DNA fragments binding CTCF in vitro and in vivo are capable of blocking enhancer activity

<p>Abstract</p> <p>Background</p> <p>Earlier we identified ten 100-300-bp long CTCF-binding DNA fragments selected earlier from a 1-Mb human chromosome 19 region. Here the positive-negative selection technique was used to check the ability of CTCF-binding human genomic fragments to block enhancer-promoter interaction when inserted into the genome.</p> <p>Results</p> <p>Ten CTCF-binding DNA fragments were inserted between the CMV enhancer and CMV minimal promoter driving the herpes simplex virus thymidine kinase (HSV<it>-tk</it>) gene in a vector expressing also the <it>neo</it>^Rgene under a separate promoter. The constructs were then integrated into the genome of CHO cells, and the cells resistant to neomycin and ganciclovir (positive-negative selection) were picked up, and their DNAs were PCR analyzed to confirm the presence of the fragments between the enhancer and promoter in both orientations.</p> <p>Conclusions</p> <p>We demonstrated that all sequences identified by their CTCF binding both <it>in vitro </it>and <it>in vivo </it>had enhancer-blocking activity when inserted between the CMV minimal promoter and enhancer in stably transfected CHO cells.</p

DNA methylation signal has a major role in the response of human breast cancer cells to the microenvironment

International audienceBreast cancer-associated fibroblasts (CAFs) have a crucial role in tumor initiation, metastasis and therapeutic resistance by secreting various growth factors, cytokines, protease and extracellular matrix components. Soluble factors secreted by CAFs are involved in many pathways including inflammation, metabolism, proliferation and epigenetic modulation, suggesting that CAF-dependent reprograming of cancer cells affects a large set of genes. This paracrine signaling has an important role in tumor progression, thus deciphering some of these processes could lead to relevant discoveries with subsequent clinical implications. Here, we investigated the mechanisms underlying the changes in gene expression patterns associated with the cross-talk between breast cancer cells and the stroma. From RNAseq data obtained from breast cancer cell lines grown in presence of CAF-secreted factors, we identified 372 upregulated genes, exhibiting an expression level positively correlated with the stromal content of breast cancer specimens. Furthermore, we observed that gene expression changes were not mediated through significant DNA methylation changes. Nevertheless, CAF-secreted factors but also stromal content of the tumors remarkably activated specific genes characterized by a DNA methylation pattern: hypermethylation at transcription start site and shore regions. Experimental approaches (inhibition of DNA methylation, knockdown of methyl-CpG-binding domain protein 2 and chromatin immunoprecipitation assays) indicated that this set of genes was epigenetically controlled. These data elucidate the importance of epigenetics marks in the cancer cell reprogramming induced by stromal cell and indicated that the interpreters of the DNA methylation signal have a major role in the response of the cancer cells to the microenvironment

Data Cleaning, Linking and Enriching with OpenRefine: Part of the Data Science Training for Librarians series

Free Your Metadata: Data cleaning, linking and enriching with OpenRefine. http://www.altbibl.io/dtu/speakers/simon/info:eu-repo/semantics/nonPublishe

Identification of Variants in the 4q35 Gene FAT1 in Patients with a Facioscapulohumeral Dystrophy-Like Phenotype

International audienceFacioscapulohumeralmuscular dystrophy (FSHD) is linked to copy-number reduction (N < 10) of the 4q D4Z4 subtelomeric array, in association with DUX4-permissive haplo-types. This main form is indicated as FSHD1. FSHD-like phenotypes may also appear in the absence of D4Z4 copy-number reduction. Variants of the SMCHD1 gene have been reported to associate with D4Z4 hypomethylation in DUX4-compatible hap-lotypes, thus defining FSHD2. Recently, mice carrying a muscle-specific knockout of the protocadherin gene Fat1 or its consti-tutive hypomorphic allele were shown to develop muscular and nonmuscular defects mimicking human FSHD. Here, we report FAT1 variants in a group of patients presenting with neuro-muscular symptoms reminiscent of FSHD. The patients do not carry D4Z4 copy-number reduction, 4q hypomethylation, or SM-CHD1 variants. However, abnormal splicing of the FAT1 transcript is predicted for all identified variants. To determine their pathogenicity, we elaborated a minigene approach coupled to an antisense oligonucleotide (AON) assay. In vitro, four out of five selected variants induced partial or complete alteration of splicing by creating new splice sites or modifying splicing regulators. AONs confirmed these effects. Altered transcripts may affect FAT1 protein interactions or stability. Altogether, our data suggest that defective FAT1 is associated with an FSHD-like phenotype. Hum Mutat 36:443–453, 2015. C 2015 Wiley Periodicals, Inc

OpenRefine/OpenRefine: OpenRefine v3.7.6

New in 3.7.6 A missing space was added in the layout of the text facet, by @frafra (#6071) Browser launching on startup was fixed for Snap-packaged OpenRefine, by @kristbaum (#6065) The selection of Wikibase statement merging strategies was fixed, by @wetneb (#6066) A resizing issue in the presence of the Wikibase extension and facets was fixed, by @Abbe98 (#6070) Vulnerabilities (fixed since 3.7.5) A moderate vulnerabilities in the database extension was fixed. Connecting to a malicious MySQL server could read files or execute arbitrary code on the machine running OpenRefine. The vulnerabilities were assigned CVE-2023-41886 and CVE-2023-41887 identifiers respectively, and were reported by @nbxiglk0. (fixed since 3.7.4) A moderate vulnerability in project import was fixed. Importing a maliciously crafted project could execute arbitrary code on the machine running OpenRefine. This vulnerability has been assigned the CVE-2023-37476 identifier. It was reported by Stefan Schiller from SonarSource. New features Most text exposed to users in OpenRefine's UI can now be translated. Some strings (generated server-side) were not translatable so far. To help translators catch up on this backlog, do not hesitate to join us on Weblate. (#5030) New media files can be uploaded to Wikibase instances such as Wikimedia Commons. The wikitext of existing files can also be edited thanks to the new fields introduced. (#4682) A button "Discover Wikibase instances…" was added on the dialog which lists the registered Wikibase instances (#5007), whose design was improved (#5009) In the Wikibase schema editor, statements with non-standard datatypes (such as EDTF dates or musical notations) are now supported, assuming they use strings as underlying representation (#3263) The Wikibase issues tab now makes it possible to locate which rows are responsible for certain issues, using facets (#5033) The default throttle delay for the "Add column by fetching URLs" operation was reduced to 500ms and the error reporting for this field was improved (#5188) Wikibase templates (incomplete Wikibase schemas) can be saved and shared, as a way of helping contributors use the same way of structuring data in a Wikibase instance (#5043, #5303) The line-based importer now supports a custom delimiter, instead of only newlines (#4103) The Excel importer can be configured to import all cells as text, disabling the use of other datatypes supported by OpenRefine (#4838) The "some value" and "no value" Wikibase values can now be uploaded by OpenRefine (#5360) The Excel importer will also avoid coercing cell values to OpenRefine datatypes which do not fully fit them, such as representing a date as a date with time (#5389, #5390). GREL changes Improved error handling in number formatting with the GREL toString function (#816) The behaviour of the GREL function wholeText() has changed slightly in the way it handles newlines, following an upstream change in the jsoup library (jsoup issue #1636) A new parent GREL function, to obtain the parent element of an XML element, was added (#5176) Bug fixes The layout of the dialog to select a reconciliation match was improved so that the auto-complete widget does not hide the other options (#4821) Better in-tool documentation around the way the scatterplot facet detects numerical columns (#4890) The detection of URLs in cell values was fixed (#4546) The error message displayed when trying to add a Wikibase manifest with a manifest version that is too old or recent was improved (#4847) Errors returned by Jython expressions are more readable (#3012) The ODS exporter no longer creates a default sheet "Sheet1" in the documents it creates (#4864) Longer descriptions in auto-completion widget are not cut off anymore (#4988) The interface for editing cell values was improved to better explain how to input dates (#3082) The Windows refine.bat script was made more consistent with the Unix refine script (#4949, #5404) The "Search for Match" dialog was rearranged so that the dropdown does not cover the buttons (#4945) Error handling in the scatterplot facet was improved (#4893) The "Collapse consecutive whitespaces" operation now handles unicode whitespace correctly (#4898) (#4991) The handling of GZIP-compressed files without .gz extension was improved in the importing pipeline (#547) (#5153) The "Add column based on this column dialog" can be submitted by pressing "Enter" in the column field (#5143) The editing of redirected Wikibase items was fixed (#5162) The user experience was improved in the case of incomplete Wikibase schemas (#5131) The memory usage display was improved to show the used memory instead of the total memory, and was made more precise (#5222) The association of labels to form inputs was improved, enhancing the accessibility of the interface (#5239, #5242, #5249, #5284) An overflow issue in the reconciliation dialog was fixed (#5285) The Wikibase manifests now properly support locally-running reconciliation endpoints (#5035) The aspect ratio of Wikibase logos is now properly preserved (#5306) The SQL exporter interface was improved (#5224) The cell edit popup and dialogs with textbox inputs became resizable (#5330) When marking a set of cells as "New" in an unreconciled column, the user is prompted for the reconciliation service to use (#4985) More quality assurance checks were introduced in the Wikibase extension, such as checking for identical label and description in new Wikibase items (#4980) The caching of auto-completion results in the Wikibase extension was fixed (#5190) The Wikidata extension was fully renamed to "Wikibase extension" (#4525) The controls of the cluster and edit dialog are greyed out while clustering is taking place (#5369) The handling of unicode whitespace was improved throughout the application (#5105) Our MacOS packages (.DMG) are now properly signed and notarized, which should make their installation easier (#4586). Also, the presentation of the DMG image was made more user-friendly by including the customary link to the Applications folder. (#5509) The parsing of the unary minus sign in GREL was fixed (#5465) (From 3.7-beta3 on) The clustering dialog no longer introduces non-breaking spaces when selecting options with spaces in them (#5581) (From 3.7.1 on) The display of the memory usage during project import was fixed (#5665) (From 3.7.2 on) The localization in German was fixed (#5750) (From 3.7.3 on) Starting openrefine.exe on Windows with Java 17 was fixed (#5583) (From 3.7.3 on) Wikibase edits on deleted items are skipped and do not stall the entire batch (#5385) (From 3.7.3 on) The HTML document language is aligned with the language of the interface (#5925) (From 3.7.3 on) The default reconciliation types are displayed with both name and id (#5907) (From 3.7.3 on) The transpose cells across columns was fixed so it treats blank cells as null (#5229

OpenRefine/OpenRefine: OpenRefine v3.7.7

&lt;p&gt;This is the seventh stable release of the 3.7 series. Please &lt;a href="https://docs.openrefine.org/manual/installing#set-where-data-is-stored"&gt;backup your workspace directory&lt;/a&gt; before installing and report any problems that you encounter.&lt;/p&gt; &lt;h2&gt;New in 3.7.7&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;A rendering issue in the Wikibase schema editor was fixed, by @wetneb (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/6165"&gt;#6165&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Attempts to fetch invalid URLs in the &quot;Add column by fetching URLs&quot; operation are properly reported to the user, by @tfmorris (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/6141"&gt;#6141&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;A missing space between the &quot;remove&quot; and &quot;configure&quot; buttons of the &quot;Add column from reconciled values&quot; operation was added, by @SrinathKadam048 (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/6151"&gt;#6151&lt;/a&gt;)&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;Vulnerabilities&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;(fixed since 3.7.5) A moderate vulnerabilities in the database extension was fixed. Connecting to a malicious MySQL server could read files or execute arbitrary code on the machine running OpenRefine. The vulnerabilities were assigned CVE-2023-41886 and CVE-2023-41887 identifiers respectively, and were reported by @nbxiglk0.&lt;/li&gt; &lt;li&gt;(fixed since 3.7.4) A moderate vulnerability in project import was fixed. Importing a maliciously crafted project could execute arbitrary code on the machine running OpenRefine. This vulnerability has been assigned the CVE-2023-37476 identifier. It was reported by Stefan Schiller from SonarSource.&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;New features&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;Most text exposed to users in OpenRefine's UI can now be translated. Some strings (generated server-side) were not translatable so far. To help translators catch up on this backlog, do not hesitate to &lt;a href="https://hosted.weblate.org/engage/openrefine/"&gt;join us on Weblate&lt;/a&gt;. (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5030"&gt;#5030&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;New media files can be uploaded to Wikibase instances such as Wikimedia Commons. The wikitext of existing files can also be edited thanks to the new fields introduced. (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4682"&gt;#4682&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;A button &quot;Discover Wikibase instances…&quot; was added on the dialog which lists the registered Wikibase instances (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5007"&gt;#5007&lt;/a&gt;), whose design was improved (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5009"&gt;#5009&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;In the Wikibase schema editor, statements with non-standard datatypes (such as EDTF dates or musical notations) are now supported, assuming they use strings as underlying representation (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/3263"&gt;#3263&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Wikibase issues tab now makes it possible to locate which rows are responsible for certain issues, using facets (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5033"&gt;#5033&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The default throttle delay for the &quot;Add column by fetching URLs&quot; operation was reduced to 500ms and the error reporting for this field was improved (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5188"&gt;#5188&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Wikibase templates (incomplete Wikibase schemas) can be saved and shared, as a way of helping contributors use the same way of structuring data in a Wikibase instance (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5043"&gt;#5043&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5303"&gt;#5303&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The line-based importer now supports a custom delimiter, instead of only newlines (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4103"&gt;#4103&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Excel importer can be configured to import all cells as text, disabling the use of other datatypes supported by OpenRefine (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4838"&gt;#4838&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The &quot;some value&quot; and &quot;no value&quot; Wikibase values can now be uploaded by OpenRefine (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5360"&gt;#5360&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Excel importer will also avoid coercing cell values to OpenRefine datatypes which do not fully fit them, such as representing a date as a date with time (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5389"&gt;#5389&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5390"&gt;#5390&lt;/a&gt;).&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;GREL changes&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;Improved error handling in number formatting with the GREL &lt;code&gt;toString&lt;/code&gt; function (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/816"&gt;#816&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The behaviour of the GREL function &lt;code&gt;wholeText()&lt;/code&gt; has changed slightly in the way it handles newlines, following &lt;a href="https://jsoup.org/news/release-1.15.1"&gt;an upstream change in the jsoup library&lt;/a&gt; (jsoup issue &lt;a href="https://github.com/jhy/jsoup/issues/1636"&gt;#1636&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;A new &lt;code&gt;parent&lt;/code&gt; GREL function, to obtain the parent element of an XML element, was added (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5176"&gt;#5176&lt;/a&gt;)&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;Bug fixes&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;The layout of the dialog to select a reconciliation match was improved so that the auto-complete widget does not hide the other options (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4821"&gt;#4821&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Better in-tool documentation around the way the scatterplot facet detects numerical columns (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4890"&gt;#4890&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The detection of URLs in cell values was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4546"&gt;#4546&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The error message displayed when trying to add a Wikibase manifest with a manifest version that is too old or recent was improved (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4847"&gt;#4847&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Errors returned by Jython expressions are more readable (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/3012"&gt;#3012&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The ODS exporter no longer creates a default sheet &quot;Sheet1&quot; in the documents it creates (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4864"&gt;#4864&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Longer descriptions in auto-completion widget are not cut off anymore (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4988"&gt;#4988&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The interface for editing cell values was improved to better explain how to input dates (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/3082"&gt;#3082&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Windows &lt;code&gt;refine.bat&lt;/code&gt; script was made more consistent with the Unix &lt;code&gt;refine&lt;/code&gt; script (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/4949"&gt;#4949&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5404"&gt;#5404&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The &quot;Search for Match&quot; dialog was rearranged so that the dropdown does not cover the buttons (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/4945"&gt;#4945&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Error handling in the scatterplot facet was improved (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/4893"&gt;#4893&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The &quot;Collapse consecutive whitespaces&quot; operation now handles unicode whitespace correctly (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/4898"&gt;#4898&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/4991"&gt;#4991&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The handling of GZIP-compressed files without &lt;code&gt;.gz&lt;/code&gt; extension was improved in the importing pipeline (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/547"&gt;#547&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5153"&gt;#5153&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The &quot;Add column based on this column dialog&quot; can be submitted by pressing &quot;Enter&quot; in the column field (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5143"&gt;#5143&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The editing of redirected Wikibase items was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5162"&gt;#5162&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The user experience was improved in the case of incomplete Wikibase schemas (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5131"&gt;#5131&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The memory usage display was improved to show the used memory instead of the total memory, and was made more precise (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5222"&gt;#5222&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The association of labels to form inputs was improved, enhancing the accessibility of the interface (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5239"&gt;#5239&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5242"&gt;#5242&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5249"&gt;#5249&lt;/a&gt;, &lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5284"&gt;#5284&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;An overflow issue in the reconciliation dialog was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5285"&gt;#5285&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Wikibase manifests now properly support locally-running reconciliation endpoints (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5285"&gt;#5035&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The aspect ratio of Wikibase logos is now properly preserved (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5306"&gt;#5306&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The SQL exporter interface was improved (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5224"&gt;#5224&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The cell edit popup and dialogs with textbox inputs became resizable (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5330"&gt;#5330&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;When marking a set of cells as &quot;New&quot; in an unreconciled column, the user is prompted for the reconciliation service to use (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4985"&gt;#4985&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;More quality assurance checks were introduced in the Wikibase extension, such as checking for identical label and description in new Wikibase items (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4980"&gt;#4980&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The caching of auto-completion results in the Wikibase extension was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5190"&gt;#5190&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The Wikidata extension was fully renamed to &quot;Wikibase extension&quot; (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4525"&gt;#4525&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The controls of the cluster and edit dialog are greyed out while clustering is taking place (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5369"&gt;#5369&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The handling of unicode whitespace was improved throughout the application (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5105"&gt;#5105&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;Our MacOS packages (.DMG) are now properly signed and notarized, which should make their installation easier (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/4586"&gt;#4586&lt;/a&gt;). Also, the presentation of the DMG image was made more user-friendly by including the customary link to the Applications folder. (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5509"&gt;#5509&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;The parsing of the unary minus sign in GREL was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5465"&gt;#5465&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7-beta3 on) The clustering dialog no longer introduces non-breaking spaces when selecting options with spaces in them (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5581"&gt;#5581&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.1 on) The display of the memory usage during project import was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5665"&gt;#5665&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.2 on) The localization in German was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5750"&gt;#5750&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.3 on) Starting openrefine.exe on Windows with Java 17 was fixed (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5583"&gt;#5583&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.3 on) Wikibase edits on deleted items are skipped and do not stall the entire batch (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5385"&gt;#5385&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.3 on) The HTML document language is aligned with the language of the interface (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/5925"&gt;#5925&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.3 on) The default reconciliation types are displayed with both name and id (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5907"&gt;#5907&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(From 3.7.3 on) The transpose cells across columns was fixed so it treats blank cells as null (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/5229"&gt;#5229&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(from 3.7.6 on) A missing space was added in the layout of the text facet, by @frafra (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/6071"&gt;#6071&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(from 3.7.6 on) Browser launching on startup was fixed for Snap-packaged OpenRefine, by @kristbaum (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/6065"&gt;#6065&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(from 3.7.6 on) The selection of Wikibase statement merging strategies was fixed, by @wetneb (&lt;a href="https://github.com/OpenRefine/OpenRefine/pull/6066"&gt;#6066&lt;/a&gt;)&lt;/li&gt; &lt;li&gt;(from 3.7.6 on) A resizing issue in the presence of the Wikibase extension and facets was fixed, by @Abbe98 (&lt;a href="https://github.com/OpenRefine/OpenRefine/issues/6070"&gt;#6070&lt;/a&gt;)&lt;/li&gt; &lt;/ul&gt

OpenRefine/OpenRefine: OpenRefine v2.8 Release

This is the official release of OpenRefine 2.8. Please backup your workspace directory before installing and report any problems that you encounter. New features: Project metadata support Enhancement of Wikidata Reconcile Support split multivalued-cells by regex/special characters Text filter exclude Add free memory detection and Notification to user Improved UI for better usability Some bug fixes See the full list of changes. OpenRefine is funded by Google Inc. News Lab