- Jun 2024
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prerequisite
Replication--getting the same result from doing the whole study again--is logically independent from whether there even exist any code/analysis from the original paper. Recommend revising and instead talking about how they are related and often conflated.
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- May 2024
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spec.matrix.org spec.matrix.org
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The user should know precisely where their data is stored
And be able to store it locally, on trusted devices, replicated.
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URL
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- Feb 2024
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Local file Local file
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Among the cognoscenti of nanotechnology, this threat has becomeknown as the “gray goo problem.” Though masses of uncon-trolled replicators need not be gray or gooey, the term “gray goo”emphasizes that replicators able to obliterate life might be less in-spiring than a single species of crabgrass. They might be superiorin an evolutionary sense, but this need not make them valuable.
quote in Bill Joy originally from the book Engines of Creation.
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- Jan 2024
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Local file Local file
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Uncontrolledself-replication in these newer technologies runs a much greater risk: arisk of substantial damage in the physical world.
As a case in point, the self-replication of misinformation on social media networks has become a substantial physical risk in the early 21st century causing not only swings in elections, but riots, take overs, swings in the stock market (GameStop short squeeze January 2021), and mob killings. It is incredibly difficult to create risk assessments for these sorts of future harms.
In biology, we see major damage to a wide variety of species as the result of uncontrolled self-replication. We call it cancer.
We also see programmed processes in biological settings including apoptosis and necrosis as means of avoiding major harms. What might these look like with respect to artificial intelligence?
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- Aug 2023
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royalsocietypublishing.org royalsocietypublishing.org
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interesting paper about replacing journals with more "modern" scholarly infrastructure
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developer.confluent.io developer.confluent.io
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Partition Leader Balancing
balance the load on leader preferred replica - first replica of each partition preferred replica is evenly distributed among brokers tries to make the preferred replica as the leader and hence balancing the load
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Replication
followers that lag behind replica lag time max ms is removed from the ISR
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Kafka
follower failure is handled by removing the lagging or failed followers from the ISR and considering only the rest and moves the high watermark
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Protocol
a log is committed when all replicas are in sync - ISR - then we move watermark
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Replication
leaders&followers leader commits log with an epoch(indicates generation of lifetime of a log) follower fetch with offset no to sync with leader leader reponds with new record logs with epoch in the next fetch request, leader moves high watermark based on offset in request (n-1) in that response it passes the high watermark to the follower
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- Mar 2023
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static-content.springer.com static-content.springer.com
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(a)colE1(b)SC101(c)RSF1010
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- Nov 2022
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www.wikipathways.org www.wikipathways.org
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Can broadly split the process into three parts. Initiation, elongation and termination
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DNAPolymerase A
Primase and DNA polymerase A work in close association.
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CDK2
This is the S-phase CDK.
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Assembly of the pre-replicative complex
- Replication origin licensing.
- All of this occurs in G1 phase
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Orc complex
Orc1-5 complex.
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Cdc6
Cdc6 is only present in G1 phase.
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DNA replication pathway in humans. Orc complex binds the origin of replication.
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bio.libretexts.org bio.libretexts.org
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The initial sample consisted of 1 band. F = 0. 1st generation = The sample overall less dense, still one band. Intermediate density. dsDNA made of one strand heavy and one light. After 2 generations, there was a band for intermediate density and for strands of just light, N-14, dsDNA.
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Three methods of replication were initially hypothesized: * Conservative * Semi-conservative * Dispersive
Semi-conservative method was eventually determined to be correct based on empirical evidence from Messelson & Stahl, in 1958.
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Parental strands consist of N-15 isotopes. Replicated daughter strands consist of N-14 isotopes. The CsCl ultracentrifugation process creates density gradient. This allows DNA fragments of different densities to migrate and form a band at the point at which their buoyant density equals that of the salt.
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- E.coli grown in an heavy nitrogen, N-15, enriched medium
- Then transferred to N-14 based media to reproduce
- As several points in the experiment, cells were lysed and underwent ultracentrifugation through a CsCl concentration gradient
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- Aug 2022
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www.nature.com www.nature.com
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Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature, 1–1. https://doi.org/10.1038/s41586-022-04474-x
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www.nature.com www.nature.com
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McDiarmid, A. D., Tullett, A. M., Whitt, C. M., Vazire, S., Smaldino, P. E., & Stephens, J. E. (2021). Psychologists update their beliefs about effect sizes after replication studies. Nature Human Behaviour, 5(12), 1663–1673. https://doi.org/10.1038/s41562-021-01220-7
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- Dec 2021
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www.nature.com www.nature.com
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Replicating scientific results is tough—But essential. (2021). Nature, 600(7889), 359–360. https://doi.org/10.1038/d41586-021-03736-4
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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. This is the first reported case of conjugative transfer of a naturally occurring plasmid between gram-negative and gram-positive bacteria.
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- Oct 2021
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Serra-Garcia, M., & Gneezy, U. (2021). Nonreplicable publications are cited more than replicable ones. Science Advances, 7(21), eabd1705. https://doi.org/10.1126/sciadv.abd1705
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Bekkers, R. (2021). Course Manual: Replication and Preregistration in the Social Sciences. https://osf.io/bh3yp/
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- Jul 2021
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www.statnews.com www.statnews.com
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Short interview that covers the findings of a systematic review that aimed to identify the number of studies trying to replicate the outcomes of clinical decision support systems.
Article being discussed in this piece: Coiera, E., & Tong, H. L. (2021). Replication studies in the clinical decision support literature-frequency, fidelity, and impact. Journal of the American Medical Informatics Association: JAMIA, ocab049. https://doi.org/10/gmb35n
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www.sciencedirect.com www.sciencedirect.com
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Logg, Jennifer M., and Charles A. Dorison. “Pre-Registration: Weighing Costs and Benefits for Researchers.” Organizational Behavior and Human Decision Processes 167 (November 1, 2021): 18–27. https://doi.org/10.1016/j.obhdp.2021.05.006.
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psyarxiv.com psyarxiv.com
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Markowitz, D. M., Song, H. (Jin), & Taylor, S. H. (2021). Tracing the Adoption and Effects of Open Science in Communication Research. PsyArXiv. https://doi.org/10.31234/osf.io/dsf67
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- Jun 2021
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twitter.com twitter.com
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Thomas Rhys Evans on Twitter: “🚨 Get Involved 🚨 #OpenScience practices and preregistration are all well and good, but do they help with applied and consultancy research? 🧵...” / Twitter. (n.d.). Retrieved June 27, 2021, from https://twitter.com/ThomasRhysEvans/status/1395752110088675328
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Study finds potentially druggable process of SARS-CoV-2 replication. (n.d.). Retrieved June 24, 2021, from https://phys.org/news/2021-06-potentially-druggable-sars-cov-replication.html
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- May 2021
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psyarxiv.com psyarxiv.com
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Braud, M., Gaboriaud, A., Ferry, T., Mardi, W. E., Silva, L. D., Lemouzy, M., Guttierrez, J., Petit, S., Szabelska, A., & IJzerman, H. (2021). COVID-19-related conspiracy beliefs and their relationship with perceived stress and pre-existing conspiracy beliefs in a Prolific Academic sample: A replication and extension of Georgiou et al. (2020). PsyArXiv. https://doi.org/10.31234/osf.io/t62s7
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twitter.com twitter.com
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Maarten van Smeden on Twitter. (n.d.). Twitter. Retrieved 4 March 2021, from https://twitter.com/MaartenvSmeden/status/1328093246829064192
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www.sciencemag.org www.sciencemag.org
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Moutinho, S., WadmanApr. 30, M., 2021, & Pm, 5:40. (2021, April 30). Is Russia’s COVID-19 vaccine safe? Brazil’s veto of Sputnik V sparks lawsuit threat and confusion. Science | AAAS. https://www.sciencemag.org/news/2021/04/russias-covid-19-vaccine-safe-brazils-veto-sputnik-v-sparks-lawsuit-threat-and
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- Apr 2021
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bmcmicrobiol.biomedcentral.com bmcmicrobiol.biomedcentral.com
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The pUB origin of replication stems from Staphylococcus aureus and is known to be active in a wide range of low GC Gram-positive bacteria (Firmicutes)
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- Mar 2021
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osf.io osf.io
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Breznau, N., Rinke, E. M., Wuttke, A., Adem, M., Adriaans, J., Alvarez-Benjumea, A., Andersen, H. K., Auer, D., Azevedo, F., Bahnsen, O., Balzer, D., Bauer, G., Bauer, P. C., Baumann, M., Baute, S., Benoit, V., Bernauer, J., Berning, C., Berthold, A., … Nguyen, H. H. V. (2021). Observing Many Researchers using the Same Data and Hypothesis Reveals a Hidden Universe of Data Analysis. MetaArXiv. https://doi.org/10.31222/osf.io/cd5j9
Tags
- noise
- behavioural science
- meta-science
- economics
- crowdsourcing
- psychology
- scientific method
- crowd sourced replication initiative
- reseach
- researcher variability
- garden of forking paths
- analytical flexibility
- lang:en
- political science
- social policy
- researcher degrees of freedom
- is:preprint
- immigration
- sociology
Annotators
URL
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psyarxiv.com psyarxiv.com
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Ryan, W., Baum, S., & Evers, E. (2021). People Behave as if they Anticipate Regret Conditional on Experiencing a Bad Outcome. PsyArXiv. https://doi.org/10.31234/osf.io/dcgpy
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Gernsbacher, M. A. (2018). Three ways to make replication mainstream. The Behavioral and Brain Sciences, 41, e129. https://doi.org/10.1017/S0140525X1800064X
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journals.sagepub.com journals.sagepub.com
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Hoogeveen, S., Sarafoglou, A., & Wagenmakers, E.-J. (2020). Laypeople Can Predict Which Social-Science Studies Will Be Replicated Successfully: Advances in Methods and Practices in Psychological Science. https://doi.org/10.1177/2515245920919667
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daniellakens.blogspot.com daniellakens.blogspot.com
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Lakens, D. (2020, November 29). The 20% Statistician: Why I care about replication studies. The 20% Statistician. https://daniellakens.blogspot.com/2020/11/why-i-care-about-replication-studies.html
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- Feb 2021
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Peyton, Kyle, Gregory A. Huber, and Alexander Coppock. “The Generalizability of Online Experiments Conducted During The COVID-19 Pandemic.” SocArXiv, November 28, 2020. https://doi.org/10.31235/osf.io/s45yg.
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brief19.com brief19.com
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Vaccinations Could Limit Further Mutations. (n.d.). Retrieved 18 February 2021, from https://brief19.com/2021/02/17/brief
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- Dec 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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All replication in R6K relies on the two essential components of a minimal replicon, the γ ori, and its cognate Rep, π protein, encoded by the pir gene
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psyarxiv.com psyarxiv.com
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Corker, K. S., Arnal, J., Bonfiglio, D. B. V., Curran, P. G., Chartier, C. R., Chopik, W. J., Guadagno, R., Kimbrough, A., Schmidt, K., & Wiggins, B. J. (2020). Many Labs 5: Registered Replication of Albarracín et al. (2008), Experiment 7. PsyArXiv. https://doi.org/10.31234/osf.io/qzspr
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- Nov 2020
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psyarxiv.com psyarxiv.com
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Schindler, S., Reinhardt, N., & Reinhard, M.-A. (2020). Defending one’s worldviews under mortality salience – Testing the validity of an established idea. PsyArXiv. https://doi.org/10.31234/osf.io/7bxcs
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journals.plos.org journals.plos.org
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Replication begins
Rolling circle replication overview
Replication begins when the Rep protein, which is encoded on the plasmid (ORF A), recognizes a specific site on the plasmid (double-strand origin, or DSO) and catalyzes the nicking of one DNA strand. The Rep protein remains bound to the 5′ phosphate after the nicking action. The newly released 3′ hydroxyl on the opposite end serves as a primer for DNA synthesis. The host DNA polymerase uses the unnicked circular strand as a template, so that a single replication fork moves around a plasmid until it regenerates the DSO. A second copy of Rep protein catalyzes the cleavage of the newly formed DSO, effectively releasing a single stranded copy of the plasmid. In the absence of Rep, the replication fork continues to move around the template, forming a single stranded concatemer. The single strand origin (SSO), a non-coding element that forms extensive secondary structure, is required for synthesis of the lagging strand. SSO sequences vary considerably among different RCR plasmids, but are extremely important for robust replication of the plasmid in the cell [10]. Here we describe the engineering of the pWV01 RCR origin to create pBAV1K-T5, a very broad-host range expression vector.
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- Oct 2020
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worksinprogress.co worksinprogress.co
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Escaping science’s paradox. (n.d.). Works in Progress. Retrieved 21 October 2020, from https://www.worksinprogress.co/issue/escaping-sciences-paradox/
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- Sep 2020
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journals.sagepub.com journals.sagepub.com
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Spellman, B. A. (2015). A Short (Personal) Future History of Revolution 2.0. Perspectives on Psychological Science, 10(6), 886–899. https://doi.org/10.1177/1745691615609918
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jamanetwork.com jamanetwork.com
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Kouzy, R., Jaoude, J. A., Garcia, C. J. G., Alam, M. B. E., Taniguchi, C. M., & Ludmir, E. B. (2020). Characteristics of the Multiplicity of Randomized Clinical Trials for Coronavirus Disease 2019 Launched During the Pandemic. JAMA Network Open, 3(7), e2015100–e2015100. https://doi.org/10.1001/jamanetworkopen.2020.15100
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www.youtube.com www.youtube.com
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JNOLive | Multiplicity of Randomized Clinical Trials for Coronavirus Disease 2019. (2020, July 14). https://www.youtube.com/watch?v=H-MWPqgLUvA&feature=youtu.be
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www.thelancet.com www.thelancet.com
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Chu, H., Chan, J. F.-W., Yuen, T. T.-T., Shuai, H., Yuan, S., Wang, Y., Hu, B., Yip, C. C.-Y., Tsang, J. O.-L., Huang, X., Chai, Y., Yang, D., Hou, Y., Chik, K. K.-H., Zhang, X., Fung, A. Y.-F., Tsoi, H.-W., Cai, J.-P., Chan, W.-M., … Yuen, K.-Y. (2020). Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: An observational study. The Lancet Microbe, 1(1), e14–e23. https://doi.org/10.1016/S2666-5247(20)30004-5
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- Aug 2020
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journals.sagepub.com journals.sagepub.com
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Hohn, R. E., Slaney, K. L., & Tafreshi, D. (2020). An Empirical Review of Research and Reporting Practices in Psychological Meta-Analyses. Review of General Psychology, 1089268020918844. https://doi.org/10.1177/1089268020918844
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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Frias‐Navarro, D., Pascual‐Llobell, J., Pascual‐Soler, M., Perezgonzalez, J., & Berrios‐Riquelme, J. (n.d.). Replication crisis or an opportunity to improve scientific production? European Journal of Education, n/a(n/a). https://doi.org/10.1111/ejed.12417
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osf.io osf.io
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Nelson, N. C., Ichikawa, K., Chung, J., & Malik, M. (2020). Mapping the discursive dimensions of the reproducibility crisis: A mixed methods analysis [Preprint]. MetaArXiv. https://doi.org/10.31222/osf.io/sbv3q
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Luban, J., Sattler, R., Mühlberger, E., Graci, J. D., Cao, L., Weetall, M., Trotta, C., Colacino, J. M., Bavari, S., Strambio-De-Castillia, C., Suder, E. L., Wang, Y., Soloveva, V., Cintron-Lue, K., Naryshkin, N. A., Pykett, M., Welch, E. M., O’Keefe, K., Kong, R., … Peltz, S. (2020). The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines. BioRxiv, 2020.08.05.238394. https://doi.org/10.1101/2020.08.05.238394
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www.latimes.com www.latimes.com
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C. L., & Print. (2020, August 14). Op-Ed: We rely on science. Why is it letting us down when we need it most? Los Angeles Times. https://www.latimes.com/opinion/story/2020-08-14/replication-crisis-science-cancer-memory-rewriting
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- Jul 2020
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www.newscientist.com www.newscientist.com
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Vaughan, A. (n.d.). Which covid-19 treatments work and how close are we to getting more? New Scientist. Retrieved 31 July 2020, from https://www.newscientist.com/article/2250176-which-covid-19-treatments-work-and-how-close-are-we-to-getting-more/
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marketplace.digitalocean.com marketplace.digitalocean.com
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Listens to changes in a PostgreSQL Database and broadcasts them over WebSocket. It works like this:the Phoenix server listens to PostgreSQL's replication functionality (using Postgres' logical decoding).it converts the byte stream into JSON.it then broadcasts over WebSocket.
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science.sciencemag.org science.sciencemag.org
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Barton, C. M., Alberti, M., Ames, D., Atkinson, J.-A., Bales, J., Burke, E., Chen, M., Diallo, S. Y., Earn, D. J. D., Fath, B., Feng, Z., Gibbons, C., Hammond, R., Heffernan, J., Houser, H., Hovmand, P. S., Kopainsky, B., Mabry, P. L., Mair, C., … Tucker, G. (2020). Call for transparency of COVID-19 models. Science, 368(6490), 482.2-483. https://doi.org/10.1126/science.abb8637
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www.youtube.com www.youtube.com
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King’s Open Research Conference | Anne Scheel | The Importance of Registered Reports. (n.d.). Retrieved June 18, 2020, from https://www.youtube.com/watch?v=d_gT2GLH1jM&feature=youtu.be
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psyarxiv.com psyarxiv.com
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Olsson-Collentine, A., van Assen, M. A. L. M., & Wicherts, J. M. (2020). Postprint—Heterogeneity in direct replications in psychology and its association with effect size [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/m23v4
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- Jun 2020
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rss.onlinelibrary.wiley.com rss.onlinelibrary.wiley.com
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Mathur, M. B., & VanderWeele, T. J. (2020). New statistical metrics for multisite replication projects. Journal of the Royal Statistical Society: Series A (Statistics in Society), 183(3), 1145–1166. https://doi.org/10.1111/rssa.12572
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psyarxiv.com psyarxiv.com
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Syed, M., & Donnellan, B. (2020). Registered Reports with Developmental and Secondary Data: Some Brief Observations and Introduction to the Special Issue [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/gnhxk
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twitter.com twitter.com
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Nivi Mani on Twitter. "I cannot stop smiling! Here is a first peek at the data from our online browser-based intermodal preferential looking set-up! We replicate the prediction effect (boy eats big cake, Mani & Huettig, 2012) using our online webcam testing software @julien__mayor @Kindskoepfe_Lab" / Twitter. (n.d.). Twitter. Retrieved June 15, 2020, from https://twitter.com/nivedita_mani/status/1265556217486815232
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www.cos.io www.cos.io
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Science, C. for O. (2020 May 5). TOP Factor to appear in Master Journal List. https://www.cos.io/about/news/cos-and-the-web-of-science-collaborate-to-bring-top-factor-to-master-journal-list
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www.bmj.com www.bmj.com
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Glasziou, P. P., Sanders, S., & Hoffmann, T. (2020). Waste in covid-19 research. BMJ 2020;369. doi: https://doi.org/10.1136/bmj.m1847
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www.theatlantic.com www.theatlantic.com
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Zhang, S. (2020, April 8). The Best Hopes for a Coronavirus Drug. The Atlantic. https://www.theatlantic.com/science/archive/2020/04/what-coronavirus-drug-will-look-like/609661/
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journals.sagepub.com journals.sagepub.com
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Rosenbusch, H., Hilbert, L. P., Evans, A. M., & Zeelenberg, M. (2020). StatBreak: Identifying “Lucky” Data Points Through Genetic Algorithms. Advances in Methods and Practices in Psychological Science, 2515245920917950. https://doi.org/10.1177/2515245920917950
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psyarxiv.com psyarxiv.com
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Leplaa, H. J., Rietbergen, C., & Hoijtink, H. (2020). Bayesian evaluation of replication studies [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/49tbz
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www.pnas.org www.pnas.org
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Yang, Y., Youyou, W., & Uzzi, B. (2020). Estimating the deep replicability of scientific findings using human and artificial intelligence. Proceedings of the National Academy of Sciences, 117(20), 10762–10768. https://doi.org/10.1073/pnas.1909046117
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- May 2020
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psycnet.apa.org psycnet.apa.org
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Schauer, J. M., & Hedges, L. V. (2020). Assessing heterogeneity and power in replications of psychological experiments. Psychological Bulletin. Advance online publication. https://doi.org/10.1037/bul0000232
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psyarxiv.com psyarxiv.com
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Uygun Tunç, D., & Tunç, M. N. (2020, May 13). Replication Under Underdetermination: Introducing Systematic Replications Framework. https://doi.org/10.31234/osf.io/pdm7y
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psyarxiv.com psyarxiv.com
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Haaf, J. M., Hoogeveen, S., Berkhout, S., Gronau, Q. F., & Wagenmakers, E. (2020, April 14). A Bayesian Multiverse Analysis of Many Labs 4: Quantifying the Evidence against Mortality Salience. https://doi.org/10.31234/osf.io/cb9er
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- Apr 2020
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psyarxiv.com psyarxiv.com
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Jamieson, R. K., & Pexman, P. M. (2020, April 20). Moving Beyond 20 Questions: We (Still) Need Stronger Psychological Theory. https://doi.org/10.1037/cap0000223
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IJzerman, H., Lewis, N. A., Jr., Weinstein, N., DeBruine, L. M., Ritchie, S. J., Vazire, S., … Przybylski, A. K. (2020, April 27). Psychological Science is Not Yet a Crisis-Ready Discipline. https://doi.org/10.31234/osf.io/whds4
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Wölfel, R., Corman, V.M., Guggemos, W. et al. Virological assessment of hospitalized patients with COVID-2019. Nature (2020). https://doi.org/10.1038/s41586-020-2196-x
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- Feb 2020
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www.sciencedirect.com www.sciencedirect.com
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0.506 (0.532)
can we find any measures of dispersion here?
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For the 12 studies with an original p < 0.005, 10 (83%) replicated. For the 12 studies with an original p > 0.005, only 1 (8%) replicated. Further work is needed to test if prediction markets outperform predictions based only on the initial p-value, to test if the market also aggregates other information important for reproducibility.
p values may capture all the information?
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- Dec 2019
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societyinmind.com societyinmind.com
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"The replication crisis, if nothing else, has shown that productivity is not intrinsically valuable. Much of what psychology has produced has been shown, empirically, to be a waste of time, effort, and money. As Gibson put it: our gains are puny, our science ill-founded. As a subject, it is hard to see what it has to lose from a period of theoretical confrontation. The ultimate response to the replication crisis will determine whether this bout is postponed or not."
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- Jul 2019
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microbialcellfactories.biomedcentral.com microbialcellfactories.biomedcentral.com
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pUC origin carries a point mutation in the sense RNA that stabilizes the priming complex, resulting in higher copy number
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- Jun 2016
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Local file Local file
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etter writing continued as a medium for theinformal exchange of information and for requesting fellowscientists to replicate experiments (Manten, 1980, p. 8).
replication happened outside of journals, via letter writing
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- Mar 2016
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download.springer.com download.springer.com
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Schmidt, S. (2009). Shall we really do it again? The powerful concept of replication is neglected in thesocial sciences.Review of General Psychology, 13(2), 90–100.
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Evanschitzky, H., Baumgarth, C., Hubbard, R., & Armstrong, J. S. (2007). Replication research’s disturbingtrend.Journal of Business Research, 60(4), 411–415. doi
replication research
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- Jan 2015
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liliputing.com liliputing.com
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Teachers can save digital content to the built-in storage and up to 50 students at a time can connect to the Access Point to download or access documents, videos, or other files on their own devices even if there’s no internet signal.
CouchDB replication anyone?
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- Oct 2013
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www.ploscompbiol.org www.ploscompbiol.org
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Replication is the cornerstone of a cumulative science
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