DNA replication is a semiconservative process. It means that each strand acts as a template for the synthesis of a new complementary strand. Therefore, this process takes us from one parent molecule to two daughter molecules, with each newly formed double helix containing one new and one old strand.
DNA replication is a semiconservative process. It means that each strand acts as a template for the synthesis of a new complementary strand. Therefore, this process takes us from one parent molecule to two daughter molecules, with each newly formed double helix containing one new and one old strand.
State v. Mott: A Case Study in Forensic Sciencegcpolando
Presentation to Manchester College\'s Science Department; describes the legal aspects of forensic science in a trial presented by my elected prosecutor, Curtis Hill, and chief deputy, Vicki Becker.
C. Contaldi, F. Vafaee, P. C. Nelson - GECCO'17 Conference TalkCarlo Contaldi
The manuscript I wrote about my new crossover operator for Genetic Algorithms has been accepted as a full paper for the Genetic and Evolutionary Computation Conference 2017 (GECCO'17 - http://gecco-2017.sigevo.org/index.html/HomePage).
Here is the presentation I used for my GECCO'17 conference talk, held in Berlin on 19 July 2017.
Check out my conference proceeding on the ACM Digital Library @https://doi.org/10.1145/3071178.3071240
Check out an excerpt from my conference talk @https://www.youtube.com/watch?v=JOZuTsAHaAs
Mastering RNA-Seq (NGS Data Analysis) - A Critical Approach To Transcriptomic...Elia Brodsky
This workshop will address critical issues related to Transcriptomics data:
Processing raw Next Generation Sequencing (NGS) data:
1. Next Generation Sequencing data preprocessing:
Trimming technical sequences
Removing PCR duplicates
2. RNA-seq based quantification of expression levels:
Conventional pipelines (looking at known transcripts)
Identification of novel isoforms
Analysis of Expression Data Using Machine Learning:
3. Unsupervised analysis of expression data:
Principal Component Analysis
Clustering
4. Supervised analysis:
Differential expression analysis
Classification, gene signature construction
5. Gene set enrichment analysis
The workshop will include hands-on exercises utilizing public domain datasets:
breast cancer cell lines transcriptomic profiles (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r110),
patient-derived xenograft (PDX) mouse model of tumor and stroma transcriptomic profiles (http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=8014&path[]=23533), and
processed data from The Cancer Genome Atlas samples (https://cancergenome.nih.gov/).
Team: The workshops are designed by the researchers at the Tauber Bioinformatics Research Center at University of Haifa, Israel in collaboration with academic centers across the US. Technical support for the workshops is provided by the Pine Biotech team. https://edu.t-bio.info/a-critical-approach-to-transcriptomic-data-analysis/
A Configurable CEGAR Framework with Interpolation-Based RefinementsAkos Hajdu
Presentation of our paper at the the 36th IFIP International Conference on Formal Techniques for Distributed Objects, Components and Systems (FORTE 2016). Heraklion, Greece
Neuroscience core lecture given at the Icahn school of medicine at Mount Sinai. This is the version 2 of the same topic. I have made some modifications to give a more gentle introduction and add a new example for ngs.plot.
State v. Mott: A Case Study in Forensic Sciencegcpolando
Presentation to Manchester College\'s Science Department; describes the legal aspects of forensic science in a trial presented by my elected prosecutor, Curtis Hill, and chief deputy, Vicki Becker.
C. Contaldi, F. Vafaee, P. C. Nelson - GECCO'17 Conference TalkCarlo Contaldi
The manuscript I wrote about my new crossover operator for Genetic Algorithms has been accepted as a full paper for the Genetic and Evolutionary Computation Conference 2017 (GECCO'17 - http://gecco-2017.sigevo.org/index.html/HomePage).
Here is the presentation I used for my GECCO'17 conference talk, held in Berlin on 19 July 2017.
Check out my conference proceeding on the ACM Digital Library @https://doi.org/10.1145/3071178.3071240
Check out an excerpt from my conference talk @https://www.youtube.com/watch?v=JOZuTsAHaAs
Mastering RNA-Seq (NGS Data Analysis) - A Critical Approach To Transcriptomic...Elia Brodsky
This workshop will address critical issues related to Transcriptomics data:
Processing raw Next Generation Sequencing (NGS) data:
1. Next Generation Sequencing data preprocessing:
Trimming technical sequences
Removing PCR duplicates
2. RNA-seq based quantification of expression levels:
Conventional pipelines (looking at known transcripts)
Identification of novel isoforms
Analysis of Expression Data Using Machine Learning:
3. Unsupervised analysis of expression data:
Principal Component Analysis
Clustering
4. Supervised analysis:
Differential expression analysis
Classification, gene signature construction
5. Gene set enrichment analysis
The workshop will include hands-on exercises utilizing public domain datasets:
breast cancer cell lines transcriptomic profiles (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r110),
patient-derived xenograft (PDX) mouse model of tumor and stroma transcriptomic profiles (http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=8014&path[]=23533), and
processed data from The Cancer Genome Atlas samples (https://cancergenome.nih.gov/).
Team: The workshops are designed by the researchers at the Tauber Bioinformatics Research Center at University of Haifa, Israel in collaboration with academic centers across the US. Technical support for the workshops is provided by the Pine Biotech team. https://edu.t-bio.info/a-critical-approach-to-transcriptomic-data-analysis/
A Configurable CEGAR Framework with Interpolation-Based RefinementsAkos Hajdu
Presentation of our paper at the the 36th IFIP International Conference on Formal Techniques for Distributed Objects, Components and Systems (FORTE 2016). Heraklion, Greece
Neuroscience core lecture given at the Icahn school of medicine at Mount Sinai. This is the version 2 of the same topic. I have made some modifications to give a more gentle introduction and add a new example for ngs.plot.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
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/
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Searching for Configurations in Clone Evaluation: A Replication Study [SSBSE'16]
1. Searching for Configurations
in Clone Evaluation:
A Replication Study
C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke
J. H. Drake
CENTRE FOR RESEARCH ON EVOLUTION, SEARCH AND TESTING
DEPARTMENT OF COMPUTER SCIENCE
UNIVERSITY COLLEGE LONDON
2. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Code Clone
2
3. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Clone Detectors
3
if (x==0) then y=y+1;
if (check==0) then count=count+1;
$p ($p==0) $p $p=$p+1;
$p ($p==0) $p $p=$p+1;
if_s
if ( cond_e ) then assign_e
if_s
if ( cond_e ) then assign_e
Deckard
CCFinder
Simian
NiCad
4. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Oracle Problem in Code Clone
Absence of the possibility to establish a ground truth, we do
not know if code is actually cloned
4
?
5. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Agreement
5
?
6. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Parameters Tuning
6
7. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
EvaClone
7
T. Wang, M. Harman., Y. Jia, & J. Krinke. Searching for Better
Configurations: A Rigorous Approach to Clone Evaluation. in FSE’13
6 Clone Detectors:
PMD, iClones
ConQAT, Simian,
NiCad, CCFinder
8 Software Projects:
weltab, cook, snns,
psql, javadoc, ant,
jdtcore, swing
15 years
8. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Maximising Agreement
8
C D N S
Maximise
Clone detectors
9. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
EvaClone (cont.)
9
EvaClone favors recall over precision
and more candidates will be reported.
10. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Replication Study
10
11. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Fitness Function
11
4x3x2x1x ++ +
4 x (All clone lines)
12. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Replication Study (cont.)
12
Deckard
CCFinder
Simian
NiCad 25 parameters
Population size 100
No. of Generation 100
Crossover 0.8
Mutation 0.1
Elitism 0.25
2 x 1012
13. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
13
Ver. 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 2.0.0 2.0.44
SLOC
(k)
5.5 6.7 6.78 6.82 7.2 7.6 8.4 8.9 10.1 12.4 17.9 22.8 23.6 25.3
%Inc N/A 21% 2% 1% 6% 5% 11% 7% 13% 23% 44% 28% 3% 8%
Note: there are 2 complete libraries (cglib and asm) embedded in release 1.5 — 1.9 and have been removed before the analysis
14. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
RQ1: Optimised Agreement
How do the default parameters perform in terms of
clone agreement on each Mockito release compared
to the optimised ones?
14
0.30
0.35
0.40
0.45
0.50
0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 2.0.0 2.0.44
Mockito
FitnessValue
Default
EvaClone Highest
EvaClone Lowest
Comparison of optimised tools agreement (the highest and the lowest in 20 runs) to the default agreement over 14 Mockito releases
17. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
RQ3: Clones over Releases
17
How many clones in Mockito are reported with the
highest agreement over releases?
DefaultEvaClone
18. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Maximising Agreement
18
C D N S
Maximise
Clone detectors
19. Searching for Configurations in Clone Evaluation: A Replication Study — C. Ragkhitwetsagul, M. Paixao, M. Adham, S. Busari, J. Krinke, J. H. Drake
Open Challenge
A better fitness function
for EvaClone is needed
It must not only rely on the number of cloned
lines, but also include other aspects:
How often a line is found to be cloned to other
places?
Precision vs. Recall?
Location of clones
19
???