Life Sciences Commons^™

3b Project Data - Raw Tiff Series And Cropped Series, George Mcnamara

George McNamara

Fluorescence microscopy data acquired for 3B Bayesian localization microscopy.

Settings: 100 nm XY pixel size. 50 millisecond exposures, MetaMorph stream acquisition mode (as fast as possible). Stellaris FISH mammalian cells labeled with Quasar 670 fluorophores, one molecule per 20mer FISH probe, ~48 probes to TOP1 mRNA (Topoisomerase 1).

More on the 3B project and Stellaris FISH data at http://works.bepress.com/gmcnamara/38/

and at Susan Cox's web sites http://www.coxphysics.com/3b/ http://superresolved.com/

Effectiveness Of Communication Skills In Decreasing Addiction Tendencies Among Male Students From Cities Within Tehran Province, Seyed Mohammad, Kalantarkousheh, دکتر سید محمد کلانتر کوشه

Seyed Mohammad Kalantarkousheh

This research investigates the effectiveness of teaching communication skills in decreasing the tendency to addiction in guidance school male students. Communication skills are considered to be a component of life skills. This research entails a pre-test /post-test with control group design that includes all guidance school mal e students studying in the cities of Tehran Province. A total of 30 male students were selected according to the random sample cluster method. Half of the population was classified as the test group and the remainder comprised th e control group. This research used the addiction potential s cale (APS) that has …

Synthesis, Physico-Chemical And Antimicrobial Studies Of Ionic Liquid, Mohammad Oves

Mohammad Oves

No abstract provided.

Time Series Data For 3b Image Processing, George Mcnamara

George McNamara

Time series data for 3B image processing

Four time series data sets of Stellaris single molecules RNA FISH (fluorescence in situ hybridization). All four datasets are 301 imaqe planes. FISH probes are to TOP1 mRNA (Topoisomerase I)in Saos osterosarcoma cells.

One dataset is 10 millisecond exposures (very dim), acquired in Streaming acquisition mode (no hardware overhead).

The other three datasets are a three consecutive planes of the same XY field of view.

I have included image processing results for:

PiMP - a fast method developed by Sebastian Munck et al 2012, http://www.ncbi.nlm.nih.gov/pubmed/?term=22357945

and greatly improved performance by Glen Macdonald (Seattle). …

Selection And Phenotypic Characterization Of A Core Collection Of Brachypodium Distachyon Inbred Lines, Ludmilla Tyler, Johnathan U. Fangel, Alexandra D. Fagerström, Michael A. Steinwand, Ted K. Raab, William Gt Willats, John P. Vogel

Ted K. Raab

The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, …

Blood Vessel Z-Series Image Data Set From Confocal Microscopy 2013 Book, George Mcnamara

George McNamara

Blood Vessel Z-series image data set from Confocal Microscopy 2013 book chapter:

McNamara G, Yanai A, Khankaldyyan V, Laug WE, Boden J, Webster K, Li Y, Wen R. Low magnification confocal microscopy of tumor angiogenesis. Methods Mol Biol. 2014; 1075: 149-75.

doi: 10.1007/978-1-60761-847-8_6. PubMed PMID: 24052350.

See also:

Jeffrey Boden, Jianqin Wei, George McNamara, Hans Layman, Midhat Abdulreda, Fotios Andreopoulos, and Keith A. Webster. Whole-mount imaging of the mouse hindlimb vasculature using the lipophilic carbocyanine dye DiI. Biotechniques Rapid Dispatches, July 2012, pp. 1–4

http://www.biotechniques.com/rapiddispatches/Whole-mount-imaging-of-the-mouse-hindlimb-vasculature-using-the-lipophilic-carbocyanine-dye-DiI./biotechniques-333144.html

Supplemental file:

http://www.biotechniques.com/multimedia/archive/00182/BTNRD-BM-WebsterSUP_182355a.pdf

You may find useful to download Leica LAS AF Lite from

ftp://ftp.llt.de/softlib/LAS_AF_Lite/ …

Seedling Growth Rates And Light Requirements Of Subtropical Rainforest Trees Associated With Basaltic And Rhyolitic Soils, C H. Lusk, Kerrie M. Sendall, P J. Clarke

Kerrie M Sendall

A trade-off between shade tolerance and growth in open conditions is widely believed to underlie the dynamics of humid forests. Little is known about how the growth versus shade tolerance trade-off interacts with other major trade-offs associated with differential adaptation to major environmental factors besides light. We asked whether the growth versus shade tolerance trade-off differed between subtropical rainforest tree assemblages native to basaltic (fertile) and rhyolitic (infertile) soils in northern New South Wales, because of the allocational costs of adaptation to low nutrient availability. Seedling relative growth rates of six basalt specialists and five rhyolite specialists were measured in …

Epa Targets Nanotechnology: Hi-Ho, Nanosilver, Away?, David L. Wallace, Justin Schenck

David L Wallace

No abstract provided.

Avian Influenza Virus Prevalence In Migratory Waterfowl In The United States, 2007-2009, Scott R. Groepper Mr., Thomas Deliberto, Mark Vrtiska, Kerri Pedersen, Seth Swafford, Scott Hyngstrom

Scott R Groepper

SUMMARY. We analyzed 155,535 samples collected for surveillance of avian influenza viruses (AIVs), in the United States from 2007 to 2009, from migratory waterfowl (ducks, geese, and swans). The goal was to elucidate patterns of prevalence by flyway and functional groups to determine targets for future surveillance. Apparent prevalence of AIV was highest in the Pacific Flyway in 2007–2008 (14.2% and 14.1%, respectively), in the Mississippi Flyway in 2009 (16.8%), and lowest each year in the Atlantic Flyway (range, 7.3%–8.9%). Dabbling ducks had higher apparent prevalence of AIV (12.8%–18.8%) than diving ducks (3.9%–6.0%) or geese and swans (3.6%–3.9%). We observed …

Recreating Mesquite Mounds (Nebkas) In The Colorado Desert, David A. Bainbridge

David A Bainbridge

Accretion dunes or mounds (also known as nebkas or nebkhas) are formed when plants capture and then are partially buried in wind-blown sand. In the San Felipe drainage in the western Colorado Desert, mesquite (Prosopis glandulosa Torrey var. torreyana (L. D. Benson) M. C. Johnston)) forms dunes up to 5 m high. These are ecologically important for both ecosystem structure (primarily habitat) and function (soil accumulation, moisture retention and nutrient cycling). The widening of California state highway 86 damaged and removed several mesquite mounds and the California Department of Transportation asked us to explore techniques for recreating them to reduce …

Soil Penetrometer, David A. Bainbridge

David A Bainbridge

A simple easy to build impact soil penetrometer can provide very useful information on soil strength. This can be very important for restoration planning and management of soils in agriculture and forestry.

Soil Solarization, David A. Bainbridge

David A Bainbridge

Soil solarization makes use of the energy of the sun to heat soil and kill weeds and pathogens. Single, double, or bubblepack plastic and be used to increase soil temperature. Multiple growth benefits are often realized.

Bayesian Joint Selection Of Genes And Pathways: Applications In Multiple Myeloma Genomics, Lin Zhang, Jeffrey S. Morris, Jiexin Zhang, Robert Orlowski, Veerabhadran Baladandayuthapani

Jeffrey S. Morris

It is well-established that the development of a disease, especially cancer, is a complex process that results from the joint effects of multiple genes involved in various molecular signaling pathways. In this article, we propose methods to discover genes and molecular pathways significantly associ- ated with clinical outcomes in cancer samples. We exploit the natural hierarchal structure of genes related to a given pathway as a group of interacting genes to conduct selection of both pathways and genes. We posit the problem in a hierarchical structured variable selection (HSVS) framework to analyze the corresponding gene expression data. HSVS methods conduct …

Modelling And Optimal Control Of A Time-Delayed Switched System In Fed-Batch Process, Chongyang Liu, Zhaohua Gong

Chongyang Liu

The main control goal of the fed-batch process is to maximize the yield of target product as well as to minimize the operation costs simultaneously. Considering the existence of time delay and the switching nature in the fed-batch process, a time-delayed switched system is proposed to formulate the 1,3-propanediol (1,3-PD) production process. Some important properties of the system are also discussed. Taking the switching instants and the terminal time as the control variables, a free terminal time delayed optimal control problem is then presented. Using a time-scaling transformation and parameterizing the switching instants into new parameters, an equivalently optimal control …

Sensitivity Analysis And Parameter Identification For A Nonlinear Time-Delay System In Microbial Fed-Batch Process, Chongyang Liu

Chongyang Liu

Developing suitable dynamic models of bioprocess is a difficult issue in bioscience. In this paper, considering the microbial metabolism mechanism, i.e., the production of new biomass is delayed by the amount of time it takes to metabolize the nutrients, in glycerol bioconversion to 1,3-propanediol, we propose a nonlinear time-delay system to formulate the fed-batch fermentation process. Some important properties are also discussed. Then, in view of the effect of time-delay and the high number of kinetic parameters in the system, the parametric sensitivity analysis is used to determine the key parameters. Finally, a parameter identification model is presented and a …

Pitfalls Of Ascertainment Biases In Genome Annotations—Computing Comparable Protein Domain Distributions In Eukarya, Arli A. Parikesit, Lydia Steiner, Peter F. Stadler, Sonja J. Prohaska

Arli A Parikesit

Most investigations into the large-scale patterns of protein evolution are based on gene annotations that have been compiled in reference databases. The use of these resources for quantitative comparisons, however, is complicated by sometimes vast differences in coverage. More importantly, however, we also observe substantial ascertainment biases that cannot be removed by simple normalization procedures. A striking example is provided by the correlations between protein domains. We observe that statistics derived from different computational gene annotation procedure show dramatic discrepancies, and even qualitative changes from negative to positive correlation, when compared to statistics obtained from annotation databases.

Disease Risks Posed By Wild Birds Associated With Agricultural Landscapes, Larry Clark

Larry Clark

No abstract provided.

Chapter 7: The Chemical Senses In Birds, Larry Clark

Larry Clark

No abstract provided.

Changing Climate And The Altitudinal Range Of Avian Malaria In The Hawaiian Islands – An Ongoing Conservation Crisis On The Island Of Kaua`I, Carter T. Atkonson, Ruth B. Utzurrum, Dennis A. Lapointe, Richard J. Camp, Lisa H. Crampton, Jeffrey T. Foster, Thomas W. Giambelluca

Richard J. Camp

Transmission of avian malaria in the Hawaiian Islands varies across altitudinal gradients and is greatest at elevations below 1500 m where both temperature and moisture are favorable for the sole mosquito vector, Culex quinquefasciatus, and extrinsic sporogonic development of the parasite, Plasmodium relictum. Potential consequences of global warming on this system have been recognized for over a decade with concerns that increases in mean temperatures could lead to expansion of malaria into habitats where cool temperatures currently limit transmission to highly susceptible endemic forest birds. Recent declines in two endangered species on the island of Kaua’i, the ‘Akikiki (Oreomystis bairdi) …

Inducing A Dielectric Barrier Discharge Plasma Within A Package, Vladimir Milosavljevic

Vladimir Milosavljevic

Cold atmospheric plasma offers significant potential as a nonthermal decontamination tool for food and medical applications. We present results of a dielectric barrier discharge (DBD) plasma induced in a gas confined by a polymer package. The resultant discharge and contained afterglow are found to have a strong antimicrobial effect.

Inducing A Dielectric Barrier Discharge Plasma Within A Package, Vladimir Milosavljevic

Vladimir Milosavljevic

Cold atmospheric plasma offers significant potential as a nonthermal decontamination tool for food and medical applications. We present results of a dielectric barrier discharge (DBD) plasma induced in a gas confined by a polymer package. The resultant discharge and contained afterglow are found to have a strong antimicrobial effect.

Decision-Making In Economics: Critical Lessons From Neurobiology, Renato Alas Msc, Kuldeep Kumar, Avik Mukherjee, Munirul Haque Nabin, Sukanto Bhattacharya

Renato A Martins MSc

Book Description: Game Theory has provided an extremely useful tool in enabling economists to venture into unknown areas. Its concepts of conflict and cooperation apply whenever the actions of several agents are interdependent; providing language to formulate as well as to structure, analyze, and understand strategic scenarios. Economic Behavior, Game Theory, and Technology in Emerging Markets explores game theory and its deep impact in developmental economics, specifically the manner in which it provides a way of formalizing institutions. This is particularly important for emerging economies which have not yet received much attention in the academic world. This publication is useful …

Fungal Solid-State Fermentation And Various Methods Of Enhancement In Cellulase Production, Li Wan Yoon, Teck Nam Ang Dr., Gek Cheng Ngoh Dr, Adeline Seak May Chua Dr

Teck Nam Ang Dr.

Cellulase serves vast applications in the industries of biofuel, pulp and paper, detergent and textile. With the presence of its three components i.e. endoglucanase, exoglucanase and β-glucosidase, the enzyme can effectively depolymerize the cellulose chains in lignocellulosic substrate to produce smaller sugar units that consists of cellobiase and glucose. Fungi are the most suitable cellase producers attributing to its ability to produce a complete cellulase system. Solid state fermentation (SSF) by fungi is a preferable production route for cellulase as it imposes lower cost and enables the production of cellulase with higher titre. This article gives an overview on the …

Population Dynamics Of Spiders In Ayya Nadar Janaki Ammal College Campus, Sivakasi, Virudhunagar District, Tamil Nadu, India, Jeyaparvathi S

JOZS JOURNAL

Spiders play an important role in regulating insect pests in the agricultural ecosystem. There are a large number of species, many of them with high population densities. A survey was conducted in the Ayya Nadar Janaki Ammal College campus from January, 2011 - March, 2011. 29 individuals were collected representing 11 families and 21 genera. From these, 25 species were present throughout the campus; however, only 5 of these were taken in the ground, they are the ground dwellers. Peucetia viridana (Stolizcka), Oxyopes hindostanicus (Tikader), Lycosa pseudoannulata (Bosenberg) and Plexippus petersi, were common. P. viridana was the dominant species followed …

Characterization Of Bovine-Derived Porous Hydroxyapatite Scaffold And Its Potential To Support Osteogenic Differentiation Of Human Bone Marrow Derived Mesenchymal Stem Cells., Krishnamurithy G, Murali Mr, Hamdi M, Abbas Aa, Raghavendran Hb, Kamarul T

Murali Malliga Raman

Porous three-dimensional hydroxyapatite (HA) scaffolds were prepared using bovine cortical bone derived HA (BDHA). Analyses of the morphology, chemical composition, and phase purity of the scaffold were performed using scanning electron microscopy (SEM), micro-computer tomography (micro-CT), Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction (XRD). SEM images revealed the rough and porous surface of the scaffold, while micro-CT showed the average porous volume of 76.7±0.6% and pore size of 0.04–0.25 mm. Single phase corresponding to standard HA was observed using XRD, and FTIR confirmed the presence of functional groups similar to HA. The EDX analysis …

Histology, Glycosaminoglycan Level And Cartilage Stiffness In Monoiodoacetate-Induced Osteoarthritis: Comparative Analysis With Anterior Cruciate Ligament Transection In Rat Model And Human Osteoarthritis, Naveen Sv, Ahmad Re, Hui Wj, Suhaeb Am, Murali Malliga Raman, Shanmugam R, Kamarul T

Murali Malliga Raman

Monosodium -iodoacetate (MIA)-induced animal model of osteoarthritis (OA) is under-utilised despite having many inherent advantages. At present, there is lack of studies that directly compare the degenerative changes induced by MIA with the surgical osteoarthritis induction method and human osteoarthritis, which would further verify a greater use of this model. Therefore, we compared the histological, biochemical and biomechanical characteristics in rat model using MIA against the anterior cruciate ligament transection (ACLT) and human cartilage with clinically established osteoarthritis. The right knees of Sprague-Dawley rats were subjected to either MIA or ACLT (n=18 in each group). Six rats were used as …

Fluoroscopy Assisted Minimally Invasive Transplantation Of Allogenic Mesenchymal Stromal Cells Embedded In Hystemtm Reduce The Progression Nucleus Pulposus Degeneration In The Damaged Intervertebral Disc - A Preliminary Study In Rabbits, Suhban Ra, Puvanan K, Murali Mr, Raghavendran Hb, Shani S, Abdullah Bj, Abbas Aa, Mohamad Ja, Kamarul T

Murali Malliga Raman

This study was conducted to develop a technique for minimally invasive and accurate delivery of stem cells to augment nucleus pulposus (NP) in damaged intervertebral discs (IVD). IVD damage was created in noncontiguous discs at L4-L5 level; rabbits (N = 12) were randomly divided into three groups: group I treated with MSCs in HyStem hydrogel, group II treated with HyStem alone, and group III received no intervention. MSCs and hydrogel were administered to the damaged disc under guidance of fluoroscopy. Augmentation of NP was assessed through histological and MRI T2 mapping of the NP after eight weeks of transplantation. T2 …

Pearl Millet Breeding Lines Developed At Icrisat:A Reservoir Of Variability And Useful Source, Mahalingam Govindaraj

Mahalingam Govindaraj

The International Crops Research Institute for the Semi- Arid Tropics (ICRISAT) conducts inter-disciplinary and partnership-based research for the genetic improvement of its mandate crops. During the 1970s and 1980s, the pearl millet improvement at ICRISAT, Patancheru, emphasized on: (i) developing a diverse range of traitspecific composites, based on the germplasm largely from the Western and Central Africa; (ii) improving them by the process of recurrent selection, principally for grain yield and downy mildew (Sclerospora graminicola (Sacc.) Schroet ) resistance; and (iii) developing open-pollinated varieties (OPVs)

Forest Biomass Supply Chains In Ireland: A Life Cycle Assessment Of Ghg Emissions And Primary Energy Balances, Fionnuala Murphy

Fionnuala Murphy

The demand for wood for energy production in Ireland is predicted to double from 1.5 million m3 over bark (OB) in 2011 to 3 million m3 OB by 2020. There is a large potential for additional biomass recovery for energetic purposes from both thinning forest stands and by harvesting of tops and branches, and stumps. This study builds on research within the wood-for-energy concept in Ireland by analysing the energy requirements and greenhouse gas emissions associated with thinning, residue bundling and stump removal for energy purposes. To date there have been no studies on harvesting of residues and stumps in …

Surveillance Of Feral Swine For Trichinella Spp. And Toxoplasma Gondii In The Usa And Host-Related Factors Associated With Infection, John A. Baroch

John A Baroch

No abstract provided.