The document summarizes Monica Munoz-Torres' thought process and analysis of two protein families - PTHR16771 and PTHR23074 - in relation to the GO term "recombinational repair". For PTHR16771 (DSS1), she inspects literature linking it to homologous recombination and prunes three species from the family. For PTHR23074 (AAA ATPase), she analyzes FIGNL1 and its role in double-strand break repair, and decides to propagate the relevant GO term only to the MRCA of FIGNL1 homologs. She also notes software issues with PAINT.
In this slide contains principle, types, methods and application of Western Blotting Technique.
Presented by: T.NIRANJAN REDDY (Department of pharmacology).
RIPER, anantapur
We have created a large Neo4j database that integrates the results from text mining, experimental data and biological background knowledge. The utility of this graph is two fold:
- Identify promising compounds to be tested as a starting point for drug development.
- Better understand the results of large scale compound testing in cellular assays using imaging technology.
Currently the database contains 25 million article abstracts, data for 2 million compounds and 60000 genes – overall 29 million nodes and 270 million relationships.
We show some details about how the graph was built and show examples how combining text mining with experimental results leads to new insights and to better understanding and design in biological experiments.
Continuing with the theme of DNA repair via homologous recombination, I will discuss the following family during the PAINT call:
PTHR13451 CLASS II CROSSOVER JUNCTION ENDONUCLEASE MUS81
Seminario basado en el artículo "Structural determination of group A Streptococcal surface
dehydrogenase and characterization of its interaction with
urokinase-type plasminogen activator receptor"
I presented two fascinating stories where Molecular Dynamics simulations contributed to enhancing our understanding of immunodeficiencies. In one of the projects, the treatment of patients could be improved. These slides were presented at the Basler Modeller Stammtisch, 26.02.2021
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
In this slide contains principle, types, methods and application of Western Blotting Technique.
Presented by: T.NIRANJAN REDDY (Department of pharmacology).
RIPER, anantapur
We have created a large Neo4j database that integrates the results from text mining, experimental data and biological background knowledge. The utility of this graph is two fold:
- Identify promising compounds to be tested as a starting point for drug development.
- Better understand the results of large scale compound testing in cellular assays using imaging technology.
Currently the database contains 25 million article abstracts, data for 2 million compounds and 60000 genes – overall 29 million nodes and 270 million relationships.
We show some details about how the graph was built and show examples how combining text mining with experimental results leads to new insights and to better understanding and design in biological experiments.
Continuing with the theme of DNA repair via homologous recombination, I will discuss the following family during the PAINT call:
PTHR13451 CLASS II CROSSOVER JUNCTION ENDONUCLEASE MUS81
Seminario basado en el artículo "Structural determination of group A Streptococcal surface
dehydrogenase and characterization of its interaction with
urokinase-type plasminogen activator receptor"
I presented two fascinating stories where Molecular Dynamics simulations contributed to enhancing our understanding of immunodeficiencies. In one of the projects, the treatment of patients could be improved. These slides were presented at the Basler Modeller Stammtisch, 26.02.2021
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
genes addiion\deeion\ediionthat lead to a therapeutic, prophylactic or diagnostic effect
Plasmid DNA
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•Genetically engineered micro-organisms
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2016 Presentation at the University of Hawaii Cancer CenterCasey Greene
Date: February 19, 2016
Time: 10:30 am
Place: University of Hawaii Cancer Center 701 Ilalo Street, Sullivan Conference Room
Details: Dr. Casey Greene
Department of Systems Pharmacology and Translational Therapeutics
Department of Genetics
University of Pennsylvania
Moore Investigator, Gordon and Betty Moore Foundation
Deep learning for extracting protein-protein interactions from biomedical lit...Yifan Peng
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This presentation contains details about the Apollo genome annotation editor functionality. It also includes a step-by-step example about curating a gene of interest.
This presentation explains the meaning of curation and includes an introduction to the Apollo genome annotation editing tool and its curation environment.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction to use and functionality for the IAGC and BIPAA research communities.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction on gene annotation & curation for the IAGC and BIPAA research communities.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
Apollo annotation guidelines for i5k projects Diaphorina citriMonica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
A Workshop at the Stowers Institute for Medical Research.
This is a brief update about the genome browser JBrowse and the genome annotation editor Apollo, addressed to the members of the Alliance of Genome Resources (AGR).
Learn more about JBrowse at jbrowse.org
Learn more about Apollo at GenomeArchitect.org
Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integra...Monica Munoz-Torres
Manual curation is crucial to improving the quality of the annotations for a genome sequencing project. During this portion of the genome sequencing workflow, curators use a variety of experimental evidence to improve on automated predictions to more accurately represent the underlying biology.
Apollo is a web-based genome annotation editor that allows curators to manually revise and edit genomic elements. It provides a reporting structure for annotated genomic elements and an ‘Annotator Panel’ that allows users to quickly browse the genome and all available annotations. Users can manually edit the structure of a genomic element as well as add metadata, including references to other databases, adding functional assignments to genes and gene products with specific lookup support for Gene Ontology (GO) terms, as well as including references to published literature in support of these annotations.
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Introduction to Apollo - i5k Research Community – Calanoida (copepod)Monica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
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Scientific research is inherently a collaborative task; in our case it is a dialog among different researchers to reach a shared understanding of the underlying biology. To facilitate this dialog we have developed two web-based annotation tools: Apollo (http://genomearchitect.org/), a genomic feature editor, designed to support structural annotation of gene models, and Noctua (http://noctua.berkeleybop.org/), a biological-process model builder designed for describing the functional roles of gene products. Here we wish to outline an inventory of essential requirements that, in our experience, enable an annotation tool to meet the needs of both professional biocurators as well as other members of the research community. Here are the general requirements, beyond specific functional requirements, that any annotation tool must satisfy.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
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Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
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Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project Species.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
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The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
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This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
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Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
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Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
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Thesis Statement for students diagnonsed withADHD.ppt
PAINT Conf Call 062414
1. PAINT conference call
GO:0000725 recombinational repair
PTHR16771 and PTHR23074
Monica Munoz-Torres, PhD | @monimunozto
Berkeley Bioinformatics Open-Source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
24 June, 2014
UNIVERSITY OF
CALIFORNIA
2. Outline
1. Thought process
2. GO Term: recombinational repair
3. PTHR16771
• Proteasome Complex Subunit DSS.
4. PTHR23074
• AAA ATPase.
PAINT Conf Call
GO:0000725
recombinational repair
Outline 2
3. Thought Process
• Find gene with annotation to GO term of interest
• Inspect details at UniProt (FASTA, GO terms, etc.)
• Link to PubMed, extract information
• Inspect CDD (e.g. BLAST vs nr)
• Inspect all annotations associated with gene in
question reviewing both tree and MSA
• Propagate as appropriate
Thought Process 3
4. GO Term
Accession: GO:0000725
Name: recombinational repair
Ontology: biological_process
Definition: A DNA repair process that involves the
exchange, reciprocal or nonreciprocal, of genetic
material between the broken DNA molecule and a
homologous region of DNA. Source: GOC:elh
GO Term 4
6. PTHR16771: Proteasome Complex Subunit DSS1
• BRCA2 is a breast cancer susceptibility gene implicated in
the repair of double-strand breaks by homologous
recombination with RAD51.
• DSS1 interacts with BRCA2 in a domain-specific way
• DSS1 is required for the BRCA2-RAD51 complex to
become associated with sites of DNA damage and for the
maintenance of genomic stability, a function conserved
from lower eukaryotes to humans.
• DSS1 is involved in DNA damage repair via homologous
recombination.
PTHR16771 6
7. DSS1_SEM1 [cd13768, pfam05160]
proteasome complex subunit DSS1/SEM1 (s:CDD)
• The evolutionarily conserved deleted in split hand/split foot
protein 1 (DSS1)/Sem1 is a subunit of the regulatory particle
(RP) of the proteasome.
PTHR16771 7
8. Pruned
• Inspecting MSA and comparing with the Conserved
domains of DSSm1/SEM1 family, I pruned the following
species:
20140505: Pruned TETTS_TTHERM_00227230
20140505: Pruned ORYSJ_P0693B08.32
20140505: Pruned PUCGT_PGTG_08936
PTHR16771 8
9. Reasons for pruning
• ORYSJ_P0693B08.32 and PUCGT_PGTG_08936 have
long (20 - 40 aa) strings of residues interrupting the
conserved domain of DSS1 (increasing the length of the
peptide), which has been very well characterized to 71aa
in length.
• TETTS_TTHERM_00227230 has an extended string of
~40 aa at the beginning of the protein, and the second
portion of its conserved domain is severely corrupted
(degenerate) in comparison to all other proteins in the
family
PTHR16771 9
11. Decision
# cellular_component
20140513: Has function proteasome complex (GO:0000502) in
Eukaryota_PTN000423400
20140513: Colocalizes with nucleus (GO:0005634) in
Eukaryota_PTN000423400
# biological_process
20140513: Has function proteolysis (GO:0006508) in
Eukaryota_PTN000423400
20140509: Has function double-strand break repair via homologous
recombination (GO:0000724) in Eukaryota_PTN000423400
# Pruned from tree
20140513: Pruned ORYSJ_P0693B08.32
20140513: Pruned TETTS_TTHERM_00227230
20140513: Pruned PUCGT_PGTG_08936
PTHR16771 11
12. Questions
• Should I annotate other terms? or only concentrate on the
one I am reviewing?
• I find myself hesitating about propagating due to
degeneracy of conserved domains in MSA (thus, I pruned
three species).
How much weight should MSA have on decisions?
Does everyone else rely heavily on them?
PTHR16771 12
13. MF: Peptidase activity?
• Although Human_SHFM1 has an annotation to peptidase activity GO:
0008233, the paper reporting the IDA does not make any claims of
peptidase activity, or any of its synonyms (i.e. hydrolase, acting on
peptide bonds; peptide hydrolase activity; protease activity; proteinase
activity).
• “Yeast and mammalian two-hybrid assays showed that DSS1 can
associate with BRCA2 in the region of amino acids 2472 to 2957 in the
C terminus of the protein. Using coimmunoprecipitation of epitope-
tagged BRCA2 and DSS1 cDNA constructs transiently expressed in
COS cells, authors demonstrated an association. Furthermore,
endogenous BRCA2 could be coimmunoprecipitated with endogenous
DSS1 in MCF7 cells, demonstrating an in vivo association.”
• No further details on the nature of the bond are discussed. Should this
term be removed? or changed to 'catalytic activity' instead?
PTHR16771 13
14. Questions
From the "Evidence" tab:
• What does "has function nucleus" mean?
and "has function proteasome complex"?
and how can I avoid that syntax?
am I supposed to avoid the syntax?
“has function” vs “contributes to”?
• Warnings: (see next)
PTHR16771 14
15. Warnings that disappear…
#WARNINGS
WARNING: Experimental data changed!
The following annotations are no longer supported by experimental
evidence
and have been removed:
Opisthokonta_PTN000423402 to double-strand break repair via homologous
recombination
Bilateria_PTN000423403 to double-strand break repair via homologous
recombination
PTHR16771 15
• I got a warning about experimental evidence being removed, but
the experimental evidence is still being displayed. My initial thought
was that the culprit was my "redundant" propagation of a process
annotation to a less derived node, then a more ancestral one. Is
this the cause? ---> Update: the errors disappeared. ???
16. Previously: Decision
#cellular component
20140513: Has function proteasome complex (GO:0000502) in Eukaryota_PTN000423400
20140513: Colocalizes with nucleus (GO:0005634) in Bilateria_PTN000423403
20140513: Colocalizes with nucleus (GO:0005634) in Eukaryota_PTN000423400
20140507: Has function nucleus (GO:0005634) in Bilateria_PTN000423403
#biological process
20140513: Has function proteolysis (GO:0006508) in Eukaryota_PTN000423400
20140509: Has function proteolysis (GO:0006508) in Opisthokonta_PTN000423402
20140509: Has function double-strand break repair via homologous recombination (GO:0000724) in
Eukaryota_PTN000423400
#Pruned
20140513: Pruned ORYSJ_P0693B08.32
20140513: Pruned TETTS_TTHERM_00227230
20140513: Pruned PUCGT_PGTG_08936
PTHR16771 16
18. PTHR23074: AAA ATPase
• AAA+ Superfamily: “ATPases Associated with a wide variety of
cellular Activities”
• An ancient group of ATPases belonging to the ASCE (for
additional strand, catalytic E) division of the P-loop NTPase fold.
• Members function as molecular chaperons, ATPase subunits of
proteases, helicases, or nucleic-acid stimulated ATPases.
• AAA+ proteins contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and the
Walker A and B motifs of the P-loop NTPases.
PTHR23074 18
19. FIGNL1: RAD51-binding protein fidgetin-like 1
• RAD51 recombinase plays central role in homologous
recombination (HR), which is critical for repair of DNA double-
strand breaks.
• FIGNL1 specifically interacts with RAD51 through its conserved
RAD51 binding domain.
• Forms part of protein complex FIGNL1 + KIAA0146/SPIDR,
required for DNA repair
PTHR23074 19
23. Decision
FIGNL1's RAD51 binding domain (FRBD) is required for "regulation
of double-strand break repair via homologous
recombination" (GO:0010569) activity.
FIGNL1 and its homologs contain also an AAA superfamily domain,
and vsp4 domain. The required binding domain is only present
in this family. Members from other clades were reviewed.
Neither family had the required FRBD and one did not have a
vsp4 domain either.
Decision to propagate GO:0010569 only to
Eukaryota_PTN000553645 as the Most Recent Common
Ancestor for this biological process for the FIGNL1 gene.
PTHR23074 23
26. Evidence (text)
# molecular_function
20140603: Contributes to ATPase activity (GO:0016887) in
root_PTN000553509
# cellular_component
20140603: Has function nucleus (GO:0005634) in root_PTN000553509
# biological_process
20140603: Has function regulation of double-strand break repair via
homologous recombination (GO:0010569) in
Eukaryota_PTN000553645
# Notes
PTHR23074 26
27. Software Reports
• Space to enter PANTHER protein
family ID not visible
• Arrow heads do not act as
expected: i.e. do not move spaces
along MSA
Software Reports 27
28. Software Reports
• Large family eats up CPUs; PAINT freezes (tmp)
• Is right-click on experimental annotation supposed to highlight
the MRCA node for them? If so, not evident.
• Permanent Tree ID (PANTREE) links broken / blank pages
• Resizing a window takes several seconds
• Challenging to propagate to “off-screen” node
Software Reports 28