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RNA binding proteins (RBPs) regulate nearly all post-transcriptional processes within cells. To fully understand RBP function, it is essential to identify their in vivo targets. Standard techniques for profiling RBP targets, such as crosslinking immunoprecipitation (CLIP) and its variants, are limited or suboptimal in some situations, e.g. when compatible antibodies are not available and when dealing with small cell populations such as neuronal subtypes and primary stem cells. This review summarizes and compares several genetic approaches recently designed to identify RBP targets in such circumstances. TRIBE (targets of RNA binding proteins identified by editing), RNA tagging, and STAMP (surveying targets by APOBEC-mediated profiling) are new genetic tools useful for the study of post-transcriptional regulation and RBP identification. We describe the underlying RNA base editing technology, recent applications, and therapeutic implications.

The temporal distribution of earthquakes provides important basis for earthquake prediction and seismic hazard analysis. The relatively limited records of strong earthquakes have often made it difficult to study the temporal distribution models of regional strong earthquakes. However, there are hundreds of years of complete strong earthquake records in North China Seismic Zone, providing abundant basic data for studying temporal distribution models. Using the data of M ≥ 6.5 earthquakes in North China as inputs, this paper estimates the model parameters using the maximum likelihood method with exponential, Gamma, Weibull, Lognormal and Brownian passage time (BPT) distributions as target models. The optimal model for describing the temporal distribution of earthquakes is determined according to Akaike information criterion (AIC), determination coefficient R2 and Kolmogorov-Smirnov test (K-S test). The results show that Lognormal and BPT models perform better in describing the temporal distribution of strong earthquakes in North China. The mean recurrence periods of strong earthquakes (M ≥ 6.5) calculated based on these two models are 8.1 years and 13.2 years, respectively. In addition, we used the likelihood profile method to estimate the uncertainty of model parameters. For the BPT model, the mean and 95% confidence interval of recurrence interval µ is 13.2 (8.9–19.1) years, and the mean and 95% confidence interval of α is 1.29 (1.0-1.78). For the Lognormal model, the mean value and 95% confidence interval of v is 2.09 (1.68–2.49), the mean value exp (v) corresponding to earthquake recurrence interval is 8.1 (5.4–12.1) years. In this study, we also calculated the occurrence probability of M ≥ 6.5 earthquakes in North China Seismic Zone in the future, and found that the probability and 95% confidence interval in the next 10 years based on the BPT model is 35.3% (26.8%-44.9%); the mean value and 95% confidence interval of earthquake occurrence probability based on the Lognormal distribution is 35.4% (22.9%-49.7%); the mean probability and 95% confidence interval based on the Poisson model is 53.1% (41.1%-64%). The results of this study may provide important reference for temporal distribution model selection and earthquake recurrence period calculation in future seismic hazard analysis in North China.

Pedestrian detection based on visual sensors has made significant progress, in which region proposal is the key step. There are two mainstream methods to generate region proposals: anchor-based and anchor-free. However, anchor-based methods need more hyperparameters related to anchors for training compared with anchor-free methods. In this paper, we propose a novel multiscale anchor-free (MSAF) region proposal network to obtain proposals, especially for small-scale pedestrians. It usually has several branches to predict proposals and assigns ground truth according to the height of pedestrian. Each branch consists of two components: one is feature extraction, and the other is detection head. Adapted channel feature fusion (ACFF) is proposed to select features at different levels of the backbone to effectively extract features. The detection head is used to predict the pedestrian center location, center offsets, and height to get bounding boxes. With our classifier, the detection performance can be further improved, especially for small-scale pedestrians. The experiments on the Caltech and CityPersons demonstrate that the MSAF can significantly boost the pedestrian detection performance and the log-average miss rate (MR) on the reasonable setting is 3.97% and 9.5%, respectively. If proposals are reclassified with our classifier, MR is 3.38% and 8.4%. The detection performance can be further improved, especially for small-scale pedestrians.

Background A variety of diabetes self-management instruments have been developed but few of them consist of the preparedness for diabetes self-management behavior. The novel psychometric evaluation tool “the LMC Skills, Confidence & Preparedness Index (SCPI)” measures three key aspects of a patient’s diabetes self-management: knowledge of the skill, confidence in being able to perform skill and preparedness to implement the skill. The objective of this study was to translate, adapt and validate the SCPI for use in Chinese adult patients with type 2 diabetes. Methods This study followed the guideline recommended by the American Academy of Orthopaedic Surgeons Evidence Based Medicine Committee (AAOS) to indigenize the scale. Forward and back translation, and cross-cultural language debugging were completed according to the recommended steps. A convenience sample of Chinese patients with type 2 diabetes (n = 375) were recruited from a university-affiliated hospital in Shanghai. The validity (criterion, discriminant validity, and construct validity), reliability (internal consistency and test–retest reliability) and the interpretability of the instrument were examined. The content validity was calculated by experts’ evaluation. Results The Chinese version of SCPI (C-SCPI) has good internal consistency with a Cronbach’s alpha of 0.92. The ceiling effects of the preparedness subscales is 21%. The criterion validity of three dimensions of C-SCPI was established with significantly moderate correlations between the DKT, DES-SF and SDSCA (p 2/df = 2.775, RMSEA = 0.069, CFI = 0.903, GFI = 0.873, TLI = 0.889, IFI = 0.904. The test–retest reliability coefficient was 0.61 (p Conclusion We established a Chinese version of SCPI through translation and cross-cultural adaptation. The C-SCPI is reliable and valid for assessment of the level of self-management in Chinese patients with type 2 diabetes.

RNA translation is tightly regulated to ensure proper protein expression in cells and tissues. Translation is often assayed with biochemical assays such as ribosome profiling and TRAP, which are effective in many contexts. These assays are however not ideal with limiting amounts of biological material when it can be difficult or even impossible to make an extract with sufficient signal or sufficient signal:noise. Because of our interest in translational regulation within the few Drosophila adult circadian neurons, we fused the ADAR catalytic domain (ADARcd) to several small subunit ribosomal proteins and assayed mRNA editing in Drosophila S2 cells. The strategy is named RiboTRIBE and is analogous to a recently published APOBEC-based method. The list of RiboTRIBE-edited transcripts overlaps well with ribosome profiling targets, especially with more highly ranked targets. There is also an enriched number of editing sites in ribosome-associated mRNA comparing to total mRNA, indicating that editing occurs preferentially on polyribosome-associated transcripts. The use of cycloheximide to freeze translating ribosomes causes a substantial increase in the number of RiboTRIBE targets, which is decreased by pretreating cells with the chain terminating drug puromycin. NOTE: Additional experiments performed after first submitting this manuscript to BioRxiv estimate that less than 5% of Rps28b-ADAR is ribosome-associated. This is because the vast majority of the fusion protein sediments at the top of a polyribosome gradient. We therefore suggest that most editing reported in the manuscript is not catalyzed by ribosome-associated ADAR (10/2/2021).

Additional file 1. Process of cross-cultural adaptation & General information of experts & Modified content after interviewing.

We used a relatively new method, HyperTRIBE, to identify in vivo RNA targets of the translation inhibitor 4E-BP., 4E-BP (eIF4E-BP) represses translation initiation by binding to the 5′ cap–binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity, and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used HyperTRIBE (targets of RNA binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. The protein associates with specific mRNAs, and ribosome profiling data show that mTOR inhibition changes the translational efficiency of 4E-BP TRIBE targets more substantially compared to nontargets. In both systems, these targets have specific motifs and are enriched in translation-related pathways, which correlate well with the known activity of 4E-BP and suggest that it modulates the binding specificity of eIF4E and contributes to mTOR translational specificity.

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein which forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, altered neuronal dendritic morphology is a common theme among several neurological disorders and is thought to precede neurodegeneration. We previously found that both TDP-43 overexpression (OE) and knockdown (KD) result in reduced dendritic branching of cortical neurons. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as an approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 RNA targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescues defects in dendritic branching. Finally, we demonstrate, using RNA sequencing, that TDP-43 OE and KD cause similar changes in the abundance of specific messenger RNAs, consistent with their ability to produce similar morphological defects. Our data therefore provide a mechanism by which TDP-43 dysfunction interferes with dendritic branching, and may define pathways for therapeutic intervention in neurodegenerative diseases.

RNA-binding proteins (RBPs) accompany RNA from birth to death, affecting RNA biogenesis and functions. Identifying RBP-RNA interactions is essential to understanding their complex roles in different cellular processes. However, detecting in vivo RNA targets of RBPs, especially in a small number of discrete cells, has been a technically challenging task. We previously developed a novel technique called TRIBE (targets of RNA-binding proteins identified by editing) to overcome this problem. TRIBE expresses a fusion protein consisting of a queried RBP and the catalytic domain of the RNA-editing enzyme ADAR (adenosine deaminase acting on RNA) (ADARcd), which marks target RNA transcripts by converting adenosine to inosine near the RBP binding sites. These marks can be subsequently identified via high-throughput sequencing. In spite of its usefulness, TRIBE is constrained by a low editing efficiency and editing-sequence bias from the ADARcd. Therefore, we developed HyperTRIBE by incorporating a previously characterized hyperactive mutation, E488Q, into the ADARcd. This strategy increases the editing efficiency and reduces sequence bias, which markedly increases the sensitivity of this technique without sacrificing specificity. HyperTRIBE provides a more powerful strategy for identifying RNA targets of RBPs with an easy experimental and computational protocol at low cost, that can be performed not only in flies, but also in mammals. The HyperTRIBE experimental protocol described below can be carried out in cultured Drosophila S2 cells in 1 week, using tools available in a common molecular biology laboratory; the computational analysis requires 3 more days.

Disaster preparedness is critical for reducing potential impact. This paper contributes to current knowledge of disaster preparedness using representative national sample data from China, which faces high earthquake risks in many areas of the country. The adoption of earthquake preparedness activities by the general public, including five indicators of material preparedness and five indicators of awareness preparedness, were surveyed and 3245 respondents from all 31 provinces of Mainland China participated in the survey. Linear regression models and logit regression models were used to analyze the effects of potential influencing factors. Overall, the preparedness levels are not satisfied, with a material preparation score of 3.02 (1–5), and awareness preparation score of 2.79 (1–5), nationally. Meanwhile, residents from western China, which has higher earthquake risk, have higher degrees of preparedness. The concern for disaster risk reduction (DRR) and the concern for building safety and participation in public affairs are consistent positive predictors of both material and awareness preparedness. The demographic and socioeconomic variables' effects, such as gender, age, education, income, urban/rural division, and building size, vary according to different preparedness activities. Finally, the paper concludes with a discussion of the theoretical contribution and potential implementation.

A particle swarm optimization (PSO) algorithm which can dynamically adjust learning factors is proposed to solve the problems of low efficiency and unstable operation of traditional industrial robots. The method uses piecewise polynomial interpolation to fit the trajectory, and uses an improved particle swarm algorithm to optimize the trajectory of industrial robots with time as a fitness function. This method effectively combines the piecewise polynomial interpolation function with PSO, avoids the complex process of particle swarm algorithm to construct the adaptation function, and improves the problem that the traditional PSO is more likely to fall into local extreme value in the early stage and convergence speed is slow in the later stage. Through experiments to obtain the motion pose, velocity and acceleration trajectory of each joint of the manipulator, we can know that this method can effectively realize the trajectory optimization of the industrial robot, and ensure the stability of the overall operation while improving the operating efficiency.

The environment project in the greater Mekong sub-region was the largest multi-field environmental cooperation launched by six countries (China, Vietnam, Laos, Myanmar, Thailand and Cambodia) in 2006, since the cooperation mechanism was established by Asian Development Bank (ADB) in 1992. How to establish the indicators to assess the achievements of the biological corridor construction and the status of ecological environment quantitatively is one of the prerequisites for the future project ongoing phase. The popular Pressure-State-Response (PSR) framework was employed in this study to assess the natural and human pressure, the healthy state of regional natural environment, and the subsequent response of ecosystem dynamic change in the Greater Mekong Subregion. Instead of using surveying based data as driving parameters, large amount of driving factors were retrieved from multi-source remote sensing data from 2000 to 2017, which provides access to larger updated and real-time databases, more tangible data allowing more objective goal management, and better spatially covered. The driving factors for pressure analysis included digital elevation, land surface temperature, evapotranspiration, light index, road network map, land cover dynamic change and land use degree, which were derived directly and indirectly from remote sensing. The indicators for state evaluation were composed of vegetation index, leaf area index, and fractional vegetation cover from remote sensing directly. The comprehensive response index was mainly determined by the pressure and state indicators. Through the analysis based on an overlay technique, it showed that the ecological environment deteriorated firstly from 2000 to 2010 and then started to improve from 2010 to 2017. The proofs indicated that the natural forest and wetland ecosystems were improved and the farmland area was decreased between 2000 and 2017. This study explored effective indicators from remote sensing for the ecological and environmental assessment, which can provide a strong decision-making basis for promoting the sustainable development of the ecological environment in the greater Mekong subregion, as well as the technological support for the construction of the biodiversity corridor.

With the development of e-commerce, delivery time is regarded as a key competitive advantage in an oligopoly market, as shortening the delivery time can stimulate demand for products. Many firms adopt a variety of strategies to shorten delivery time, and holding sufficient inventory is reported as an effective way. This study integrates a market share attraction model based on delivery time competition with the traditional inventory model to determine the optimal delivery time and order quantity. With the use of supermodular game method, we investigate the effect of changes in marketing and operations factors on the equilibrium delivery time and order quantity in non-dominated and dominated oligopolistic markets. The results reveal that the equilibrium delivery time and order quantity exhibit a directional response to changes in marketing and operations factors, and the response differs between the non-dominated oligopoly and the dominated oligopoly. Furthermore, under a cooperative oligopolistic market with asymmetry, it is beneficial for the firms with high competitive strength to adopt the delivery time strategy, but it fails to do so for the firm with the low competitive strength. Lastly, numerical analysis suggests that marketing factors play a more important role in affecting equilibrium measures than operations factors.

Disaster preparedness is critical for reducing potential impact. This paper contributes to current knowledge of disaster preparedness using a representative national sample data from China, which faces high earthquake risks in many areas of the country. The adoption of earthquake preparedness activities by the general public, including five material preparation, and five awareness preparation were surveyed, and 3,245 respondents from all of the 31 provinces of mainland China participated in the survey. Linear regression models and Logit regression models were used to analyze the effects of potential influencing factors. Overall, the preparedness levels are not satisfied, with a material preparation score of 3.02 (1–5), and awareness preparation score of 2.79 (1–5), nationally. Meanwhile, residents from west China where have higher earthquake risk have higher preparedness degrees. The concern of disaster risk reduction, the concern of building safety and participation in public affairs are consistent positive predictors of both material and awareness preparedness. The demographic and socioeconomic variables' effects, such as gender, age, education, income, urban/rural division, and occupied building type, vary according to different preparedness activities. Finally, the paper concludes with a discussion of the theoretical contribution and potential implementation.

We previously developed TRIBE, a method for the identification of cell-specific RNA binding protein targets. TRIBE expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR and performs Adenosine-to-Inosine editing on RNA targets of the RBP. However, target identification is limited by the low editing efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites, many of which are also edited by TRIBE but at a much lower editing frequency. HyperTRIBE therefore more faithfully recapitulates the known binding specificity of its RBP than TRIBE. In addition, separating RNA binding from the enhanced editing activity of the HyperTRIBE ADAR catalytic domain sheds light on the mechanism of ADARcd editing as well as the enhanced activity of the HyperADARcd.

IL-2 is the major regulatory cytokine of the immune system. It plays a key role in T cell survival, growth and activation. IL-2 may induce the expression of multiple genes including some cytokine genes. The induction of these genes is triggered by different signal pathways, one of them being the Jak-STAT signal pathway. The genes regulated by this pathway remain to be determined. By studying IL-2-inducible genes, we have confirmed that the TNF-beta gene is one of the immediate early genes activated by IL-2. By analysis of the DNA sequences around 180-300 bases upstream of the transcription initiation point of the mouse TNF-beta gene, we demonstrate that there is a STAT5 binding site which is essential to the inducibility of the TNF-beta gene. Furthermore, in BA/F3 cells co-transfected with the STAT5A gene and IL-2R beta gene, the activation of the TNF-beta gene promoter by IL-2 was greatly promoted, whereas the TNF-beta gene promoter became IL-2-non-inducible if the STAT5A gene was substituted with a dominant negative STAT5A, i.e. a C-terminally truncated mutant. Taken together, our results show that the Jak-STAT signal pathway is involved in induction of the TNF-beta gene in cells stimulated by IL-2.

Background The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this study, we conducted a comprehensive evolutionary analysis of CDK and cyclin proteins in metazoans and their unicellular relatives. Results Our analysis divided the CDK family into eight subfamilies. Seven subfamilies (CDK1/2/3, CDK5, CDK7, CDK 20, CDK8/19, CDK9, and CDK10/11) are conserved in metazoans and fungi, with the remaining subfamily, CDK4/6, found only in eumetazoans. With respect to cyclins, cyclin C, H, L, Y subfamilies, and cyclin K and T as a whole subfamily, are generally conserved in animal, fungi, and amoeba Dictyostelium discoideum. In contrast, cyclin subfamilies B, A, E, and D, which are cell cycle-related, have distinct evolutionary histories. The cyclin B subfamily is generally conserved in D. discoideum, fungi, and animals, whereas cyclin A and E subfamilies are both present in animals and their unicellular relatives such as choanoflagellate Monosiga brevicollis and filasterean Capsaspora owczarzaki, but are absent in fungi and D. discoideum. Although absent in fungi and D. discoideum, cyclin D subfamily orthologs can be found in the early-emerging, non-opisthokont apusozoan Thecamonas trahens. Within opisthokonta, the cyclin D subfamily is conserved only in eumetazoans, and is absent in fungi, choanoflagellates, and the basal metazoan Amphimedon queenslandica. Conclusions Our data indicate that the CDK4/6 subfamily and eumetazoans emerged simultaneously, with the evolutionary conservation of the cyclin D subfamily also tightly linked with eumetazoan appearance. Establishment of the CDK4/6-cyclin D complex may have been the key step in the evolution of cell cycle control during eumetazoan emergence.