Introduction to the peer review workshop for the PhD students of the Wageningen Graduate Schools. The goal is to explain peer review, entice PhD students to take part in the peer review process and give some tips on how to start with peer review.
Introduction to the peer review workshop for the PhD students of the Wageningen Graduate Schools. The goal is to explain peer review, entice PhD students to take part in the peer review process and give some tips on how to start with peer review.
Peer Review is the Process used to judge the quality of articles submitted for publication in a scholarly journal. Peer Reviewed articles are considered the best source to use when writing a research paper.
Researcher KnowHow session presented by Michelle Maden PhD MA FHEA, Postdoc research associate in evidence synthesis, Liverpool Reviews and Implementation Group
Presentation at: Developing Search Methods for Systematic Review Workshop; September 19, 2015; Sina Trauma and Surgery Research Centre , Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
Included Topics: developing search protocols for systematic reviews, search strategies, search resources, search levels, search operators, management of search results, search and information management methods.
Science is ever evolving, and replication studies and negative findings play a major role in helping science grow. But journals are not always open to publishing these. What role do replication studies play in scientific discovery? And how does publishing negative results help further the cause of science? View this presentation to learn more.
Researcher KnowHow session presented by Ruaraidh Hill PhD MSc FHEA Lecturer in evidence synthesis at the University of Liverpool and Angela Boland MSc PhD PGCert (LTHE)Director –Liverpool Reviews & Implementation Group
Peer Review is the Process used to judge the quality of articles submitted for publication in a scholarly journal. Peer Reviewed articles are considered the best source to use when writing a research paper.
Researcher KnowHow session presented by Michelle Maden PhD MA FHEA, Postdoc research associate in evidence synthesis, Liverpool Reviews and Implementation Group
Presentation at: Developing Search Methods for Systematic Review Workshop; September 19, 2015; Sina Trauma and Surgery Research Centre , Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
Included Topics: developing search protocols for systematic reviews, search strategies, search resources, search levels, search operators, management of search results, search and information management methods.
Science is ever evolving, and replication studies and negative findings play a major role in helping science grow. But journals are not always open to publishing these. What role do replication studies play in scientific discovery? And how does publishing negative results help further the cause of science? View this presentation to learn more.
Researcher KnowHow session presented by Ruaraidh Hill PhD MSc FHEA Lecturer in evidence synthesis at the University of Liverpool and Angela Boland MSc PhD PGCert (LTHE)Director –Liverpool Reviews & Implementation Group
ScienceOpen: Rethinking Peer Review / Young Academy of ScotlandScienceOpen
Hosted by the RSE Young Academy of Scotland Open Data Working Group
The scholarly publishing paradigm is changing – Open Access, altmetrics, data-mining are increasingly setting new standards. A recent Royal Society conference on “The Future of Scholarly Scientific Communication” called in particular for sweeping reforms to the current system of peer review. The new platform ScienceOpen has taken up the challenge. In order to put the evaluation of research back in the hands of researchers, we are experimenting with new forms of author-mediated pre-publication peer review. Published articles are open for transparent post-publication peer review and versioning to reflect feedback as the scientific community reads, works with, attempts to reproduce and builds on the results. The essential efforts of peer reviewers in this process are recognized with a citable CrossRef DOI for their report. ScienceOpen goes further to extend this open research evaluation process to over 1.5 million aggregated Open Access publications. We are taking advantage of this transitional moment to rethink how scientific communication, and particularly peer review could function in the future, because we believe that scholarly publishing is not an end in itself, but the beginning of a dialogue to move the whole scientific venture forward.
Ulrich Pöschl (MPIC/ ACP) -- Multi-stage open peer review integrating the str...OpenAIRE
Presentation of Ulrich Pöschl from the Max Planck Institute for Chemistry, Mainz/Germany and ACP (Atmospheric Chemistry and Physics) on the OpenAIRE workshop "Open Peer Review: Models, Benefits and Limitations"
Science in the context of journals, Open, and the futureBenjamin Laken
The state of science, journals, peer-review, thoughts on Open Science, reproducibility, and Science 2.0.
Accompanying article at https://thewinnower.com/papers/open-evolution-and-revolution-in-science
This material was presented in front of grad students of Institut Teknologi Bandung and journal managers to open their perspective to this new approach of scholarly publishing. I borrowed the materials from F1000research website containing their standard publication slides.
5 hours course taught by Nicolás Robinson-García and Evaristo Jiménez-Contreras in June 23-July 3, 2014 in the University of Granada within the exchange program with Al-Faraby Kazakh National University students 'Current problems of modern philology'.
This webinar is part of the activities related to the Pathway Open Access : Repositories and Publishers, and organized by the CIARD Community.
*About the webinar*
The Open Science journal F1000Research was launched in 2012 in order to address many of the shortcomings of conventional life science publishing, particularly those that exacerbate publication bias, publishing inefficiencies and irreproducibility of findings.
Open Science goes beyond Open Access in making every element of the scientific process free to use, reuse and redistribute. This includes ensuring the availability of raw data, software and referee reports, which are often at least as important as the article with which they are associated.
This webinar will provide an overview of F1000Research's approach to Open Science publishing and highlight other unique aspects of the journal's model including post-publication peer review, article versioning and non-traditional article types.
*Presented by Thomas Ingraham*
Thomas Ingraham is Development Editor at F1000Research and has been involved with the journal's Open Science and editorial development since its inception.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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 .
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.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
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.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...
I conf2016
1. Peiling Wang1, Manasa Rath1, Michael Deike1, Qiang Wu2
1University of Tennessee at Knoxville, USA
2University of Science and Technology, China
Open Post-Publication Peer Review: An
Innovation in Scientific Publishing
2. Peer Review: Bedrock of Modern Science
Evaluation of scientific findings
Quality assurance for scholarly or scientific
publications
Criticisms:
long delay in publishing
high quality work not recognized thus rejected
flawed research published
o a scientist published 126 fabricated papers
o “peer review ring” scandal
3. Globalization of Modern Science
Big science
volume (e.g., 2006 1,346,000 articles published in
23,750 peer-reviewed journals)
growth (e.g., > 3.31% for refereed journals)
increased collaboration: number of co-authors;
number of participating countries
Prolific authors
Hirsch index ~100
Increased accessibility to publications and
data
4. Open Peer Review: Much Needed
Modernization
Peer review is an established practice of
scientific publishing for centuries
Blind (double or single) referee process
for objectivity may compromise
transparency
Open science and open research
Open access
Open peer review
Open assessments (reader comments)
5. Open Science & Open Research
Open Access (OA)
Open Assessment
F1000Prime (peer recommendation)
Reader comments (open or registered users)
Open Peer Review (OPR)
Process transparent
Identity known (author, or/and referee)
Review history (published alongside)
6. Two Basic OPR Models
Post-publication open peer review
Articles published online upon submission
Peers are invited to review
Signed review report immediately online
Must pass Indexation threshold
Pre-publication open peer review
Blind (non blind) review moderated by editors
Publish review history alongside accepted
article (democratic decisions)
7.
8. Indexation vs. Publication Timelag
If an article is published before peer review,
what is the quality assurance?
A threshold is set for indexing a post-
publication article:
Two referees assigned “Approval”
or
One referee assigned “Approval” plus two
referees assigned “Approval with reservation”
9. OPR: Innovation
New and less known by scientists who
publish or review
Review history – never before published
as a part of the article
Authors and reviewers become
collaborators in open research
Future of OPR is still in the making
10. Research Method
Comparing four OPR journals
Timelag (publication vs. indexation)
Openness policy (review history, anonymity,
…)
Analyzing F1000Research (as the post-
publication peer review model)
focus on only research articles
11. Timelags
OPR Journals Timelag (Median)
F1000Research Publication: ~7 days Indexation: 35 / 69 days
PeerJ Acceptance: 74 days Publication: 22 days
eLife Acceptance: 90 days Publication: 29 days
GigaScience
Acceptance: 102
days
Publication: 22 days
13. OPR Policies (Cont’d)
eLife
Decision letter
published (Editor)
Reviewer identity
(optional)
Author’s response
GigaScience
Notes on datasets
Non-anonymity
(may honor
reviewer’s request)
Review history
Author’s responses
14. F1000Research: A Fully Open Model
F1000Research dataset, harvested on
March 20, 2015, 215 indexed research
articles
58% were approved in their first version
and being indexed in Scopus & PubMed
For the articles approved in their original
submissions, 21% published a revised
version
15. F1000Research Articles (215 indexed)
929 authors from 50 countries
544 referees from 46 countries
Top 5 contributing countries:
Authors from
US, UK, Australia, Germany, Canada
Reviewers from
US, UK, Canada, Australia, Germany
16. Where else do these authors publish?
Searching WoS and Scopus for the top
downloaded F1000Research articles’ 96
authors:
The authors’ H-index (mean 11; the highest H-
index 97)
Journals’ high impact factor (mean 9.7; the
highest IF 42.3)
Journals are reputable, such as Science, Nature,
and Annual Review of Entomology
17. Advantages of OPR
transparency
openness
review history as an integral part of
published research work
accountability of both authors and
reviewers to their work
open research to involve readers in
evaluation of published work
18. Further Research on OPR
Investigate the state-of-the-art of OPR
Identify the best practice
Investigate the effect of OPR on referees
What are the differences between the signed
review reports and anonymous review
reports?
Investigate the effect of OPR on authors
Willingness to adopt OPR
19. Dual Models: Open or Traditional
Papers in Physics: % of Articles under OPR
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
70.00%
80.00%
90.00%
100.00%
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