Online biomedical named entities recognition by data and knowledge-driven model.

Named entity recognition (NER) is an important task for the natural language processing of biomedical text. Currently, most NER studies standardized biomedical text, but NER for unstandardized biomedical text draws less attention from researchers. Named entities in online biomedical text exist with errors and polymorphisms, which negatively impact NER models' performance and impede support from knowledge representation methods. In this paper, we propose a neural network method that can effectively recognize entities in unstandardized online medical/health text. We introduce a new pre-training scheme that uses large-scale online question-answering pairs to enhance transformers' model capacity on online biomedical text. Moreover, we supply models with knowledge representations from a knowledge base called multi-channel knowledge labels, and this method overcomes the restriction from languages, like Chinese, that require word segmentation tools to represent knowledge. Our model outperforms other baseline methods significantly in experiments on a dataset for Chinese online medical entity recognition and achieves state-of-the-art results.

Synaptic excitation underlies processing of paired stimulation in the mouse inferior colliculus.

The inferior colliculus (IC) receives inputs from the ascending auditory pathway and helps localize the sound source by shaping neurons' responses. However, the contributions of excitatory or inhibitory synaptic inputs evoked by paired binaural stimuli with different inter-stimulus intervals to auditory responses of IC neurons remain unclear. Here, we firstly investigated the IC neuronal response to the paired binaural stimuli with different inter-stimulus intervals using in vivo loose-patch recordings in anesthetized C57BL/6 mice. It was found that the total acoustic evoked spikes remained unchanged under microsecond interval conditions, but persistent suppression would be observed when the time intervals were extended. We further studied the paired binaural stimuli evoked excitatory/inhibitory inputs using in vivo whole-cell voltage-clamp techniques and blockage of the auditory nerve. The amplitudes of the contralateral excitatory inputs could be suppressed, unaffected or facilitated as the interaural delay varied. In contrast, contralateral inhibitory inputs and ipsilateral synaptic inputs remained almost unchanged. Most IC neurons exhibited the suppression of contralateral excitatory inputs over the interval range of dozens of milliseconds. The facilitative effect was generated by the summation of contralateral and ipsilateral excitation. Suppression and facilitation were completely abolished when ipsilateral auditory nerve was blocked pharmacologically, indicating that these effects were exerted by ipsilateral stimulation. These results suggested that the IC would inherit the binaural inputs integrated at the brainstem as well as within the IC and synaptic excitations, modulated by ipsilateral stimulation, underlie the binaural acoustic response.

Frameshift mutation of Timm8a1 gene in mouse leads to an abnormal mitochondrial structure in the brain, correlating with hearing and memory impairment.

BACKGROUND: Deafness-dystonia-optic neuronopathy (DDON) syndrome is a progressive X-linked recessive disorder characterised by deafness, dystonia, ataxia and reduced visual acuity. The causative gene deafness/dystonia protein 1 (DDP1)/translocase of the inner membrane 8A (TIMM8A) encodes a mitochondrial intermembrane space chaperon. The molecular mechanism of DDON remains unclear, and detailed information on animal models has not been reported yet. METHODS AND RESULTS: We characterized a family with DDON syndrome, in which the affected members carried a novel hemizygous variation in the DDP1 gene (NM_004085.3, c.82C>T, p.Q28X). We then generated a mouse line with the hemizygous mutation (p.I23fs49X) in the Timm8a1 gene using the clustered regularly interspaced short palindromic repeats /Cas9 technology. The deficient DDP1 protein was confirmed by western blot assay. Electron microscopic analysis of brain samples from the mutant mice indicated abnormal mitochondrial structure in several brain areas. However, Timm8a1I23fs49X/y mutation did not affect the import of mitochondria inner member protein Tim23 and outer member protein Tom40 as well as the biogenesis of the proteins in the mitochondrial oxidative phosphorylation system and the manganese superoxide dismutase (MnSOD / SOD-2). The male mice with Timm8a1I23fs49X/y mutant exhibited less weight gain, hearing impairment and cognitive deficit. CONCLUSION: Our study suggests that frameshift mutation of the Timm8a1 gene in mice leads to an abnormal mitochondrial structure in the brain, correlating with hearing and memory impairment. Taken together, we have successfully generated a mouse model bearing loss-of-function mutation in Timm8a1.

An attention-based multi-task model for named entity recognition and intent analysis of Chinese online medical questions.

In this paper, we propose an attention-based multi-task neural network model for text classification and sequence tagging and then apply it to the named entity recognition and the intent analysis of Chinese online medical questions. We found that the use of both attention and multi-task learning improved the performance of these tasks. Our method achieved superior performance in named entity recognition and intent analysis compared with other baseline methods; the method is a light-weight solution that is suitable for deployment on small servers. Furthermore, we took advantage of the model's capabilities for these two tasks and built a simple question-answering system for cardiovascular issues. Users and service providers can monitor the logic of the answers generated by this system.

Anti-fibrotic effect of iguratimod on pulmonary fibrosis by inhibiting the fibroblast-to-myofibroblast transition.

PURPOSE: Pulmonary fibrosis (PF) is a severe lung disease causing significant morbidity and mortality. PF pathogenesis is attributed to the fibroblast-to-myofibroblast transition (FMT) driven by the most potent pro-fibrogenic factor TGF-ß1 activating the Smad3-dependent TGF-ß1 canonical pathway. Iguratimod (IGU) is a novel anti-rheumatic drug that suppresses the secretion of inflammatory factors, but is also able to modulate the differentiation of multiple cells. Therefore, the aim of this work was to investigate the effect of IGU on FMT. MATERIALS/METHODS: PF mouse model was induced in C57BL/6 male mice by bleomycin. The effect of IGU was assessed through the evaluation of lung morphology by H&E and through the collagen accumulation in the lung by Masson staining. Primary human lung fibroblasts (pHLFs) were also used to evaluate the effect of IGU in vitro on TGF-ß1-stimulated cells, and proliferation, migration and invasion were measured, together with genes and proteins involved in FMT. RESULTS: IGU attenuated bleomycin-induced PF in mice and improved the pathological changes in their lungs. In addition, IGU significantly inhibited proliferation, migration and invasion in TGF-ß1-stimulated pHLFs without causing apoptosis. Moreover, IGU significantly reduced TGF-ß1-induced increase of collagen I and III mRNA expression, thus reducing lung function impairment, and α-SMA, Smad2 and Smad3 phosphorylation, fibronectin expression and F-actin microfilament formation, thus attenuating FMT through the inhibition of the Smad3 pathway. CONCLUSIONS: Our results collectively revealed the beneficial effect of IGU on the inhibition of FMT, thus suggesting that it might act as an effective anti-fibrotic agent in preventing the progression of PF.

Inhibitory effects of pirfenidone on fibroblast to myofibroblast transition in rheumatoid arthritis-associated interstitial lung disease via the downregulation of activating transcription factor 3 (ATF3).

OBJECTIVE: Pirfenidone (PFD) is an oral anti-fibrotic drug used for idiopathic pulmonary fibrosis (IPF) therapy. We determined the role of activating transcription factor 3 (ATF3) and the effect of PFD on fibroblast to myofibroblast transition (FMT) in rheumatoid arthritis-associated interstitial lung disease (RA-ILD). METHODS: RA-ILD lung specimens were obtained by CT-guided percutaneous transthoracic biopsy. A pulmonary fibrosis mouse model was established by the intratracheal injection of bleomycin. Pathological variation and the expression of α-SMA and ATF3 were observed by H&E, Masson and immunofluorescence staining. Primary human lung fibroblasts (pHLFs) were isolated from lung tissues that were pathologically confirmed to be normal by pneumonectomy. Cell viability was detected using an MTT assay. Cell migration and invasion were detected using a Transwell chamber. The protein levels of α-SMA, ATF3, Smad3 and p-Smad3 were measured by Western blot. HLFs were infected with lentiviruses expressing ATF3 or scrambled shRNA. RESULTS: ATF3 was dramatically upregulated in lung tissues from both bleomycin-induced mice and patients with RA-ILD compared with controls. The upregulation of ATF3 and the accumulation of collagen in the lung tissues of mice with pulmonary fibrosis were reduced by PFD. PFD significantly inhibited increases in the proliferation, invasion and migration of pHLFs stimulated by TGF-ß1. Moreover, we observed the inhibitory effect of PFD on FMT via the downregulation of ATF3, which was further confirmed in ATF3 knockdown (KD) pHLFs. CONCLUSIONS: This work shows the inhibitory effect of PFD on FMT in pHLFs, which is mediated by the downregulation of ATF3. Our findings suggest that PFD might have therapeutic potential for the treatment of RA-ILD.

Molecular basis of 5-hydroxytryptophan synthesis in Saccharomyces cerevisiae.

We report for the first time that 5-hydroxytryptophan can be synthesized in Saccharomyces cerevisiae by heterologously expressing prokaryotic phenylalanine 4-hydroxylase or eukaryotic tryptophan 3/5-hydroxylase, together with enhanced synthesis of MH4 or BH4 cofactors. The innate DFR1 gene in the folate synthesis pathway was found to play pivotal roles in 5-hydroxytryptophan synthesis.