Domain transformation on biological event extraction by learning methods.

Event extraction and annotation has become a significant focus of recent efforts in biological text mining and information extraction (IE). However, event extraction, event annotation methods, and resources have so far focused almost exclusively on a single domain. State-of-the-art studies on biological event extraction and annotation are typically domain-dependent and domain-restricted. In this paper, we adopt an approach aimed at extracting events and relations for two different tasks by generating a common dataset using transfer learning and structural correspondence learning (SCL). A deep learning event extraction system was developed to evaluate our results. Our approach comprises two stages: (1) generating a dataset from two independent event extraction tasks or domains, and (2) using a classifier model to learn feature patterns from the generated dataset for event and relation extraction. The classifier in the proposed model can extract events and relations irrespective of the domain of the test input. Our study shows that this approach performs competitively compared to domain specific or dependent tasks.

The complete chloroplast genome of Blechnopsis orientalis (Linnaeus) C. Presl 1753 (Blechnaceae).

Blechnopsis orientalis (Linnaeus) C. Presl (1753) is a fern used both as food and medicine. It is found primarily in southern China and Southeast Asia, thriving in warm, humid shrublands or sparse forest. The total length of the chloroplast genome is 155,211 bp, including a large single-copy region (LSC, 81,877 bp), a small single-copy region (SSC, 21,500 bp), and two inverted repeat regions (IRs, 25,917 bp). The GC content is 41.3%. A total of 131 genes were annotated, including 88 protein-coding genes, eight rRNA genes, and 35 tRNA genes. The phylogenetic analysis using the maximum-likelihood method showed that B. orientalis and Oceaniopteris gibba were closely related. This study provides genomic resources for phylogenetic genetics and resource exploitation of B. orientalis.

The complete chloroplast genome of Leonurus sibiricus Linnaeus (Labiatae, Leonurus Miller).

Leonurus sibiricus Linnaeus 1753, an annual or biennial herb found in northern China, Mongolia, and Russia, typically grows in stony, sandy grasslands, and pine forests. This study sequenced and reported the complete chloroplast genome of L. sibiricus for the first time. The entire circular genome measures 151,689 bp in length, with a GC content of 38.4%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNAs, and eight rRNAs. The genome exhibits a typical quadripartite structure, comprising a large single-copy (LSC 82,820 bp) region, a small single-copy (SSC 17,619 bp) region, and a pair of inverted repeat (IR 25,625 bp each) regions. Phylogenetic analysis using the maximum-likelihood method indicates that L. sibiricus is most closely related to L. japonicus Houttuyn. This study provides valuable genomic resources for further research on the phylogenetics and biodiversity of the genus Leonurus.

The complete chloroplast genome of Pulsatilla chinensis f. alba D. K. Zang (Ranunculaceae, Pulsatilla Miller).

Pulsatilla chinensis f. alba D. K. Zang 1993 is a forma of Pulsatilla chinensis (Bge.) Regel, the root of P. chinensis is traditional Chinese medicine called Pulsatillae radix. The biggest difference between P. chinensis f. alba and P. chinensis is that P. chinensis f. alba sepals is white. The complete chloroplast genome of P. chinensis f. alba was sequenced using the Illumina NovaSeq platform for the first time. The lengths of the genome, large single-copy (LSC), small single-copy (SSC), two inverted repeats (IRs), and GC content were 163,654 bp, 82,355 bp, 19,069 bp, 31,115 bp, and 37.2%, respectively. It had 134 genes, including 90 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The maximum-likelihood tree indicated that P. chinensis f. alba had a closer relationship with P. chinensis. This study would provide a theoretical basis for the further study of Pulsatilla plants genetics phylogenetic research.

The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis.

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae).

Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (1933), a shrub or small tree, is native to northern and southern China. It is an excellent relief and medicinal plant. The complete chloroplast genome is 158,043 bp in length, with a large single-copy region of 86,957 bp, a small single-copy region of 20,138 bp, two inverted repeat regions of 25,474 bp each, and a GC content of 37.4%. There were 129 genes annotated, including 84 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic trees are constructed using plastome data from 38 species and the maximum-likelihood method. The results of the chloroplast genome-wide analysis and the phylogenetic tree show the taxonomic phylogeny of the G. biloba var. parviflora in relation to other species, increasing the accuracy of the phylogenetic classification of the plant.

Dorsal raphe nucleus to anterior cingulate cortex 5-HTergic neural circuit modulates consolation and sociability.

Consolation is a common response to the distress of others in humans and some social animals, but the neural mechanisms underlying this behavior are not well characterized. By using socially monogamous mandarin voles, we found that optogenetic or chemogenetic inhibition of 5-HTergic neurons in the dorsal raphe nucleus (DR) or optogenetic inhibition of serotonin (5-HT) terminals in the anterior cingulate cortex (ACC) significantly decreased allogrooming time in the consolation test and reduced sociability in the three-chamber test. The release of 5-HT within the ACC and the activity of DR neurons were significantly increased during allogrooming, sniffing, and social approaching. Finally, we found that the activation of 5-HT1A receptors in the ACC was sufficient to reverse consolation and sociability deficits induced by the chemogenetic inhibition of 5-HTergic neurons in the DR. Our study provided the first direct evidence that DR-ACC 5-HTergic neural circuit is implicated in consolation-like behaviors and sociability.

CRF-CRFR1 system within the dorsal medial prefrontal cortex are involved in consolation deficits under acute restraint stress in mandarin voles.

Consolation is a complex empathic behavior that has recently been observed in some socially living rodents. Despite the growing body of literature suggesting that stress affects some simple form of empathy, the relationship between stress and consolation remains largely understudied. Using monogamous mandarin voles, we found that an acute restraint stress exposure significantly reduced consolation-like behaviors and induced anxiety-like behaviors. Along with these behavioral changes, corticotropin-releasing factor (CRF) and CRF receptor 1 (CRFR1) neurons were activated within the anterior cingulate cortex (ACC) and prelimbic cortex (PrL) but not within the infralimbic cortex (IL). Chemogenetic activation of CRF neurons in the ACC and PrL, recaptured acute stress-induced behavioral dysfunctions. We further observed that intracellular PKA and PKC signaling pathways mediate CRF-induced behavioral dysfunctions, but they work in a regional-specific, sex-biased manner. Together, these results suggest that the local CRF-CRFR1 system within the ACC and PrL is involved in the consolation deficits and anxiety induced by acute stress.

Different baseline physical activity predicts susceptibility and resilience to chronic social defeat stress in mice: Involvement of dopamine neurons.

Physical inactivity, the fourth leading mortality risk factor worldwide, is associated with chronic mental illness. Identifying the mechanisms underlying different levels of baseline physical activity and the effects of these levels on the susceptibility to stress is very important. However, whether different levels of baseline physical activity influence the susceptibility and resilience to chronic social defeat stress (CSDS), and the underlying mechanisms in the brain remain unclear. The present study segregated wild-type mice into low baseline physical activity (LBPA) and high baseline physical activity (HBPA) groups based on short term voluntary wheel running (VWR). LBPA mice showed obvious susceptibility to CSDS, while HBPA mice were resilient to CSDS. In addition, the expression of tyrosine hydroxylase (TH) in the ventral tegmental area (VTA) was lower in LBPA mice than in HBPA mice. Furthermore, activation of TH neurons in the VTA of LBPA mice by chemogenetic methods increased the levels of VWR and resilience to CSDS. In contrast, inhibiting TH neurons in the VTA of HBPA mice lowered the levels of VWR and increased their susceptibility to CSDS. Thus, this study suggests that different baseline physical activities might be mediated by the dopamine system. This system also affects the susceptibility and resilience to CSDS, possibly via alteration of the baseline physical activity. This perspective on the neural control and impacts on VWR may aid the development of strategies to motivate and sustain voluntary physical activity. Furthermore, this can maximize the impacts of regular physical activity toward stress-reduction and health promotion.

[Heavy Metal Contamination and Migration in Correspondence of an Electroplating Site on the Hilly Lands of the Guangdong-Hong Kong-Macau Greater Bay Area, China].

The Guangdong-Hong Kong-Macau Greater Bay Area presents the highest number of electroplating corporations in China; some of them of very large scale. Electroplating emissions are the cause of widespread heavy metal contamination of both soil and groundwater in the Guangdong-Hong Kong-Macau Greater Bay Area. Hence, the reuse of electroplating sites in this area should be preceded by an analysis of heavy metal characteristics and migration in the soil and groundwater. We performed such analyses in correspondence of a relocated electroplating site on the hilly lands of the Guangdong-Hong Kong-Macau Greater Bay Area, and quantitatively determined the spatial distribution of heavy metals. Moreover, we discussed the migration of heavy metals under the specific hydrogeological conditions of the area. The results showed that the soil and groundwater in correspondence of the electroplating factory were polluted by heavy metals in different degrees. The over-standard rates of Ni, Cr6+, and Cu in the soil were 20.5%, 12.8%, and 2.7%, respectively; meanwhile, those of Ni, Pb, and Cr6+ in the groundwater were 41.7%, 33.3%, and 33.3%, respectively. The pattern of heavy metal pollution reflected the functional division of the electroplating factory, the contaminants should have mainly derived from the leakage of electroplating wastes. A low-permeable silt clay layer located below the fill soil layer limited the downward transportation of heavy metals, which were hence mainly concentrated in the surface soils. However, in another area of the site characterized by shallow-buried and completely decomposed granite (having high permeability), heavy metals could be transported much deeper. The adsorption of Cr6+ by the soil tends to be weak in an acid-acidic environment, explaining the relatively high concentrations of Cr6+ recorded in the upper 10 m of soil. Although the conductivity of the shallow aquifers was low, the occurrence of acid soil and of an oxidizing water environment should have favored the transport of Cr6+ and Ni in the groundwater, causing high concentrations of Cr6+ and Ni in correspondence of the electroplating workshops (characterized by a relatively low water table and deep heavy metal transport depth). The excess of Pb in the groundwater probably resulted from the high Pb content of granite in the Guangdong-Hong Kong-Macau Greater Bay Area. Overall, we observed high concentrations of Ni, Cr6+, and Cu in the shallow soil and groundwater located in correspondence of the electroplating site on the hilly lands of the Guangdong-Hong Kong-Macau Greater Bay Area. The presence of low permeable clay restricted the downward diffusion of heavy metals. However, in the presence of acid soil and shallow buried granite, or of oxidized groundwater, the migration depth of Ni and Cr6+ was significantly higher.

Voluntary Wheel Running Reverses Deficits in Social Behavior Induced by Chronic Social Defeat Stress in Mice: Involvement of the Dopamine System.

Voluntary exercise has been reported to have a therapeutic effect on many psychiatric disorders and social stress is known to impair social interaction. However, whether voluntary exercise could reverse deficits in social behaviors induced by chronic social defeat stress (CSDS) and the underlying mechanism remain unclear. The present study shows CSDS impaired social preference and induced social interaction deficiency in susceptible mice. Voluntary wheel running (VWR) reversed these effects. In addition, CSDS decreased the levels of tyrosine hydroxylase in the ventral tegmental area and the D2 receptor (D2R) in the nucleus accumbens (NAc) shell. These changes can be recovered by VWR. Furthermore, the recovery effect of VWR on deficits in social behaviors in CSDS mice was blocked by the microinjection of D2R antagonist raclopride into the NAc shell. Thus, these results suggest that the mechanism underlying CSDS-induced social interaction disorder might be caused by an alteration of the dopamine system. VWR may be a novel means to treat CSDS-induced deficits in social behaviors via modifying the dopamine system.

Involvement of oxytocin and GABA in consolation behavior elicited by socially defeated individuals in mandarin voles.

Consolation, which entails comforting contact directed toward a distressed party, is a common empathetic response in humans and other species with advanced cognition. Here, using the social defeat paradigm, we provide empirical evidence that highly social and monogamous mandarin voles (Microtus mandarinus) increased grooming toward a socially defeated partner but not toward a partner who underwent only separation. This selective behavioral response existed in both males and females. Accompanied with these behavioral changes, c-Fos expression was elevated in many of the brain regions relevant for emotional processing, such as the anterior cingulate cortex (ACC), bed nucleus of the stria terminalis, paraventricular nucleus (PVN), basal/basolateral and central nucleus of the amygdala, and lateral habenular nucleus in both sexes; in the medial preoptic area, the increase in c-Fos expression was found only in females, whereas in the medial nucleus of the amygdala, this increase was found only in males. In particular, the GAD67/c-Fos and oxytocin (OT)/c-Fos colocalization rates were elevated in the ACC and PVN, indicating selective activation of GABA and OT neurons in these regions. The "stressed" pairs matched their anxiety-like behaviors in the open-field test, and their plasma corticosterone levels correlated well with each other, suggesting an empathy-based mechanism. This partner-directed grooming was blocked by pretreatment with an OT receptor antagonist or a GABAA receptor antagonist in the ACC but not by a V1a subtype vasopressin receptor antagonist. We conclude that consolation behavior can be elicited by the social defeat paradigm in mandarin voles, and this behavior may be involved in a coordinated network of emotion-related brain structures, which differs slightly between the sexes. We also found that the endogenous OT and the GABA systems within the ACC are essential for consolation behavior in mandarin voles.

Extraction of drug-drug interaction using neural embedding.

Information on changes in a drug's effect when taken in combination with a second drug, known as drug-drug interaction (DDI), is relevant in the pharmaceutical industry. DDIs can delay, decrease, or enhance absorption of either drug and thus decrease or increase their action or cause adverse effects. Information Extraction (IE) can be of great benefit in allowing identification and extraction of relevant information on DDIs. We here propose an approach for the extraction of DDI from text using neural word embedding to train a machine learning system. Results show that our system is competitive against other systems for the task of extracting DDIs, and that significant improvements can be achieved by learning from word features and using a deep-learning approach. Our study demonstrates that machine learning techniques such as neural networks and deep learning methods can efficiently aid in IE from text. Our proposed approach is well suited to play a significant role in future research.

Gene ontology annotation by density and gravitation models.

Gene Ontology (GO) is developed to provide standard vocabularies of gene products in different databases. The process of annotating GO terms to genes requires curators to read through lengthy articles. Methods for speeding up or automating the annotation process are thus of great importance. We propose a GO annotation approach using full-text biomedical documents for directing more relevant papers to curators. This system explores word density and gravitation relationships between genes and GO terms. Different density and gravitation models are built and several evaluation criteria are employed to assess the effects of the proposed methods.

Rule extraction in gene-disease relationship discovery.

BACKGROUND: Biomedical data available to researchers and clinicians have increased dramatically over the past years because of the exponential growth of knowledge in medical biology. It is difficult for curators to go through all of the unstructured documents so as to curate the information to the database. Associating genes with diseases is important because it is a fundamental challenge in human health with applications to understanding disease properties and developing new techniques for prevention, diagnosis and therapy. METHODS: Our study uses the automatic rule-learning approach to gene-disease relationship extraction. We first prepare the experimental corpus from MEDLINE and OMIM. A parser is applied to produce some grammatical information. We then learn all possible rules that discriminate relevant from irrelevant sentences. After that, we compute the scores of the learned rules in order to select rules of interest. As a result, a set of rules is generated. RESULTS: We produce the learned rules automatically from the 1000 positive and 1000 negative sentences. The test set includes 400 sentences composed of 200 positives and 200 negatives. Precision, recall and F-score served as our evaluation metrics. The results reveal that the maximal precision rate is 77.8% and the maximal recall rate is 63.5%. The maximal F-score is 66.9% where the precision rate is 70.6% and the recall rate is 63.5%. CONCLUSIONS: We employ the rule-learning approach to extract gene-disease relationships. Our main contributions are to build rules automatically and to support a more complete set of rules than a manually generated one. The experiments show exhilarating results and some improving efforts will be made in the future.

Enhancing performance of protein and gene name recognizers with filtering and integration strategies.

Named entity (NE) recognition is a fundamental task in biological relationship mining. This paper considers protein/gene collocates extracted from biological corpora as restrictions to enhance the precision rate of protein/gene name recognition. In addition, we integrate the results of multiple NE recognizers to improve the recall rates. Yapex and KeX, and ABGene and Idgene are taken as examples of protein and gene name recognizers, respectively. The precision of Yapex increases from 70.90 to 85.84% at the low expense of the recall rate (i.e., it only decreases 2.44%) when collocates are incorporated. When both filtering and integration strategies are employed together, the Yapex-based integration with KeX shows good performance, i.e., the F-score increases by 7.83% compared to the pure Yapex method. The results of gene recognition show the same tendency. The ABGene-based integration with Idgene shows a 10.18% F-score increase compared to the pure ABGene method. These successful methodologies can be easily extended to other name finders in biological documents.