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 …

Analysis Of Genetic Diversity Using Simple Sequence Repeat (Ssr) Markers And Growth Regulator Response In Biofield Treated Cotton (Gossypium Hirsutum L.), Mahendra Kumar Trivedi, Alice Branton, Dahryn Trivedi, Gopal Nayak, Mayank Gangwar, Snehasis Jana

Mahendra Kumar Trivedi

Cotton is the most important crop for the production of fiber that plays a key role in economic and social affairs. The aim of the study was to evaluate the impact of biofield energy treatment on cotton seeds regarding its growth, germination of seedling, glutathione (GSH) concentration, indole acetic acid (IAA) content and DNA fingerprinting using simple sequence repeat (SSR) markers for polymorphism analysis. The seeds of cotton cv. Stoneville-2 (Gossypium hirsutum L.) was obtained from DNA Land Marks Inc., Canada and divided into two groups. One group was remained as untreated, while the other was subjected to Mr. Trivedi …

Spectroscopic Characterization Of Chloramphenicol And Tetracycline: An Impact Of Biofield Treatment, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

Objective: Chloramphenicol and tetracycline are broad-spectrum antibiotics and widely used against variety of microbial infections. Nowadays, several microbes have acquired resistance to chloramphenicol and tetracycline. The present study was aimed to evaluate the impact of biofield treatment for spectroscopic characterization of chloramphenicol and tetracycline using FT-IR and UV-Vis spectroscopy. Methods:The study was performed in two groups (control and treatment) of each antibiotic. The control groups remained as untreated, and biofield treatment was given to treatment groups. Results: FT-IR spectrum of treated chloramphenicol exhibited the decrease in wavenumber of NO2 from 1521 cm-1 to 1512 cm-1 and increase in wavenumber of …

An Effect Of Biofield Treatment On Multidrug-Resistant Burkholderia Cepacia: A Multihost Pathogen, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

Burkholderia cepacia (B. cepacia) is an opportunistic, Gram negative pathogen which causes infection mainly in immunocompromised population and associated with high rate of morbidity and mortality in cystic fibrosis patients. Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinical sample of B. cepacia was divided into two groups i.e. control and biofield treated. The analysis was done after 10 days of treatment and compared with control group. Control and treated group were analyzed for susceptibility pattern, MIC value, biochemical studies and biotype number using MicroScan Walk-Away® system.Sensitivity assay results showed …

Bio-Field Treatment: An Effective Strategy To Improve The Quality Of Beef Extract And Meat Infusion Powder, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP). The treated powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), particle size analysis, surface area analysis, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). The FT-IR results showed disappearance of triglycerides peaks in both the treated powders as compared to control. XRD results corroborated the amorphous nature of both control and treated samples. The BEP showed enhanced average particle size (d50) and d99 (size exhibited by 99% …

Studies Of The Atomic And Crystalline Characteristics Of Ceramic Oxide Nano Powders After Bio Field Treatment, Mahendra Kumar Trivedi

Mahendra Kumar Trivedi

Transition metal oxides (TMOs) have been known for their extraordinary electrical and magnetic properties. In the present study, some transition metal oxides (Zinc oxide, iron oxide and copper oxide) which are widely used in the fabrication of electronic devices were selected and subjected to biofield treatment. The atomic and crystal structures of TMOs were carefully studied by Fourier transform infrared (FT-IR) spectroscopy and X-ray diffraction (XRD) studies. XRD analysis reveals that biofield treatment significantly changed the lattice strain in unit cells, crystallite sizes and densities in ceramics oxide powders. The computed molecular weight of the treated samples exhibited significant variation. …

Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock

Thomas Van Horn

Phage Enkatz is a temperate mycobacteriophage isolated from an un-enriched soil sample collected from the South Forty housing area of the Washington University in St. Louis campus. Enkatz displays unequally sized plaques with a clear center that become cloudier with radial distance from the center. Genome analysis indicates that Enkatz is a cluster A1 mycobacteriophage with a genome size of 49,738 bases and 82 identified genes, 33 of which have been assigned functions. This analysis reveals that the majority of the genes in the positive strand code for structural proteins, while the majority of the genes in the negative strand …

The Pollution Of River Ibër With Heavy Metals From Landfill Of Kelmend, Innovative Research Publications Irp India, Rafet Zeqiri, Izet Zeqiri, Sadija Nikshiq -Kadriu, Mehush Aliu

Innovative Research Publications IRP India

In this paper treated the degree of water pollution that emerges from mining and mixed with industrial wastes and as such in the form of pulp thrown in landfills. From the landfill through drainage and water flows in the river Ibër, penetrate the different pollutants that affect in water quality of this river. The degree of contamination of the river Ibër is monitored at several points, on which it is made water sampling of landfill and where we have reached the conclusion on the possibilities of prevention of water pollution of the river Ibër

Ordinal Probit Wavelet-Based Functional Models For Eqtl Analysis, Mark J. Meyer, Jeffrey S. Morris, Craig P. Hersh, Jarret D. Morrow, Christoph Lange, Brent A. Coull

Jeffrey S. Morris

Current methods for conducting expression Quantitative Trait Loci (eQTL) analysis are limited in scope to a pairwise association testing between a single nucleotide polymorphism (SNPs) and expression probe set in a region around a gene of interest, thus ignoring the inherent between-SNP correlation. To determine association, p-values are then typically adjusted using Plug-in False Discovery Rate. As many SNPs are interrogated in the region and multiple probe-sets taken, the current approach requires the fitting of a large number of models. We propose to remedy this by introducing a flexible function-on-scalar regression that models the genome as a functional outcome. The …

Open Consent, Biobanking And Data Protection Law: Can Open Consent Be ‘Informed’ Under The Forthcoming Data Protection Regulation?, Dara Hallinan, Michael Friedewald

Michael Friedewald

This article focuses on whether a certain form of consent used by biobanks – open consent – is compatible with the Proposed Data Protection Regulation. In an open consent procedure, the biobank requests consent once from the data subject for all future research uses of genetic material and data. However, as biobanks process personal data, they must comply with data protection law. Data protection law is currently undergoing reform. The Proposed Data Protection Regulation is the culmination of this reform and, if voted into law, will constitute a new legal framework for biobanking. The Regulation puts strict conditions on consent …

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 …

Iniadi Pearl Millet Germplasm As A Valuable Genetic Resource For High Grain Iron, Mahalingam Govindaraj

Mahalingam Govindaraj

Crop biofortification is increasingly being recognized as a cost-effective and sustainable approach to address the widespread micronutrient malnutrition arising from Fe and Zn deficiencies. Pearl millet as a cereal crop species has higher Fe density than all other major cereals. Earlier studies in pearl millet have shown that breeding lines, hybrid parents, improved populations and composites having high Fe and Zn densities were often based largely or entirely on iniadi pearl millet germplasm. In an attempt to identify additional sources of high Fe density in this group of germplasm, 297 accessions were screened using Perl’s Prussian Blue staining, of which …

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 …

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, …

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.

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)

Molecular Detection, Genetic Characterization And Zoonotic Potenial Of Porcine Rotaviruses, Joshua O. Amimo

Joshua O Amimo

Virus induced enteritis is one of the serious problems accounting for maximum deaths in neonatal animals and human throughout the world. The absence of appropriate surveillance programs and laboratory facilities have resulted in a scarcity of accessible data on virus associated diarrheas (especially rotavirus) in pigs in the East African region. The aim of this study was to provide detailed molecular epidemiological information on the prevalence and genetic diversity of rotaviruses (RVs) and also the distribution of genotypes of group A RVs (RVA) circulating in high intensive commercial pig production systems in the USA and smallholder pig production systems (1-25 …

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 …

The Empire Of Cancer: Gene Patents And Cancer Voices, Matthew Rimmer

Matthew Rimmer

In his book, The Emperor of All Maladies, Siddhartha Mukherjee writes a history of cancer — ‘It is a chronicle of an ancient disease — once a clandestine, “whispered-about” illness — that has metamorphosed into a lethal shape-shifting entity imbued with such penetrating metaphorical, medical, scientific, and political potency that cancer is often described as the defining plague of our generation’.Increasingly, an important theme in the history of cancer is the role of law, particularly in the field of intellectual property law. It is striking that a number of contemporary policy debates over intellectual property and public health have concerned …

Metagenomic Insights Into Anaerobic Metabolism Along An Arctic Peat Soil Profile, David A. Lipson, John M. Haggerty, Archana Srinivas, Ted K. Raab, Shashank Sathe, Elizabeth A. Dinsdale

Ted K. Raab

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance …

Flash4 Dark Reference Images, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 dark reference images, acquired with 10 second exposure times, no light to camera. Camera offset (set by Hamamatsu( is ~100 (the average intensity of the first image is always ~1 intensity level higher - an odd feature, but trivial in practice for a 16-bit camera).

George McNamara, Ph.D.

Single Cells Analyst at L.J.N. Cooper Lab

University of Texas M.D. Anderson Cancer Center

Video Codec Performance (Excel Spreadsheet), George Mcnamara

George McNamara

Video codec performance (Excel spreadsheet). Movie was made in 2005-2006 when I worked at City of Hope National Medical Center. VTLF refers to Video Timelapse Light Facility. Videos were outputted from MetaMorph as AVI files. Personally, I always recommend uncompressed video files fro scientific uses. I also encourage posting the original scientific data format (ex. .lsm, .zvi, .lif, .stk).

Pubspectra Tattletales, George Mcnamara

George McNamara

Tattletales for Multiplex Fluorescent Reporters in Single Cells for Metabolomics

George McNamara

As of April 2013: L.J.N. Cooper & D.A. Lee Cellular Immunotherapy Lab, University of Texas M.D. Anderson Cancer Center, Houston, TX

Email: gtmcnamara@mdanderson.org, geomcnamara@earthlink.net

Tattletales is my concept for spatial multiplexing many fluorescent protein (FP) biosensors in the same live cell. For example, there are excellent FP biosensors to Ca++ ions, pH, glucose, ribose, glutamine, glutamate, ATP, redox, ROS, pyruvate, cAMP, cGMP, IP3, PI(3,4,5)P3, cell cycle indicators (Fucci2), PKA, PKC, photsphatases, caspase(s) [1, 2]. However, these are typically used one biosensor per experiment, due in part to flooding …

Global Quantitative Assessment Of The Colorectal Polyp Burden In Familial Adenomatous Polyposis Using A Web-Based Tool, Patrick M. Lynch, Jeffrey S. Morris, William A. Ross, Miguel A. Rodriguez-Bigas, Juan Posadas, Rossa Khalaf, Diane M. Weber, Valerie O. Sepeda, Bernard Levin, Imad Shureiqi

Jeffrey S. Morris

Background: Accurate measures of the total polyp burden in familial adenomatous polyposis (FAP) are lacking. Current assessment tools include polyp quantitation in limited-field photographs and qualitative total colorectal polyp burden by video.

Objective: To develop global quantitative tools of the FAP colorectal adenoma burden.

Design: A single-arm, phase II trial.

Patients: Twenty-seven patients with FAP.

Intervention: Treatment with celecoxib for 6 months, with before-treatment and after-treatment videos posted to an intranet with an interactive site for scoring.

Main Outcome Measurements: Global adenoma counts and sizes (grouped into categories: less than 2 mm, 2-4 mm, and greater than 4 mm) were …

Screening Of Commercial Cyclic Peptides As Inhibitor Envelope Protein Dengue Virus (Denv) Through Molecular Docking And Molecular Dynamics, Arli A. Parikesit, Kinanty Kinanty, Usman Sumo F. Tambunan

Arli A Parikesit

Dengue virus (DENV) has spread throughout the world, especially in tropical climates. Effective treatment of DENV infection is not yet available although several candidate vaccines have been developed. Treatment at this time is only to reduce symptoms and reduce the risk of death. Therefore, antiviral treatment is much needed. Envelope protein is one of the structural proteins of DENV which is known and could be a target of antiviral inhibitors and plays a special role in the fusion process. The aim of this research is to screen the commercial cyclic peptides which are used as inhibitors of envelope protein DENV …

The New Frontier Of Advanced Reproductive Technology: Reevaluating Modern Legal Parenthood, Yehezkel H. Margalit Dr., John D. Loike Dr., Orrie Levy Adv.

Hezi Margalit

Assisted reproductive technologies (ARTs) have challenged our deepest conceptions of what it means to be a parent by fragmenting traditional aspects of parenthood. The law has been slow to respond to this challenge, and numerous academic articles have proposed models for adapting parentage laws to ARTs. In the coming years, however, scientific advancements in reproductive technologies, such as somatic cell nuclear transfer and stem cell technologies, will challenge both parentage laws and proposed legal models for traditional ARTs in new and fascinating ways. For instance, these advanced technologies could allow two women to create a child without any male genetic …

Piscine Myocarditis Virus (Pmcv) In Wild Atlantic Salmon Salmo Salar, Torstein Tengs Dr.

Dr. Torstein Tengs

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of sea-farmed Atlantic salmon Salmo salar L., but CMS-like lesions have also been found in wild Atlantic salmon. In 2010 a double-stranded RNA virus of the Totiviridae family, provisionally named piscine myocarditis virus (PMCV), was described as the causative agent of CMS. In the present paper we report the first detection of PMCV in wild Atlantic salmon. The study is based on screening of 797 wild Atlantic salmon by real-time RT-PCR. The samples were collected from 35 different rivers along the coast of Norway, and all individuals included in the study were …

Molecular Surveillance Of Low Pathogenic Avianinfluenza Viruses In Wild Birds Across The United States:Inferences From The Hemagglutinin Gene, Antoinette J. Piaggio, Susan A. Shriner, Kaci Van Dalen, Alan B. Franklin, Theodore D. Anderson, Sergios-Orestis Kolokotronis

Alan B Franklin

A United States interagency avian influenza surveillance plan was initiated in 2006 for early detection of highly pathogenic avian influenza viruses (HPAIV) in wild birds. The plan included a variety of wild bird sampling strategies including the testing of fecal samples from aquatic areas throughout the United States from April 2006 through December 2007. Although HPAIV was not detected through this surveillance effort we were able to obtain 759 fecal samples that were positive for low pathogenic avian influenza virus (LPAIV). We used 136 DNA sequences obtained from these samples along with samples from a public influenza sequence database for …

Democracia E Biotecnologia: Argumentos Para A Construção De Um Discurso Pautado Na Agência Humana Como Vetor Transformador Da Realidade, Carolina Altoé Velasco

Carolina Altoé Velasco

O artigo objetiva demonstrar que os processos biotecnológico e democrático têm em comum a interferência da agência humana como vetor transformador de suas realidades. Utiliza-se como marco teórico-metodológico as obras de Guillermo O’Donnell e Adela Cortina. Guillermo O’Donnell reconhece o impacto motivado pela tecnologia e globalização na sociedade e a agência humana como fomentadora do processo democrático. Já Adela Cortina considera a pessoa (contemplada por sujeito autônomo e solidário) a medida da democracia e esta como forma de vida. A eleição de Cortina para travar um diálogo com o pensamento de O’Donnell se dá em razão da abordagem feita a …

Halloween 2012 Jack O'Lanterns Trick Or Treat, George Mcnamara

George McNamara

Halloween 2012 makes trick or treating more visual and interactive than in past years.

the download is a ZIP file containing three files.

Print out the (unnumbered) image on as large and nice printer paper as possible - I used glossy 44" wide here in Miami (University of Miami, MillerSchool of Medicine, Calder Library, Biomedical Communications dept - I also made another print on "fabric", also 44" wide to take with me to an HHMI Janelia Farm conference on 'turning images into knowledge' that ends on Oct 31 - might stay up for a second conference, "GFP..." that start Nov …