Life Sciences Commons^™

Functional Car Models For Spatially Correlated Functional Datasets, Lin Zhang, Veerabhadran Baladandayuthapani, Hongxiao Zhu, Keith A. Baggerly, Tadeusz Majewski, Bogdan Czerniak, Jeffrey S. Morris

Jeffrey S. Morris

We develop a functional conditional autoregressive (CAR) model for spatially correlated data for which functions are collected on areal units of a lattice. Our model performs functional response regression while accounting for spatial correlations with potentially nonseparable and nonstationary covariance structure, in both the space and functional domains. We show theoretically that our construction leads to a CAR model at each functional location, with spatial covariance parameters varying and borrowing strength across the functional domain. Using basis transformation strategies, the nonseparable spatial-functional model is computationally scalable to enormous functional datasets, generalizable to different basis functions, and can be used on …

Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), Elizabeth C. Craig, Brian S. Dorr, Katie C. Hanson-Dorr, Jed P. Sparks, Paul D. Curtis

Brian S Dorr

The diet-tissue discrimination factor is the amount by which a consumer’s tissue varies isotopically from its diet, and is therefore a key element in models that use stable isotopes to estimate diet composition. In this study we measured discrimination factors in blood (whole blood, red blood cells and plasma), liver, muscle and feathers of Double- crested Cormorants (Phalacrocorax auritus) for stable isotope ratios of carbon, nitrogen and sulfur. Cormorants exhibited discrimination factors that differed significantly among tissue types (for carbon and nitrogen), and differed substantially (in the context of the isotopic variation among relevant prey species) from those observed in …

Satpdb: A Database Of Structurally Annotated Therapeutic Peptides, Sandeep Singh

Sandeep Singh

SATPdb (http://crdd.osdd.net/raghava/satpdb/) is a database of structurally annotated therapeutic peptides, curated from 22 public domain peptide databases/datasets including 9 of our own. The current version holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids. It covers peptides having natural, non-natural and modified residues. These peptides were systematically grouped into 10 categories based on their major function or therapeutic property like 1099 anticancer, 10585 antimicrobial, 1642 drug delivery and 1698 antihypertensive peptides. We assigned or annotated structure of these therapeutic peptides using structural databases (Protein Data Bank) and state-of-the-art structure prediction methods like I-TASSER, …

The Influence Of Riparian Vegetation And Season On Stream Metabolism Of Valley Creek, Minnesota, Daniel J. Hornbach, Rick Beckel, Erin N. Husted, Dylan P. Mcadam, Inga M. Roen, Amanda J. Wareham

Daniel J. Hornbach

No abstract provided.

Mcnamara 2010 Metamatters Newletter Series - Rogers Pmn The Chase And Temporal Area Maps, George Mcnamara

George McNamara

My four 2010 MetaMorph MetaMatters newsletter articles on "The Chase" (video available for download here on my bepress site) and history / use of temporal area maps.

Comparative Analysis Of Biodegradability Of Biodiesel Obtained By Conventional And Non-Conventional Methods, Innovative Research Publications Irp India, Nagaraja Y. P, Chandrashekhar Biradar

Innovative Research Publications IRP India

Biodiesel is an alternative to conventional diesel fuel made from renewable resources. No engine modifications are required to use biodiesel in place of crude oil-based diesel. The use of biodiesel resulted in lower emissions of unburned hydrocarbons, carbon monoxide and particulate matter. Biodiesel also increased catalytic converter efficiency in reducing particulate emissions. Chemical characterization also revealed lower levels of some toxic and reactive hydrocarbon species when biodiesel fuels were used. In the present work, biodiesel is produced by both conventional and non-conventional methods to determine the biodegradability effect using microorganisms obtained from soil collected from the vicinity of a petrol …

Production And Purification Of Tannase From Aspergillus Aculeatus Using Plant Derived Raw Tannin, Innovative Research Publications Irp India, Jasbir Bagga, Soumya Kanti Pramanik, Vibha Pandey

Innovative Research Publications IRP India

Tannase, an enzyme with immense potential has lot of applications in food, beverage, pharmaceutical and chemical industries. During the present study, tannin content of different plant materials was determined. Tannase has been produced from Aspergillus aculeatus through fermentation of tannin rich plant materials. Among the plant materials used, Cassia ciamia gives better result. Maximum oxygen is utilized by the organism after 24 h of growth. pH of the fermented broth falls to 4.1 after 28 h of growth. Organism utilizes wheat bran as a solid substrate to produce maximum tannase. Maximum enzyme production through solid state fermentation was achieved after …

Social Science Contributions Compared In Synthetic Biology And Nanotechnology, Philip Shapira, Jan Youtie, Yin Li

Philip Shapira

With growing attention to societal issues and implications of synthetic biology, we investigate sources of social science publication knowledge in synthetic biology and probe what might be learned by comparison with earlier rounds of social science research in nanotechnology. “Social science” research is broadly defined to include publications in conventional social science as well as humanities, law, ethics, business, and policy fields. We examine the knowledge clusters underpinning social science publications in nanotechnology and synthetic biology using a methodology based on the analysis of cited references. Our analysis finds that social science research in synthetic biology already has traction and …

Annual Variation In Autumn Migration Phenology And Energetic Condition At A Stopover Site In The Western United States, Robert A. Miller, Jay D. Carlisle, Neil Paprocki, Gregory S. Kaltenecker, Julie A. Heath

Robert Miller

Climate change is having a dramatic effect on many migratory species. Changes in climate may lead to changes in food availability or other proximate cues that affect migratory behavior. We used 13 years (2000–2012) of data on songbird banding and raptor migration counts and captures during autumn migration in the intermountain West to evaluate whether regional temperature or precipitation or hemispheric climate indices predicted autumn migratory timing and energetic condition. We examined overall trends and evaluated the effects of diet and migratory distance on phenology and conditional responses. For the 13-year study period, no temperature, precipitation, or climate index trends …

Importance Of Genetic Diversity Assessment In Crop Plants And Its Recent Advances: An Overview Of Its Analytical Perspectives, Mahalingam Govindaraj

Mahalingam Govindaraj

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world.Agricultural scientists realized that PGD can be captured and stored in the formof plant genetic resources (PGR) such as gene bank,DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security.This paper comprehensively reviews four important areas; (i) the …

Exploring Behavioral And Hormonal Flexibility Across Light Environments In Guppies From Low-Predation Populations, Gita R. Kolluru

Gita R. Kolluru

No abstract provided.

Warm Microhabitats Drive Both Increased Respiration And Growth Rates Of Intertidal Consumers, Luke P. Miller, Bengt J. Allen, Felicia A. King, Daisy R. Chilin, Vanessa M. Reynoso, Mark W. Denny

Luke P. Miller

Rocky intertidal organisms are often exposed to broadly fluctuating temperatures as the tides rise and fall. Many mobile consumers living on the shore are immobile during low tide, and can be exposed to high temperatures on calm, warm days. Rising body temperatures can raise metabolic rates, induce stress responses, and potentially affect growth and survival, but the effects may differ among species with different microhabitat preferences. We measured aerial and aquatic respiration rates of 4 species of Lottia limpets from central California, and estimated critical thermal maxima. In a variety of microhabitats in the field, we tracked body temperatures and …

Cloning And Expression Analysis Of Drosophila Extracellular Cu Zn Superoxide Dismutase, Michael J. Blackney, Rebecca Cox, David Shepherd, Joel D. Parker

Joel D Parker

In the present study, we cloned and sequenced the mRNAs of the Sod3 [extracellular Cu Zn SOD (superoxide dismutase)] gene in Drosophila and identified two mRNA products formed by alternative splicing. These products code for a long and short protein derived from the four transcripts found in global expression studies (Flybase numbers Dmel\CG9027, FBgn0033631). Both mRNA process variants contain an extracellular signalling sequence, a region of high homology to the Sod1 (cytoplasmic Cu Zn SOD) including a conserved AUG start, with the longer form also containing a hydrophobic tail. The two fully processed transcripts are homologous to Caenorhabditis elegans Sod3 …

Climate Change Enhances The Negative Effects Of Predation Risk On An Intermediate Consumer, Luke P. Miller, Catherine M. Matassa, Geoffrey C. Trussell

Luke P. Miller

Predators are a major source of stress in natural systems because their prey must balance the benefits of feeding with the risk of being eaten. Although this ‘fear’ of being eaten often drives the organization and dynamics of many natural systems, we know little about how such risk effects will be altered by climate change. Here, we examined the interactive consequences of predator avoidance and projected climate warming in a three-level rocky intertidal food chain. We found that both predation risk and increased air and sea temperatures suppressed the foraging of prey in the middle trophic level, suggesting that warming …

Thermal Stress And Predation Risk Trigger Distinct Transcriptomic Responses In The Intertidal Snail Nucella Lapillus, Nathaniel D. Chu, Luke P. Miller, Stefan T. Kaluziak, Geoffrey C. Trussell, Steven V. Vollmer

Luke P. Miller

Thermal stress and predation risk have profound effects on rocky shore organisms, triggering changes in their feeding behaviour, morphology and metabolism. Studies of thermal stress have shown that underpinning such changes in several intertidal species are specific shifts in gene and protein expression (e.g. upregulation of heat-shock proteins). But relatively few studies have examined genetic responses to predation risk. Here, we use next-generation RNA sequencing (RNA-seq) to examine the transcriptomic (mRNA) response of the snail Nucella lapillus to thermal stress and predation risk. We found that like other intertidal species, N. lapillus displays a pronounced genetic response to thermal stress …

Mcnamara 20140911 Bepress Author Utilization Counts Cannot Be Trusted Due To Poor Design And Support, George Mcnamara

George McNamara

McNamara 20140911 Bepress author utilization counts cannot be trusted due to poor design and support

//

20140912 update: bepress support finally 'gets' my problem and should have my author counts fixed soon.

I have left the text below and the original download as is.

//

Email exchange 9/2014 (also available as a PDF download):

Your bepress system “database” is pretty lame if there is no way for your team to correct this ‘bot inflation.

You are serving an academic research community that has a very high expectation in the quality of our scholarship and data. That you cannot correct “bad …

Enhancement Of Chronically Induced Breast Carcinogenesis By Combined Environmental And Dietary Carcinogens And Suppression By Dietary Agents, Lenora A. Pluchino Ph.D.

Lenora A. Pluchino, Ph.D.

Most breast cancers occur sporadically due to long-term exposure to low-dose carcinogens present in our environment and diet. American lifestyles involve frequent exposures to smoke, polluted air, and high temperature-cooked meats comprising multiple carcinogens, such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), benzo[α[alpha]]pyrene (B[α[alpha]]P), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). To investigate whether these carcinogens may act together to enhance breast cell carcinogenesis, we used our chronically-induced breast cell carcinogenesis model wherein we repeatedly expose non-cancerous human breast epithelial MCF10A cells to physiologically-achievable doses of carcinogens to progressively induce cellular acquisition of cancer-associated properties including reduced dependence on growth factors, anchorage-independent growth, increased cell proliferation, migration and …

Mathematical Structure Of Fuzzy Modeling Of Medical Diagnoses By Using Clustering Models, R.W. W. Hndoosh

R. W. Hndoosh

An Adaptive-Network-based Fuzzy Inference System ANFIS with different techniques of clustering is successfully developed to solve one of the problems of medical diagnoses, because it has the advantage of powerful modeling ability. In this paper, we propose the generation of an adaptive neuro-Fuzzy Inference System model using different clustering models such as a subtractive fuzzy clustering (SFC) model and a fuzzy c-mean clustering (FCM) model in the Takagi-Sugeno (TS) fuzzy model for selecting the hidden node centers. An experimental result on datasets of medical diagnoses shows the proposed model with two models of clustering (ANFIS-SFC & ANFIS-FCM) while comparing the …

Timelapse Data - Gm Imaging Cytometer Needs Stitching Part 1 Of 2, George Mcnamara

George McNamara

Timelapse data - GM imaging cytometer needs stitching part 1 of 2

Imaging challenge: align multiple time series over time to overcome "stage slop" in the imaging cytometer used in this experiment.

http://works.bepress.com/gmcnamara/53 (this)

and

http://works.bepress.com/gmcnamara/54 (next)

are zip files containing 8-bit stacks (MetaMorph multiplane TIFF files) acquired on an imaging cytometer.

"53" is the brightfield data, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6).

"54" is GFP fluorescence, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6). The GFP fluorescence decreases over time due to photobleaching. GFP disappears from cells when they die (soluble GFP diffusing …

Pathscan Enabler At Md Anderson Cancer Center, George Mcnamara

George McNamara

McNamara 20140703 - Additional Pathscan and Tiki_Goddess related resources

http://works.bepress.com/gmcnamara/52

http://home.earthlink.net/~tiki_goddess/

http://works.bepress.com/gmcnamara/1/

http://works.bepress.com/gmcnamara/11/

https://www.linkedin.com/in/georgemcnamara

Our Pathscan Enabler IV, delivered July 2014, uses the QuickScan software to scan a histology slide in "two clicks" (after loading the

slide):

1. Push the QuickScan button on the front of the Pathscan Enabler.

2. Click the Scan button in the QuickScan pop-up application (optional: change scan area in the Prescan image window).

The image gets saved as a TIFF file to the Windows 7 (64-bit) desktop.

I have been using Pathscan Enabler's since version I in 2000. See Chantrain et al 2003:

Chantrain CF, …

Real-Time Pcr And Real-Time Rt-Pcr Applications In Food Labelling And Gene Expression Studies, Arash Kashani, Tasmanian Institute Of Agriculture

Emily Scott

Polymerase chain reaction (PCR) as a scientific invention, has revolutionized molecular biology and led to real-time PCR and later, real-time reverse transcription PCR (Real-Time RT-PCR). These two techniques enable scientists to conduct PCR detection of amplified gene products and expression analysis of targeted genes. Quantitative polymerase chain reaction (qPCR), also called real-time polymerase chain reaction, is a recent modification to PCR that utilizes fluorescent reporter molecular techniques to monitor the production of amplified products during each cycle of the PCR reaction, and enables both detection and quantification of specific sequences in complex mixtures. Over the past decade, real-time PCR applications …

Mechanisms Of Photoperiod In Regulation Of Rice Flowering, Abdulrahman Mahmoud Dogara, Salisu Muhammad Tahir, Idris Shehu, Mustapha Abbah

Emily Scott

A study on the photoperiodic control of flower in rice is advancing and rice has become an example of short day plant. Many genes used in flowering time determination in rice have been identified by many methods. The conclusion from these molecular studies is a remarkable conservation of genes which play an important role in the control of flowering time in rice. The rice photoperiod sensitivity gene Hd3a was originally detected as a heading date related quantitative trait locus found on chromosome 6 of rice. High resolution linkage mapping of Hd3a was carried using a huge segregating population derived from …

Effects Of Prey Abundance On Breeding Season Diet Of Northern Goshawks (Accipiter Gentilis) Within An Unusual Prey Landscape, Robert A. Miller, Jay D. Carlisle, Marc J. Bechard

Robert Miller

A critical element of diet analysis is species adaptability to alternative prey sources. The breeding season diet of Northern Goshawks (Accipiter gentilis) includes both mammalian and avian species, varies geographically, and is often dependent upon tree squirrels of the genera Sciurus and Tamiasciurus>/i>. We studied alternative prey sources of Northern Goshawks in the South Hills of south-central Idaho, an area where tree squirrels are naturally absent and other prey frequently important in the diet of goshawks, such as smaller corvids, are uncommon. We quantified the diet of goshawks using nest cameras and surveyed abundance of prey using line …

Lichens Of Six Vernal Pools In Acadia National Park, Maine, Usa, Jason Barton, Brett Ciccotelli, Jillian E. Gall, Fred C. Olday, Bruce Connery, Tanner B. Harris, Alan M. Fryday, Nishanta Rajakaruna

Nishanta Rajakaruna

Whereas lichen-habitat relations have been well-documented globally, literature on lichens of vernal pools is scant. We surveyed six vernal pools at Acadia National Park on Mount Desert Island, Maine, USA for their lichen diversity. Sixty-seven species were identified, including seven species that are new reports for Acadia National Park: Fuscidea arboricola, Hypogymnia incurvoides, Lepraria finkii, Phaeographis inusta, Ropalospora viridis, Usnea flammea, and Violella fucata. Five species are considered uncommon or only locally common in New England: Everniastrum catawbiense, Hypogymnia krogiae, Pseudevernia cladonia, Usnea flammea, and Usnea merrillii. This …

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). …

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 …

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 …

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.

Comparative Genomics Of Closely Related Salmonella Enterica Serovar Typhi Strains Reveals Genome Dynamics And The Acquisition Of Novel Pathogenic Elements, Kien-Pong Yap

Kien-Pong Yap

Background Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.

Results A comparative genomics analysis combined with a phylogenomic analysis revealed that the strains from the outbreak and carrier were closely related with microvariations and possibly derived from a common ancestor. Additionally, the …