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  1. Last 7 days
    1. Jonathan Rothberg 🦋. (2021, March 2). Testing works. I test daily. Insist on HOME testing. @michaelmina_lab @JoeBiden Research suggests B.1.526 needs to be closely watched “for its ability to evade both monoclonal antibody and, to a certain extent, the vaccine-induced antibody,” said Fauci [Tweet]. @JMRothberg. https://twitter.com/JMRothberg/status/1366755339912306688

  2. Apr 2021
    1. Ich kann irgendwie keinen Text auswählen aber die PageNotes klappen :D

  3. Mar 2021
    1. Create a note by selecting some text and clicking the button

      example

    1. 命令总结 指令 描述 /start Just a greeting /uptime returns Lupin Uptime /ver returns Lupin running Version /help help command (WIP) /anno URL Import hypothesis annotations from URL /importFC Imports your Flashcards into Lupin /srs import alias of /importFC /srs x starts a round of SRS for x flashcards /getMM pageTitle Generates a dynamic MindMap for pageTitle /pullNow Pulls all pages from your Git for fast access /themes calls the theme changer /encryptAll Encrypts all your pages with AGE keys /decryptAll Decrypts all your pages back to clear text

      tewat

    1. There is obvious connections between the flow paths of a use case and its test cases. Deriving functional test cases from a use case through its scenarios (running instances of a use case) is straightforward.
    2. With content based upon an action or event flow structure, a model of well-written use cases also serves as an excellent groundwork and valuable guidelines for the design of test cases
    1. TRAILBLAZER-STORY will follow as it turned out to be inevitable for setting up application state for tests. Instead of fumbling around with factories and traits in your tests, you “tell a story” about what to create in which order, easily customizable, and all written using activities.
    1. It is absolutely advisable to use factory in combination with let. let(:song) { factory( Song::Create, { title: "Timebomb", band: "Rancid" } ) }
    2. You should always use operations as factories in tests.
    3. There are several helpers to deal with operation tests and operations used as factories.
    4. In production, you will never trigger one specific callback or a particular validation, only. Your application will run all code required to create a Song object, for instance. In Trailblazer, this means running the Song::Create operation, and testing that very operation with all its side-effects.
    5. Unit tests for operations: They test all edge cases in a nice, fast unit test environment without any HTTP involved.
    1. Coronavirus Pandemic Data Explorer. (n.d.). Our World in Data. Retrieved March 3, 2021, from https://ourworldindata.org/coronavirus-data-explorer

      is:webpage lang:en COVID-19 graph case death Germany Sweden UK Afghanistan Africa Albania Algeria Andorra Angola Anguilla Antigua Barbuda Argentina Armenia Asia Australia Austria Azerbaijan Bahamas Bahrain Bangladesh Barbados Belarus Belgium Belize Benin Bermuda Bhutan Bolivia Bosnia Herzegovina Botswana Brazil Bulgaria Burkina Faso Burundi Cambodia Cameroon Canada Cape Verde Cayman Islands Central African Republic Chad Chile China Colombia Comoros Congo Costa Rica Cote d'ivoire Croatia Cuba Cyprus Czechia Democratic Republic of Congo Denmark Djobouti Dominica Dominician Republic Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Eswatini Ethiopia Europe Europian Union Faeroe Islands Falkland Islands Fiji Finland France Gabon Gambia Georgia Ghana Gibraltar Greece Greenland Grenada Guatemala Guernsey Guinea Guinea-Bissau Guyana Haiti Honduras Hong Kong Hungary Iceland India Indonesia Iran Iraq Ireland Isle of Man israel Italy Jamaica Japan Jersey Jordan Kazakhstan Kenya Kosovo Kuwait Kyrgyzstan Laos Latvia Lebanon Lesotho Liberia Libya Liechtenstein Lithuania Luxembourg Macao Madagascar Malawi Malaysia Maldives Mali Malta Mashall Islands Mauritania Mauritius Mexico Micronesia Moldova Monaco Mongolia Montenegro Morocco Mozambique Myanmar Namibia Nepal Netherlands New Zealand Nicaragua Niger Nigeria North America North Macedonia Northern Cyprus Norway Oceania Oman Pakistan Palestine Panama Papua New Guinea Paraguay Peru Philipines Poland Portugal Qatar Romania Russia Rwanda Saint Helena Saint Kitts and Nevis Saint Lucia Saint Vincent Grenadines Samoa San Marino Sao Tome and Principe Saudi Arabia Senegal Serbia Seychelles Sierra Leone Singapore Slovakia Slovenia Solomon Islands Somalia South Africa South America South Korea South Sudan Spain Sri Lanka Sudan Suriname Switzerland Syria Taiwan Tajikistan Tanzania Thailand Timor Togo Trinidad Tobago Tunisia Turkey Turks and Caicos Islands Uganda Ukraine United Arab Emirates USA Uruguay Uzbekistan Vanuatu Vatican Venezuela Vietnam World Yemen Zambia Zimbabwe test vaccine chart map table data case fatality rate mortality

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    1. 서울대학교 UX lab에서 하이포테시스를 사용한 첫 사례가 되어보았습니다. 저는 인턴 이윤수입니다.

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    1. Kevin McConway. ‘Media: Worst Ever Week for Test & Trace; They Only Reached 59.9% of Identified Contacts. But the % Reached Went up This Week for Contacts Managed by Local Health Protection Teams AND for Contacts Not Managed by Them (What Used to Be Called “complex” and “Non-Complex” Cases.) How?’ Tweet. @kjm2 (blog), 5 November 2020. https://twitter.com/kjm2/status/1324417367477264386.

    1. Why separate out red tests from green tests? Because my green tests serve a fundamentally different purpose. They are there to act as a living specification, validating that the behaviors work as expected. Regardless of whether they are implemented in a unit testing framework or an acceptance testing framework, they are in essence acceptance tests because they’re based upon validating behaviors or acceptance criteria rather than implementation details.
    2. Conversely, red tests are tests I write after the code is written to lock down some implementation.
    3. Have you ever played the game 20 questions? Most of us have played that game at one point in our lives. One person thinks of something that could be an animal, vegetable, or mineral and then they answer yes/no questions that are asked of them. The point of the game is to ask as few questions as possible in order to accurately guess what the person is thinking.  This is how I think of the unit tests that I write the specified behavior as I’m doing test-first development. I ask what are the fewest tests that I need to write in order to assert the behavior I want to create.
    4. I am a big advocate of having a complete test base and even erring on the side of caution when it comes to quality engineering and software validation but that is not what we’re talking about here. What we’re talking about here are the tests that we write when we’re doing test-first development and I’m proposing that writing those tests from the perspective of specifying the behaviors that we want to create is a highly valuable way of writing tests because it drives us to think at the right level of abstraction for creating behavioral tests and that allow us the freedom to refactor our code without breaking it.
  4. Feb 2021
    1. How do you know if source maps are working correctly? Try adding a syntax error to one of your assets and use the console to debug. Does it show the correct file and source location? Or does it reference the top level application.js file?
    1. Release from cell cycle arrest with Cdk4/6 inhibitors generates highly synchronised cell cycle progression in human cell culture

      [TEST] Reviewer 2: In their manuscript “Release from cell cycle arrest with Cdk4/6 inhibitors generates highly synchronised cell cycle progression in human cell culture” Trotter and Hagan investigated cell synchronization via CDK4 inhibitors as an alternative approach to commonly used thymidine-release regimes. The authors find that CDK4 inhibitor-based synchronization is suitable in 5 out of 25 tested cell lines (they show only data of 4 cell lines!) and provide FACS and Western blot data confirming this notion. Overall, the manuscript has the character of a methods study and does not explore the consequences and potential side-effects of CDK4 inhibitor based synchronization beyond the first two mitoses. Using CDK4 inhibitors to (pre)-synchronize cells in G1 phase is not a novel idea and has been used/published before (e.g. recently by Jackman et al., JCB 2020), however, to my knowledge a methodological study as presented here comparing different cell lines and different CDK4 inhibitors to synchronize cells has not been performed. Precise and as much as possible perturbation-free cell cycle synchronization remains key to cell cycle research, hence I think the presented manuscript has the potential to be a valuable addition to the field.

      Except for the missing information on the number of experimental repeats for most experiments (see below) and a request to also include a tabular overview of all cell lines investigated, I do not have major criticisms precluding publication from my point of view. There are several points, however, the authors should address to make the manuscript stronger and more useful to the community.

      1) Discussion & Introduction

      -In recent years, live imaging studies of asynchronous cells, e.g. by the Meyer, Spencer, Mansfeld, Purvis or Bakal labs, have demonstrated that at least for single cell analyses no synchronization regimes are required anymore because singe cells tracks can be aligned computationally to a common cell cycle starting point after the experiment. Of course, such approaches are not compatible with biochemical experiments, but certainly support diverse functional analyses that previously were only possible by synchronized populations such as monitoring degradation/expression profiles of proteins. Hence, to my opinion at least the introduction would benefit from a short paragraph putting the “old school” bulk synchronization regimes to which also their approach belongs into context with such single cell alternatives.

      -Can the authors provide a reference/results for their statement that RPE-1 cells are “refractory to double thymidine block induction synchronization” and that the levels of synchrony are low after serum starvation (l251ff)?

      -Contact inhibition as an alternative method for synchronization, especially in RPE-1 cells, should be mentioned as well.

      -p21, l516ff and p22, l534ff. Can the authors please indicate the names of the cell lines they refer to and not just the references. Also, does this argumentation then hold true for the altered genotypes we know of the non-responsive cell lines? E.g. MCF10A, which lack p16 and amplify myc signaling? Here, it would make sense to include known restriction-point genotype information in the table of all cell lines tested as suggested below. This would greatly benefit researchers choosing the right synchronization protocol for their individual cell line models.

      -p23, l580ff. The closing statement is weak and does not connect well to the text before. Could be completely omitted.

      -p20, l494. While the authors show based on gH2AX staining that there is not increased DNA damage due to CDK4i synchronization in S phase and mitosis they have no own data showing that chromosome segregation is not affected by CDK4 inhibition. While they reference a personal communication with the Pines lab, they should tone down this claim sufficiently.

      P19, l474. The authors should remove the claim of novelty, because CDK4 inhibitors have been used before to synchronize cells, e.g. by refs 56 and 57 and others, e.g. Spencer et al., 2013 have use MEKK inhibitors, which target CDK4 indirectly via cyclin D.

      P20, l501. This holds also true for contact inhibition!

      2) Figures

      -For data presentations with bar charts showing lower n (<10) it would be useful if the authors over plot the single data points on top of the bar charts to enable the reader estimating the distribution of the data. Also, the precise number of repetitions should be indicated, e.g. Fig 1, 4, 6,7,8, 9. It should be indicated if bars show the mean or median!

      -All Western blot analyses should indicate molecular markers (Figs 3 &5) and in the absence of quantifications, it should be mentioned of how many experiments the data is representative of.

      -Generally, for all experiments/data it should be indicated of how many independent repeats the data is representative/shown. E.g. it is not clear of how many repeats the data without error bars is representative of in basically all figures with such data.

      -Generally, the authors should carefully re-read their figure captions and make sure that the referrals to explanations in other figures are correct and provide sufficient data. As a reader, I find it somewhat cumbersome, if I have read the legends of 3 figures to get all the required information – e.g. legend to figure 8 refers to figure legend 7, which refers to Figure legend …

      -Figure 9, the unit of the concentrations of palbociclib is not given.

      Experiments

      -Western blot analyses in Figures 3 and 5. I am not sure if I understand the data and the corresponding description in the figure legend (l916ff). Eg5 is degraded by the APC/C at the G1 phase (Eguren et al., Cell Rep. 2014) and S10 on histone H3 is phosphorylated at the end of G2 phase and trough-out mitosis. To better define mitosis (and the end of M) the authors should also blot for cyclin B1 and/or cyclin A2. The choice of Eg5 and Wee1 is not ideal as their degradation profile is not as sharp and poorly visible in the data presented. Furthermore, it would benefit their comparison between different cell lines if in both experiments the same markers are analysed. Finally, the pS10 blotting and the FACS profiles in Figure 5 indicate that the cells are still significantly enriched in G2 or M phase as the pS10 peak is still very high by the end of the experiment. This indicates that THP-1 cells have a longer cell cycle than RPE-1 cells or that the release in THP-1 is slower than in RPE-1 cells at a certain cell cycle stage. Can the authors comment on this and better describe their data?

      -The authors should include a table with all 25 cell lines tested indicating, which cell lines are suitable for CDK4 inhibitor based synchronization and which are not. They mention in the text only few non-responsive ones, but this information is important for the reproducibility of their data and will save the time of others applying this approach to non-responsive cells. Also, the identity of 5th cell line that responded well to CDK4i synchronization is not given.

    2. Release from cell cycle arrest with Cdk4/6 inhibitors generates highly synchronised cell cycle progression in human cell culture

      [TEST] Reviewer 1: Release from the cell cycle arrest with Cdk4/6 inhibitors generates highly synchronised cell cycle progression in human cell culture by Trotter and Hagan

      In this very interesting manuscript Trotter and Hagan use Cdk4/6 inhibitors, predominately the drug palbociclib, to arrest hTERT-RPE1 cells close to 100% in G1 phase of the cell cycle. Wash out of the drug then triggers synchronized progression of the cells through the cell cycle. The authors carefully define the conditions that allow high efficient synchronisation with palbociclib and establish that this arrest and release protocol does not cause DNA damage as this is the case for the conventional thymidine block and release scheme. The synchronisation protocol described by Trotter and Hagan will help many researchers to perform highly reproducible and meaningful cell cycle analysis experiments in cell lines that before resisted the conventional protocols. I therefore strongly support publishing of this manuscript in Open Biology. I have only minor points that the authors may want to address before publication.

      Specific points

      1. Line 276: “indicated by black and red line sin the FACS plots”.
      2. Lines 291-295: complicated long sentence. Please simplify.
      3. Line 294; remove “data”.
      4. Line 300: “open black squares”.
      5. Fig. 7d: why do authors use grey and blue colours? I guess that two synchronized cultures were used. The colour code on top should follow the colour code in the bars: light, medium, high. The colour code is not completely clear. I guess EdU means EdU positive (+/- gamma-H2AX) and gamma-H2AX (+/- EdU). Please clarify.
      6. An alternative way of analysing Fig. 7d is counting G2 cells (CENP-F positive) for gamma-H2AX staining with and without synchronization. The synchronized cells would be analysed after 14-16 h. This would address whether the synchronisation scheme leads to cells with DNA damage.
      7. The authors should explain better how the experiment in Fig. 9 was done. I guess that cells were incubated with the given palbociclib concentrations for the stated time. The medium was then changed (no palbociclib + nocodazole) and cells were incubated for 24 h followed by FACS analysis. How do the authors explain the behaviour of A549? Shorter incubation
    1. Cell-density effects are generally thought to be mediatedby external signal molecules that affect gene expressionwhen they reach a certain threshold concentration, aphenomenon called quorum sensing

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    1. A tramping of sea boots was heard in the entry; the door was flung open, and in rolled a wild set of mariners enough. Enveloped in their shaggy watch coats, and with their heads muffled in woollen comforters, all bedarned and ragged, and their beards stiff with icicles, they seemed an eruption of bears from Labrador. They had just landed from their boat, and this was the first house they entered. No wonder, then, that they made a straight wake for the whale’s mouth—the bar—when the wrinkled little old Jonah, there officiating, soon poured them out brimmers all round. One complained of a bad cold in his head, upon which Jonah mixed him a pitch-like potion of gin and molasses, which he swore was a sovereign cure for all colds and catarrhs whatsoever, never mind of how long standing, or whether caught off the coast of Labrador, or on the weather side of an ice-island.

      Testing the API

  5. Jan 2021
    1. An important aspect of the environmental management literature considers the strength and nature of the relationship between economic development and environmental degradation, more specifically whether the former can feasibly be achieved without the latter. Some research has supported the existence of an Environmental Kuznets Curve (EKC), according to which environmental degradation increases up to a point as economies grow but then declines with further affluence [1–5]; however, a substantial body of research has cast doubts on whether countries can truly “grow” their way out of environmental problems [6–10]. As a result, the conventional economic growth paradigm is being challenged from multiple sources, with critics arguing that not only are we in danger of exceeding planetary boundaries [11,12], but that unrestrained growth is also a root cause of unsustainability and contributes to political disaffection, social inequality,

      Annotation in pdf

  6. Dec 2020
  7. www.investopedia.com www.investopedia.com
    1. Essentially, a t-test allows us to compare the average values of the two data sets and determine if they came from the same population.

      Comparing datasets to see if they came from the same population.

    1. Nothing has any purpose. Life is meaningless. Any purposes you imagine you have are illusions, errors, or lies. This is the stance of nihilism. It appears quite logical. It might seem to follow naturally from some scientific facts: everything is made of subatomic particles; they certainly don’t have purposes; and you can’t get purpose by glomming together a bunch of purposeless bits. It is easy to fall into nihilism in moments of despair; but, fortunately, it is difficult to maintain, and hardly anyone holds it for long. Nevertheless, the seemingly compelling logic of nihilism needs an answer. It turns out that it is quite wrong, as a matter again of science and logic. But because that is not obvious, three other stances try (and fail) to find a middle way between eternalism and nihilism.

      Hypothesis is reporting the HTML of this selection contains a number of newlines that don't appear in the HTML on the page.

  8. Nov 2020
    1. If you get a positive PCR test and you want to be sure that what you’re finding is a true positive, then you have to perform a viral culture. What this means is that you take the sample, add it to respiratory cells in a petri dish, and see if you can get those cells to start producing new virus particles. If they do, then you know you have a true positive result. For this reason, viral culture is considered the “gold standard” method for diagnosis of viral infections. However, this method is rarely used in clinical practice, which means that in reality, a diagnosis is often made based entirely on the PCR test.

      [[Z: A positive PCR should be followed by a viral culture test to see if you're dealing with a live infection]]

      After a positive PCR test, you don't know if the virus is alive or not. To find this out you can add it to respiratory cells (in the case of a respiratory virus) and see if they start producing virus particles).

      [[Z: Viral culture tests are rarely used in clinical practice]]

      Positive diagnoses of COVID-19 are done base on PCR only.

  9. Oct 2020
    1. Standing in solidarity with black activists, artists, researchers, and communities

      This is a test annotation.

    1. 可惜的是,Hypothesis 官网的检索功能比较简陋,也没有提供批量导出功能。对此,最简单的解决方案是使用前面提到的 Facet 工具

      Q: Facet工具是做什么的

    1. This is a page note test.

    2. Hypothesis users can create their own annotations, and you can reply to each other’s comments in the side panel.

      This is an annotation test.

  10. Sep 2020
    1. hypothes.is

      Hello this is a test !

      Hypothesis is a new effort to implement an old idea: A conversation layer over the entire web that works everywhere, without needing implementation by any underlying site

      Thank you Chris https://twitter.com/choldgraf !

    1. Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) cause familialParkinson’s disease, and sequence variations are associated with the sporadic form of the disease.LRRK2 phosphorylates a subset of RAB proteins implicated in secretory and recycling traffickingpathways, including RAB8A and RAB10. Another RAB protein, RAB29, has been reported to recruitLRRK2 to the Golgi,

      this is a test

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  11. twitter.com