AutoLit® User Guide
Examining Results in Synthesis
Administrative Tools
Support and FAQs
Best Nest Building Practices
SLR Basics: How to Perform Systematic Review
NMA Basics: How to Perform a Meta-Analysis
Best Practices for Writing a Publishable Manuscript
The Settings page allows you to create and edit a nest description and nest protocol, as well as manage User Keywords. Only the Owner and Admins of a nest can view its Settings page.
The Settings page is found in the top left of the page, underneath Nest Home and Activity. This link will only appear to the Owner and Admins in the nest; Settings are hidden from Users.
Add or remove User and/or Admin privileges for individuals and access and/or Ownership for Organizations in your specific nest. To learn how to do so for individuals or organizations, see the Manage Access page.
Note: Nest-level Admin functions are separate from Organization-level Admin functions.
From the Synthesis section, you can toggle ‘on’ or ‘off’ any Synthesis page: Qualitative Synthesis (QLS), Quantitative Synthesis (QNS), Manuscript, Dashboard, Critical Appraisal, or PRISMA.
By default:
Choose which QLS diagram is displayed when you open the Synthesis page: Sunburst or Dendrogram.
By default, the Sunburst diagram is selected and displayed in Synthesis:
But if the Dendrogram is selected, it will be displayed in Synthesis:
Note: both diagrams may still be accessed at anytime (circled in red) but this Setting decides which is shown by default.
Abstracts are automatically shown alongside records displayed in Synthesis. If you wish to also display Full Texts, toggle this on here. Due to copyright reasons, this cannot be turned on if your nest is public, only protected or private (see above).
Upload a pdf to be shown in Synthesis when Manuscript is toggled on and empty.
Manuscript in Synthesis will then display the pdf as such:
As an Admin, you can configure the Screening Mode to be:
Standard Screening means that each record will be screened by one user in a single session. The user will have the option of designating “Full Text Review”, but there is no separate Full Text step.
Dual Screening means that each record will be screened by two different users and adjudicated by a third.
Two-Pass Screening means that each record will be screened at the Abstract level by one user, and advanced to a second, separate Full Text screening step, where the record must have a full text PDF uploaded and a final Screening decision made by a single user.
Dual Two-Pass Screening combines these functions, meaning each record is screened by two different users and adjudicated at the Abstract step, and then two users must screen at the Full Text step followed by adjudication.
Toggling between Standard, Two-Pass, and Dual Screening (see image) can lead to loss of data, as only the final Inclusion and Exclusion decisions will be saved if you switch between Screening Modes!
Manual vs. Automatic: By default, the Screening Model will be on Manual, meaning that it will only run when a user selects Train Screening Model during the Screening process.
For Automatic Training, head to Nest Settings–> Screening Model. This will cause the Model to run as soon as a sufficient number of studies are screened, and this Model will be re-run automatically as more screening occurs.
As probabilities are generated, they are displayed in place of the “Train Screening Model” text in the Screening module, in the below case it is “P(Inclusion): 0.87.”.
Displayed vs. Hidden: By default, the Screening Model will be displayed, meaning that any user will be able to see the probabilities on the Screening panel:
If you want this probability to be hidden from all users, Admins, and Owners on each individual study, toggle “Hide Probabilities.” If hidden, you can still run the model from the Admin page and have the option to turn on Automatic updating. Learn more about the Screening model here.
If there are screening decisions from a previous nest that are relevant to your current nest, you can import existing screening decisions for any record already in your nest by uploading a spreadsheet. To do this, under Screening on the Settings page, selecting “Begin” under Import.
Tagging, by default, is in Form-based mode or you can turn on Standard mode:
In this mode, your configured tags will be displayed as an open-ended list to be selected from in order to extract data.
Standard tag recommendations are available to all users to assist in the Tagging process. Smart Tag recommendations are only available to enterprise users, but utilize OpenAI GPT 3.5/4 to search Abstracts and Full Texts. Toggling on “Smart (Beta)” will automatically generate recommendations for any included studies with available full texts. This will run in the background.
You have a limited number of regenerations due to the costliness of each generation. After full text smart recommendations are generated, and for further assistance, you have the option to also generate smart tag recommendations for included abstracts. Learn more about Tag Recommendations.
If there are tags from a previous nest that are relevant to your current nest, you can import existing tags for any record already in your nest by uploading a spreadsheet. To do this, under Tagging on the Settings page, selecting “Begin” under Import.
As an Admin, you can configure the Meta-Analytical Extraction Mode to be:
Standard MA Extraction means that each record will be extracted for quantitative data only once.
Dual MA Extraction means that each record will be extracted by two different users and adjudicated by a third. To toggle Dual MA Extraction 'on', select it in the Admin page:
To avoid bias in your review where multiple reviewers are participating, you may want to consider blinding certain aspects of the process. The Blinding settings allow you turn off or hide features.
Reviewers' identities are shown to adjudicators by default. You can hide these identities for each adjudication decision as to not influence the ultimate decision. To do this, toggle on “Blind Adjudication”:
For example:
Adjudicate Screening before Blinding:
After Blinding:
By default, records shown in the screening queue to reviewers is in order of Ref ID. You may wish to randomize the studies shown to avoid bias or order them by inclusion probability after the model is trained. Selecting the queue order affects the remainder of studies left in the screening queue.
When you have trained a Screening Model either manually or via automatic training these values are displayed in Screening. To avoid bias, you may wish to hide these probabilities. You can hide these probabilities in Nest Settings. This allows you to remove the advancement or inclusion probabilities for each study if turned on, so the reviewer can make a completely independent decision.
Note: Advancement probabilities are shown in Two-Pass Screening at the Abstract level, and Inclusion probabilities are shown in Standard Screening in the singular round of screening.
Screening before hiding probabilities:
After hiding probabilities:
If Robot Screener is on, these probabilities are automatically removed.
This removes the right-hand Comments tab in the workflow modules (Screening, Tagging, MA Extraction, Critical Appraisal), allowing you to hide any comments made on studies when viewing them. As a result comments can't directly be made as they appear in the queue but can be made and seen when the study is accessed in Study Inspector.
Right hand side tabs before hiding comments:
After hiding comments:
During Screening you may remove the Tagging tab available as you screen. We offer the ability to Tag during screening to be able to apply preliminary tags, but similarly it also exposes users to bias after a previous reviewer has screened and tagged. The before and after mirrors the above Comments removal but for the Tagging tab instead in Screening alone.
Copying a nest will copy the data and configurations, such as the search terms, references, exclusion reasons, the tagging hierarchy, applied tags, data elements, full-text PDFs, Critical Appraisal systems, the protocol and manuscript, and other configurations. The copied nest is entirely independent of the original nest. Access privileges will not be copied from the old nest and must be configured.
Only Owners have the right to delete a nest. “Delete” can be found next to “Rename”; deleting a nest is irreversible and will completely delete all data related to the project in question!
Deleting a nest has wide-reaching and irreversible effects, including loss of all nest data. Proceed with caution!
These features are only available to admins within an organization subscribed at the Enterprise level.
Allocation allows you to assign work in specific modules to various members of your team. Learn more about Allocation.
Nest Versions allow you to manually save up a version of your nest at a specific date and time. Learn more about Nest Versions.
