Biovista Vizit: Overview and Quick Start Guide
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Vizit is a visual search engine that helps scientists explore connections between biomedical concepts, such as Genes, Diseases, Pathways, Organisms, etc. as they appear on PubMed. http://www.biovista.com/vizit/
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PubMed Basics
Pubmed is a free database of over 23 million biomedical research references and abstracts provided by the National Library of Medicine. It covers fields of medicine, nursing, dentistry, and healthcare. While some full text articles are available directly, Pubmed also links out to full text articles available through institutional subscriptions. Key features of Pubmed include searching by PMID number, publication type, MeSH terms, and filters to limit searches. Tips for effective searching include using Boolean operators and filters to refine results, as well as saving relevant references for later use.
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This document describes an encyclopedia called E-BABE that contains over 5,000 bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. E-BABE allows searching by drug name, chemical formula, or structure to find relevant methods. It includes information from published studies and pharmacopeias to aid in method development and validation for bioavailability and bioequivalence studies. E-BABE is intended to help pharmaceutical companies and testing laboratories select appropriate analytical methods.
Utet gdu
The document provides instructions for using the GDU (Grande Dizionario dell'Uso) dictionary. It outlines the two search modes: simplified and full. The full mode allows the user to access additional search options through the menu, including statistics about search terms, earliest sources of words, and saving custom dictionaries. It warns that the USB drive containing the database must be connected for the system to function properly.
Abstract template
The document describes E-BABE, an encyclopedia of bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. It contains over 5,000 thoroughly curated methods from literature and pharmacopeias. Each method includes details needed for development/validation, like chemical structure, analytical conditions, and pharmacokinetic parameters. Users can search by drug name, chemical formula, or structure to select appropriate quality control and bioequivalence study methods. E-BABE aims to support the pharmaceutical industry and testing laboratories in selecting bioanalytical methods.
Abstract template
The document describes E-BABE, an encyclopedia of bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. It contains over 5,000 thoroughly curated methods from literature and pharmacopeias. Each method includes details needed for development/validation, like analytical parameters, sample preparation, and pharmacokinetic values. Users can search by drug name, chemical formula, or structure to select appropriate quality control and bioanalytical methods. E-BABE aims to support the pharmaceutical industry and testing laboratories in conducting bioavailability and bioequivalence studies.
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PubMed Basics
Pubmed is a free database of over 23 million biomedical research references and abstracts provided by the National Library of Medicine. It covers fields of medicine, nursing, dentistry, and healthcare. While some full text articles are available directly, Pubmed also links out to full text articles available through institutional subscriptions. Key features of Pubmed include searching by PMID number, publication type, MeSH terms, and filters to limit searches. Tips for effective searching include using Boolean operators and filters to refine results, as well as saving relevant references for later use.
Abstract Template
This document describes an encyclopedia called E-BABE that contains over 5,000 bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. E-BABE allows searching by drug name, chemical formula, or structure to find relevant methods. It includes information from published studies and pharmacopeias to aid in method development and validation for bioavailability and bioequivalence studies. E-BABE is intended to help pharmaceutical companies and testing laboratories select appropriate analytical methods.
Utet gdu
The document provides instructions for using the GDU (Grande Dizionario dell'Uso) dictionary. It outlines the two search modes: simplified and full. The full mode allows the user to access additional search options through the menu, including statistics about search terms, earliest sources of words, and saving custom dictionaries. It warns that the USB drive containing the database must be connected for the system to function properly.
Abstract template
The document describes E-BABE, an encyclopedia of bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. It contains over 5,000 thoroughly curated methods from literature and pharmacopeias. Each method includes details needed for development/validation, like chemical structure, analytical conditions, and pharmacokinetic parameters. Users can search by drug name, chemical formula, or structure to select appropriate quality control and bioequivalence study methods. E-BABE aims to support the pharmaceutical industry and testing laboratories in selecting bioanalytical methods.
Abstract template
The document describes E-BABE, an encyclopedia of bioanalytical methods for studying the bioavailability and bioequivalence of pharmaceuticals. It contains over 5,000 thoroughly curated methods from literature and pharmacopeias. Each method includes details needed for development/validation, like analytical parameters, sample preparation, and pharmacokinetic values. Users can search by drug name, chemical formula, or structure to select appropriate quality control and bioanalytical methods. E-BABE aims to support the pharmaceutical industry and testing laboratories in conducting bioavailability and bioequivalence studies.
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This document is a literature review on the contribution of iron and oxidative stress to cell death. It discusses how iron is essential but can also catalyze oxidative stress through Fenton chemistry reactions. Reactive oxygen species are produced endogenously and can cause damage. Excess iron accumulation leads to oxidative stress and is implicated in diseases. The review examines how iron and reactive oxygen species induce different forms of cell death including apoptosis, necrosis, autophagy and the newly discovered iron-dependent form called ferroptosis. Therapeutic strategies aim to reduce oxidative stress and iron levels.
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This document summarizes various antigen-antibody reactions and diagnostic tests. It describes complement fixation tests, which use complement to detect antigen-antibody complexes. It also discusses neutralization tests, opsonization tests, radioimmunoassays, enzyme immunoassays, chemiluminescence immunoassays, Western blots, immunochromatographic tests, immunofluorescence, and flow cytometry. The types of ELISA are described as direct, indirect, competitive, sandwich, and capture. The document provides details on the procedures, components, applications, and advantages/disadvantages of these various antigen-antibody reaction diagnostic methods.
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Loop Control
PURPOSE
The purpose of this lab is to introduce you to HCS12 C and assembly programming using loop control. This is
a two-week project.
EXPERIMENT
(1) (50%) Using CodeWarrior to create a new project that uses C language. During the project setup, most
steps are similar to when you created an assembly project except the following two extra steps:
For “Rapid Application Development Option”, select None and press “Next>”.
Select “ANSI startup code”, “Small” memory model, and “None” for floating point format. Press
“Next>”.
Write a simple C program that declares a character array of 32 elements and uses a for loop, with an
ascending loop index variable, to write a constant value of -1 to every array element. The program also
declares an integer array of 32 elements and uses a while loop with a descending loop index variable to
write a constant value of -1 to every array element. At the end, the program should get into an infinite loop
using a while loop. Make sure both arrays and both loop indices are all declared as global variables. Using
CodeWarrior debug window to find out and record the following information inside the listing file
(generated by the C compiler).
The assembly code segment that corresponds to the for loop. Put comments on the code segment
after studying it. For each assembly instruction, also record its starting address and its machine
code.
Repeat the above process for the while loop.
Turn in (only) the listing file that contains the above information
Hint: From time to time, it helps to study the assembly listing file produced by the C compiler. In order for
CodeWarrior C compiler to produce assembly listing, do the following:
1. Get the “Standard Setting” dialog box by using Alt F7 (alternatively, clicking the corresponding icon, or
select Menu “Edit” and then SubMenu “Standard Setting”).
2. Select “Compiler for HC12” at the left hand side of the box and click on the “Options” button on the
right hand side. An “HC12 Compiler Option Settings” dialog box shows up.
3. Select the “Output” tab and put a check mark on “Generate Listing File”. Click the “OK” button.
4. Make the project.
5. Use Windows Explorer to reach the project folder. Inside the “bin” folder, there are multiple files with
their file types as “MASM Listing”. Double click the file “main” to open the file with a text editor.
(2) (50%) Write an assembly program that calculates the (two-byte-long) sum of N unsigned two-byte values in
a memory area. It also turns on LED1 (refer to Lab 1, part 2) if and only if the sum is more than a value,
THRESHOLD. In the data section, use assembler directives ds.b or ds.w to reserve the following:
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Cover.docxA Brief Overview of Bovine Respirato.docx
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A Brief Overview of Bovine Respiratory Disease Sequencing Study
Student Name
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Ahmed_Exp22_Word_Ch04_Cumulative_Cattle.docx
Name 4
Many large-scale genomics projects in progress today relate to sequencing human genomes, and finding relationships between certain sequences and disease, in addition to creating large storehouses of genetic data for later research. Most goals of genomic projects relate to strategies for early detection, prevention, and cures for diseases. However, a lesser-known area of genomic research is that of farm animals, particularly those that are integral to the national food supply. By understanding many of the same correlations and sequencing patterns found in human genomic research, farm animal genomics can fosteroften fosters practices that lead to increased livestock health and productivity, and the bioengineering of new animal-related technologies. Additionally, research related to farm-animal genetics proves valuable for humans, as farm animals are often models for physiological and pathological studies. Comment by Exploring Series: This report needs a cover page. It is also incorrectly formatted as a research paper.
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CEG 3310/5310 Laboratory 3
Loop Control
PURPOSE
The purpose of this lab is to introduce you to HCS12 C and assembly programming using loop control. This is
a two-week project.
EXPERIMENT
(1) (50%) Using CodeWarrior to create a new project that uses C language. During the project setup, most
steps are similar to when you created an assembly project except the following two extra steps:
For “Rapid Application Development Option”, select None and press “Next>”.
Select “ANSI startup code”, “Small” memory model, and “None” for floating point format. Press
“Next>”.
Write a simple C program that declares a character array of 32 elements and uses a for loop, with an
ascending loop index variable, to write a constant value of -1 to every array element. The program also
declares an integer array of 32 elements and uses a while loop with a descending loop index variable to
write a constant value of -1 to every array element. At the end, the program should get into an infinite loop
using a while loop. Make sure both arrays and both loop indices are all declared as global variables. Using
CodeWarrior debug window to find out and record the following information inside the listing file
(generated by the C compiler).
The assembly code segment that corresponds to the for loop. Put comments on the code segment
after studying it. For each assembly instruction, also record its starting address and its machine
code.
Repeat the above process for the while loop.
Turn in (only) the listing file that contains the above information
Hint: From time to time, it helps to study the assembly listing file produced by the C compiler. In order for
CodeWarrior C compiler to produce assembly listing, do the following:
1. Get the “Standard Setting” dialog box by using Alt F7 (alternatively, clicking the corresponding icon, or
select Menu “Edit” and then SubMenu “Standard Setting”).
2. Select “Compiler for HC12” at the left hand side of the box and click on the “Options” button on the
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4. Make the project.
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(2) (50%) Write an assembly program that calculates the (two-byte-long) sum of N unsigned two-byte values in
a memory area. It also turns on LED1 (refer to Lab 1, part 2) if and only if the sum is more than a value,
THRESHOLD. In the data section, use assembler directives ds.b or ds.w to reserve the following:
a two-byte space for THRESHO.
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The document discusses the launch of a new online platform for the medical journal Anesthesiology. The goals are to make content easier to find, read, and keep up with areas of interest automatically. Key features include Google-like searching, enhanced displays of articles and figures, links to related content, topic collections, alerts and RSS feeds to track areas of interest, and mobile optimization. The changes aim to provide a more personalized experience for readers to find and access relevant information.
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Cover.docxA Brief Overview of Bovine Respirato.docx
Cover.docx
A Brief Overview of Bovine Respiratory Disease Sequencing Study
Student Name
11/23/2024
Ahmed_Exp22_Word_Ch04_Cumulative_Cattle.docx
Name 4
Many large-scale genomics projects in progress today relate to sequencing human genomes, and finding relationships between certain sequences and disease, in addition to creating large storehouses of genetic data for later research. Most goals of genomic projects relate to strategies for early detection, prevention, and cures for diseases. However, a lesser-known area of genomic research is that of farm animals, particularly those that are integral to the national food supply. By understanding many of the same correlations and sequencing patterns found in human genomic research, farm animal genomics can fosteroften fosters practices that lead to increased livestock health and productivity, and the bioengineering of new animal-related technologies. Additionally, research related to farm-animal genetics proves valuable for humans, as farm animals are often models for physiological and pathological studies. Comment by Exploring Series: This report needs a cover page. It is also incorrectly formatted as a research paper.
A developing area of livestock genomics is that of pathogen sequencing. Specifically, the Agricultural Research Service (ARS) branch of the United States Department of Agriculture (USDA) is conducting a genetics study to sequence the respiratory microbiome and virome associated with Bovine Respiratory Disease (BRD) in beef cattle. This disease is one of the most costly and prevalent diseases within the cattle industry, causing severe respiratory distress that usually results in death. As such, BRD results in lost revenue for cattle farmers each year. To combat this, in 2021 the ARS began following specific populations of beef cattle in the US and Ireland to study the microbiome and virome profiles at various points of time during the animal’s life cycle. Specifically, profiles are evaluated in calves prior to weaning and again after entering the feedlot, at which time the animal is most likely to contract BRD. This study will continue through 2022. as funding permits.
Objectives of the study are three-fold; to gather information about the prevalence of BRD, develop scientific methods to identify the pathogenic agents that cause the disease, and to understand the dynamics of secondary infection in cattle that contract the disease a second time, provided the first infection is survived. These objectives will help researchers uncover and understand any connections between microbiome profiles of cattle that develop BRD and those that do not. Consequently, this study has the potential for large positive impacts to the beef cattle industry. As detailed in Table 1, several research activities are ongoing, contributing to the understanding of pathogen sequencing in cattle.
Research Activity
.
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Rob Camp goes through various online tools and search engines which enable
patients to search for clinical trials. Rob’s background includes serving as
Executive Director of the EATG (European AIDS Treatment Group), the creation
of an HIV organisation in Barcelona, the creation of national groups in Spain
and other countries (organising seminars on how to create organisations in EU
Eastern States, Southern States), leading projects supported by the European
Commission department for Public Health (DG SANCO), working on funding for
NGOs. Rob is currently working half time in the US as liaison between patient
organisations and the FDA, and spends the rest of his time in Europe. Rob
speaks English and Spanish
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Mini manual-database-instruction-sanders
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Mark2Cure is developing a crowdsourcing platform to engage large groups of people, including microtask workers and volunteers, in annotating biomedical literature. Recent studies show non-experts can generate high-quality annotations. The platform will direct workers to complete "quests" assigned by scientific leaders to extract targeted knowledge. An initial prototype uses Amazon Mechanical Turk to evaluate disease mention annotation on PubMed abstracts, achieving expert-level precision and outperforming natural language processing tools. The goal is to structure all published biomedical knowledge with human-level accuracy and completeness on the same day as publication.
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Biovista Vizit: Overview and Quick Start Guide
- 1. Vizit Quick Start Guide www.biovista.com/vizit © 2016 Biovista Inc. All rights reserved.
- 2. © 2016 Biovista Inc. All rights reserved. 2 Vizit helps you find connections between entities such as genes, pathways, diseases, drugs and more. Vizit displays these connection in a graph. You can select a connection between any 2 concepts and ask Vizit to show you all the PubMed publications that mention these 2 concepts. A Vizit query (called “Explore”) works with 2 parameters: parameter 1 is a specific concept such as the BRCA1 gene; parameter 2 is a class of concepts such as PATHWAYS. In this example, the Explore query means: find me all the pathways associated with BRCA1. Vizit can help you explore and understand an area of research you are working in by helping you find non-obvious connections between genes, pathways, disease, drugs and other biologically relevant entities and processes in which you may be interested. With PubMed you need to know the specific genes, pathways an so on that you are interested in in order to find relevant publications. With Vizit you can (a) review connections between genes, pathways and more (b) pick interesting connections you were not aware of and (c) then access the relevant publications. Vizit helps your discovery work by letting you generate scientific hypotheses based on the existing scientific bibliography. Vizit Basic Concepts: How it helps you – How it works 1 2 3 4 Pathway Link to PubMed publications Gene A VIZIT Graph
- 3. © 2016 Biovista Inc. All rights reserved. 3 Bring up the “Add a Term” panel. 1.Click on the Add icon. Vizit will display the “Add a Term” panel. 1.Click on “Gene, Pathway, Drug etc.” and select an option. 2.Start typing in your search term. Vizit will auto-complete as you type. 3.Select your search term when you see it in the auto-complete suggestions. Vizit will display your search term in the “whiteboard”. 4.Click on your search term in the whiteboard to start your exploration, or repeat these steps to add more terms to the whiteboard. Starting your Query – Add a search term (keyword) to your graph 1 2 The Add icon The Add a Term panel
- 4. © 2016 Biovista Inc. All rights reserved. 4 EXPLORE What it does: EXPLORE lets you find genes, pathways, diseases etc. that are related to your selected node (i.e. a specific gene like BRCA1 or pathway like APOPTOSIS). For example it lets you answer a question such as: In which pathways is BRCA1 involved? How it works: Click on a node (circle) in a Vizit graph. Select “Explore” from the pop-up menu. CONNECT What it does: CONNECT lets you see if your selected node is related to any of the genes, pathways, diseases etc. that are displayed in your current Vizit graph. How it works: Click on a node (circle) in a Vizit graph. Select “Connect” from the pop-up menu, then select one of Genes, Pathways, Diseases etc. in the pop-up menu. BRIDGE What it does: BRIDGE lets you find any genes, pathways, diseases etc. that are common to two selected nodes. For example it lets you answer a question such as: What genes are involved in both the “CELL CYCLE” and the “DNA REPAIR” pathways? How it works: Select any two nodes in your Vizit graph. Click on first, then Ctrl- (Cmd- in Mac) Click on the second. Click on any of the selected nodes. Select “Bridge” from the pop-up menu, then select one of Genes, Pathways, Diseases etc. in the pop-up menu. Main VIZIT Commands 1 2 3 Click on a node to select it. A selected node is greyed in. Then select one of the commands.
- 5. © 2016 Biovista Inc. All rights reserved. 5 Click on the bibliography icon to access PubMed publications mentioning the 2 linked nodes (gene BCL2 and pathway APOPTOSIS). Vizit will display the titles of PubMed articles. Click on the PubMed ID to access the article on PubMed. Accessing Scientific Publications 1 2 The Bibliography icon
- 6. © 2016 Biovista Inc. All rights reserved. 6 You can share your Vizit graphs: •if you are member of a research team and want to share your findings with your colleagues or ask them for their ideas. •if you want to contribute or comment on an idea regarding a research problem discussed at a blog, conference or other public forum. Share your Graphs 1 2 Click on the Share icon. Copy-paste the graph URL in an email or Select any of the social media options to share your graph with the public. The Share icon The graph URL Vizit graphs you share are “live” which means that if the recipient of your email clicks on the URL not only will they see your graph but they will also be able to work on it freely.
- 7. © 2016 Biovista Inc. All rights reserved. For more Information 1 2 Be our guest: Take the Vizit tours. Send us an email: info@biovista.com