This document proposes InterPlanetary Wayback (IPWB), a system to archive web pages using the InterPlanetary File System (IPFS) in a peer-to-peer manner. It extracts HTTP headers and payloads from WARC files and stores them as objects in IPFS, generating corresponding CDXJ indexes. Pages can then be replayed by dereferencing the CDXJ locators through IPFS. While a proof of concept, IPWB has potential to solve archival permanence through distributed storage, though performance requires further optimization for large-scale use.
InterPlanetary Wayback: The Next Step Towards Decentralized Web ArchivingSawood Alam
InterPlanetary Wayback (IPWB) facilitates permanence and collaboration in web archives by disseminating the contents of WARC files into the InterPlanetary File System (IPFS) network. IPFS is a peer-to-peer content-addressable file system that inherently allows deduplication and facilitates opt-in replication. IPWB splits the header and payload of WARC response records before disseminating into IPFS to leverage the deduplication, builds a CDXJ index with references to the IPFS hashes returns, and combines the headers and payload from IPFS at the time of replay. We also explore the possibility of an index-free, fully decentralized collaborative web archiving system as the next step.
Introducing Web Archiving and WSDL Research GroupSawood Alam
My talk to introduce Web Archiving and the Web Science and Digital Libraries Research Group to some invited students from India for a summer workshop in Old Dominion University, Norfolk, VA
Profiling Web Archival Voids for Memento RoutingSawood Alam
Slides of the paper presentation, "Profiling Web Archival Voids for Memento Routing", for JCDL 2021.
Authors: Sawood Alam, Michele C. Weigle, Michael L. Nelson
Preprint: https://arxiv.org/abs/2108.03311
Recording: https://youtu.be/ImJWkndNoS8
Have you ever been stuck downloading a module you already have? Have you ever been stuck without internet, unable to npm install when all the modules you need are stored in your coworkers' computers in the same LAN? Well no more! With the IPFS companion for npm, you get (a) distributed discovery: install modules seamlessly from any other computer you can reach; (b) cryptographic versioning: never install the same version twice; (c) free deduplication: don't download or store the same things multiple times.
npm-over-ipfs uses IPFS (the InterPlanetary Filesystem), a new file distribution protocol. IPFS is like Git meets Bittorrent; it is perfect for Node.js modules, it enables devs to have local caches, work offline or work in LANs, and use modules present in nearby machines.
MementoMap Framework for Flexible and Adaptive Web Archive ProfilingSawood Alam
In this work we propose MementoMap, a flexible and adaptive framework to efficiently summarize holdings of a web archive. We described a simple, yet extensible, file format suitable for MementoMap. We used the complete index of the arquivo.pt comprising 5B mementos (archived web pages/files) to understand the nature and shape of its holdings. We generated MementoMaps with varying amount of detail from its HTML pages that have an HTTP status code of 200 OK. Additionally, we designed a single-pass, memory-efficient, and parallelization-friendly algorithm to compact a large MementoMap into a small one and an in-file binary search method for efficient lookup. We analyzed more than three years of MemGator (a Memento aggregator) logs to understand the response behavior of 14 public web archives. We evaluated MementoMaps by measuring their Accuracy using 3.3M unique URIs from MemGator logs. We found that a MementoMap of less than 1.5% Relative Cost (as compared to the comprehensive listing of all the unique original URIs) can correctly identify the presence or absence of 60% of the lookup URIs in the corresponding archive while maintaining 100% Recall (i.e., zero false negatives).
Video and slides synchronized, mp3 and slide download available at URL http://bit.ly/1RJcfss.
Juan Batiz-Benet makes a short intro of IPFS (the InterPlanetary File System), a new hypermedia distribution protocol, addressed by content and identities. He also discusses the IPLD data model and example data structures (unixfs, keychain, post). Filmed at qconsf.com.
Juan Batiz-Benet is an Independent Scientist.
InterPlanetary Wayback: The Next Step Towards Decentralized Web ArchivingSawood Alam
InterPlanetary Wayback (IPWB) facilitates permanence and collaboration in web archives by disseminating the contents of WARC files into the InterPlanetary File System (IPFS) network. IPFS is a peer-to-peer content-addressable file system that inherently allows deduplication and facilitates opt-in replication. IPWB splits the header and payload of WARC response records before disseminating into IPFS to leverage the deduplication, builds a CDXJ index with references to the IPFS hashes returns, and combines the headers and payload from IPFS at the time of replay. We also explore the possibility of an index-free, fully decentralized collaborative web archiving system as the next step.
Introducing Web Archiving and WSDL Research GroupSawood Alam
My talk to introduce Web Archiving and the Web Science and Digital Libraries Research Group to some invited students from India for a summer workshop in Old Dominion University, Norfolk, VA
Profiling Web Archival Voids for Memento RoutingSawood Alam
Slides of the paper presentation, "Profiling Web Archival Voids for Memento Routing", for JCDL 2021.
Authors: Sawood Alam, Michele C. Weigle, Michael L. Nelson
Preprint: https://arxiv.org/abs/2108.03311
Recording: https://youtu.be/ImJWkndNoS8
Have you ever been stuck downloading a module you already have? Have you ever been stuck without internet, unable to npm install when all the modules you need are stored in your coworkers' computers in the same LAN? Well no more! With the IPFS companion for npm, you get (a) distributed discovery: install modules seamlessly from any other computer you can reach; (b) cryptographic versioning: never install the same version twice; (c) free deduplication: don't download or store the same things multiple times.
npm-over-ipfs uses IPFS (the InterPlanetary Filesystem), a new file distribution protocol. IPFS is like Git meets Bittorrent; it is perfect for Node.js modules, it enables devs to have local caches, work offline or work in LANs, and use modules present in nearby machines.
MementoMap Framework for Flexible and Adaptive Web Archive ProfilingSawood Alam
In this work we propose MementoMap, a flexible and adaptive framework to efficiently summarize holdings of a web archive. We described a simple, yet extensible, file format suitable for MementoMap. We used the complete index of the arquivo.pt comprising 5B mementos (archived web pages/files) to understand the nature and shape of its holdings. We generated MementoMaps with varying amount of detail from its HTML pages that have an HTTP status code of 200 OK. Additionally, we designed a single-pass, memory-efficient, and parallelization-friendly algorithm to compact a large MementoMap into a small one and an in-file binary search method for efficient lookup. We analyzed more than three years of MemGator (a Memento aggregator) logs to understand the response behavior of 14 public web archives. We evaluated MementoMaps by measuring their Accuracy using 3.3M unique URIs from MemGator logs. We found that a MementoMap of less than 1.5% Relative Cost (as compared to the comprehensive listing of all the unique original URIs) can correctly identify the presence or absence of 60% of the lookup URIs in the corresponding archive while maintaining 100% Recall (i.e., zero false negatives).
Video and slides synchronized, mp3 and slide download available at URL http://bit.ly/1RJcfss.
Juan Batiz-Benet makes a short intro of IPFS (the InterPlanetary File System), a new hypermedia distribution protocol, addressed by content and identities. He also discusses the IPLD data model and example data structures (unixfs, keychain, post). Filmed at qconsf.com.
Juan Batiz-Benet is an Independent Scientist.
Supporting Web Archiving via Web PackagingSawood Alam
We describe challenges related to web archiving, replaying archived web resources, and verifying their authenticity. We show that Web Packaging has significant potential to help address these challenges and identify areas in which changes are needed in order to fully realize that potential.
Position Paper: https://arxiv.org/abs/1906.07104
Presented in the Internet Architecture Board's ESCAPE 2019 Workshop (Exploring Synergy between Content Aggregation and the Publisher Ecosystem)
https://www.iab.org/activities/workshops/escape-workshop/
Combining Heritrix and PhantomJS for Better Crawling of Pages with JavascriptMichael Nelson
Justin F. Brunelle
Michele C. Weigle
Michael L. Nelson
Web Science and Digital Libraries Research Group
Old Dominion University
@WebSciDL
IIPC 2016
Reykjavik, Iceland, April 11, 2016
Archive Assisted Archival Fixity Verification FrameworkSawood Alam
The number of public and private web archives has increased, and we implicitly trust content delivered by these archives. Fixity is checked to ensure an archived resource has remained unaltered since the time it was captured. Some web archives do not allow users to access fixity information and, more importantly, even if fixity information is available, it is provided by the same archive from which the archived resources are requested. In this research, we propose two approaches, namely Atomic and Block, to establish and check fixity of archived resources.
Readying Web Archives to Consume and Leverage Web BundlesSawood Alam
Potential utilization of the emerging Web technology, Web Bundles, in Web archiving, presented at the IIPC WAC 2021 in Session 8 by Sawood Alam.
Recording: https://youtu.be/lQX9v9V0FRQ
Impact of HTTP Cookie Violations in Web ArchivesSawood Alam
Certain HTTP Cookies on certain sites can be a source of content bias in archival crawls. Accommodating Cookies at crawl time, but not utilizing them at replay time may cause cookie violations, resulting in defaced composite mementos that never existed on the live web. To address these issues, we propose that crawlers store Cookies with short expiration time and archival replay systems account for values in the Vary header along with URIs.
MementoMap: A Web Archive Profiling Framework for Efficient Memento RoutingSawood Alam
Topic: Doctoral Dissertation Defense
Title: MementoMap: A Web Archive Profiling Framework for Efficient Memento Routing
Student: Sawood Alam
University: Old Dominion University
Date: Friday, December 4, 2020
Clipper project presentation at the Jisc Research Data Network meeting, Cambridge, 6th September 2016.
Clipper: A web annotation toolkit for research & practice with online audio visual media
Minerva is a storage plugin of Drill that connects IPFS's decentralized storage and Drill's flexible query engine. Any data file stored on IPFS can be easily accessed from Drill's query interface, just like a file stored on a local disk.
Visit https://github.com/bdchain/Minerva to learn more and try it out!
Evaluating the SiteStory Transactional Web Archive with the ApacheBench ToolMichael Nelson
Evaluating the SiteStory Transactional Web Archive with the ApacheBench Tool
Justin F. Brunelle
Michael L. Nelson
Lyudmila Balakireva
Robert Sanderson
Herbert Van de Sompel
TPDL 2013, September 24, 2013
These slides go with the paper "Reminiscing About 15 Years of Interoperability Efforts" which is available at http://dx.doi.org/10.1045/november2015-vandesompel
Slides were used for a presentation at the Fall 2015 Membership Meeting of the Coalition for Networked Information.
Supporting Web Archiving via Web PackagingSawood Alam
We describe challenges related to web archiving, replaying archived web resources, and verifying their authenticity. We show that Web Packaging has significant potential to help address these challenges and identify areas in which changes are needed in order to fully realize that potential.
Position Paper: https://arxiv.org/abs/1906.07104
Presented in the Internet Architecture Board's ESCAPE 2019 Workshop (Exploring Synergy between Content Aggregation and the Publisher Ecosystem)
https://www.iab.org/activities/workshops/escape-workshop/
Combining Heritrix and PhantomJS for Better Crawling of Pages with JavascriptMichael Nelson
Justin F. Brunelle
Michele C. Weigle
Michael L. Nelson
Web Science and Digital Libraries Research Group
Old Dominion University
@WebSciDL
IIPC 2016
Reykjavik, Iceland, April 11, 2016
Archive Assisted Archival Fixity Verification FrameworkSawood Alam
The number of public and private web archives has increased, and we implicitly trust content delivered by these archives. Fixity is checked to ensure an archived resource has remained unaltered since the time it was captured. Some web archives do not allow users to access fixity information and, more importantly, even if fixity information is available, it is provided by the same archive from which the archived resources are requested. In this research, we propose two approaches, namely Atomic and Block, to establish and check fixity of archived resources.
Readying Web Archives to Consume and Leverage Web BundlesSawood Alam
Potential utilization of the emerging Web technology, Web Bundles, in Web archiving, presented at the IIPC WAC 2021 in Session 8 by Sawood Alam.
Recording: https://youtu.be/lQX9v9V0FRQ
Impact of HTTP Cookie Violations in Web ArchivesSawood Alam
Certain HTTP Cookies on certain sites can be a source of content bias in archival crawls. Accommodating Cookies at crawl time, but not utilizing them at replay time may cause cookie violations, resulting in defaced composite mementos that never existed on the live web. To address these issues, we propose that crawlers store Cookies with short expiration time and archival replay systems account for values in the Vary header along with URIs.
MementoMap: A Web Archive Profiling Framework for Efficient Memento RoutingSawood Alam
Topic: Doctoral Dissertation Defense
Title: MementoMap: A Web Archive Profiling Framework for Efficient Memento Routing
Student: Sawood Alam
University: Old Dominion University
Date: Friday, December 4, 2020
Clipper project presentation at the Jisc Research Data Network meeting, Cambridge, 6th September 2016.
Clipper: A web annotation toolkit for research & practice with online audio visual media
Minerva is a storage plugin of Drill that connects IPFS's decentralized storage and Drill's flexible query engine. Any data file stored on IPFS can be easily accessed from Drill's query interface, just like a file stored on a local disk.
Visit https://github.com/bdchain/Minerva to learn more and try it out!
Evaluating the SiteStory Transactional Web Archive with the ApacheBench ToolMichael Nelson
Evaluating the SiteStory Transactional Web Archive with the ApacheBench Tool
Justin F. Brunelle
Michael L. Nelson
Lyudmila Balakireva
Robert Sanderson
Herbert Van de Sompel
TPDL 2013, September 24, 2013
These slides go with the paper "Reminiscing About 15 Years of Interoperability Efforts" which is available at http://dx.doi.org/10.1045/november2015-vandesompel
Slides were used for a presentation at the Fall 2015 Membership Meeting of the Coalition for Networked Information.
10 Ways to Win at SlideShare SEO & Presentation OptimizationOneupweb
Thank you, SlideShare, for teaching us that PowerPoint presentations don't have to be a total bore. But in order to tap SlideShare's 60 million global users, you must optimize. Here are 10 quick tips to make your next presentation highly engaging, shareable and well worth the effort.
For more content marketing tips: http://www.oneupweb.com/blog/
Web Archiving Activities of ODU’s Web Science and Digital Library Research G...Michael Nelson
Michael L. Nelson
@phonedude_mln
Michele C. Weigle
@weiglemc
National Symposium on Web Archiving Interoperability
2017-02-21
Many projects joint with LANL
Funding from NSF, IMLS, NEH, and AMF
This is our team presentation in Archived Unleashed 3.0 in San Francisco. Our team work on twitter data about the U.S. second presidential debate in October 2016.
Workshop: Archive Unleashed 3.0
Team: Good News/ Bad News
Category: Local News
Location/Date: Internet Archive, San Francisco, CA, February 23 – 24, 2017
Team members:
Sawood Alam, Old Dominion University
Lulwah Alkwai, Old Dominion University
Mark Beasley, Rhizome
Brenda Berkelaar, University of Texas at Austin
Frances Corry, University of Southern California
Ilya Kreymer, Rhizome
Nathalie Casemajor, INRS
Lauren Ko, University of North Texas
German slides for different use cases for Elasticsearch: Document Store, full text search, flexible query cache, geospatial search, logfile analytics, analytics.
Static Sites Can be the Solution (Simon Wood)Future Insights
Taken from this month's (17th July) London Web meet-up (http://londonweb.org) - we were joined by Simon Wood. Based in Kent, Simon is a passionate tech/geek and is currently Head of Technology and Innovation at the Shortbreaks and New Ventures division of Holiday Extras, a travel technology company. Simon is also acting CTO for miDrive an in-house Start Up incubator.
Simon's session description for Static Sites Can be the Solution:
"We build complex dynamic websites as a first port of call but these are slow, have issues with scaling and can be complex to host. I believe we should more often look to static sites first. I will demonstrate why static sites are such a good choice and show you how you can build static sites, using tools like Jekyll and other static site generators. We will cover how they can be hosted on S3 and GitHub pages and talk about how they can be frequently updated with the correct workflow even though they are static. You can have a blog on a static site and still make regular new blog posts and have dynamic content."
In this talk we will demonstrate and unveil the latest developments on browser specific weaknesses including creative new mechanisms to compromise confidentiality, successfully perform login and history detection, serve mixed content, deliver malicious ghost binaries without a C&C server, exploit cache / timing side channels to extract secrets from third-party domains and leverage new HTML5 features to carry out more stealthy attacks. This is a fast-paced practical presentation with live demos that will challenge your knowledge of the Same Origin Policy and push the limits of what is possible with today’s web clients.
Topics will include: Current XSS filter bypass for IE & Chrome. Same Origin Policy timing attacks on Chrome. Data URI malware with spoofed URLs and ‘download’ attribute. HTML5 drag & drop exploitation. History stealing attacks. Clipboard stealing attacks. Cross-domain hijacking attacks with flash content sniffing, Blob URLs and SVGs. Spoofing URL address bars on modern browsers. Advanced browser encoding quirks and exploitation techniques.
Linked Open Data is the most usable kind of Open Data. An example of a well integrated source of Linked Open Data on tourism and mobility is the Open Data Hub operated by NOI. We will use the SPARQL querying language, a W3C standard, to query the data and show how this differs from other access methods. The tour will start by querying the end point directly from the command line with tools, like curl. Then, one by one, well known data science software packages. like R and Pandas, will be used to directly work with these datasets, to perform statistical calculations and generating graphs from data.
In the final part, these software packages will be used to query data from other well known data sources, like Wikidata and DBpedia.
A review of the webshells used by bad guys. How they are protected but also mistakes in their implementation. This talk was presented at the OWASP Belgium Chapter Meeting in May 2017.
Uma breve descrição sobre o HTML 5 e suas principais características como: forms, a nova estrutura, aúdio e vídeo, etc.
An overview about HTML 5 and its main features such as: forms, new structure, audio and video, etc.
An examination of the current data portability design patterns used in Social Media sites. Looking at a possible new Open Stack concept to create true plug and play interfaces for user to exchange data
Learn about the exciting new REST Resource API powered by Python's new asyncio library. In this talk you'll learn about some of the amazing things you can do with Guillotina and how you can leverage it to build your next JavaScript web application.
Similar to InterPlanetary Wayback: Peer-To-Peer Permanence of Web Archives (20)
CDX Summary: Web Archival Collection InsightsSawood Alam
Large web archival collections are often opaque about their holdings. We created an open-source tool called, CDX Summary, to generate statistical reports based on URIs, hosts, TLDs, paths, query parameters, status codes, media types, date and time, etc. present in the CDX index of a collection of WARC files. Our tool also surfaces a configurable number of potentially good random memento samples from the collection for visual inspection, quality assurance, representative thumbnails generation, etc. The tool generates both human and machine readable reports with varying levels of details for different use cases. Furthermore, we implemented a Web Component that can render generated JSON summaries in HTML documents. Early exploration of CDX insights on Wayback Machine collections helped us improve our crawl operations.
Venue: TPDL 2022
Recording: https://www.youtube.com/watch?v=K5i3XShqW6A
Video Archiving and Playback in the Wayback MachineSawood Alam
At the Internet Archive (IA) we collect static and dynamic lists of seeds from various sources (like Save Page Now, Wikipedia EventStream, Cloudflare, etc.) for archiving. Some of these seeds include web pages with videos on them. Those URLs are curated based on certain criteria to identify potential videos that should be archived or excluded. Candidate video page URLs for archiving are placed in a queue (currently using Kafka) to be consumed by a separate process. We maintain a persistent database of videos we have already archived, which is used both for status tracking as well as a seen-check system to avoid duplicate downloads of large media files that usually do not change. We use youtube-dl (or one of its forks) to download videos and their metadata. We archive the container HTML page, associated video metadata, any transcriptions, thumbnails, and at least one of the many video files with different resolutions and formats. These pieces are stored in separate WARC records (some with “response” type and others as “metadata”). Some popular video streaming services do not have static links to embed video files, which makes it difficult to identify and serve video files corresponding to their container HTML pages on archival replay. To glue related pieces together for replay we are currently using a key-value store, but exploring ways to get away with an additional index. We are using a custom video player and perform necessary rewriting in the container HTML page for a more reliable video playback experience. We create a daily summary of metadata of videos that we have archived and load it in a custom-built Video Archiving Insights dashboard to identify any issues or biases, which are utilized as a feedback loop for quality assurance and to enhance our curation criteria and archiving strategies. We are always looking forward to ways to improve the system that works at scale as well as means to interoperate.
Recording: youtube.com/watch?v=6MiYKOq_DKo
MementoMap: An Archive Profile Dissemination FrameworkSawood Alam
We introduce MementoMap, a framework to express and disseminate holdings of web archives (archive profiles) by themselves or third parties. The framework allows arbitrary, flexible, and dynamic levels of details in its entries that fit the needs of archives of different scales. This enables Memento aggregators to significantly reduce wasted traffic to web archives.
A brief introduction to WARC File Format used for long-term Web Archival preservation. These slides were initially prepared to give a guest lecture in the CS 531 Web Server Design (Fall 2018) course at Old Dominion University.
MemGator - A Memento Aggregator CLI and Server in GoSawood Alam
MemGator - A Portable Concurrent Memento Aggregator CLI and Server Written in Go.
The corresponding poster can be found at http://www.cs.odu.edu/~salam/presentations/memgator-jcdl16-poster.pdf
Avoiding Zombies in Archival Replay Using ServiceWorkerSawood Alam
Live-leakage (zombie resource) is an issue in archival replay of web pages. This work proposes a mechanism to avoid such live-leakage using ServiceWorker. This work was presented in WADL 2017 on June 22 in Toronto, Ontario, Canada.
Client-side Reconstruction of Composite Mementos Using ServiceWorkerSawood Alam
Live-leakage (zombie resource) is an issue in archival replay of web pages. This work proposes a mechanism to avoid such live-leakage using ServiceWorker. This work was presented in JCDL 2017 on June 20 in Toronto, Ontario, Canada.
A talk given to final year B.Tech. Computer Science students at Jamia Millia Islamia, New Delhi, India with the intent of spreading awareness about web archiving and digital preservation and motivating the students for research.
HTTP Mailbox - Asynchronous RESTful CommunicationSawood Alam
A Thesis Presentation to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of Master of Science Computer Science
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
InterPlanetary Wayback: Peer-To-Peer Permanence of Web Archives
1. InterPlanetary Wayback
Peer-to-Peer Permanence of Web Archives
Mat Kelly, Sawood Alam, Michael L. Nelson, Michele C. Weigle
Old Dominion University
Web Science and Digital Libraries Research Group
Norfolk, Virginia, USA
@WebSciDL
TPDL 2016
Hannover, Germany
September 7, 2016
http://github.com/oduwsdl/ipwb
2. Background - IPFS
● Hypermedia distributed protocol
● IPFS entity hashes are content addressed
○ Content changes → different hash produced
○ Inherent potential for de-duplication of content
● Files accessible via HTTP: http://ipfs.io/<hash>
● Built on trust chains for provenance
6. Motivation
● Persistence of archived web data dependent on resilience
of organization and availability of data
● Remove massive redundancy in web archive files of exact
duplicate content
● Determine feasibility of pushing WARCs into IPFS
19. ● Reported IPFS slowness https://github.com/ipfs/go-ipfs/issues/1216
○ Has since been fixed, subsequent to IPWB-TPDL
570 files per minute~10% overhead
20. Replay Time
● 600 requests in 222 seconds
● Slower than PyWB (which took 5.26 seconds)
● File vs. rich object based retrieval
● Never expiring cache
21. Future Works
● Evaluate the improved IPFS on large dataset
● Evaluate deduplication
● Implement an index-free collaborative archiving system
● Utilize IPNS to reference URI-Rs
22. Conclusions
● A proof of concept system to leverage a novel approach to
archiving and retrieval
● Evaluated storage and time costs and qualitative analysis
● It can only work for small archives in it’s current state
● A path to answer “who will archive the archives?” question
23. InterPlanetary Wayback
Peer-to-Peer Permanence of Web Archives
@WebSciDL
http://github.com/oduwsdl/ipwb
Support: NSF #1624067 via the Archives Unleashed Hackathon
Mat Kelly, Sawood Alam, Michael L. Nelson, Michele C. Weigle