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Satpdb: A Database Of Structurally Annotated Therapeutic Peptides, Sandeep Singh Oct 2015

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 ...


Constructos Teóricos En Economía Común Informática, Rodrigo Lopez-Pablos Aug 2015

Constructos Teóricos En Economía Común Informática, Rodrigo Lopez-Pablos

Lopez-Pablos, Rodrigo

Repasando elementos de economía comunitaria, solidaría y de la información, se construyen abstracciones teóricas fundamentales en una proto-explicación del rol de la información y el tiempo en la explicación del hecho económico digital y convencional. Infoagregadamente, se sitúa a la emisión informacional como expresión ontológica micro y macroinformática individual y colectiva del ser: el aseguramiento de la infodiversidad civilizatoria generacional; luego, se argumenta sobre la falacia filosófica computacional cognoscitiva detrás de una presunción teórica conceptual equivocada en el estudio y aplicación de lógicas artificiales: su potencial real para la generación de conocimiento híbrido y la creación de conocimiento sin precedentes ...


Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock Apr 2015

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 ...


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 Jan 2015

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 ...


The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft Nov 2014

The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus was devised. The polymerase pac-pb1n enzyme is responsible for the replication of H1N1 virus. Thus, novel inhibitors were developed to ward off the functionality of the enzyme. In this research, cyclic peptides has been chosen to inhibit PAc-PB1n due to its proven stability in reaching the drug target. Thus, computational method for elucidating the molecular interaction between cyclic ...


The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft Nov 2014

The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

No abstract provided.


Biokimia Dan Teknologi Farmasi: Desain Obat Dan Vaksin Dengan Pendekatan Biomedis Molekular, Usman Sumo Friend Tambunan Usft, Arli A. Parikesit Aap Jun 2014

Biokimia Dan Teknologi Farmasi: Desain Obat Dan Vaksin Dengan Pendekatan Biomedis Molekular, Usman Sumo Friend Tambunan Usft, Arli A. Parikesit Aap

Arli A Parikesit

No abstract provided.


Time Series Data For 3b Image Processing, George Mcnamara Jan 2014

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 ...


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 Jan 2014

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.


Comparative Genomics Of Closely Related Salmonella Enterica Serovar Typhi Strains Reveals Genome Dynamics And The Acquisition Of Novel Pathogenic Elements, Kien-Pong Yap Jan 2014

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 ...


Software To Accompany "A Kernel Machine Approach For Differential Expression Analysis Of Mass Spectrometry-Based Metabolomics Data", Debashis Ghosh Jan 2014

Software To Accompany "A Kernel Machine Approach For Differential Expression Analysis Of Mass Spectrometry-Based Metabolomics Data", Debashis Ghosh

Debashis Ghosh

No abstract provided.


Ultra-Deep Pyrosequencing Of Partial Surface Protein Genes From Infectious Salmon Anaemia Virus (Isav) Suggest Novel Mechanisms Involved In Transition To Virulence, Torstein Tengs Dr. Nov 2013

Ultra-Deep Pyrosequencing Of Partial Surface Protein Genes From Infectious Salmon Anaemia Virus (Isav) Suggest Novel Mechanisms Involved In Transition To Virulence, Torstein Tengs Dr.

Dr. Torstein Tengs

Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA ...


Sequence Analysis Of The Genome Of Piscine Orthoreovirus (Prv) Associated With Heart And Skeletal Muscle Inflammation (Hsmi) In Atlantic Salmon (Salmo Salar), Torstein Tengs Dr. Jul 2013

Sequence Analysis Of The Genome Of Piscine Orthoreovirus (Prv) Associated With Heart And Skeletal Muscle Inflammation (Hsmi) In Atlantic Salmon (Salmo Salar), Torstein Tengs Dr.

Dr. Torstein Tengs

Piscine orthoreovirus (PRV) is associated with heart- and skeletal muscle inflammation (HSMI) of farmed Atlantic salmon (Salmo salar). We have performed detailed sequence analysis of the PRV genome with focus on putative encoded proteins, compared with prototype strains from mammalian (MRV T3D)- and avian orthoreoviruses (ARV-138), and aquareovirus (GCRV-873). Amino acid identities were low for most gene segments but detailed sequence analysis showed that many protein motifs or key amino acid residues known to be central to protein function are conserved for most PRV proteins. For M-class proteins this included a proline residue in μ2 which, for MRV, has been ...


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 May 2013

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 ...


A Mobile Genetic Element With Unknown Function Found In Distantly Related Viruses, Torstein Tengs Dr. Apr 2013

A Mobile Genetic Element With Unknown Function Found In Distantly Related Viruses, Torstein Tengs Dr.

Dr. Torstein Tengs

BACKGROUND

The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.

METHODS

We have searched GenBank in order to identify all viral accessions that have s2m(-like) sequence motifs. Rigorous phylogenetic analyses and constrained tree topology testing were also performed in order to investigate the apparently mobile nature of s2m.

RESULTS

The stem-loop s2m structure can be found in four families of + ssRNA viruses; Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae. In all of these virus families, with the ...


Cfp: Handbook Of Research On Technological Applications And Innovation For Economic Development, Deogratias Harorimana Mr Mar 2013

Cfp: Handbook Of Research On Technological Applications And Innovation For Economic Development, Deogratias Harorimana Mr

Dr Deogratias Harorimana

The innovation in the 21st century goes significantly beyond the high-tech picture driven by small or large industry clusters in a specific region-typically Silicon Valley and M4Corridor. The future of innovation will lie within knowledge management and seamless technological applications. These will be supported by planned funding strategies, possibly with clients as drivers of the innovation. This view seems to be supported by the UK government “Technology and Innovation Futures” (2011); the USA government (2011), study into which leading scholars concede that the future innovation and technological applications for economic growth will include products and processes, improvements in areas such ...


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 Jan 2013

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 Jan 2013

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 ...


Online Model Selection Approach Based On Unscented Kalman Filtering, René Schenkendorf, Michael Mangold Jan 2013

Online Model Selection Approach Based On Unscented Kalman Filtering, René Schenkendorf, Michael Mangold

René Schenkendorf

Highly predictive mathematical models are of inestimable value in systems biology. Their application ranges from investigations of basic processes in living organisms up to model based drug design in the field of pharmacology. For the development of reliable models suitable model candidates and related model parameters have to be identified by minimising the difference between the model outcome and available measurement data. Due to the complexity of the analysed processes mathematical models capture only the essential features of interest. This approximate representation, which is usually combined with a vague knowledge of basic processes, leads in many cases to a variety ...


How Can Pacific Island Economies Benefits From The Advent Of Ict’S – Review Of Best Practices In Education, Deogratias Harorimana Sr Oct 2012

How Can Pacific Island Economies Benefits From The Advent Of Ict’S – Review Of Best Practices In Education, Deogratias Harorimana Sr

Dr Deogratias Harorimana

This paper explored implementation and use of information and communication technologies in Fiji, in order to gain insight into recent government initiatives to introduce computers and other ICTs for the community of Fiji. The focus of this paper in that it provided the framework for an in-depth exploration of e-learning centers around the country and the benefits from the advent of ICT’s in e-learning community centers in Fiji. Areas concentrated on are outcome of ICT’s in formal education to students and community as a whole in areas of agriculture, health, environment and infrastructure etc. The research sought understanding ...


Technical Assistance, Knowledge Gatekeeping And Indigenous Knowledge: Re-Thinking The International Development Practice, Deogratias Harorimana Sr Sep 2012

Technical Assistance, Knowledge Gatekeeping And Indigenous Knowledge: Re-Thinking The International Development Practice, Deogratias Harorimana Sr

Dr Deogratias Harorimana

This paper presents results from a multi-disciplinary conceptual analysis of development theory and practice. It reviews issues raised and proposes a shift in the epistemology of possession towards an epistemology of practice which is guided by the following aspects (1) The consideration of the learning culture of parties involved, (2) the ability and willingness for decontextualisation of the knowledge by the source and (3) the ability to embedded it by recipients (embededness ), (4) the importance that is attached to knowledge of the host country as reflected through (5) Similarity in culture, values, understanding of context and knowledge bases; (6) the ...


Mis Mock Questions (Why Mis In Corporate Turbulant Times), Deogratias Harorimana Sr May 2012

Mis Mock Questions (Why Mis In Corporate Turbulant Times), Deogratias Harorimana Sr

Dr Deogratias Harorimana

With corporate strategy becoming more and more dependent on speed,focus, innovation and strategy, what can MIS do? and what should be MIS role ? what is the relationship between Corporate Strategy KPI and MIS? These questions are answered in an MBA Management Information Systems at USP. This programme is delivered across the entire Pacific region through the Graduate School of Business. It is my privilege to post here few questions that students who attended one of the course in Nadi, at Tanoa International Hotel had to answer in one of the Quiz test.


Economic Benefits Analysis Of Mining Industries In Png And Solomon Islands, Deogratias Harorimana Sr Apr 2012

Economic Benefits Analysis Of Mining Industries In Png And Solomon Islands, Deogratias Harorimana Sr

Dr Deogratias Harorimana

This paper discusses mining and mineral operations in the two countries Papua New Guinea and Solomon Islands with regards to its contribution to the overall Gross domestic Product and the economic development of each country.

Our finding shows that mining is an excellent contributor to economic growth and development as in the case of Papua New Guinea.Tax revenue from PNG Mining industries contributions to the PNG fiscal basket remains strong and growing steadily. The mining and minerals tax revenue remains an important contributor to the government fiscal budget over the last 10 years. This has been a strong contributor ...


Understanding Economics Of The Pacific Island Nations: Issues And Cases, Deogratias Harorimana Sr Apr 2012

Understanding Economics Of The Pacific Island Nations: Issues And Cases, Deogratias Harorimana Sr

Dr Deogratias Harorimana

No abstract provided.


Job Creation In The Tuna Industry Of The Solomon Islands- A Tentative Strategic Analysis, Deogratias Harorimana Sr Apr 2012

Job Creation In The Tuna Industry Of The Solomon Islands- A Tentative Strategic Analysis, Deogratias Harorimana Sr

Dr Deogratias Harorimana

The principal objective of this paper is to review the current Tuna Fisheries Policies in the Solomon Islands with a view to proposing strategies that will maximize Job creation while at the same time address the issues that currently exist in this sector. Although the Tuna Industry’s contribution to GDP is quite significant, the Solomon Island Government (SIG) gets little or close to nothing out of it in the form of revenue and Job creation with the majority of vessels being foreign owned and fishing license fees amongst the lowest in the Pacific. SOLTAI which is partly owned by ...


Review Of Solomon Islands’ Policies And Programs To Promote Private Sector Development And Small Business, Deogratias Harorimana Sr Apr 2012

Review Of Solomon Islands’ Policies And Programs To Promote Private Sector Development And Small Business, Deogratias Harorimana Sr

Dr Deogratias Harorimana

Solomon Islands is a nation with vast resources with huge potential to excel economically if proper business atmosphere is provided for both private sector development and small and medium enterprises entrepreneurship. Conducive policies that, not only, a mere statement but is broken down to workable strategies with quantitative expected outcome with a strong mentoring mechanism is very important. Previous governments have continuously ignored the importance of having small business policies until lately when NCRA government came up with a set of policies that strategically addresses the significance of small and medium businesses. However, notwithstanding foreign investment is very important in ...


Using The Case Study Methodology In Teaching, Deogratias Harorimana Mr Jan 2012

Using The Case Study Methodology In Teaching, Deogratias Harorimana Mr

Dr Deogratias Harorimana

This paper reviews the Why, How, to use the Case Study Methods in MBA teaching. The Presentation was prepared for and delivered as part of MBA students induction Programme in the Graduate School of Business.


Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris Jan 2012

Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris

Jeffrey S. Morris

In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational ...


Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do Jan 2012

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple ...


The Evolution Of Cooperation: How Patience Matters, Atin Basu Choudhary, Raja Mazumder, Vahan Simoyan Jan 2012

The Evolution Of Cooperation: How Patience Matters, Atin Basu Choudhary, Raja Mazumder, Vahan Simoyan

Atin Basu Choudhary

The evolution of cooperation has been the focus of much attention from evolutionary game theorists. Of course, conventional game theorists often cite the Folk Theorem to suggest that cooperation is very likely as long as people are patient. However, experimental and real world evidence of the Folk Theorem has been sparse. We investigate whether cooperation can evolve endogenously in a population where people have different patience levels. We motivate our model by asking the following question: why don’t biologists cooperate with each other by contributing to biological databases? We apply the Folk theorem from conventional game theory and assume ...