The structure of BgaR, a transcriptional regulator of the lactose operon in Clostridium perfringens, has been solved by SAD phasing using a mercury derivative. BgaR is an exquisite sensor of lactose, with a binding affinity in the low-micromolar range. This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form, and was compared with AraC, another saccharide-binding transcriptional regulator. It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold, but that part of the saccharide is exposed to bulk solvent. This differs from the classical AraC saccharide-binding site, which is mostly sequestered from the bulk solvent. The structures of BgaR bound to lactose and to lactulose highlight how specific and nonspecific interactions lead to a higher binding affinity of BgaR for lactose compared with lactulose. Moreover, solving multiple structures of BgaR in different space groups, both bound to saccharides and unbound, verified that the dimer interface along a C-terminal helix is similar to the dimer interface observed in AraC.

David Guerit, Pauline Marie, Anne Morel, Justine Maurin, Christel Verollet, Brigitte Raynaud-Messina, Serge Urbach, and Anne Blangy

Among hematopoietic cells, osteoclasts (Oc) and immature dendritic cells (Dc) are closely related myeloid cells with distinct functions; Oc participate skeleton maintenance while Dc sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during Oc and Dc differentiation. We provide global proteomic and transcriptomic analyses of primary mouse Oc and Dc, based on original SILAC and RNAseq data. We established specific signatures for Oc and Dc including genes and proteins of unknown functions. In particular, we showed that Oc and Dc have the same α and β tubulin isotypes repertoire but that Oc express much more β tubulin isotype Tubb6. In both mouse and human Oc, we demonstrate that elevated expression of Tubb6 in Oc is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hindered Oc resorption activity. Overall, we highlight here potential new regulators of Oc and Dc biology and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.

Mei Wang, Luping Yu, Shu Wang, Fan Yang, Min Wang, Lufan Li, and Xin Wu

RNA-binding protein LIN28A is required for maintaining tissue homeostasis, including the reproductive system, but the underlying mechanisms on how LIN28A regulates germline progenitors remain unclear. Here, we dissected LIN28A-binding targets using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse testes. LIN28A preferentially binds to CDS or 3'UTR regions through these sites with GGAG(A) sequences enriched within mRNAs. Further investigation of Lin28a null mouse testes indicated that meiosis-associated mRNAs mediated by LIN28A were differentially expressed. Next, ribosome profiling revealed that the mRNA levels of these targets were significantly reduced in polysome fractions, and their protein expression levels decreased in the Lin28a null mouse testes, even when meiotic arrest in null mouse testes was not apparent. Collectively, these findings provide a set of binding targets that are regulated by LIN28A, which may potentially be the mechanism for the prominent role of LIN28A in regulating mammalian undifferentiated spermatogonia fates and male fertility.

Stephen Kershaw, David J. Morgan, James Boyd, David G. Spiller, Gareth Kitchen, Egor Zindy, Mudassar Iqbal, Magnus Rattray, Chris M. Sanderson, Andrew Brass, Claus Jorgensen, Tracy Hussell, Laura C. Matthews, and David W. Ray

Glucocorticoids (GCs) act through the glucocorticoid receptor (GR) to regulate immunity, energy metabolism, and tissue repair. Upon ligand binding, activated GR mediates cellular effects by regulating gene expression, but some GR effects can occur rapidly without new transcription. We show GCs rapidly inhibit cell migration, in response to both GR agonist and antagonist ligand binding. The inhibitory effect on migration is prevented by GR knockdown with siRNA, confirming GR specificity, but not by actinomycin D treatment, suggesting a non-transcriptional mechanism. We identified a rapid onset increase in microtubule polymerisation following glucocorticoid treatment, identifying cytoskeletal stabilisation as the likely mechanism of action. HDAC6 overexpression, but not knockdown of αTAT1, rescued the GC effect, implicating HDAC6 as the GR effector. Consistent with this hypothesis, ligand-dependent cytoplasmic interaction between GR and HDAC6 was demonstrated by quantitative imaging. Taken together, we propose that activated GR inhibits HDAC6 function and thereby increases the stability of the microtubule network to reduce cell motility. We therefore report a novel, non-transcriptional mechanism whereby GCs impair cell motility through inhibition of HDAC6 and rapid reorganization of the cell architecture.

The integration within PROSECUTORbyKarpel (PbK) and DEFENDERbyKarpel (DbK) enables legal professionals to streamline their transcript processes

Back in late 2016, we introduced Speech Recognition at Auphonic. This allows our users to create transcripts of their recordings, and more usefully, this means podcasts become searchable.
Now we integrated two more speech recognition engines: Amazon Transcribe and Speechmatics. Whilst integrating these services, we also took the opportunity to develop a complete new Transcription Editor:

Screenshot of our Transcript Editor with word confidence highlighting and the edit bar.
Try out the Transcript Editor Examples yourself!

The new Auphonic Transcript Editor is included directly in our HTML transcript output file, displays word confidence values to instantly see which sections should be checked manually, supports direct audio playback, HTML/PDF/WebVTT export and allows you to share the editor with someone else for further editing.

The new services, Amazon Transcribe and Speechmatics, offer transcription quality improvements compared to our other integrated speech recognition services.
They also return word confidence values, timestamps and some punctuation, which is exported to our output files.

The Auphonic Transcript Editor

With the integration of the two new services offering improved recognition quality and word timestamps alongside confidence scores, we realized that we could leverage these improvements to give our users easy-to-use transcription editing.
Therefore we developed a new, open source transcript editor, which is embedded directly in our HTML output file and has been designed to make checking and editing transcripts as easy as possible.

• Edit the transcription directly in the HTML document.
• Show/hide word confidence, to instantly see which sections should be checked manually (if you use Amazon Transcribe or Speechmatics as speech recognition engine).
• Listen to audio playback of specific words directly in the HTML editor.
• Share the transcript editor with others: as the editor is embedded directly in the HTML file (no external dependencies), you can just send the HTML file to some else to manually check the automatically generated transcription.
• Export the edited transcript to HTML, PDF or WebVTT.
• Completely useable on all mobile devices and desktop browsers.

Examples: Try Out the Transcript Editor

Here are two examples of the new transcript editor, taken from our speech recognition audio examples page:

1. Singletrack Transcript Editor Example

Singletrack speech recognition example from the first 10 minutes of Common Sense 309 by Dan Carlin. Speechmatics was used as speech recognition engine without any keywords or further manual editing.

2. Multitrack Transcript Editor Example

A multitrack automatic speech recognition transcript example from the first 20 minutes of TV Eye on Marvel - Luke Cage S1E1. Amazon Transcribe was used as speech recognition engine without any further manual editing.
As this is a multitrack production, the transcript includes exact speaker names as well (try to edit them!).

Transcript Editing

By clicking the Edit Transcript button, a dashed box appears around the text. This indicates that the text is now freely editable on this page. Your changes can be saved by using one of the export options (see below).
If you make a mistake whilst editing, you can simply use the undo/redo function of the browser to undo or redo your changes.

When working with multitrack productions, another helpful feature is the ability to change all speaker names at once throughout the whole transcript just by editing one speaker. Simply click on an instance of a speaker title and change it to the appropriate name, this name will then appear throughout the whole transcript.

Word Confidence Highlighting

Word confidence values are shown visually in the transcript editor, highlighted in shades of red (see screenshot above). The shade of red is dependent on the actual word confidence value: The darker the red, the lower the confidence value. This means you can instantly see which sections you should check/re-work manually to increase the accuracy.

Once you have edited the highlighted text, it will be set to white again, so it’s easy to see which sections still require editing.
Use the button Add/Remove Highlighting to disable/enable word confidence highlighting.

NOTE: Word confidence values are only available in Amazon Transcribe or Speechmatics, not if you use our other integrated speech recognition services!

Audio Playback

The button Activate/Stop Play-on-click allows you to hear the audio playback of the section you click on (by clicking directly on the word in the transcript editor).
This is helpful in allowing you to check the accuracy of certain words by being able to listen to them directly whilst editing, without having to go back and try to find that section within your audio file.

If you use an External Service in your production to export the resulting audio file, we will automatically use the exported file in the transcript editor.
Otherwise we will use the output file generated by Auphonic. Please note that this file is password protected for the current Auphonic user and will be deleted in 21 days.

If no audio file is available in the transcript editor, or cannot be played because of the password protection, you will see the button Add Audio File to add a new audio file for playback.

Export Formats, Save/Share Transcript Editor

Save/Share Editor

The Save Editor button stores the whole transcript editor with all its current changes into a new HTML file. Use this button to save your changes for further editing or if you want to share your transcript with someone else for manual corrections (as the editor is embedded directly in the HTML file without any external dependencies).

Export HTML / Export PDF / Export WebVTT

Use one of these buttons to export the edited transcript to HTML (for WordPress, Word, etc.), to PDF (via the browser print function) or to WebVTT (so that the edited transcript can be used as subtitles or imported in web audio players of the Podlove Publisher or Podigee).
Every export format is rendered directly in the browser, no server needed.

Amazon Transcribe

The first of the two new services, Amazon Transcribe, offers accurate transcriptions in English and Spanish at low costs, including keywords, word confidence, timestamps, and punctuation.

UPDATE 2019:
Amazon Transcribe offers more languages now - please see Amazon Transcribe Features!

Pricing

The free tier offers 60 minutes of free usage a month for 12 months. After that, it is billed monthly at a rate of $0.0004 per second ($1.44/h).
More information is available at Amazon Transcribe Pricing.

Custom Vocabulary (Keywords) Support

Custom Vocabulary (called Keywords in Auphonic) gives you the ability to expand and customize the speech recognition vocabulary, specific to your case (i.e. product names, domain-specific terminology, or names of individuals).
The same feature is also available in the Google Cloud Speech API.

Timestamps, Word Confidence, and Punctuation

Amazon Transcribe returns a timestamp and confidence value for each word so that you can easily locate the audio in the original recording by searching for the text.
It also adds some punctuation, which is combined with our own punctuation and formatting automatically.

The high-quality (especially in combination with keywords) and low costs of Amazon Transcribe make it attractive, despite only currently supporting two languages.
However, the processing time of Amazon Transcribe is much slower compared to all our other integrated services!

Try it yourself:
Connect your Auphonic account with Amazon Transcribe at our External Services Page.

Speechmatics

Speechmatics offers accurate transcriptions in many languages including word confidence values, timestamps, and punctuation.

Many Languages

Speechmatics’ clear advantage is the sheer number of languages it supports (all major European and some Asiatic languages).
It also has a Global English feature, which supports different English accents during transcription.

Timestamps, Word Confidence, and Punctuation

Like Amazon, Speechmatics creates timestamps, word confidence values, and punctuation.

Pricing

Speechmatics is the most expensive speech recognition service at Auphonic.
Pricing starts at £0.06 per minute of audio and can be purchased in blocks of £10 or £100. This equates to a starting rate of about $4.78/h. Reduced rate of £0.05 per minute ($3.98/h) are available if purchasing £1,000 blocks.
They offer significant discounts for users requiring higher volumes. At this further reduced price point it is a similar cost to the Google Speech API (or lower). If you process a lot of content, you should contact them directly at sales@speechmatics.com and say that you wish to use it with Auphonic.
More information is available at Speechmatics Pricing.

Speechmatics offers high-quality transcripts in many languages. But these features do come at a price, it is the most expensive speech recognition services at Auphonic.

Unfortunately, their existing Custom Dictionary (keywords) feature, which would further improve the results, is not available in the Speechmatics API yet.

Try it yourself:
Connect your Auphonic account with Speechmatics at our External Services Page.

What do you think?

Any feedback about the new speech recognition services, especially about the recognition quality in various languages, is highly appreciated.

We would also like to hear any comments you have on the transcript editor particularly - is there anything missing, or anything that could be implemented better?
Please let us know!

We propose Cotatron, a transcription-guided speech encoder for speaker-independent linguistic representation. Cotatron is based on the multispeaker TTS architecture and can be trained with conventional TTS datasets. We train a voice conversion system to reconstruct speech with Cotatron features, which is similar to the previous methods based on Phonetic Posteriorgram (PPG). By training and evaluating our system with 108 speakers from the VCTK dataset, we outperform the previous method in terms of both naturalness and speaker similarity. Our system can also convert speech from speakers that are unseen during training, and utilize ASR to automate the transcription with minimal reduction of the performance. Audio samples are available at https://mindslab-ai.github.io/cotatron, and the code with a pre-trained model will be made available soon.

Described herein are techniques for assembling a polynucleotide encoding a transcription activator-like effector nucleases (TALEN). The techniques ligate and digest necessary modules for a TALEN assembly in one reactor or system. Methods and Kits for generating a TALEN are also described.

Sir Howard Elston, our community affairs editor, lifts the lid on local social media groups.