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11 08, 2021

New preprint – A spatiotemporal complexity architecture of human brain activity

2021-08-12T11:09:46+02:00

New preprint – A spatiotemporal complexity architecture of human brain activity

The human brain is a complex network. Ever since the first description of “functional connectivity” in the 1990s, network neuroscience has emerged as one of the leading approaches to study the brain, including unparalleled international collaborations like the Human Connectome Project (HCP).

While our understanding of the connectome is rapidly increasing, some fundamental questions about brain networks remain: How does a functional connection between two brain regions form? Why are some regions more functionally connected than others? And what determines the spatial and temporal organization of the network?

In our latest preprint, we shed some light on these questions through complexity analysis of resting-state data from the HCP. In this manuscript, we report a mechanism by which the brain’s network architecture arises from spontaneous episodes of neural regularity. These episodes become visible as “complexity drops” and provide a unifying explanation for many known properties of the human brain, including functional connectivity, brain states, structure-function relationships, and network hierarchies. For more on this human “complexome”, check out the preprint!

New preprint – A spatiotemporal complexity architecture of human brain activity2021-08-12T11:09:46+02:00
14 07, 2021

New study published in JAMA Oncology!

2021-07-14T09:28:04+02:00

New study published in JAMA Oncology!

Our recent article shows that brain-targeting autoantibodies found in lung cancer patients may be responsible for cancer-related cognitive impairment.

In this prospective, cross-sectional study we included 167 patients with lung cancer. Brain-directed autoantibodies were found in 36.5% of all patients: 19.8% had known neuronal autoantibodies and 16.8% had autoantibodies against currently unknown antigens that were detected by immunohistochemistry. Cognitive impairment was found in as much as 67.0% of patients. Importantly, patients with neuronal autoantibodies had increased odds of cognitive impairment compared with patients without autoantibodies. Interestingly, autoantibodies against currently unknown neuronal antigens were also associated with higher odds of cognitive impairment.

Therefore, our study suggests that neuronal autoantibodies might represent a pathogenic factor in cancer-related cognitive impairment among patients with lung cancer.

There is a JAMA Oncology podcast interview with Frederik and Carsten at: https://edhub.ama-assn.org/jn-learning/audio-player/18621621 and an editorial about our study at: https://jamanetwork.com/journals/jamaoncology/article-abstract/2781393

The full study can be found online here and downloaded as a pdf here!

New study published in JAMA Oncology!2021-07-14T09:28:04+02:00
2 06, 2021

German translation of the MMQ

2021-06-02T11:12:14+02:00

German translation of the MMQ

Interested in assessing subjective memory? The German translation by @JosephineHeine and @SophiaRekers of the Multifactorial Memory Questionnaire (MMQ) is now freely available for clinicians and researchers here. Normative and psychometric data coming soon. Stay tuned!

German translation of the MMQ2021-06-02T11:12:14+02:00
31 08, 2020

New paper in Annals of Neurology on clinical and MRI outcomes in pediatric NMDAR encephalitis

2020-09-28T12:30:03+02:00

New paper in Annals of Neurology: Clinical and Magnetic Resonance Imaging Outcome Predictors in Pediatric Anti–N-Methyl-D-Aspartate Receptor Encephalitis

Longitudinal volumetric MRI analyses revealed significant brain volume loss and failure of age-expected brain growth in pediatric anti-NMDA receptor encephalitis. Abnormal MRI findings, a clinical presentation with sensorimotor deficits, and a treatment delay of over 4 weeks were identified as predictors of poor clinical outcome.

Find the full publication here.

New paper in Annals of Neurology on clinical and MRI outcomes in pediatric NMDAR encephalitis2020-09-28T12:30:03+02:00
23 03, 2020

Archiv and Ablage

2020-04-01T10:24:30+02:00

Archiv and Ablage

[Written by Johanna on 2019/06/20]

The title will probably be the key word that appears in the wiki and is thus directly linked to your entry.

Table of content

  1. What is it for?
    • Ablage
    • Archiv
  2. How do I get access?
    • Ablage
    • Archiv
  3. How do I store my data there?
    • Ablage
    • Archiv
  4. Links

What is it for?

The Ablage and Archiv can be used to store your data. There are a few differences between the two:

Ablage

If you want to back-up data from a running project or want to save files/data your currently working with on a Charité-Server, you can use this folder. The Ablage has space for 8TB.

Archiv

Additionally to the Datenablage, we now have access to the Archiv (10TB). The Archiv can be used for data which won’t be modified anymore. Everybody should think about what they can put in the Archiv to save space in the Datenablage, e.g. already finished projects.

How do I get access?

Ablage

To store data in the Ablage, you need to get permission by the Charité IT.

You must fill out this form: https://intranet.charite.de/fileadmin/user_upload/microsites/gb/it/sys/Beantragung-Rechte.pdf

Johanna/Leonie can help you if you should have questions.

You then find the folder DATEN here:

(S:) CHARITE-DATEN-ABLAGE

– AG

-AG-Finke

-Daten

Archiv

Because we seriously cannot modify the data once it is uploaded in the Archiv, we have to be very careful what we put there. Everybody who got granted access to the Datenablage is also able to read the Archiv. However, only Maron and Johanna/Leonie have the possibility to upload data.

How do I store my data there?

Ablage

The folder structure is the following: \NAME\PROJECT

Please keep in mind that the space is limited to 8TB for the whole lab. To keep track of the Datenablage, Carsten made this google doc:

https://docs.google.com/spreadsheets/d/1a956pDa-BgsnxDtLHnEnZSvzaWu471Fp3_y3dLyh7tQ/edit#gid=0

Please put all the relevant information concerning the data you want to store in this spreadsheet.

Archiv

If you want to store data in the Archiv

(1) put your data in the folder ‘ready_for_archiv’ in the Datenablage

(2) Write a mail to Maron and/or Johanna/Leonie and we will move the data to the Archiv

Links

https://intranet.charite.de/fileadmin/user_upload/microsites/gb/it/sys/Beantragung-Rechte.pdf

Archiv and Ablage2020-04-01T10:24:30+02:00
23 03, 2020

Ethics

2020-04-01T10:23:10+02:00

How to Ethics

Initially the most important task is to find out when the ethics committee meets, and then submit to them at least 14 days prior so that your application can be scheduled in for that meeting. Meeting dates for 2019 can be found here. The committee should generally get back to you within 10 days of the Meeting with a decision.

For your ethics submission you will require the following documents

  1. Ethikantrag (Ethics Application)
  2. Anschreiben (Cover Letter)
  3. Studieninformation (Study Information for Participants),
  4. Einwilligungserklärung (Participant Consent Form)
  5. Case Report Form – in most cases this is not needed, but be sure to check first.

The Ethikantrag can be downloaded here. However, check on the website if there is a newer version.

The key to writing the Ethikantrag is to be clear and precise, but not too detailed. The latter may seem counter-intuitive, but being too specific in your explanations may then require you to submit amendments to ethics for every small change you want to make. Reviewers are unlikely to care about the specificities of your research, as their priority is ensuring that you have identified potential risks for participants and that participants are aware of their rights. Furthermore, in many cases, ethics is time-pressured and often submitted before you yourself have an extremely clear idea of the ins and outs of your study. An example of this would be saying “validated and commonly used tests of memory, attention and speed will be used to test the cognitive functioning of participants”, instead of listing out each and every test, and then later having to make an ethics amendment if you wish to change one. However, if you are already quite sure of what test you will be using, then by all means, list it.

There are many sections (e.g. data protection, insurance, participant rights) from each of the required documents which can be copied directly from previous submissions. Just ask a lab member if they could forward you one of the previous applications.

As for a general template or structure of the various required documents, Stephan kindly shared around approved Study Information and Consent forms for the V-Reha project in 2018 which can be found here.

Ethics2020-04-01T10:23:10+02:00
23 03, 2020

Github

2020-03-23T15:51:03+01:00

HOW TO: GitHub for Version Control

[Written by Graham Cooper on 2019/15/01]

Table of content

  1. Version Control in GitHub
  2. Set up Git and GitHub
  3. Git Commands
  4. Links
  5. Literature

Version Control in GitHub

Reproducibility ensures that anyone (including you in 6 months’ time!) can take your data and get the same results and tables that you originally found/generated. Problems with reproducibility (and how to overcome these) have been widely discussed in recent years, particularly in the behavioral sciences. One major obstacle standing in the way of reproducibility in research is good curation of data, i.e. storing everything in a sensible place, keeping track of changes in files by various collaborators. This is a particular challenge for us as researchers as (generally) we have been taught how to collect and analyze data to a high level of skill but have received next to no training in how to curate that data once it exists. Git (and GitHub) is one popular version control system that enables such data curation and is widely used in the field of software engineering, where the skills of data science/data management are taught to a gold standard. Using Git and GitHub, you have one space where all your relevant documents can be stored. Every version of your documents is saved so you can easily go back and check previous versions without needing to search through endless files names “manuscript_draft_version_16_FINAL_draft_ACTUAL_FINAL_DRAFT.doc”, for example! It also makes collaboration easier as everyone can work on the same document at once and merge versions, while keeping track of who did what. At the end of the project it also facilitates sharing of data and code as you can make a private repository public and add a link that everyone can access.

Currently GitHub allow users to have unlimited private repositories!

See Vuorre & Corley (2018) for a more detailed tutorial on Git and GitHub including how to set it up. A link to the online pdf is available in the links section.

Git Commands

Below is a list of common commands for Git and what they are used for.

git init

Initializes an empty git repository

git status

Shows all changes made since last “commit”

git add

Adds changes to the file to be committed

git commit -m “added file”

Commit all changes (signify that these changes should be included in the document). The text after the -m flag is the commit message that describes the changes you made

Links

Literature

  1. Vuorre, M. & Curley, J. P. (2018) Curating Research Assets: A Tutorial on the Git Version Control System. Advances in Methods and Practices in Psychological Science, 1(2).
Github2020-03-23T15:51:03+01:00
23 03, 2020

How to hire an intern

2020-04-01T10:24:05+02:00

How to hire an intern

[Written by Sophia on 2019/01/14]

Lot’s of work and only 24 hours in a day. That’s why you need an intern or more than one. In order to do it efficiently and without getting in trouble with administration, there are a couple of things you need to be consider.

Table of content

  1. Approaches
  2. Job analysis
  3. Sourcing
    • Heading 2.1
      • Heading 2.1.1
  1. Screening and selection
  2. Desk space
  3. Payment
  4. Organization
    • Documents for Annette
  1. Links
  2. Literature

Approaches

Two ways to go with ups and downs:

Passive (being wooed): Wait for people to contact the lab or you

+ little effort

– bit of a gamble whether the person is a good fit

Active (looking for people you need): Put out an ad with what you need

+ a bit of work

– more likely to find a person who is a good fit

Job analysis

  • What is the job I want the person to do (Main task, Side tasks, Project)
  • Knowledge, skills, abilities and other characteristics necessary to complete the tasks (language, programming, analysis, …)
  • What are the skills which are useful but not mandatory
  • What can you offer the person (be realistic)
  • Time Frame: Full-time, part-time, How many weeks, months
  • Can you offer to supervise a thesis following the internship
  • Specify which documents (e.g. CV, transcript of records, X-pages cover letter) you want until which date on which you base your decision to invite them for a telephone/skype call or personal interview.

Sourcing

  • Identify the target group (Students of which subject, Bachelor/ Master, the year)
  • Where do I find this target group: FU, HU, TU, Charité, Mind and Brain
  • Contact the respective institution: Mailing list, lecturers, teaching coordinators

Screening and selection

  • Try to give every candidate equal chance of proving their ability by asking roughly the same questions / giving same task
  • Figure out before meeting: What do you want to know from them?
  • Tell them when they are going to hear from you regarding your decision
  • Might be good idea to ask them to get back to you after xy days on whether they want to do the internship before you tell them your decision

Payment

  • In most of cases, you will not be able to pay your intern with money. In Germany the only way not to pay an intern is, when the internship is mandatory for their study
    • You need prove of that by the sending institution (Erklaerung A, signed and stamped by the sending institution, if not HU student)
    • You pay the person with knowledge, professional growth and a Confirmation of what they did in the internship and how well they did that
  • At least for longer internships, it’s a token of appreciation, if you give them a little something (e.g. book and a thank you card)

Work Space

Where your intern will be working depends also on where you work. There are 2-4 computers in the attic which are occupied by Finke lab interns. However, if you plan on using one of those, talk to the other lab members and how they are currently occupied. At least on one computer we have special rotation/ intern log-ins the person can use.

For the attic, the intern will need a key-card you can order from Laura (mb-office@hu-berlin.de). This will take a couple of days.

There are also interns at the Charité offices. Same thing applies about desk space – talk to your colleagues regarding availability. Depending on the office they will sit in, they will need either 70.105 or 725.1, which you can get from the Schlüsselverwaltung CCM.

Documents you need for Mind and Brain

The checked and signed Laufzettel (see attachemnts), including but not necessarily exclusively

  • If not Mind and Brain student: proof of mandatory internship (Erklaerung A)
  • Proof of liability insurance
  • Matriculation certificate
  • Hospitationsvereinbarung (signed by intern and Carsten)
  • Confirmation fireprotection (signed by intern)
  • Lab safety protocol they will be working in (signed by intern)
  • HU Keycard for Haus 1, Luisenstr. 56 with access to the rooms they will be working at
    • Contact Laura beforehand, otherwise you will have to open doors for them all day (mb-office@hu-berlin.de)
    • You will only get the keycard, if you hand out a copy of the completed Laufzettel
  • Internet access with HU account (usefull, if they stay for longer), CMS

All documents except for the MB_Laufzettel Praktikanten_Interns_Mitarbeiter.pdf can be found in the ZIP_folder_documents_1-11__18__and_3_x_extras and ZIP_folder_Praktika

Attachments

MB_Laufzettel Praktikanten_Interns_Mitarbeiter

Zip folders

ZIP_folder_documents_1-11__18__and_3_x_extras

ZIP_folder_Praktika Ausschreibung Praktikant

Example of an ad I posted in German: Ausschreibung Praktikant

How to hire an intern2020-04-01T10:24:05+02:00
23 03, 2020

How to: Get a Charité e-mail address / SAP access

2020-04-01T10:23:05+02:00

How to: Get a Charité e-mail address / SAP access

[Written by Josephine on 2019/01/14]

Table of content

  1. Charité e-mail address
    • Why do I need it?
    • How do I get it?
  2. SAP access
    • Why do I need it?
    • How do I get it?

Charité e-mail address

1.1.          Why do I need it?

Your Charité e-mail address will not only make a more professional impression when contacting study participants, it is also needed to access various applications at the Charité workplace, including:

  • Log in to the Charité desktop PCs (‘Klinischer Arbeitsplatz’)
  • Using the T: drive as your personal backup, accessible from every desktop PC on campus
  • Getting access to the Charité intranet website
  • Getting access to the Charité corporate benefit system
  • Providing an official e-mail for correspondence authorships

1.2.          How do I get it?

You will need a Charité e-mail address in order to apply for SAP. Fill out the attached application form for external employees if you do not have an official contract with Charité. The form needs to be signed by the head of the group (including stamp) and faxed to the IT office.

The ‘HR-OE’ organizational unit of the Department of Neurology (CCM) is: MNE-FO.

Heading 2

2.1.     Why do I need it?

Your SAP log in will allow you to access the digital patient documentation system. This includes information about:

  • Patients’ medical documentation and letters
  • Current patient lists of the wards
  • Scheduled appointments, tests and diagnostic findings of in-patients

2.2.     How do I get it?

Fill out the attached application form for external employees if you do not have an official contract with Charité. The form needs to be signed by the head of the group (including stamp) and faxed to the IT office.

Downloads: [Form Email] [Form SAP]

How to: Get a Charité e-mail address / SAP access2020-04-01T10:23:05+02:00
23 03, 2020

Order Retourenkleber

2020-04-01T10:24:57+02:00

Order Retourenkleber

[Written by Johanna on 2019/06/17]

Table of content

  1. What are Retourenkleber?
  2. Quick and easy: How to order them

What are “Retourenkleber”?

Retourenkleber are stickers you can hand out to patients or study participants when you want them to not have to pay the postage for the return of documents.

It means that we (aka Carstens third-party funds) pay for it once it arrives at the post office at Charité.

Currently, only the lab in Sauerbruchweg 5 uses Retourenkleber and we store them there.

They look like this:

Quick and easy: How to order them

  1. Ask Carsten which Kostenstelle should be used for the new Retourenkleber.
  2. Take the one of the old Retourenkleber and go to the post office in Charité Mitte (Hufelandweg 9, on the ground floor. Follow the signs.)
  3. Fill in a form to order the new ones, the friendly person behind the corner will help.
  4. Pick them up the next day at the post office.
Order Retourenkleber2020-04-01T10:24:57+02:00