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A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics Nature Precedings
I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7052/version/1
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A new outlook towards kidney injuries Nature Precedings
Mahesh Satwekar; Abhijeet Satwekar.
Acute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate...
Tipo: Manuscript Palavras-chave: Biotechnology; Immunology; Microbiology.
Ano: 2012 URL: http://precedings.nature.com/documents/7021/version/1
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A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements- (v.4) Nature Precedings
Valentin Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional “wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6231/version/4
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A novel strategy for the targeted analysis of protein and peptide metabolites Nature Precedings
Nicholas A. Williamson; Charles Reilly; Chor-Teck Tan; Sri-Harsha Ramarathinam; Alun Jones; Christie L. Hunter; Francis R. Rooney; Anthony W. Purcell.
The detection and quantitation of exogenously administered biological macromolecules (e.g. vaccines, peptide and protein therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related compounds. We describe a method that incorporates stable isotope labeling of the compound of interest allowing the selective screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low molecular weight fragment ions produced during MS/MS that distinguish isotopically labelled material from related endogenous compounds. All isotopically labelled substances can be selected using this scanning technique for further analysis whilst other...
Tipo: Manuscript Palavras-chave: Biotechnology; Immunology; Pharmacology.
Ano: 2009 URL: http://precedings.nature.com/documents/3812/version/1
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A theory for the tissue specificity of BRCA1/2 related and other hereditary cancers Nature Precedings
Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high and seem so selective that many mutation carriers choose to have prophylactic surgery. There has been much conjecture to explain such apparently striking tissue specificity. All these suggestions share the assumption that some disabled function of normal tumor suppressor genes leads to a tissue specific cancer response. Here the idea is proposed and tested that major determinants of where BRCA1/2 hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic inflammation or the carcinogen. The target tissue may have receptors for the pathogen, become selectively exposed to an inflammatory process...
Tipo: Manuscript Palavras-chave: Cancer; Genetics & Genomics; Immunology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4881/version/1
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A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains Nature Precedings
Claudiu I. Bandea.
The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3888/version/1
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Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin Nature Precedings
Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The evolution of H5N1 has attracted significant interest 1-4 due to linkages with avian 5,6 and human infections 7,8. The basic tenets of influenza genetics 9 attribute genetic drift to replication errors caused by a polymerase complex that lacks a proof reading function. However, recent analysis 10 of swine influenza genes identifies regions copied with absolute fidelity for more than 25 years. In addition, polymorphism tracing of clade 2.2 H5N1 single nucleotide polymorphisms identify concurrent acquisition 11 of the same polymorphism onto multiple genetic backgrounds in widely dispersed geographical locations. Here we show the aggregation of regional clade 2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa onto a human Nigerian H5N1...
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/743/version/1
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Allicin from garlic suppresses TNF-α and augments IFN-γ expressions in monocyte cultures from patients with Vaginitis Nature Precedings
Najmul Islam; Jawed Iqbal; Nazarul Hasan; Zeeshan Fatima; Hamida Thakur; Nazia Hasan; Abbas Ali Mahdi; Tamkin Khan; Farzana Bano; Irfan Ahmad Ansari.
Objective: We tried to explore beneficial effects of allicin- a natural antioxidant from garlic in the possible management of vaginitis. 
Methods: Peripheral blood mononuclear cells (PBMC’s) were isolated from blood of patients having vaginal infections as well as normal healthy subjects as per our published protocol. Monocytes (MN’s) from above PBMC’s were adhered, rested overnight and cultured without or with varying doses of allicin (0-500 ng/ml). Some cultures received SN50 and SN50M (100 ug/ml). After 24 hrs cultures, the cells were harvested and the supernatants subjected to secreted TNF-α and sIFN-γ assays by ELISA. Treated/untreated harvested cells were subjected to glutathione...
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1560/version/1
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Alzheimer's disease is TH17 related autoimmune disease against misfoded beta amyloid Nature Precedings
Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5934/version/1
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Alzheimer's disease is TH17 related autoimmune disease against misfolded beta amyloid Nature Precedings
Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5934/version/2
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Alzheimer's disease is TH17 related autoimmune disease against misfolded beta amyloid Nature Precedings
Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5934/version/3
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An Ontology for Designing Models of Epidemics Nature Precedings
Geoffrey Frank; William Wheaton; Vesselina Bakalov; Phillip Cooley; Diane Wagener.
Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics.
An ontology has been developed for MIDAS to support the collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious disease ontology) that define the scope of its models and supporting documentation.
The ontology is used to aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the MIDAS repository...
Tipo: Presentation Palavras-chave: Immunology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3555/version/1
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Angiogenesis in Chronic Obstructive Pulmonary Disease Nature Precedings
Alessandro Matarese; Gaetano Santulli.
Angiogenesis is a crucial component of lung pathophysiology, not only in cancer but also in other disorders, such as chronic obstructive pulmonary disease (COPD). In COPD angiogenesis is definitely able to control and orchestrate the progression of airway remodeling. Herein, we provide several remarkable translational aspects of angiogenesis in COPD, exploring both basic and clinical research in this field. Indeed, we present a number of pro- and anti-angiogenic factors, which can be also used as potential biomarkers to monitor disease progression. 

This pre-print has subsequently been published at http://www.unisa.it/uploads/7100/06.pdf
Tipo: Manuscript Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7112/version/1
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Antibodies targeting Cancer stem cells, A novel pattern in Immunotherapy Nature Precedings
Sarfaraz Alam.
Antibody targeting of cancer is showing clinical and commercial success after deep research and development over the last 3 decades. They have the great potential to deliver long-term cures but a shift in thinking towards a cancer stem cell (CSC) model for tumour development is certain to have an impact on how antibodies are selected and developed, the targets they bind to and the drugs used in combination with them. CSCs have been identified from many human tumours and share many of the characteristics of normal stem cells such as the ability to renew and metabolically or physically protect themselves from xenobiotic and DNA damage. Targeting CSCs could be a strategy to improve the outcome of cancer therapy. Monoclonal antibodies are clinically and...
Tipo: Presentation Palavras-chave: Cancer; Immunology; Molecular Cell Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5428/version/1
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Antibody responses to a Cryptosporidium parvum rCP15/60 vaccine Nature Precedings
Alexandra J. Burton; Daryl V. Nydam; Gary Jones; Jennifer Zambriski; Thomas C. Linden; Graham Cox; Randy Davis; Alicia Brown; Dwight D. Bowman.
Cryptosporidium parvum is a zoonotic apicomplexa-protozoan pathogen that causes gastroenteritis and diarrhoea in mammals worldwide. The organism is transmitted by ingestion of oocysts, which are shed in faeces, and completes its lifecycle in a single host.^1^ C. parvum is ubiquitous on dairy operations worldwide and is one of the leading causes of diarrhoea in calves on these farms.^2,3^ Here, for the first time, we describe the antibody response in a large group of cows to a recombinant C. parvum oocyst surface protein (rCP15/60) vaccine and the antibody response in calves fed rCP15/60-immune colostrum produced by these vaccinated cows. Results of recent genotype surveys indicate that calves are the only major reservoir for C. parvum infections in...
Tipo: Manuscript Palavras-chave: Immunology.
Ano: 2009 URL: http://precedings.nature.com/documents/3988/version/1
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Anti-HIV therapy: pipeline approaches and future directions Nature Precedings
Lavkush Dwivedi; Mansi Shrivastava.
Human immunodeficiency virus (HIV), with about 30 million deaths and double infections (in developing countries), is an open challenge today for global scientists. Developing safe and effective measurements against it has become the prime need of hour. Though, putting it at health priority, various efforts like chemotherapy, vaccines and others are attempted globally over last decade. Consequently, highly active antiretroviral therapy was introduced but fails to completely block the viral replication due to drug resistance and various other severe side effects. The antigenic variability and lack of appropriate experimental models is the major obstacle in the development of an ever effective treatment against HIV. However, to overcome the present hurdles...
Tipo: Manuscript Palavras-chave: Immunology.
Ano: 2011 URL: http://precedings.nature.com/documents/5540/version/1
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Artificial Antigen Presenting Cells With Preclustered anti-CD28/-CD3/-LFA-1 Monoclonal Antibodies Are Highly Effective To Induce The Ex-Vivo Expansion Of Functional Human Antitumor T Cells Nature Precedings
Roberta Zappasodi; Massimo Di Nicola; Carmelo Carlo-Stella; Roberta Mortarini; Alessandra Molla; Claudia Vegetti; Lorena Passoni; Salvatore Albani; Andrea Anichini; Alessandro M. Gianni.
Effective adoptive T cell therapy requires the _ex vivo_ generation of functional T lymphocytes with a long lifespan _in vivo_. We evaluated _in vitro_ T cell expansion by artificial antigen presenting cells (aAPC) generated with activating (human anti-CD3), co-stimulating (human anti-CD28) and adhesion (human anti-LFA-1) monoclonal antibodies pre-clustered in microdomains (MDs) held by a liposome scaffold. The co-localization of T cell ligands in MDs and the targeting of an adhesion protein, increasing the efficiency of immunological synapse formations, represent the novelties of our system. These aAPCs allowed increased expansion of polyclonal CD4^+^ and CD8^+^ T cells and of tumor antigen-specific CD8^+^ T cells compared to anti-CD28- and...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2007 URL: http://precedings.nature.com/documents/1250/version/1
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Bacterial Capnine Blocks Transcription of Human Antimicrobial Peptides Nature Precedings
Trevor G. Marshall.
The US CDC believes that 65% of all infections in developed countries may be caused by pathogens in biofilms. Electron Microscopy has shown that these bacterial communities can evade phagocytosis, and persist in the cytoplasm of monocytes, macrophages, lymphocytes and neutrophils. Three decades ago, Wirostko _et al._ found such intraphagocytic communities in Crohn’s disease, Juvenile Rheumatoid Arthritis and Sarcoidosis. However, the mechanism(s) by which such persistent bacteria could evade the immune system have remained elusive. Recently, 16S RNA from species of gliding bacteria never thought to be able to survive _in vivo_, have been found in surgically removed biofilms. This study set out to identify whether the genomes of these gliding...
Tipo: Poster Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/164/version/1
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BBSRC Data Sharing Policy Nature Precedings
Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6015/version/1
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Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates Nature Precedings
Rodrick Wallace.
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a 'biological renormalization' perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Tipo: Manuscript Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6849/version/1
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