and reduced corticosteroid burden. However, many will have disease flares even on treatment. Only a few small studies directly compare outcomes between alternate anti-TNFα (infliximab and adalimumab). The use of different uveitis grading systems, inclusion criteria, and outcome measures makes cross-study comparisons difficult. Whether the achievement and maintenance of inactive disease occurs more frequently with certain anti-TNFα remains controversial. Newer biologics that modulate the immune system differently (e.g., interfere with Th17 activation through IL-17a and IL-6 blockade, limit T lymphocyte costimulation, and deplete B lymphocytes), have shown promise for uveitis. Studies of these agents are small and include mostly adults. Additional biologics are also being explored to treat uveitis. With their advent, we are hopeful that outcomes will ultimately be improved for children with AU. With many biologics available, much work remains to identify the optimal inflammatory pathway to target in AU.

Biological objectives for bird populations

Treesearch

Jonathan Bart; Mark Koneff; Steve Wendt

2005-01-01

This paper explores the development of population based objectives for birds. The concept of population based objectives for bird conservation lies at the core of planning in the North American Bird Conservation Initiative. Clear objectives are needed as a basis for partnership, and a basis for program evaluation in an adaptive context. In the case of waterfowl,...

The development of a UGV-mounted automated refueling system for VTOL UAVs

NASA Astrophysics Data System (ADS)

Wills, Mike; Burmeister, Aaron; Nelson, Travis; Denewiler, Thomas; Mullens, Kathy

2006-05-01

This paper describes the latest efforts to develop an Automated UAV Mission System (AUMS) for small vertical takeoff and landing (VTOL) unmanned air vehicles (UAVs). In certain applications such as force protection, perimeter security, and urban surveillance a VTOL UAV can provide far greater utility than fixed-wing UAVs or ground-based sensors. The VTOL UAV can operate much closer to an object of interest and can provide a hover-and-stare capability to keep its sensors trained on an object, while the fixed wing UAV would be forced into a higher altitude loitering pattern where its sensors would be subject to intermittent blockage by obstacles and terrain. The most significant disadvantage of a VTOL UAV when compared to a fixed-wing UAV is its reduced flight endurance. AUMS addresses this disadvantage by providing forward staging, refueling, and recovery capabilities for the VTOL UAV through a host unmanned ground vehicle (UGV), which serves as a launch/recovery platform and service station. The UGV has sufficient payload capacity to carry UAV fuel for multiple launch, recovery, and refuel iterations. The UGV also provides a highly mobile means of forward deploying a small UAV into hazardous areas unsafe for personnel, such as chemically or biologically contaminated areas. Teaming small UAVs with large UGVs can decrease risk to personnel and expand mission capabilities and effectiveness. There are numerous technical challenges being addressed by these development efforts. Among the challenges is the development and integration of a precision landing system compact and light enough to allow it to be mounted on a small VTOL UAV while providing repeatable landing accuracy to safely land on the AUMS. Another challenge is the design of a UGV-transportable, expandable, self-centering landing pad that contains hardware and safety devices for automatically refueling the UAV. A third challenge is making the design flexible enough to accommodate different types of VTOL UAVs, such as the AAI iSTAR ducted-fan vehicle and small helicopter UAVs. Finally, a common command-and-control architecture which supports the UAV, UGV, and AUMS must be developed and interfaced with these systems to allow fully autonomous collaborative behaviors. Funded by the Joint Robotics Program, AUMS is part of a joint effort with the Air Force Research Laboratory and the Army Missile Research Development and Engineering Command. The objective is to develop and demonstrate UGVUAV teaming concepts and work with the warfighter to ensure that future upgrades are focused on operational requirements. This paper describes the latest achievements in AUMS development and some of the military program and first responder situations that could benefit from this system.

A Bird's-Eye View of Eco-Geomorphology From a Small Unmanned Aircraft System (UAS)

NASA Astrophysics Data System (ADS)

LeClair, A. J.; Hugenholtz, C.

2012-12-01

Physical disturbance regimes play important roles in shaping ecosystems and landscapes; however, our ability to detect disturbance often depends on the method and scale of observation. Here we use a relatively new method in order to detect and map the eco-geomorphic impacts of fossorial mammals in a grassland setting. It is well-known that digging and mound building activity by these animals is a form of biological disturbance that has a number of eco-geomorphic consequences, including: soil formation, hydrology, nutrient cycling, and succession. All these processes contribute to landscape heterogeneity and often increase local micro-topographic variations through mound formation. Most studies that have examined the eco-geomorphic role of fossorial mammals have been limited to observations using traditional field-based methods. While this has yielded important data about the localized effects, the cumulative, landscape-level impacts of such small-scale disturbance events are still largely unknown. While fossorial mammals such as pocket gophers (family Geomyidae) are assumed to be ubiquitous in the environments in which they occur, the small size of individual mounds has meant that mapping their biological footprint using traditional methods has been extremely difficult. Individual mounds disappear in the pixels of conventional remote sensing imagery, while their spatial distribution makes it impractical to study them beyond the plot scale. However, recent advances in both low cost, high-resolution digital cameras, and unmanned aerial systems (UAS), have made it possible to acquire landscape-level data that matches the scale of their disturbance, thus potentially bridging the gap between ground-based field methods and traditional remote sensing imagery. In this study we used UAS-acquired, sub-decimeter resolution imagery to map and quantify the extent of fossorial mammal disturbance in a 4 km2 area of the Great Sand Hills - a stabilized dune field in southwestern Saskatchewan, Canada. This area is densely populated by both the northern pocket gopher (Thomomys talpoides) and the thirteen-lined ground squirrel (Ictidomys tridecemlineatus), both of which are active throughout the growing season. Mounds of bare sand occur both singly, and in larger, clustered networks. Older mounds are darker due to higher vegetation cover and litter accumulation, while more recent mounds are brighter due to absence of vegetation and litter. Based on objective image classification we estimate that nearly 20% of the landscape is affected by mound disturbance, while in some localized regions up to 50% of the surface is affected by recent disturbance. Overall, our case study demonstrates the potential value of UAS platforms for acquiring high-resolution remote sensing data for detecting and mapping small-scale biological disturbance.

Assessment of metals exposure and sub-lethal effects in voles and small birds captured near the DeLong Mountain Regional Transportation System Road, Cape Krusenstern National Monument, Alaska, 2006

USGS Publications Warehouse

Brumbaugh, William G.; Mora, Miguel A.; May, Thomas W.

2008-01-01

Voles (n=6) and small ground-nesting birds (n=12) were live-captured near the DeLong Mountain Regional Transportation System haul road in Cape Krusenstern National Monument in northwest Alaska in 2006 to assess metals exposure and sub-lethal biological effects. Similar numbers of animals were captured from a reference site in southern Cape Krusenstern National Monument for comparison. Histopathological examination of selected organs, blood analysis, and analysis for aluminum, barium, cadmium, lead, and zinc concentrations in liver and blood samples were performed. Voles and small birds captured from near the haul road had about 20 times greater blood and liver lead concentrations and about 3 times greater cadmium concentrations when compared to those from the reference site. Barium and zinc tissue concentrations of animals collected from different sites were not remarkably different, and aluminum concentrations were below the reporting limits in most samples. There was no clear evidence of serious sub-lethal biological effects such as lesions in internal organs or DNA damage in blood in any of the animals. Accordingly, blood and liver lead concentrations in animals captured near the haul road generally were less than tissue concentration thresholds associated with serious biological effects reported from other studies; however, subtle effects resulting from lead exposure, such as the suppression of the activity of certain enzymes, cannot be ruled out for those animals nearest the haul road. Notably, liver lead concentrations of voles and small birds at the reference location were considerably less than those previously reported for similar animals at reference sites in other parts of the United States, Canada, and Europe. Results from this reconnaissance-level study indicate that voles and small birds inhabiting this area are not suffering serious biological effects as a result of metals exposure; however, continued monitoring of lead and other metals is recommended because of uncertainties noted and because biological effects thresholds might be approached if exposure levels were to increase.

Chemical, Biological, and Radiological (CBR) Contamination Survivability, Small Items of Equipment

DTIC Science & Technology

2012-06-22

thickness (number of coats), paint condition, and surface cleanliness (mud, grease, and other). j. Pretest (baseline) and posttest (30 days after...survivability testing of small items of mission-essential (ME) Army materiel. Small items, for example , include personal gear, small arms, radios...their effects. An example would be the age of the paint on the surface (aged, new, etc.). f. The only current mechanism for converting agent mass

Biological productivity in small impoundments

USDA-ARS?s Scientific Manuscript database

Most ponds and small impoundments are built or used with a principal use in mind. That use may be recreational fishing, commercial aquaculture, waterfowl hunting, potable water storage, irrigation water supply, livestock watering, stormwater retention, landscaping, swimming, or others. In practice, ...

An autonomous robot inspired by insect neurophysiology pursues moving features in natural environments

NASA Astrophysics Data System (ADS)

Bagheri, Zahra M.; Cazzolato, Benjamin S.; Grainger, Steven; O'Carroll, David C.; Wiederman, Steven D.

2017-08-01

Objective. Many computer vision and robotic applications require the implementation of robust and efficient target-tracking algorithms on a moving platform. However, deployment of a real-time system is challenging, even with the computational power of modern hardware. Lightweight and low-powered flying insects, such as dragonflies, track prey or conspecifics within cluttered natural environments, illustrating an efficient biological solution to the target-tracking problem. Approach. We used our recent recordings from ‘small target motion detector’ neurons in the dragonfly brain to inspire the development of a closed-loop target detection and tracking algorithm. This model exploits facilitation, a slow build-up of response to targets which move along long, continuous trajectories, as seen in our electrophysiological data. To test performance in real-world conditions, we implemented this model on a robotic platform that uses active pursuit strategies based on insect behaviour. Main results. Our robot performs robustly in closed-loop pursuit of targets, despite a range of challenging conditions used in our experiments; low contrast targets, heavily cluttered environments and the presence of distracters. We show that the facilitation stage boosts responses to targets moving along continuous trajectories, improving contrast sensitivity and detection of small moving targets against textured backgrounds. Moreover, the temporal properties of facilitation play a useful role in handling vibration of the robotic platform. We also show that the adoption of feed-forward models which predict the sensory consequences of self-movement can significantly improve target detection during saccadic movements. Significance. Our results provide insight into the neuronal mechanisms that underlie biological target detection and selection (from a moving platform), as well as highlight the effectiveness of our bio-inspired algorithm in an artificial visual system.

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism

PubMed Central

Korecka, Agata; Dona, Anthony; Lahiri, Shawon; Tett, Adrian James; Al-Asmakh, Maha; Braniste, Viorica; D’Arienzo, Rossana; Abbaspour, Afrouz; Reichardt, Nicole; Fujii-Kuriyama, Yoshiaki; Rafter, Joseph; Narbad, Arjan; Holmes, Elaine; Nicholson, Jeremy; Arulampalam, Velmurugesan; Pettersson, Sven

2016-01-01

The ligand-induced transcription factor, aryl hydrocarbon receptor (AhR) is known for its capacity to tune adaptive immunity and xenobiotic metabolism—biological properties subject to regulation by the indigenous microbiome. The objective of this study was to probe the postulated microbiome-AhR crosstalk and whether such an axis could influence metabolic homeostasis of the host. Utilising a systems-biology approach combining in-depth 1H-NMR-based metabonomics (plasma, liver and skeletal muscle) with microbiome profiling (small intestine, colon and faeces) of AhR knockout (AhR−/−) and wild-type (AhR+/+) mice, we assessed AhR function in host metabolism. Microbiome metabolites such as short-chain fatty acids were found to regulate AhR and its target genes in liver and intestine. The AhR signalling pathway, in turn, was able to influence microbiome composition in the small intestine as evident from microbiota profiling of the AhR+/+ and AhR−/− mice fed with diet enriched with a specific AhR ligand or diet depleted of any known AhR ligands. The AhR−/− mice also displayed increased levels of corticosterol and alanine in serum. In addition, activation of gluconeogenic genes in the AhR−/− mice was indicative of on-going metabolic stress. Reduced levels of ketone bodies and reduced expression of genes involved in fatty acid metabolism in the liver further underscored this observation. Interestingly, exposing AhR−/− mice to a high-fat diet showed resilience to glucose intolerance. Our data suggest the existence of a bidirectional AhR-microbiome axis, which influences host metabolic pathways. PMID:28721249

Enhancement of polarizabilities of cylinders with cylinder-slab resonances

PubMed Central

Xiao, Meng; Huang, Xueqin; Liu, H.; Chan, C. T.

2015-01-01

If an object is very small in size compared with the wavelength of light, it does not scatter light efficiently. It is hence difficult to detect a very small object with light. We show using analytic theory as well as full wave numerical calculation that the effective polarizability of a small cylinder can be greatly enhanced by coupling it with a superlens type metamaterial slab. This kind of enhancement is not due to the individual resonance effect of the metamaterial slab, nor due to that of the object, but is caused by a collective resonant mode between the cylinder and the slab. We show that this type of particle-slab resonance which makes a small two-dimensional object much “brighter” is actually closely related to the reverse effect known in the literature as “cloaking by anomalous resonance” which can make a small cylinder undetectable. We also show that the enhancement of polarizability can lead to strongly enhanced electromagnetic forces that can be attractive or repulsive, depending on the material properties of the cylinder. PMID:25641391

History of the Fort Collins Science Center, U.S. Geological Survey

USGS Publications Warehouse

O'Shea, Thomas J. (compiler)

2006-01-01

At various times during the period when it was part of the National Biological Service (1993–96), the Center served as the administrative and programmatic home base for a wide number of science activities in numerous Western states (table 1). This reflected the previous fragmentation of biological and related science efforts across resource management agencies in the U.S. Department of the Interior. The organization of the 2 Center within the National Biological Service was a manifestation of the desire of the Secretary of the Interior to consolidate its biological science activities in administratively independent entities that would ensure that the science retained its objectivity. Congress later recognized the need to maintain a hierarchical independence between biological science and resource management in the Department. However, Congress also saw that the U.S. Geological Survey, with its long history of objective science support to the nation in geology, water resources, geography, and remote sensing, was a suitable alternative home for these biological science functions. Thus, in 1996 Congress transferred the biological resources functions of the National Biological Service to the U.S. Geological Survey. Detailed overviews and opinions about the history and policy issues surrounding the formation and subsequent fate of the National Biological Service can be found elsewhere (for example Cohn, 1993, 2005; Kaufman, 1993; Kreeger, 1994; Pulliam, 1995, 1998a,b; Reichhardt, 1994; Wagner, 1999)

Neuroendocrine small cell carcinoma of the uterine cervix.

PubMed

Reig Castillejo, Anna; Membrive Conejo, Ismael; Foro Arnalot, Palmira; Rodríguez de Dios, Nuria; Algara López, Manuel

2010-07-01

Neuroendocrine small cell carcinoma of the uterine cervix (SCC) is a rare disease that mixes clinical and biological characteristics of both cervical neoplasms and neuroendocrine small cell cancer. The prognosis is poor and the optimal treatment has not yet been clarified. Multimodality treatment, with surgery and concurrent chemoradiation has recently been shown to improve local control and survival rates.

Cellular manganese content is developmentally regulated in human dopaminergic neurons

NASA Astrophysics Data System (ADS)

Kumar, Kevin K.; Lowe, Edward W., Jr.; Aboud, Asad A.; Neely, M. Diana; Redha, Rey; Bauer, Joshua A.; Odak, Mihir; Weaver, C. David; Meiler, Jens; Aschner, Michael; Bowman, Aaron B.

2014-10-01

Manganese (Mn) is both an essential biological cofactor and neurotoxicant. Disruption of Mn biology in the basal ganglia has been implicated in the pathogenesis of neurodegenerative disorders, such as parkinsonism and Huntington's disease. Handling of other essential metals (e.g. iron and zinc) occurs via complex intracellular signaling networks that link metal detection and transport systems. However, beyond several non-selective transporters, little is known about the intracellular processes regulating neuronal Mn homeostasis. We hypothesized that small molecules that modulate intracellular Mn could provide insight into cell-level Mn regulatory mechanisms. We performed a high throughput screen of 40,167 small molecules for modifiers of cellular Mn content in a mouse striatal neuron cell line. Following stringent validation assays and chemical informatics, we obtained a chemical `toolbox' of 41 small molecules with diverse structure-activity relationships that can alter intracellular Mn levels under biologically relevant Mn exposures. We utilized this toolbox to test for differential regulation of Mn handling in human floor-plate lineage dopaminergic neurons, a lineage especially vulnerable to environmental Mn exposure. We report differential Mn accumulation between developmental stages and stage-specific differences in the Mn-altering activity of individual small molecules. This work demonstrates cell-level regulation of Mn content across neuronal differentiation.

Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics.

PubMed

Tolliday, Nicola; Clemons, Paul A; Ferraiolo, Paul; Koehler, Angela N; Lewis, Timothy A; Li, Xiaohua; Schreiber, Stuart L; Gerhard, Daniela S; Eliasof, Scott

2006-09-15

In 2002, the National Cancer Institute created the Initiative for Chemical Genetics (ICG), to enable public research using small molecules to accelerate the discovery of cancer-relevant small-molecule probes. The ICG is a public-access research facility consisting of a tightly integrated team of synthetic and analytical chemists, assay developers, high-throughput screening and automation engineers, computational scientists, and software developers. The ICG seeks to facilitate the cross-fertilization of synthetic chemistry and cancer biology by creating a research environment in which new scientific collaborations are possible. To date, the ICG has interacted with 76 biology laboratories from 39 institutions and more than a dozen organic synthetic chemistry laboratories around the country and in Canada. All chemistry and screening data are deposited into the ChemBank web site (http://chembank.broad.harvard.edu/) and are available to the entire research community within a year of generation. ChemBank is both a data repository and a data analysis environment, facilitating the exploration of chemical and biological information across many different assays and small molecules. This report outlines how the ICG functions, how researchers can take advantage of its screening, chemistry and informatic capabilities, and provides a brief summary of some of the many important research findings.

Reversible and long-term immobilization in a hydrogel-microbead matrix for high-resolution imaging of Caenorhabditis elegans and other small organisms

PubMed Central

Cornaglia, Matteo; Krishnamani, Gopalan; Zhang, Jingwei; Mouchiroud, Laurent; Lehnert, Thomas; Auwerx, Johan; Gijs, Martin A. M.

2018-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research and genetic studies relevant to human biology and disease. Such studies are often based on high-resolution imaging of dynamic biological processes in the worm body tissues, requiring well-immobilized and physiologically active animals in order to avoid movement-related artifacts and to obtain meaningful biological information. However, existing immobilization methods employ the application of either anesthetics or servere physical constraints, by using glue or specific microfluidic on-chip mechanical structures, which in some cases may strongly affect physiological processes of the animals. Here, we immobilize C. elegans nematodes by taking advantage of a biocompatible and temperature-responsive hydrogel-microbead matrix. Our gel-based immobilization technique does not require a specific chip design and enables fast and reversible immobilization, thereby allowing successive imaging of the same single worm or of small worm populations at all development stages for several days. We successfully demonstrated the applicability of this method in challenging worm imaging contexts, in particular by applying it for high-resolution confocal imaging of the mitochondrial morphology in worm body wall muscle cells and for the long-term quantification of number and size of specific protein aggregates in different C. elegans neurodegenerative disease models. Our approach was also suitable for immobilizing other small organisms, such as the larvae of the fruit fly Drosophila melanogaster and the unicellular parasite Trypanosoma brucei. We anticipate that this versatile technique will significantly simplify biological assay-based longitudinal studies and long-term observation of small model organisms. PMID:29509812

REVIEWS OF TOPICAL PROBLEMS: Small-scale structure of dark matter and microlensing

NASA Astrophysics Data System (ADS)

Gurevich, Aleksandr V.; Zybin, Kirill P.; Sirota, V. A.

1997-09-01

It has been revealed using microlensing that a considerable part, possibly more than half, of the dark matter in the halo of our Galaxy consists of objects with a mass spectrum ranging from 0.05 to 0.8 of the solar mass. What is the nature of these objects? There exist two hypotheses. According to one, these are Jupiter type planets or small stars (brown and white dwarfs) consisting of normal baryonic matter. According to the other, these are non-compact objects, i.e., small-scale formations in non-baryonic dark matter. Here, a theory is proposed describing the possibility of the existence of non-compact objects in the halo of our Galaxy, their structure and formation from non-baryonic matter. The theory of microlensing on compact and non-compact objects is considered in detail. The results of microlensing observations are described and compared with theory. Possible astrophysical manifestations of the presence of small-scale structure are pointed out. The field is being extensively studied and is of fundamental interest for cosmology and astrophysics.

40 CFR 142.311 - What procedures allow the Administrator to object to a proposed small system variance or overturn...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false What procedures allow the Administrator to object to a proposed small system variance or overturn a granted small system variance for a public water system serving 3,300 or fewer persons? 142.311 Section 142.311 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER...

40 CFR 142.311 - What procedures allow the Administrator to object to a proposed small system variance or overturn...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false What procedures allow the Administrator to object to a proposed small system variance or overturn a granted small system variance for a public water system serving 3,300 or fewer persons? 142.311 Section 142.311 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER...

Nano-objects as biomaterials: immense opportunities, significant challenges and the important use of surface analytical methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baer, Donald R.; Shutthanandan, Vaithiyalingam

Nano-sized objects are increasingly important as biomaterials and their surfaces play critical roles in determining their beneficial or deleterious behaviors in biological systems. Important characteristics of nanomaterials that impact their application in many areas are described with a strong focus on the importance of particle surfaces and surface characterization. Understanding aspects of the inherent nature of nano-objects and the important role that surfaces play in these applications is a universal need for any research or product development using such materials in biological applications. The role of surface analysis methods in collecting critical information about the nature of particle surfaces andmore » physicochemical properties of nano-objects is described along with the importance of including sample history and analysis results in a record of provenance information regarding specific batches of nano-objects.« less

A roadmap to success in photopharmacology.

PubMed

Broichhagen, Johannes; Frank, James Allen; Trauner, Dirk

2015-07-21

Light is a fascinating phenomenon that ties together physics, chemistry, and biology. It is unmatched in its ability to confer information with temporal and spatial precision and has been used to map objects on the scale of tens of nanometers (10(-8) m) to light years (10(16) m). This information, gathered through super-resolution microscopes or space-based telescopes, is ultimately funneled through the human visual system, which is a miracle in itself. It allows us to see the Andromeda galaxy at night, an object that is 2.5 million light years away and very dim, and ski the next day in bright sunlight at an intensity that is 12 orders of magnitude higher. Human vision is only one of many photoreceptive systems that have evolved on earth and are found in all kingdoms of life. These systems rely on molecular photoswitches, such as retinal or tetrapyrrols, which undergo transient bond isomerizations or bond formations upon irradiation. The set of chromophores that have been employed in Nature for this purpose is surprisingly small. Nevertheless, they control a wide variety of biological functions, which have recently been significantly increased through the rapid development of optogenetics. Optogenetics originated as an effort to control neural function with genetically encoded photoreceptors that use abundant chromophores, in particular retinal. It now covers a variety of cellular functions other than excitability and has revolutionized the control of biological pathways in neuroscience and beyond. Chemistry has provided a large repertoire of synthetic photoswitches with highly tunable properties. Like their natural counterparts, these chromophores can be attached to proteins to effectively put them under optical control. This approach has enabled a new type of synthetic photobiology that has gone under various names to distinguish it from optogenetics. We now call it photopharmacology. Here we trace our involvement in this field, starting with the first light-sensitive potassium channel (SPARK) and concluding with our most recent work on photoswitchable fatty acids. Instead of simply providing a historical account of our efforts, we discuss the design criteria that guided our choice of molecules and receptors. As such, we hope to provide a roadmap to success in photopharmacology and make a case as to why synthetic photoswitches, properly designed and made available through well-planned and efficient syntheses, should have a bright future in biology and medicine.

800-MeV magnetic-focused flash proton radiography for high-contrast imaging of low-density biologically-relevant targets using an inverse-scatter collimator

NASA Astrophysics Data System (ADS)

Freeman, Matthew S.; Allison, Jason; Espinoza, Camilo; Goett, John Jerome; Hogan, Gary; Hollander, Brian; Kwiatkowski, Kris; Lopez, Julian; Mariam, Fesseha; Martinez, Michael; Medina, Jason; Medina, Patrick; Merrill, Frank E.; Morley, Deborah; Morris, Chris; Murray, Matthew; Nedrow, Paul; Saunders, Alexander; Schurman, Tamsen; Sisneros, Thomas; Tainter, Amy; Trouw, Frans; Tupa, Dale; Tybo, Josh; Wilde, Carl

2016-03-01

Proton radiography shows great promise as a tool to guide proton beam therapy (PBT) in real time. Here, we demonstrate two ways in which the technology may progress towards that goal. Firstly, with a proton beam that is 800 MeV in energy, target tissue receives a dose of radiation with very tight lateral constraint. This could present a benefit over the traditional treatment energies of ~200 MeV, where up to 1 cm of lateral tissue receives scattered radiation at the target. At 800 MeV, the beam travels completely through the object with minimal deflection, thus constraining lateral dose to a smaller area. The second novelty of this system is the utilization of magnetic quadrupole refocusing lenses that mitigate the blur caused by multiple Coulomb scattering within an object, enabling high resolution imaging of thick objects, such as the human body. This system is demonstrated on ex vivo salamander and zebrafish specimens, as well as on a realistic hand phantom. The resulting images provide contrast sufficient to visualize thin tissue, as well as fine detail within the target volumes, and the ability to measure small changes in density. Such a system, combined with PBT, would enable the delivery of a highly specific dose of radiation that is monitored and guided in real time.

Structure-Based Virtual Screening of Protein Tyrosine Phosphatase Inhibitors: Significance, Challenges, and Solutions.

PubMed

Reddy, Rallabandi Harikrishna; Kim, Hackyoung; Cha, Seungbin; Lee, Bongsoo; Kim, Young Jun

2017-05-28

Phosphorylation, a critical mechanism in biological systems, is estimated to be indispensable for about 30% of key biological activities, such as cell cycle progression, migration, and division. It is synergistically balanced by kinases and phosphatases, and any deviation from this balance leads to disease conditions. Pathway or biological activity-based abnormalities in phosphorylation and the type of involved phosphatase influence the outcome, and cause diverse diseases ranging from diabetes, rheumatoid arthritis, and numerous cancers. Protein tyrosine phosphatases (PTPs) are of prime importance in the process of dephosphorylation and catalyze several biological functions. Abnormal PTP activities are reported to result in several human diseases. Consequently, there is an increased demand for potential PTP inhibitory small molecules. Several strategies in structure-based drug designing techniques for potential inhibitory small molecules of PTPs have been explored along with traditional drug designing methods in order to overcome the hurdles in PTP inhibitor discovery. In this review, we discuss druggable PTPs and structure-based virtual screening efforts for successful PTP inhibitor design.

The Viking biological investigation - Preliminary results

NASA Technical Reports Server (NTRS)

Klein, H. P.; Oyama, V. I.; Berdahl, B. J.; Horowitz, N. H.; Hobby, G. L.; Levin, G. V.; Straat, P. A.; Lederberg, J.; Rich, A.; Hubbard, J. S.

1976-01-01

A preliminary progress report is presented for the Viking biological investigation through its first month. The carbon assimilation, gas exchange, and labeled release experiments are described in detail, and the chronology of the experiments is outlined. For the first experiment, it is found that a small amount of gas was converted into organic material in one sample and that heat treatment of a duplicate sample prevented such conversion. In the second experiment, a substantial amount of O2 was detected along with significant increases in CO2 and small changes in N2. In the third experiment, a significant amount of radioactive gas was evolved from one sample, but not from a duplicate heat-treated sample. Possible biological and nonbiological interpretations are considered for these results. It is concluded that while the experiments provide clear evidence for the occurrence of chemical reactions and while the results do not violate any prima facie criteria for biological processes, a definitive answer cannot yet be given to the question of whether life exists on Mars.

Computational discovery of small open reading frames in Bacillus lehensis

NASA Astrophysics Data System (ADS)

Zainuddin, Nurhafizhoh; Illias, Rosli Md.; Mahadi, Nor Muhammad; Firdaus-Raih, Mohd

2015-09-01

Bacillus lehensis is a Gram-positive and endospore-forming alkalitolerant bacterial strain. In recent years there has been increasing interest in alkaliphilic bacteria and their ability to grow under extreme conditions as well as their ability to serve various important functions in industrial biology especially enzyme production. Small open reading frames (sORFs) have emerged as important regulators in various biological roles such as tumor progression, hormone signalling and stress response. Over the past decade, many biocomputational tools have been developed to predict genes in bacterial genomes. In this study, three softwares were used to predict sORF (≤ 80 aa) in B. lehensis by using whole genome sequence. We used comparative analysis to identify the sORFs in B. lehensis that conserved across all other bacterial genomes. We extended the analysis by doing the homology analysis against protein database. This study established the sORFs in B. lehensis that are conserved across bacteria which might has important biological function which still remain elusive in biological field.

WE-H-206-02: Recent Advances in Multi-Modality Molecular Imaging of Small Animals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsui, B.

Lihong V. Wang: Photoacoustic tomography (PAT), combining non-ionizing optical and ultrasonic waves via the photoacoustic effect, provides in vivo multiscale functional, metabolic, and molecular imaging. Broad applications include imaging of the breast, brain, skin, esophagus, colon, vascular system, and lymphatic system in humans or animals. Light offers rich contrast but does not penetrate biological tissue in straight paths as x-rays do. Consequently, high-resolution pure optical imaging (e.g., confocal microscopy, two-photon microscopy, and optical coherence tomography) is limited to penetration within the optical diffusion limit (∼1 mm in the skin). Ultrasonic imaging, on the contrary, provides fine spatial resolution but suffersmore » from both poor contrast in early-stage tumors and strong speckle artifacts. In PAT, pulsed laser light penetrates tissue and generates a small but rapid temperature rise, which induces emission of ultrasonic waves due to thermoelastic expansion. The ultrasonic waves, orders of magnitude less scattering than optical waves, are then detected to form high-resolution images of optical absorption at depths up to 7 cm, conquering the optical diffusion limit. PAT is the only modality capable of imaging across the length scales of organelles, cells, tissues, and organs (up to whole-body small animals) with consistent contrast. This rapidly growing technology promises to enable multiscale biological research and accelerate translation from microscopic laboratory discoveries to macroscopic clinical practice. PAT may also hold the key to label-free early detection of cancer by in vivo quantification of hypermetabolism, the quintessential hallmark of malignancy. Learning Objectives: To understand the contrast mechanism of PAT To understand the multiscale applications of PAT Benjamin M. W. Tsui: Multi-modality molecular imaging instrumentation and techniques have been major developments in small animal imaging that has contributed significantly to biomedical research during the past decade. The initial development was an extension of clinical PET/CT and SPECT/CT from human to small animals and combine the unique functional information obtained from PET and SPECT with anatomical information provided by the CT in registered multi-modality images. The requirements to image a mouse whose size is an order of magnitude smaller than that of a human have spurred advances in new radiation detector technologies, novel imaging system designs and special image reconstruction and processing techniques. Examples are new detector materials and designs with high intrinsic resolution, multi-pinhole (MPH) collimator design for much improved resolution and detection efficiency compared to the conventional collimator designs in SPECT, 3D high-resolution and artifact-free MPH and sparse-view image reconstruction techniques, and iterative image reconstruction methods with system response modeling for resolution recovery and image noise reduction for much improved image quality. The spatial resolution of PET and SPECT has improved from ∼6–12 mm to ∼1 mm a few years ago to sub-millimeter today. A recent commercial small animal SPECT system has achieved a resolution of ∼0.25 mm which surpasses that of a state-of-art PET system whose resolution is limited by the positron range. More recently, multimodality SA PET/MRI and SPECT/MRI systems have been developed in research laboratories. Also, multi-modality SA imaging systems that include other imaging modalities such as optical and ultrasound are being actively pursued. In this presentation, we will provide a review of the development, recent advances and future outlook of multi-modality molecular imaging of small animals. Learning Objectives: To learn about the two major multi-modality molecular imaging techniques of small animals. To learn about the spatial resolution achievable by the molecular imaging systems for small animal today. To learn about the new multi-modality imaging instrumentation and techniques that are being developed. Sang Hyun Cho; X-ray fluorescence (XRF) imaging, such as x-ray fluorescence computed tomography (XFCT), offers unique capabilities for accurate identification and quantification of metals within the imaging objects. As a result, it has emerged as a promising quantitative imaging modality in recent years, especially in conjunction with metal-based imaging probes. This talk will familiarize the audience with the basic principles of XRF/XFCT imaging. It will also cover the latest development of benchtop XFCT technology. Additionally, the use of metallic nanoparticles such as gold nanoparticles, in conjunction with benchtop XFCT, will be discussed within the context of preclinical multimodal multiplexed molecular imaging. Learning Objectives: To learn the basic principles of XRF/XFCT imaging To learn the latest advances in benchtop XFCT development for preclinical imaging Funding support received from NIH and DOD; Funding support received from GE Healthcare; Funding support received from Siemens AX; Patent royalties received from GE Healthcare; L. Wang, Funding Support: NIH; COI: Microphotoacoustics; S. Cho, Yes: ;NIH/NCI grant R01CA155446 DOD/PCRP grant W81XWH-12-1-0198.« less

Personalized disease-specific protein corona influences the therapeutic impact of graphene oxide

NASA Astrophysics Data System (ADS)

Hajipour, Mohammad Javad; Raheb, Jamshid; Akhavan, Omid; Arjmand, Sareh; Mashinchian, Omid; Rahman, Masoud; Abdolahad, Mohammad; Serpooshan, Vahid; Laurent, Sophie; Mahmoudi, Morteza

2015-05-01

The hard corona, the protein shell that is strongly attached to the surface of nano-objects in biological fluids, is recognized as the first layer that interacts with biological objects (e.g., cells and tissues). The decoration of the hard corona (i.e., the type, amount, and conformation of the attached proteins) can define the biological fate of the nanomaterial. Recent developments have revealed that corona decoration strongly depends on the type of disease in human patients from which the plasma is obtained as a protein source for corona formation (referred to as the `personalized protein corona'). In this study, we demonstrate that graphene oxide (GO) sheets can trigger different biological responses in the presence of coronas obtained from various types of diseases. GO sheets were incubated with plasma from human subjects with different diseases/conditions, including hypofibrinogenemia, blood cancer, thalassemia major, thalassemia minor, rheumatism, fauvism, hypercholesterolemia, diabetes, and pregnancy. Identical sheets coated with varying protein corona decorations exhibited significantly different cellular toxicity, apoptosis, and uptake, reactive oxygen species production, lipid peroxidation and nitrogen oxide levels. The results of this report will help researchers design efficient and safe, patient-specific nano biomaterials in a disease type-specific manner for clinical and biological applications.The hard corona, the protein shell that is strongly attached to the surface of nano-objects in biological fluids, is recognized as the first layer that interacts with biological objects (e.g., cells and tissues). The decoration of the hard corona (i.e., the type, amount, and conformation of the attached proteins) can define the biological fate of the nanomaterial. Recent developments have revealed that corona decoration strongly depends on the type of disease in human patients from which the plasma is obtained as a protein source for corona formation (referred to as the `personalized protein corona'). In this study, we demonstrate that graphene oxide (GO) sheets can trigger different biological responses in the presence of coronas obtained from various types of diseases. GO sheets were incubated with plasma from human subjects with different diseases/conditions, including hypofibrinogenemia, blood cancer, thalassemia major, thalassemia minor, rheumatism, fauvism, hypercholesterolemia, diabetes, and pregnancy. Identical sheets coated with varying protein corona decorations exhibited significantly different cellular toxicity, apoptosis, and uptake, reactive oxygen species production, lipid peroxidation and nitrogen oxide levels. The results of this report will help researchers design efficient and safe, patient-specific nano biomaterials in a disease type-specific manner for clinical and biological applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00520e

Biological Terrorism: US Policies to Reduce Global Biothreats

DTIC Science & Technology

2008-09-01

program for pro- jects that advance BEP objectives. Global Cooperation to develop bio- safety and pathogen security stan- dards that are consistent with...security. The Organization for Economic Cooperation and Development ( OECD ) has recently developed voluntary biosecurity guidelines for implementation...Abbreviations AG Australia Group BEP Biosecurity Engagement Program BSL Biosafety level BWC Biological Weapons Convention BWC-ISU Biological Weapons

BIOLOGY I, NEW APPROACHES AND OBJECTIVES.

ERIC Educational Resources Information Center

COKER, ROBERT; AND OTHERS

THE PRINCIPLES OF MODERN BIOLOGY SHOULD BE PRESENTED IN A DYNAMIC AND CHALLENGING WAY TO CAPABLE STUDENTS TO DEVELOP LASTING INTEREST IN THE SUBJECT AND TO PLACE EMPHASIS UPON THE ROLE OF THE PHYSICAL SCIENCES IN BIOLOGY IN ACCORD WITH NATIONWIDE TENDENCY. THE COURSE IS COMPLETE IN ITSELF BUT PROVIDES A BASIS FOR STUDENTS WHO ELECT ADVANCED WORK.…

Closing the Loop: Involving Faculty in the Assessment of Scientific and Quantitative Reasoning Skills of Biology Majors

ERIC Educational Resources Information Center

Hurney, Carol A.; Brown, Justin; Griscom, Heather Peckham; Kancler, Erika; Wigtil, Clifton J.; Sundre, Donna

2011-01-01

The development of scientific and quantitative reasoning skills in undergraduates majoring in science, technology, engineering, and mathematics (STEM) is an objective of many courses and curricula. The Biology Department at James Madison University (JMU) assesses these essential skills in graduating biology majors by using a multiple-choice exam…

Posing for a picture: vesicle immobilization in agarose gel

NASA Astrophysics Data System (ADS)

Lira, Rafael B.; Steinkühler, Jan; Knorr, Roland L.; Dimova, Rumiana; Riske, Karin A.

2016-05-01

Taking a photo typically requires the object of interest to stand still. In science, imaging is potentiated by optical and electron microscopy. However, living and soft matter are not still. Thus, biological preparations for microscopy usually include a fixation step. Similarly, immobilization strategies are required for or substantially facilitate imaging of cells or lipid vesicles, and even more so for acquiring high-quality data via fluorescence-based techniques. Here, we describe a simple yet efficient method to immobilize objects such as lipid vesicles with sizes between 0.1 and 100 μm using agarose gel. We show that while large and giant unilamellar vesicles (LUVs and GUVs) can be caged in the pockets of the gel meshwork, small molecules, proteins and micelles remain free to diffuse through the gel and interact with membranes as in agarose-free solutions, and complex biochemical reactions involving several proteins can proceed in the gel. At the same time, immobilization in agarose has no adverse effect on the GUV size and stability. By applying techniques such as FRAP and FCS, we show that the lateral diffusion of lipids is not affected by the gel. Finally, our immobilization strategy allows capturing high-resolution 3D images of GUVs.

Small Schools Language Arts Curriculum, 4-6: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts that do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains language arts curriculum materials for grades 4-6. Learning objectives are correlated to the Goals…

Small Schools Language Arts Curriculum, 7-8: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

ERIC Educational Resources Information Center

Hartl, David, Ed.; And Others

Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts that do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains language arts curriculum materials for grades 7-8. Learning objectives are correlated to the Goals…

A radiobiology-based inverse treatment planning method for optimisation of permanent l-125 prostate implants in focal brachytherapy.

PubMed

Haworth, Annette; Mears, Christopher; Betts, John M; Reynolds, Hayley M; Tack, Guido; Leo, Kevin; Williams, Scott; Ebert, Martin A

2016-01-07

Treatment plans for ten patients, initially treated with a conventional approach to low dose-rate brachytherapy (LDR, 145 Gy to entire prostate), were compared with plans for the same patients created with an inverse-optimisation planning process utilising a biologically-based objective. The 'biological optimisation' considered a non-uniform distribution of tumour cell density through the prostate based on known and expected locations of the tumour. Using dose planning-objectives derived from our previous biological-model validation study, the volume of the urethra receiving 125% of the conventional prescription (145 Gy) was reduced from a median value of 64% to less than 8% whilst maintaining high values of TCP. On average, the number of planned seeds was reduced from 85 to less than 75. The robustness of plans to random seed displacements needs to be carefully considered when using contemporary seed placement techniques. We conclude that an inverse planning approach to LDR treatments, based on a biological objective, has the potential to maintain high rates of tumour control whilst minimising dose to healthy tissue. In future, the radiobiological model will be informed using multi-parametric MRI to provide a personalised medicine approach.

A radiobiology-based inverse treatment planning method for optimisation of permanent l-125 prostate implants in focal brachytherapy

NASA Astrophysics Data System (ADS)

Haworth, Annette; Mears, Christopher; Betts, John M.; Reynolds, Hayley M.; Tack, Guido; Leo, Kevin; Williams, Scott; Ebert, Martin A.

2016-01-01

Treatment plans for ten patients, initially treated with a conventional approach to low dose-rate brachytherapy (LDR, 145 Gy to entire prostate), were compared with plans for the same patients created with an inverse-optimisation planning process utilising a biologically-based objective. The ‘biological optimisation’ considered a non-uniform distribution of tumour cell density through the prostate based on known and expected locations of the tumour. Using dose planning-objectives derived from our previous biological-model validation study, the volume of the urethra receiving 125% of the conventional prescription (145 Gy) was reduced from a median value of 64% to less than 8% whilst maintaining high values of TCP. On average, the number of planned seeds was reduced from 85 to less than 75. The robustness of plans to random seed displacements needs to be carefully considered when using contemporary seed placement techniques. We conclude that an inverse planning approach to LDR treatments, based on a biological objective, has the potential to maintain high rates of tumour control whilst minimising dose to healthy tissue. In future, the radiobiological model will be informed using multi-parametric MRI to provide a personalised medicine approach.

Use of micro computed-tomography and 3D printing for reverse engineering of mouse embryo nasal capsule

NASA Astrophysics Data System (ADS)

Tesařová, M.; Zikmund, T.; Kaucká, M.; Adameyko, I.; Jaroš, J.; Paloušek, D.; Škaroupka, D.; Kaiser, J.

2016-03-01

Imaging of increasingly complex cartilage in vertebrate embryos is one of the key tasks of developmental biology. This is especially important to study shape-organizing processes during initial skeletal formation and growth. Advanced imaging techniques that are reflecting biological needs give a powerful impulse to push the boundaries of biological visualization. Recently, techniques for contrasting tissues and organs have improved considerably, extending traditional 2D imaging approaches to 3D . X-ray micro computed tomography (μCT), which allows 3D imaging of biological objects including their internal structures with a resolution in the micrometer range, in combination with contrasting techniques seems to be the most suitable approach for non-destructive imaging of embryonic developing cartilage. Despite there are many software-based ways for visualization of 3D data sets, having a real solid model of the studied object might give novel opportunities to fully understand the shape-organizing processes in the developing body. In this feasibility study we demonstrated the full procedure of creating a real 3D object of mouse embryo nasal capsule, i.e. the staining, the μCT scanning combined by the advanced data processing and the 3D printing.

Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research.

PubMed

Jinawath, Natini; Bunbanjerdsuk, Sacarin; Chayanupatkul, Maneerat; Ngamphaiboon, Nuttapong; Asavapanumas, Nithi; Svasti, Jisnuson; Charoensawan, Varodom

2016-11-22

With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases.

Small silencing RNAs: an expanding universe.

PubMed

Ghildiyal, Megha; Zamore, Phillip D

2009-02-01

Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.

Grasping the pain: motor resonance with dangerous affordances.

PubMed

Anelli, Filomena; Borghi, Anna M; Nicoletti, Roberto

2012-12-01

Two experiments, one on school-aged children and one on adults, explored the mechanisms underlying responses to an image prime (hand vs. control object) followed by graspable objects that were, in certain cases, dangerous. Participants were presented with different primes (a male, a female and a robotic grasping-hand; a male and a female static-hand; a control stimulus) and objects representing two risk levels (neutral and dangerous). The task required that a natural/artifact categorization task be performed by pressing different keys. In both adults and children graspable objects activated a facilitating motor response, while dangerous objects evoked aversive affordances, generating an interference-effect. Both children and adults were sensitive to the distinction between biological and non-biological hands, however detailed resonant mechanisms related to the hand-prime gender emerged only in adults. Implications for how the concept of "dangerous object" develops and the relationship between resonant mechanisms and perception of danger are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan Chan Tseung, Hok Seum, E-mail: wanchantseung.hok@mayo.edu; Ma, Jiasen; Kreofsky, Cole R.

Purpose: Our aim is to demonstrate the feasibility of fast Monte Carlo (MC)–based inverse biological planning for the treatment of head and neck tumors in spot-scanning proton therapy. Methods and Materials: Recently, a fast and accurate graphics processor unit (GPU)–based MC simulation of proton transport was developed and used as the dose-calculation engine in a GPU-accelerated intensity modulated proton therapy (IMPT) optimizer. Besides dose, the MC can simultaneously score the dose-averaged linear energy transfer (LET{sub d}), which makes biological dose (BD) optimization possible. To convert from LET{sub d} to BD, a simple linear relation was assumed. By use of thismore » novel optimizer, inverse biological planning was applied to 4 patients, including 2 small and 1 large thyroid tumor targets, as well as 1 glioma case. To create these plans, constraints were placed to maintain the physical dose (PD) within 1.25 times the prescription while maximizing target BD. For comparison, conventional intensity modulated radiation therapy (IMRT) and IMPT plans were also created using Eclipse (Varian Medical Systems) in each case. The same critical-structure PD constraints were used for the IMRT, IMPT, and biologically optimized plans. The BD distributions for the IMPT plans were obtained through MC recalculations. Results: Compared with standard IMPT, the biologically optimal plans for patients with small tumor targets displayed a BD escalation that was around twice the PD increase. Dose sparing to critical structures was improved compared with both IMRT and IMPT. No significant BD increase could be achieved for the large thyroid tumor case and when the presence of critical structures mitigated the contribution of additional fields. The calculation of the biologically optimized plans can be completed in a clinically viable time (<30 minutes) on a small 24-GPU system. Conclusions: By exploiting GPU acceleration, MC-based, biologically optimized plans were created for small–tumor target patients. This optimizer will be used in an upcoming feasibility trial on LET{sub d} painting for radioresistant tumors.« less

Parameter space exploration within dynamic simulations of signaling networks.

PubMed

De Ambrosi, Cristina; Barla, Annalisa; Tortolina, Lorenzo; Castagnino, Nicoletta; Pesenti, Raffaele; Verri, Alessandro; Ballestrero, Alberto; Patrone, Franco; Parodi, Silvio

2013-02-01

We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.

Biology for Every Kid: 101 Easy Experiments that Really Work.

ERIC Educational Resources Information Center

Vancleave, Janice Pratt

1989-01-01

Presented are 12 biology experiments suitable for use in intermediate grade classrooms. Topics include plants, protists, fungi, animals, and osmosis. Provided are objectives, lists of materials, procedures, results, and explanations of the results. (CW)

BIOLOGICAL INTEGRITY IN MID-ATLANTIC COASTAL PLAINS HEADWATER STREAMS

EPA Science Inventory

The objective of this study was to assess the applicability of landscape metrics, in conjunction with stream water quality to estimate the biological integrity of headwater streams in the Mid-Atlantic Coastal Plains using multivariate techniques.

Biosafety- A Regulatory Primer for DOE/NNSA Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siegel, Dina Mary

2017-05-04

The objectives of a biological safety program, and this are to ensure that work with biological materials are conducted in compliance with applicable biosafety standards and ensure that protection of workers, facilities, the public, and the environment.

The yeast stands alone: the future of protein biologic production.

PubMed

Love, Kerry R; Dalvie, Neil C; Love, J Christopher

2017-12-22

Yeasts are promising alternative hosts for the manufacturing of recombinant protein therapeutics because they simply and efficiently meet needs for both platform and small-market drugs. Fast accumulation of biomass and low-cost media reduce the cost-of-goods when using yeast, which in turn can enable agile, small-volume manufacturing facilities. Small, tractable yeast genomes are amenable to rapid process development, facilitating strain and product quality by design. Specifically, Pichia pastoris is becoming a widely accepted yeast for biopharmaceutical manufacturing in much of the world owing to a clean secreted product and the rapidly expanding understanding of its cell biology as a host organism. We advocate for a near term partnership spanning industry and academia to promote open source, timely development of yeast hosts. Copyright © 2017. Published by Elsevier Ltd.

The Virtual Glovebox (VGX): An Immersive Simulation System for Training Astronauts to Perform Glovebox Experiments in Space

NASA Technical Reports Server (NTRS)

Smith, Jeffrey D.; Dalton, Bonnie (Technical Monitor)

2002-01-01

The era of the International Space Station (ISS) has finally arrived, providing researchers on Earth a unique opportunity to study long-term effects of weightlessness and the space environment on structures, materials and living systems. Many of the physical, biological and material science experiments planned for ISS will require significant input and expertise from astronauts who must conduct the research, follow complicated assay procedures and collect data and samples in space. Containment is essential for Much of this work, both to protect astronauts from potentially harmful biological, chemical or material elements in the experiments as well as to protect the experiments from contamination by air-born particles In the Space Station environment. When astronauts must open the hardware containing such experiments, glovebox facilities provide the necessary barrier between astronaut and experiment. On Earth, astronauts are laced with the demanding task of preparing for the many glovebox experiments they will perform in space. Only a short time can be devoted to training for each experimental task and gl ovebox research only accounts for a small portion of overall training and mission objectives on any particular ISS mission. The quality of the research also must remain very high, requiring very detailed experience and knowledge of instrumentation, anatomy and specific scientific objectives for those who will conduct the research. This unique set of needs faced by NASA has stemmed the development of a new computer simulation tool, the Virtual Glovebox (VGB), which is designed to provide astronaut crews and support personnel with a means to quickly and accurately prepare and train for glovebox experiments in space.

Inspiration, simulation and design for smart robot manipulators from the sucker actuation mechanism of cephalopods.

PubMed

Grasso, Frank W; Setlur, Pradeep

2007-12-01

Octopus arms house 200-300 independently controlled suckers that can alternately afford an octopus fine manipulation of small objects and produce high adhesion forces on virtually any non-porous surface. Octopuses use their suckers to grasp, rotate and reposition soft objects (e.g., octopus eggs) without damaging them and to provide strong, reversible adhesion forces to anchor the octopus to hard substrates (e.g., rock) during wave surge. The biological 'design' of the sucker system is understood to be divided anatomically into three functional groups: the infundibulum that produces a surface seal that conforms to arbitrary surface geometry; the acetabulum that generates negative pressures for adhesion; and the extrinsic muscles that allow adhered surfaces to be rotated relative to the arm. The effector underlying these abilities is the muscular hydrostat. Guided by sensory input, the thousands of muscle fibers within the muscular hydrostats of the sucker act in coordination to provide stiffness or force when and where needed. The mechanical malleability of octopus suckers, the interdigitated arrangement of their muscle fibers and the flexible interconnections of its parts make direct studies of their control challenging. We developed a dynamic simulator (ABSAMS) that models the general functioning of muscular hydrostat systems built from assemblies of biologically constrained muscular hydrostat models. We report here on simulation studies of octopus-inspired and artificial suckers implemented in this system. These simulations reproduce aspects of octopus sucker performance and squid tentacle extension. Simulations run with these models using parameters from man-made actuators and materials can serve as tools for designing soft robotic implementations of man-made artificial suckers and soft manipulators.

Benzodiazepine Synthesis and Rapid Toxicity Assay

ERIC Educational Resources Information Center

Fletcher, James T.; Boriraj, Grit

2010-01-01

A second-year organic chemistry laboratory experiment to introduce students to general concepts of medicinal chemistry is described. Within a single three-hour time window, students experience the synthesis of a biologically active small molecule and the assaying of its biological toxicity. Benzodiazepine rings are commonly found in antidepressant…

Measurements of the driving forces of bio-motors using the fluctuation theorem

PubMed Central

Hayashi, Kumiko; Tanigawara, Mizue; Kishikawa, Jun-ichi

2012-01-01

The fluctuation theorem (FT), which is a recent achievement in non-equilibrium statistical mechanics, has been suggested to be useful for measuring the driving forces of motor proteins. As an example of this application, we performed single-molecule experiments on F1-ATPase, which is a rotary motor protein, in which we measured its rotary torque by taking advantage of FT. Because fluctuation is inherent nature in biological small systems and because FT is a non-destructive force measurement method using fluctuation, it will be applied to a wide range of biological small systems in future. PMID:27857609

Carbohydrate Recognition by Boronolectins, Small Molecules, and Lectins

PubMed Central

Jin, Shan; Cheng, Yunfeng; Reid, Suazette; Li, Minyong; Wang, Binghe

2009-01-01

Carbohydrates are known to mediate a large number of biological and pathological events. Small and macromolecules capable of carbohydrate recognition have great potentials as research tools, diagnostics, vectors for targeted delivery of therapeutic and imaging agents, and therapeutic agents. However, this potential is far from being realized. One key issue is the difficulty in the development of “binders” capable of specific recognition of carbohydrates of biological relevance. This review discusses systematically the general approaches that are available in developing carbohydrate sensors and “binders/receptors,” and their applications. The focus is on discoveries during the last five years. PMID:19291708

A Reconstruction Algorithm of Magnetoacoustic Tomography with Magnetic Induction for Acoustically Inhomogeneous Tissue

PubMed Central

Zhou, Lian; Zhu, Shanan

2014-01-01

Magnetoacoustic tomography with Magnetic Induction (MAT-MI) is a noninvasive electrical conductivity imaging approach that measures ultrasound wave induced by magnetic stimulation, for reconstructing the distribution of electrical impedance in biological tissue. Existing reconstruction algorithms for MAT-MI are based on the assumption that the acoustic properties in the tissue are homogeneous. However, the tissue in most parts of human body, has heterogeneous acoustic properties, which leads to potential distortion and blurring of small buried objects in the impedance images. In the present study, we proposed a new algorithm for MAT-MI to image the impedance distribution in tissues with inhomogeneous acoustic speed distributions. With a computer head model constructed from MR images of a human subject, a series of numerical simulation experiments were conducted. The present results indicate that the inhomogeneous acoustic properties of tissues in terms of speed variation can be incorporated in MAT-MI imaging. PMID:24845284

Target selection for a hypervelocity asteroid intercept vehicle flight validation mission

NASA Astrophysics Data System (ADS)

Wagner, Sam; Wie, Bong; Barbee, Brent W.

2015-02-01

Asteroids and comets have collided with the Earth in the past and will do so again in the future. Throughout Earth's history these collisions have played a significant role in shaping Earth's biological and geological histories. The planetary defense community has been examining a variety of options for mitigating the impact threat of asteroids and comets that approach or cross Earth's orbit, known as near-Earth objects (NEOs). This paper discusses the preliminary study results of selecting small (100-m class) NEO targets and mission analysis and design trade-offs for validating the effectiveness of a Hypervelocity Asteroid Intercept Vehicle (HAIV) concept, currently being investigated for a NIAC (NASA Advanced Innovative Concepts) Phase 2 study. In particular this paper will focus on the mission analysis and design for single spacecraft direct impact trajectories, as well as several mission types that enable a secondary rendezvous spacecraft to observe the HAIV impact and evaluate it's effectiveness.

Fiber-Optic Magnetometry and Thermometry Using Optically Detected Magnetic Resonance With Nitrogen-Vacancy Centers in Diamond

NASA Astrophysics Data System (ADS)

Blakley, Sean Michael

Nitrogen--vacancy diamond (NVD) quantum sensors are an emerging technology that has shown great promise in areas like high-resolution thermometry and magnetometry. Optical fibers provide attractive new application paradigms for NVD technology. A detailed description of the fabrication processes associated with the development of novel fiber-optic NVD probes are presented in this work. The demonstrated probes are tested on paradigmatic model systems designed to ascertain their suitability for use in challenging biological environments. Methods employing optically detected magnetic resonance (ODMR) are used to accurately measure and map temperature distributions of small objects and to demonstrate emergent temperature-dependent phenomena in genetically modified living organisms. These methods are also used to create detailed high resolution spatial maps of both magnetic scalar and magnetic vector field distributions of spatially localized weak field features in the presence of a noisy, high-field background.

Physical/chemical closed-loop water-recycling

NASA Technical Reports Server (NTRS)

Herrmann, Cal C.; Wydeven, Theodore

1991-01-01

Water needs, water sources, and means for recycling water are examined in terms appropriate to the water quality requirements of a small crew and spacecraft intended for long duration exploration missions. Inorganic, organic, and biological hazards are estimated for waste water sources. Sensitivities to these hazards for human uses are estimated. The water recycling processes considered are humidity condensation, carbon dioxide reduction, waste oxidation, distillation, reverse osmosis, pervaporation, electrodialysis, ion exchange, carbon sorption, and electrochemical oxidation. Limitations and applications of these processes are evaluated in terms of water quality objectives. Computerized simulation of some of these chemical processes is examined. Recommendations are made for development of new water recycling technology and improvement of existing technology for near term application to life support systems for humans in space. The technological developments are equally applicable to water needs on Earth, in regions where extensive water recycling is needed or where advanced water treatment is essential to meet EPA health standards.

[Experiment with rats on a 22-day flight on the "Kosmos-605" biological satellite (objectives and methods)].

PubMed

Il'in, E A; Serova, L V; Noskin, A D

1976-01-01

In 1974 a rat experiment was carried out onboard the Cosmos-605 biosatellite. Inflight Wistar rats were kept unrestrained in small cages. The cages were equipped with a feeder, water supply, light source and a ventilation device. The state of the animals was assessed with respect to their motor activity. The flight experiment was preceded by a number of preparatory runs and testinns that were completed with an end-to-end experiment in a biosatellite mockup. The flight experiment was paralleled by the ground-based synchroneous experiment which simulated almost entirely the flight profile. For each experiment rats were selected and trained during a month's observation. Postflight rats were exposed to clinical, physiological, morphological, cytochemical and biochemical investigations. Tissue examinations were performed on the 2nd-3rd day (20 rats) and 26-27th day (12 rats) after flight. Four rats were kept to study remote aftereffects.

Update on Bioactive Prosthetic Material for the Treatment of Hernias.

PubMed

Edelman, David S; Hodde, Jason P

2011-12-01

The use of mesh in the repair of hernias is commonplace. Synthetic mesh, like polypropylene, has been the workhorse for hernia repairs since the 1980s. Surgisis® mesh (Cook Surgical, Bloomington, IN), a biologic hernia graft material composed of purified porcine small intestinal submucosa (SIS), was first introduced to the United States in 1998 as an alternative to synthetic mesh materials. This mesh, composed of extracellular matrix collagen, fibronectin and associated glycosaminoglycans and growth factors, has been extensively investigated in animal models and used clinically in many types of surgical procedures. SIS acts as a scaffold for natural growth and strength. We reported our initial results in this publication in July 2006. Since then, there have been many more reports and numerous other bioactive prosthetic materials (BPMs) released. The object of this article is to briefly review some of the current literature on the use of BPM for inguinal hernias, sports hernias, and umbilical hernias.

Modulation of MicroRNAs by Phytochemicals in Cancer: Underlying Mechanisms and Translational Significance

PubMed Central

Srivastava, Sanjeev K.; Arora, Sumit; Averett, Courey; Singh, Ajay P.

2015-01-01

MicroRNAs (miRNAs) are small, endogenous noncoding RNAs that regulate a variety of biological processes such as differentiation, development, and survival. Recent studies suggest that miRNAs are dysregulated in cancer and play critical roles in cancer initiation, progression, and chemoresistance. Therefore, exploitation of miRNAs as targets for cancer prevention and therapy could be a promising approach. Extensive evidence suggests that many naturally occurring phytochemicals regulate the expression of numerous miRNAs involved in the pathobiology of cancer. Therefore, an understanding of the regulation of miRNAs by phytochemicals in cancer, their underlying molecular mechanisms, and functional consequences on tumor pathophysiology may be useful in formulating novel strategies to combat this devastating disease. These aspects are discussed in this review paper with an objective of highlighting the significance of these observations from the translational standpoint. PMID:25853141

Surface biofunctionalization and production of miniaturized sensor structures using aerosol printing technologies.

PubMed

Grunwald, Ingo; Groth, Esther; Wirth, Ingo; Schumacher, Julian; Maiwald, Marcus; Zoellmer, Volker; Busse, Matthias

2010-03-01

The work described in this paper demonstrates that very small protein and DNA structures can be applied to various substrates without denaturation using aerosol printing technology. This technology allows high-resolution deposition of various nanoscaled metal and biological suspensions. Before printing, metal and biological suspensions were formulated and then nebulized to form an aerosol which is aerodynamically focused on the printing module of the system in order to achieve precise structuring of the nanoscale material on a substrate. In this way, it is possible to focus the aerosol stream at a distance of about 5 mm from the printhead to the surface. This technology is useful for printing fluorescence-marked proteins and printing enzymes without affecting their biological activity. Furthermore, higher molecular weight DNA can be printed without shearing. The advantages, such as printing on complex, non-planar 3D structured surfaces, and disadvantages of the aerosol printing technology are also discussed and are compared with other printing technologies. In addition, miniaturized sensor structures with line thicknesses in the range of a few micrometers are fabricated by applying a silver sensor structure to glass. After sintering using an integrated laser or in an oven process, electrical conductivity is achieved within the sensor structure. Finally, we printed BSA in small micrometre-sized areas within the sensor structure using the same deposition system. The aerosol printing technology combined with material development offers great advantages for future-oriented applications involving biological surface functionalization on small areas. This is important for innovative biomedical micro-device development and for production solutions which bridge the disciplines of biology and electronics.

Scientific Ground of a New Optical Device for Contactless Measurement of the Small Spatial Displacements of Control Object Surfaces

NASA Astrophysics Data System (ADS)

Miroshnichenko, I. P.; Parinov, I. A.

2017-06-01

It is proposed the computational-experimental ground of newly developed optical device for contactless measurement of small spatial displacements of control object surfaces based on the use of new methods of laser interferometry. The proposed device allows one to register linear and angular components of the small displacements of control object surfaces during the diagnosis of the condition of structural materials for forced elements of goods under exploring by using acoustic non-destructive testing methods. The described results are the most suitable for application in the process of high-precision measurements of small linear and angular displacements of control object surfaces during experimental research, the evaluation and diagnosis of the state of construction materials for forced elements of goods, the study of fast wave propagation in layered constructions of complex shape, manufactured of anisotropic composite materials, the study of damage processes in modern construction materials in mechanical engineering, shipbuilding, aviation, instrumentation, power engineering, etc.

Antibody-drug conjugates for cancer therapy: The technological and regulatory challenges of developing drug-biologic hybrids.

PubMed

Hamilton, Gregory S

2015-09-01

Antibody-drug conjugates (ADCs) are a new class of therapeutic agents that combine the targeting ability of monoclonal antibodies (mAbs) with small molecule drugs. The combination of a mAb targeting a cancer-specific antigen with a cytotoxin has tremendous promise as a new type of targeted cancer therapy. Two ADCs have been approved and many more are in clinical development, suggesting that this new class of drugs is coming to the forefront. Because of their unique nature as biologic-small drug hybrids, ADCs are challenging to develop, from both the scientific and regulatory perspectives. This review discusses both these aspects in current practice, and surveys the current state of the art of ADC drug development. Copyright © 2015 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Chemistry and Biology of the Caged Garcinia Xanthones

PubMed Central

Chantarasriwong, Oraphin; Batova, Ayse; Chavasiri, Warinthorn

2011-01-01

Natural products have been a great source of many small molecule drugs for various diseases. In spite of recent advances in biochemical engineering and fermentation technologies that allow us to explore microorganisms and the marine environment as alternative sources of drugs, more than 70% of the current small molecule therapeutics derive their structures from plants used in traditional medicine. Natural-product-based drug discovery relies heavily on advances made in the sciences of biology and chemistry. Whereas biology aims to investigate the mode of action of a natural product, chemistry aims to overcome challenges related to its supply, bioactivity, and target selectivity. This review summarizes the explorations of the caged Garcinia xanthones, a family of plant metabolites that possess a unique chemical structure, potent bioactivities, and a promising pharmacology for drug design and development. PMID:20648491

A 21st-century approach to age-old problems: the ascension of biologics in clinical therapeutics.

PubMed

Espiritu, Michael J; Collier, Abby C; Bingham, Jon-Paul

2014-08-01

Small organic molecules have been the pharmaceutical mainstay of the developed world for some time. However, in recent years, advances within the fields of genomics and proteomics have strengthened and given rise to new biologic therapies. Protein therapies, such as monoclonal antibodies and peptide drugs, have provided patients with pharmaceuticals that offer a higher level of selectivity and effectiveness that would be otherwise undeliverable within the realm of small organics. In addition to protein therapies, DNA-based therapy, such as RNA interference (RNAi) and gene therapy, have gained renewed interest within modern medicine and are potentially poised for a comeback within the biotechnology industry. As we discuss here, the advantages of such therapies continue to accumulate and have kept the biologic market strong. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Systems Biology Approach to Small Fish Ecotoxicogenomics

EPA Science Inventory

At present, a large and integrated effort in the area of ecotoxicogenomics within USEPA's Office of Research and Development is a research program titled "Linkage of exposure and effects using genomics, proteomics, and metabolomics in small fish models." The effort involves coll...

Spatial Distribution of Small Water Body Types across Indiana Ecoregions

EPA Science Inventory

Due to their large numbers and biogeochemical activity, small water bodies (SWB), such as ponds and wetlands, can have substantial cumulative effects on hydrologic, biogeochemical, and biological processes; yet the spatial distributions of various SWB types are often unknown. Usi...

Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision.

PubMed

Zhong, Bineng; Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

2016-01-01

In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method.

Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision

PubMed Central

Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

2016-01-01

In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of training data. Finally, to alleviate the tracker drifting problem caused by model updating, we jointly consider three different types of positive samples. Extensive experiments validate the robustness and effectiveness of the proposed method. PMID:27847827

40 CFR 122.30 - What are the objectives of the storm water regulations for small MS4s?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false What are the objectives of the storm... objectives of the storm water regulations for small MS4s? (a) Sections 122.30 through 122.37 are written in a... 402(p)(6) of the Clean Water Act, the purpose of this portion of the storm water program is to...