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Understanding the adoption of multiple packages of system of rice intensifica...CGIAR
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Read more: https://www.canberra.edu.au/research/faculty-research-centres/aisc/seeds-of-change and https://gender.cgiar.org/annual-conference-2019/
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Presentation given by Mauro Vigani at the recent ICAE conference in Milan.
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The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
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Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
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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.
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In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
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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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Cancer cell metabolism: special Reference to Lactate Pathway
Can improved food legume varieties increase technical efficiency in crop production?
1. Can improved food legume varieties
increase technical efficiency in crop
production?
A Case Study in Bale Highlands, Ethiopia
Girma T. Kassie, Aden Aw-Hassan, Seid A. Kemal, Luleseged Desta,
Peter Thorne, Kindu Mekonnen, Mulugeta Yitayih
29 September 2016
ILRI, Addis Ababa, Ethiopia
2. Outline
• Motivation
• The key questions
• Methodology
• Results and discussion
• Conclusion and more
questions
3. Motivation
• Faba bean (broad bean), field pea, and lentil are very important
legumes in the highlands of Ethiopia.
• Ethiopia is the largest producer of faba bean in SSA.
• In 2012/13, about 4.4 million smallholder farmers planted 574,000 ha of faba
bean producing 0.9 million tons at an average productivity of 1.6 tons per ha.
• Field pea is also an important source of protein in Ethiopia.
• In 2012, the crop ranked fourth in area coverage with an acreage of 212,890 ha
and annual production of 2.6 million tons (FAO, 2012).
• We all agree (it seems) that legumes are essential for the
regeneration of nutrient‐deficient soils.
• They fix nitrogen!
4. Motivation
Bale highlands are known for their
mono-cropping production system:
wheat and barley dominated.
Mono-cropping:
• Growing one crop year after year on
the same plot of land
• Non-diverse rotations – Only a
single crop is grown at a time within
a field.
• Associated with two problems:
• Soil degradation
• Increased vulnerability to risk
• Implies lower efficiency [broadly
defined] compared to poly-cropping
systems.
5. The key questions
• Our questions
• How efficient are improved faba bean and field pea growers compared
to non-growers?
• If there is a considerable difference in efficiency, can we attribute this
to the inclusion of improved faba bean and field pea varieties?
• Does crop productivity [crop output per unit of the most limiting
input] vary between improved faba bean and field pea growers and
non-growers?
• Our objective
• To empirically show whether the adoption of improved food legume
varieties increases the technical efficiency of crop production.
6. Methodology
•Sampling
• Multi-stage (mixed) sampling
• 3 of the 4 major legume producing districts in Bale highlands
were selected.
• Agarfa, Goba and Sinana based on relative importance of
food legumes in terms of land allocation for crops.
• 4 peasant associations in each district were selected
randomly.
• 200 farm households were randomly selected from the 4
PAs/District.
• Total sample size 600 farm HHs.
7. Analytical framework
1. Efficiency analysis (SF Model)
N,..,2i,xy iii
iii uv
),0(Ν~v 2
vi
F~ui
yi is log of total crop yield
xi vector of (log of) inputs
εi composite error
υi idiosyncratic error (iid)
ui inefficiency (one-side disturbance)
The assumption about the distribution (F) of ui term is needed to make the model
estimable. Four options so far:
1. Half normal distribution ui ~ N+(0, σu
2) (Aigner et al., 1977).
2. Exponential distribution ui ~ ε(σu) (Meesun and van den Broeck ,1977)
3. Truncated normal (Stevenson, 1980)
4. Gamma distribution (Greene, 1980, 2003).
8. SF Model (2)
• Two step estimation
1- estimates of the model parameters ĥ are obtained by
maximizing the LL-function l(ĥ)
2 – point estimates of inefficiency can be obtained thru the
mean (or the mode) of the conditional distribution
where
• Post-estimation procedures to compute efficiency
parameters:
– Jondrow et al (1982): TEi = 1-E[ui|εi]
– Battese and Coelli (1988): TEi = E[exp(-ui|εi)]
)ˆ|u(f ii
ˆxˆyˆ iii
9. SFA models
–Y= bread wheat equivalent in birr
– Efficiency model 1
• Stoc. frontier normal/tnormal model
• Jondrow et al (1982)
– Efficiency model 2
• Stoc. frontier normal/tnormal model
• Battese and Coelli (1988)
– Efficiency model 3
• Stoc. frontier normal/exponential model
• Jondrow et al (1982)
– Efficiency model 4
• Stoc. frontier normal/exponential model
• Battese and Coelli (1988)
10. Analytical framework
2. Impact analysis
Where δi is impact [technical efficiency] on individual ‘i’;
A
iY Is potential outcome of adoption for individual ‘i’.
Is potential outcome of non-adoption for individual ‘i’.
N
iY
Let D denotes adoption decision (assumed to be binary) and
takes the value 1 for adopters (A) and 0 for non adopters (N).
N
i
A
ii YY
11. 2. Impact analysis
0DifY
1DifY
Y
i
N
i
i
A
i
i
)(*)(*][][ 01 DPATUDPATETYYEEATE N
i
A
ii
]1|[]1|[]1|[ i
N
ii
A
iii DYEDYEDEATET
]0D|Y[E]0D|Y[E]0D|[EATU i
N
ii
A
iii
ATET is identified only if E[YN|D=1]-E[YN|D=0]=0: That is the TEs of HHs
from the adopter and non-adopter groups would not differ in the
absence of the improved food legume varieties.
][ iD YEPOM
12. 2. Impact analysis
• In population terms, the average trt effect (ATE) is
• ATE = E[TEadopt – TEnonadopt] = E[TEadopt] – [TEnonadopt]
• Missing data problem – we only observe one of the potential outcomes:
– We observe TEadopt for adopting farm HHs.
– We observe TEnonadopt for non-adopting farm HHs.
• When the adoption level/treatment [0/1] is randomly assigned to farm HHs,
the potential outcomes are independent of the adoption level [0/1] .
– Assuming that adoption level [0/1] is randomly assigned is hardly convincing.
• Rather, we assume that adoption level is as good as randomly assigned after
conditioning on covariates. This is called conditional independence.
• In fact, we need only conditional mean independence [CMI] – that is after
conditioning on covariates, the adoption level does not affect the means of the
potential outcomes.
– CMI restricts the dependence b/n adoption model and the potential outcomes
13. 2. Impact analysis
• Overlap assumption
– This ensures that each individual could get any adoption level.
• IID assumption
– This ensures that the potential outcomes and adoption level of each
farm HH are unrelated to potential outcomes and adoption levels of
all the other farm HHs in the population.
• Practically speaking, assuming independence of observations suffices.
14. 2. Impact analysis
• Given the fact that the potential outcomes framework formulates
the estimation of the ATE as a missing data problem, the
parameters of an auxiliary model can be used to solve it.
– The auxiliary model is how we condition on covariates so that the trt is as
good as randomly assigned:
Model Estimator
Outcome → Regression adjustment (RA)
Treatment → Inverse-probability weighted (IPW)
Outcome and treatment → Augmented IPW (AIPW)
Outcome and treatment → IPW RA
Treatment → Propensity score matching
Outcome (non-parametrically) → Nearest-neighbor matching
15. Treatment-effects estimators employed
• Adjustment and weighting
– Regression adjustment [see: Lane and Nelder (1982); Cameron and Trivedi (2005, chap. 25);
Wooldridge (2010, chap. 21); and Vittinghoff, Glidden, Shiboski, and McCulloch (2012, chap. 9).]
– Inverse probability weighting [see: Imbens (2000); Hirano, Imbens, and Ridder (2003); Tan
(2010); Wooldridge (2010, chap. 19); van der Laan and Robins (2003); and Tsiatis (2006, chap. 6).]
– Inverse probability weighting with regression adjustment (IPWRA) [see:
Wooldridge, 2007; Wooldridge, 2010]
– Augmented inverse probability weighting (AIPW) [see:Robins, Rotnitzky, and
Zhao (1995); Bang and Robins (2005); Tsiatis (2006) and Tan (2010).]
• Matching estimators
– Nearest neighbor matching [see: Abadie et al. (2004); Abadie and Imbens (2006,
2011)].
– Propensity score (treatment probability) matching [See: Rosenbaum and
Rubin (1983); Abadie and Imbens (2012)].
17. Description of the sample population
• HHs – 90% male headed and 10% female headed.
• Average land holding/hhd: 2.81 ha (reported)
• On average 37% of the farm plot is allocated to faba bean and 12% for field
pea by the sample households.
• Legume producers
• Faba bean: 50.95%
• Field pea: 31.37%
• Faba bean or field pea: 67.76%
• Adopters of improved faba bean and field pea varieties:
• Improved faba bean or field pea: 23.13%
19. The outcome variables
Variable N Mean Std. Dev. Min Max
Efficiency measure 1 575 0.781 0.108 0.094 0.937
Efficiency measure 2 575 0.794 0.103 0.101 0.939
Efficiency measure 3 575 0.782 0.108 0.094 0.937
Efficiency measure 4 575 0.794 0.103 0.100 0.939
Total bread wheat eqvt (kcl/ha) 575 2.936 2.993 0.030 29.872
Total bread wheat eqvt (birr/ha) 575 3.047 3.137 0.030 31.648
20. Simple comparison of adopters and non-adopters02468
0 .2 .4 .6 .8 1
Technical efficiency via E[exp(-u)|e] (BC approach)
Non-adopter
Adopter
kernel = epanechnikov, bandwidth = 0.0221
Kernel density estimate
0246
Density
0 .2 .4 .6 .8 1
Technical efficiency via exp[-E(u|e)] (JLMS - approach)
Non-adopter
Adopter
kernel = epanechnikov, bandwidth = 0.0241
Kernel density estimate
21. Simple comparison of adopters and non-adopters0
.1.2.3
0 10 20 30
Total bread wheat equivalent (kcal) per hectare
Non-adopter
Adopter
kernel = epanechnikov, bandwidth = 0.4076
Kernel density estimate
0
.1.2.3
Density
0 10 20 30
Total bread wheat equivalent (birr) per hectare
Non-adopter
Adopter
kernel = epanechnikov, bandwidth = 0.4010
Kernel density estimate
22. Average trt effect and Average trt effect on the treated
RA
β(Z)
IPW
β(Z)
AIPW
β(Z)
IPWRA
β(Z)
NNMATCH
β(Z)
PSMATCH
β(Z)
Efficiency measure 1
ATET
-.004 (-0.27) -.003 (-0.25) -0.006 (-.48) -.008 (-.51) -.010 (-.69)
ATE
.002 (0.16) -.01 (-0.49) 0.002 (0.07) 0.006 (0.56) 0.016 (1.01) -.001 (-.04)
Efficiency measure 2
ATET
-.004 (-0.35) -.003 (-0.3) -0.006 (-.52) -.008 (-.54) -0.009(-.69)
ATE
.001 (0.07) -.01 (-0.52) 0.002(0.08) 0.005 (0.50) 0.014 (0.95) -.002(-.09)
Efficiency measure 3
ATET
-.004 (-0.28) -.003 (-0.25) -0.006 (-.46) -.008 (-.51) -.010 (-.69)
ATE
.002 (0.16) -.01 (-0.49) 0.002 (0.07) 0.006 (0.55) 0.016 (1.01) -.001 (-.04)
Efficiency measure 4
ATET
-.004 (-0.35) -.003 (-0.3) -0.006 (-.52) -.008 (-.54) -0.009(-.69)
ATE
.001 (0.07) -.01 (-0.52) 0.002(0.08) 0.005 (0.49) 0.014 (0.95) -.002(-.09)
Total bread wheat eqvt (kcl/ha)
ATET .088 (0.33) -.067 (-.16) -.298 (-.99) 0.337 (1.03) -.778 (-1.13)
ATE
-.109 (-.44) -.392 (-1.50) -.194 (-.72) -.298 (-1.51) 0.117 (0.49) -.113 (-.31)
Total bread wheat eqvt (birr/ha) ATET
0.171(0.59) -.046 (-.09) -.180 (-.55) 0.510 (1.59) -1.034 (-1.08)
ATE
-.053(-.20) -.364 (-1.21) -.151 (-.49) -.264 (-1.25) 0.215 (0.92) -.109 (-.26)
This would have meant: For
the farm HHs who are
adopting, TE of crop
production is 0.004 less than
if none of these farm HHs
adopted.
This would have meant :
When all farmers adopt, TE of
crop production is estimated
to be 0.002 units higher than
when no farm HH adopts.
23. Conclusions and further questions
• Very low adoption of improved legume varieties – particularly faba
bean and field pea.
• No relationship with efficiency no matter how the latter was
measured.
• No relationship with productivity per unit of limiting factor no
matter what conversion [energy or price] was used.
•We observed that complementary inputs are not being
used as per the recommendations.
24. Conclusions and further questions
• Human labor is not rewarding in crop production in the
study area. Legumes are still dependent on human labor.
Would they have any future in mechanized farming?
• Would simply disseminating the ‘improved varieties’
help? How?
•Bale highlands is known for farmers heavily dependent
on machinery for their crop production. How will
legumes – produced manually – fit into this system?
• Are they meant to continue as break crops?