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Background: The Rhus gall aphid Schlechtendalia chinensis specially uses the only species Rhus chinensis and certain moss species (Mniaceae) as its primary host plant and secondary host plants, respectively. Rhus galls are formed on the primary host by the sucking of aphids, and used in traditional medicine as well as other various areas due to their high tannin contents. Chemoreception is critical for insect behaviors such as host searching, location and identification of mates and reproductive behavior. The process of chemoreception is mediated by a series of protein gene families, including odorant-binding proteins (OBPs), chemosensory proteins (CSPs), olfactory receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs). However, there have been no reports on the analysis of molecular components related to the chemoreception system of S. chinensis at the genome level. Results: We examined the genes of eight OBPs, nine CSPs, 24 ORs, 16 GRs, 22 IRs, and five SNMPs in the S. chinensis genome using homological searches, and these chemosensory genes appeared mostly on chromosome 1. Phylogenetic and gene number analysis revealed that the gene families, e.g., ORs, GRs, CSPs and SNMPs in S. chinensis, have experienced major contractions by comparing to Myzus persicae, while the two gene families OBPs and IRs had slight expansion. The current results might be related to the broader host range of M. persicae versus the specialization of S. chinensis on only a host plant. There were 28 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the chemoreceptor gene families by collinear comparison. Ka/Ks ratios (< 1) indicated that the genes of S. chinensis were mainly affected by purification selection during evolution. We also found the lower number and expression level of chemoreception genes in S. chinensis than in other 11 aphid species, such as ORs, GRs and IRs, which play an important role in host search. Conclusion: Our study firstly identified the genes of the different chemosensory protein gene families in the S. chinensis genome, and analyzed their general features and expression profile, demonstrating the importance of chemoreception in the aphid and providing new information for further functional research. [ABSTRACT FROM AUTHOR]

The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-S-transferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research. [ABSTRACT FROM AUTHOR]

Residences in poor regions always depend on rain-fed agriculture, so they urgently need suitable tools to make accurate meteorological predictions. Unfortunately, meteorological observations in these regions are usually sparse and irregularly distributed. Conventional LSTM networks only handle temporal sequences and cannot utilize the links of meteorological variables among stations. GCN-LSTM networks only capture local spatial structures through the simple structures of fixed adjacency matrices, and the CNN-LSTM can only mine gridded meteorological observations for further predictions. In this study, we propose an optimization hybrid of multiple-lag LSTM networks for meteorological predictions. Our model can make full use of observed data at partner stations under different time-lag windows and strong links among the local observations of meteorological variables to produce future predictions. Numerical experiments on the meteorological predictions of Bangladesh demonstrate that our networks are superior to the classic LSTM and its variants GCN-LSTM and CNN-LSTM, as well as the SVM and DT. [ABSTRACT FROM AUTHOR]

In his keynote lecture at the Reimagining Further Education conference in Birmingham in June 2016, Sir Frank McLoughlin was clear that the sector ‘needed a mission’ to unite around, and to let people know where it is going. This was endorsed by the attendees, who felt that it would enable the sector to regain ownership of what it stands for nationally, regionally and locally. Such a vision is needed to create a Technical and Vocational Education and Training sector that is targeted to develop an effective shared culture in the further education sector, close skills shortages and skills gaps in education, enhance community cohesion and improve productivity. This vision needs to have a robust measure of impact that aligns with the vision. One possibility is to explore a non-financial and intangible value metric where social value is aligned to the sector mission. A robust measure will enable key stakeholders to agree on areas of focus in a specific geographical location or a specific time. Such a measure might challenge the need for the existence of regulatory bodies such as Ofsted in the way they operate now. With such a robust measure of social value/impact, Government will not need to issue a white paper every time a response to a localised issue is required. We suggest that the Social Earnings Ratio (S/E or SE Ratio) is such a robust measure. For example, if the need in a certain locality is to address skills gaps/shortages or to focus on community cohesion, all that is needed is a change in the weighting of the various components of such a measure. This will allow development of a further education mission that can be utilised nationally, regionally and locally. In this article, we develop this idea and provide an illustration of how the SE Ratio could be applied to a further education college. The example we use is that of a small further education college with an annual budget of £12 m. We demonstrate, using SE Ratio, that this college produces an intangible value of approximately £40 m per annum. Such an approach will enable further education to become the strong owner of its mission and vision in the future, and allow it to develop its own culture and expertise to the maximum of its potential. [ABSTRACT FROM AUTHOR]

Under global warming scenarios, extreme climate events in South Asia will occur more frequently which will seriously threaten the safety of local residents. South Asia faces dual pressures of the obligation of carbon emissions reduction globally and the demand for a better life for huge populations. Stratospheric Aerosol Injection (SAI) climate engineering provides a potential solution to this dilemma. We compared the evolution of 12 climate extreme indices under historical scenarios, two future scenarios (SSP245, SSP585) and an implementation scenario of SAI climate engineering (G6sulfur). We showed that the intensity and frequency of extreme climates under a G6sulfur scenario would be significantly higher than those under historical scenarios, and that the difference in extreme climates under three scenarios (SSP245, SSP585, and G6sulfur) would be widely varying, with some indices being considerably mitigated while others would reflect a worse set of circumstances than would be the case without SAI climate engineering. Therefore, SAI climate engineering is not an effective tool to mitigate future climate extremes in South Asia under global warming scenarios. [ABSTRACT FROM AUTHOR]

Multifractal detrended fluctuation analysis (DFA) can extract multi-scaling behavior and measure long-range correlations in climatic time series. In this study, with the help of multifractal DFA, we investigated the scaling behavior of daily minimum/maximum temperatures during the years 1989–2019 from 34 meteorological stations in Bangladesh. We revealed spatial patterns, topographic impacts and global warming impacts of long-range correlations embedded in small and large fluctuations in temperature time series. Meanwhile, we developed a multifractal DFA-based algorithm to dynamically determine thresholds to discriminate extreme and non-extreme events in climate systems and applied it to analyze the frequency and trends of temperature extremes in Bangladesh. Compared with widely-used percentile thresholds, the extreme climate events captured in our algorithm are more reliable since they are determined dynamically by the climate system itself. [ABSTRACT FROM AUTHOR]

This paper explores the application of citizen science to help generation of scientific data and capacity-building, and so underpin scientific ideas and policy development in the area of coral reef management, on the coral reefs of Jamaica. From 2000 to 2008, ninety Earthwatch volunteers were trained in coral reef data acquisition and analysis and made over 6,000 measurements on fringing reef sites along the north coast of Jamaica. Their work showed that while recruitment of small corals is returning after the major bleaching event of 2005, larger corals are not necessarily so resilient and so need careful management if the reefs are to survive such major extreme events. These findings were used in the development of an action plan for Jamaican coral reefs, presented to the Jamaican National Environmental Protection Agency. It was agreed that a number of themes and tactics need to be implemented in order to facilitate coral reef conservation in the Caribbean. The use of volunteers and citizen scientists from both developed and developing countries can help in forging links which can assist in data collection and analysis and, ultimately, in ecosystem management and policy development. [ABSTRACT FROM AUTHOR]

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress. [ABSTRACT FROM AUTHOR]

Knowledge of factors that are important in reef resilience and integrity help us understand how reef ecosystems react following major anthropogenic and environmental disturbances. The North Jamaican fringing reefs have shown some recent resilience to acute disturbances from hurricanes and bleaching, in addition to the recurring chronic stressors of over-fishing and land development. Factors that can improve coral reef resilience are reviewed, and reef rugosity is shown to correlate with coral cover and growth, particularly for branching Acropora species. The biodiversity index for the Jamaican reefs was lowered after the 2005 mass bleaching event, as were the numbers of coral colonies, but both had recovered by 2009. The importance of coastal zone reef management strategies and the economic value of reefs are discussed, and a protocol is suggested for future management of Jamaican reefs. [ABSTRACT FROM AUTHOR]

We undertook a capacity-building exercise around marine protected areas (MPAs) that involved both local nongovernmental organization (NGO) community workers and a government fisheries officer, so that community engagement could be directly interfaced with fisheries operations and policy. Targeting a government worker is a relatively new approach. Our methodology used a modified nominal group technique and Delphi technique to develop personal action plans to facilitate the future of sustainable MPAs in the MesoAmerican Barrier Reef system. The involvement of a fisheries officer resulted in direct transfer of information from the communities to the government department. The personal action plans involve improvements to organization and management, education, support, and policy development. In addition, three NGOs, TASTE (Toledo Association for Sustainable Tourism and Empowerment), TIDE (Toledo Institute for Development and Environment), and Friends of Nature, have been incorporated into a single self-governing organization that spans four MPAs in southern Belize. This is a significant advance, allowing areas that were subject to illegal fishing to be monitored and policed. [ABSTRACT FROM AUTHOR]

The coral reef ecosystem forms part of a ‘seascape’ that includes land-based ecosystems such as mangroves and forests, and ideally should form a complete system for conservation and management. Aquaculture, including artisanal fishing for fish and invertebrates, shrimp farming, and seaweed farming, is a major part of the farming and gleaning practices of many tropical communities, particularly on small islands, and depends upon the integrity of the reefs. Climate change is making major impacts on these communities, not least through global warming and high CO2 concentrations. Corals grow within very narrow limits of temperature, provide livelihoods for millions of people in tropical areas, and are under serious threat from a variety of environmental and climate extremes. Corals survive and grow through a symbiotic relationship with photosynthetic algae: zooxanthellae. Such systems apply highly co-operative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. This review will discuss research on how climate influences reef ecosystems, and how science can lead to conservation actions, with benefits for the human populations reliant on the reefs for their survival. [ABSTRACT FROM PUBLISHER]

Abstract: Climate change and global warming have severe consequences for the survival of scleractinian (reef-building) corals and their associated ecosystems. This review summarizes recent literature on the influence of temperature on coral growth, coral bleaching, and modelling the effects of high temperature on corals. Satellite-based sea surface temperature (SST) and coral bleaching information available on the internet is an important tool in monitoring and modelling coral responses to temperature. Within the narrow temperature range for coral growth, corals can respond to rate of temperature change as well as to temperature per se. We need to continue to develop models of how non-steady-state processes such as global warming and climate change will affect coral reefs. [Copyright &y& Elsevier]

This study set out to test the hypothesis that hurricanes and tropical storms limit the recruitment and subsequent survival of massive non-branching corals on the barrier reef off the coast of Belize in the Gulf of Honduras. Overall, the surface areas of 523 individual coral specimens were measured, and recruitment dates were then modelled. There was no significant difference in coral cover or coral biodiversity between any of the sites studied (p >0.1). There were significant differences in non-branching coral recruitment in years when hurricanes impacted the area (p <0.05) compared with years when no hurricanes impacted the area. There were significantly more non-branching massive corals recruited in non-hurricane years (mean 7.7) than in hurricane years (mean 3.8; p =0.011). When years with tropical storms are added to the years with hurricanes, there was significantly lower coral recruitment (mean 4.7) relative to non-storm or hurricane years (mean 7.4; p =0.019). These results show that hurricanes and severe storms limited the recruitment and survival of massive non-branching corals of the Mesoamerican barrier reef and on patch reefs near the Belize coast in the Caribbean, and suggests that marine park managers may need to assist coral recruitment in years where there are hurricanes or severe storms. [Copyright &y& Elsevier]

Abstract: Coastal environments in the tropics can suffer from high sedimentation and low light levels. Galaxea fascicularis is a hermatypic coral that is relatively resilient to stress from bleaching and from sedimentation. Corallite dimensions – width, height, corallite densities and inter-corallite distances – of Galaxea fascicularis colonies varied significantly with depth, and so with incident light at the Sampela reef in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. Modelling studies based on our data showed that corallite width decreased with the amount of incident light, while corallite height increased with the amount of incident light (r 2 values of 0.835 for width and 0.869 for height). In all colonies, inter-corallite distance decreased significantly with the amount of incident light (r 2 =0.89). Colony width/height ratio increased in a linear fashion with inter-corallite distance for all colonies studied (r 2 =0.65). Current flow as judged using tags did not appear to be a factor in variations of corallite dimensions. Our results suggest that under low light conditions, distribution and size of corallites may optimise heterotrophic nutrition, while in conditions where light is not limiting, distribution and size of corallites may be optimal for photosynthesis. [Copyright &y& Elsevier]

Digital videophotography, computer image analysis and physical measurements have been used to monitor sedimentation rates, coral cover, genera richness, rugosity, and estimated recruitment dates of massive corals at three different sites in the Wakatobi Marine National Park, Indonesia, and on the reefs around Discovery Bay, Jamaica. Semi-structured interviews with key stakeholders in the Wakatobi Marine National Park indicated that coral mining was extensively practised, and is responsible for the absence of large non-branching corals on the Sampela reef. Blast fishing is also practised in the Wakatobi Marine Park, and the authors, together with students, showed that blast fishing resulted in coral bleaching and not mortality of two Porites lutea colonies. In addition, we showed that monitoring of bleaching in Porites colonies induced by blast fishing could be a useful way of monitoring blast fishing practices in susceptible areas in the Indo-Pacific. The techniques used in this study are appropriate for use by volunteers with sufficient training, and provide excellent projects for dissertation students reading undergraduate degrees. [ABSTRACT FROM AUTHOR]

Compares the three coral reef sites in the Wakatobi Marine National Park in Sulawesi, Indonesia. Impact of coral mining on the ecosystem habitat and biodiversity; Importance of coral growth rates to estimate recruitment dates; Role of anthropogenic and other factors on colony recruitment.

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease—cataract, the largest cause of blindness in the world—after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff’s base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes. [Copyright &y& Elsevier]

We have developed a new simple method for transport, storage, and analysis of genetic material from the corals Agaricia agaricites, Dendrogyra cylindrica, Eusmilia ancora, Meandrina meandrites, Montastrea annularis, Porites astreoides, Porites furcata, Porites porites, and Siderastrea siderea at room temperature. All species yielded sufficient DNA from a single FTA® card (19 μg–43 ng) for subsequent PCR amplification of both coral and zooxanthellar DNA. The D1 and D2 variable region of the large subunit rRNA gene (LSUrDNA) was amplified from the DNA of P. furcata and S. siderea by PCR. Electrophoresis yielded two major DNA bands: an 800-base pair (bp) DNA, which represented the coral ribosomal RNA (rRNA) gene, and a 600-bp DNA, which represented the zooxanthellar srRNA gene. Extraction of DNA from the bands yielded between 290 μg total DNA (S. siderea coral DNA) and 9 μg total DNA (P. furcata zooxanthellar DNA). The ability to transport and store genetic material from scleractinian corals without resort to laboratory facilities in the field allows for the molecular study of a far wider range and variety of coral sites than have been studied to date. [Copyright &y& Elsevier]

An understanding of the multi-step nature of cancer as it is in the breast, as a series of pivotal genetic/epigenetic modifications is irrefutably a milestone in diagnostics, prognostics and eventually providing a cure. Here we have utilised a variant of analysis of variance (ANOVA) as a model for the identification and tracking of specific mRNA species whose transcription has been significantly altered at each grade in the progression of ductal carcinoma, making it possible to correlate histological progression with the genetic events underlying breast cancer. We show that in the progression of ductal carcinomas, from grade 1 to 3, there is a reduction in the actual number of mRNA species, which are significantly over or under expressed. We also show that this technique can be employed to generate differential gene expression patterns, whereby the combined expression profile of the tailored spectra of genes in the comparison of each ductal grade is sufficient to render them on clearly separate arms of an array-wise hierarchical cluster dendrogram. [Copyright &y& Elsevier]

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function:dx/dt=a1W+a2W2+a3W3+…anWn/1+b1W+b2W2+b3W3+…bmWmwhere dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curac¸ao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village. [Copyright &y& Elsevier]

Metallothioneins (MTs) are a class of cysteine-rich metal-binding proteins. Cadmium (Cd) is one of the toxic heavy metal pollutants. In our previous research, the full-length cDNA of MT (Cd specificity) from freshwater crab (Sinopotamon henanense) (Sh MT) was cloned and genetically modified to Sh MT3 by site-directed mutagenesis to enhance the tolerance for Cd2+, however, it was limited in actual Cd2+ adsorption due to instability. Here, Sh MT3-CBM, a novel recombinant fusion protein, was prepared. CBM is a carbohydrate binding module that can specifically bind cellulose while Sh MT3 can effectively chelate Cd2+. The biosorbent Cellulose1- Sh MT3-CBM was obtained by screening suitable cellulose materials. The selective adsorption experiments showed that Cellulose1- Sh MT3-CBM had a preference for Cd2+. In low-concentration Cd2+ solutions, the removal efficiency was >99 %, and the adsorption equilibrium was reached within 15 min. The saturated adsorption capacity of Cellulose1- Sh MT3-CBM for Cd2+ is 180.35 ± 4.67 mg/g (Dry Weight). Regeneration experiments showed that adsorption efficiency was maintained after six cycles. The MTT experiment showed that Cellulose1- Sh MT3-CBM had low cytotoxicity. Meanwhile, Cellulose1- Sh MT3-CBM can preferentially remove Cd2+ in actual water samples and boiler sewage. In this study, an environmentally friendly biosorbent which can adsorb Cd2+ efficiently and quickly was prepared for actual water treatment. [Display omitted] • Sh MT3-CBM was obtained by genetic engineering technology. • Cellulose1- Sh MT3-CBM was obtained by immobilization technology. • In low concentration solution, the removal efficiency reaches >99 %. • Cellulose1- Sh MT3-CBM showed excellent reusability. • Cellulose1- Sh MT3-CBM is non-toxic to cells. [ABSTRACT FROM AUTHOR]

A computer program in BASIC has been written which will compute all scores for the Farnsworth 100-hue test, and plot them in the appropriate colour on a polar co-ordinate graph. Hard copy can be obtained on a dot-matrix printer. The program is simple to use, and considerably curtails the analysis time for this test, as well as eliminating possible computational errors. [ABSTRACT FROM AUTHOR]

The downscaling technique produces high spatial resolution precipitation distribution in order to analyze impacts of climate change in data-scarce regions or local scales. In this study, based on three statistical learning algorithms, such as support vector machine (SVM), random forest regression (RF), and gradient boosting regressor (GBR), we proposed an efficient downscaling approach to produce high spatial resolution precipitation. In order to demonstrate efficiency and accuracy of our models over traditional multilinear regression (MLR) downscaling models, we did a downscaling analysis for daily observed precipitation data from 34 monitoring sites in Bangladesh. Validation revealed that R 2 of GBR could reach 0.98, compared with RF (0.94), SVM (0.88), and multilinear regression (MLR) (0.69) models, so the GBR-based downscaling model had the best performance among all four downscaling models. We suggest that the GBR-based downscaling models should be used to replace traditional MLR downscaling models to produce a more accurate map of high-resolution precipitation for flood disaster management, drought forecasting, and long-term planning of land and water resources. [ABSTRACT FROM AUTHOR]

As a developing country with an agricultural economy as a pillar, Bangladesh is highly vulnerable to adverse effects of climate change, so the generation of high-resolution temperature maps is of great value for Bangladesh to achieve agricultural sustainable development. However, Bangladesh's weak economy and sparse meteorological stations make it difficult to obtain such maps. In this study, by mining internal features and links inside observed data, we developed an efficient data-driven downscaling technique to generate high spatial-resolution temperature distribution maps of Bangladesh directly from observed temperature data at 34 meteorological stations with irregular distribution. Based on these high-resolution historical temperature maps, we further explored a data-driven forecast technique to generate high-resolution temperature maps of Bangladesh for the period 2025–2035. Since the proposed techniques are very low-cost and fully mine internal links inside irregular-distributed observations, they can support relevant departments of Bangladesh to formulate policies to mitigate and adapt to climate change in a timely manner. [ABSTRACT FROM AUTHOR]

Motivation Virus mutation is one of the most important research issues which plays a critical role in disease progression and has prompted substantial scientific publications. Mutation extraction from published literature has become an increasingly important task, benefiting many downstream applications such as vaccine design and drug usage. However, most existing approaches have low performances in extracting virus mutation due to both lack of precise virus mutation information and their development based on human gene mutations. Results We developed ViMRT, a text-mining tool and search engine for automated virus mutation recognition using natural language processing. ViMRT mainly developed 8 optimized rules and 12 regular expressions based on a development dataset comprising 830 papers of 5 human severe disease-related viruses. It achieved higher performance than other tools in a test dataset (1662 papers, 99.17% in F1-score) and has been applied well to two other viruses, influenza virus and severe acute respiratory syndrome coronavirus-2 (212 papers, 96.99% in F1-score). These results indicate that ViMRT is a high-performance method for the extraction of virus mutation from the biomedical literature. Besides, we present a search engine for researchers to quickly find and accurately search virus mutation-related information including virus genes and related diseases. Availability and implementation ViMRT software is freely available at http://bmtongji.cn:1225/mutation/index. [ABSTRACT FROM AUTHOR]

Background: Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. Results: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. Conclusion: F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants. [ABSTRACT FROM AUTHOR]

Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome‐level genome sequence of the hawthorn cultivar "Qiu Jinxing." We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo‐chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole‐genome duplication event was specifically detected in hawthorn. The amplification of non‐specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo‐sub‐genomes in extant species of Maleae and found that these two sub‐genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo‐polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high‐quality reference genome provides a useful resource for the horticultural improvement of hawthorn. [ABSTRACT FROM AUTHOR]

Background: Dietary phytoestrogens have been suggested to influence puberty timing, a critical stage for well-being in adulthood. We hypothesized that childhood soy intake might prospectively influence puberty timing and that dietary fibre and the key isoflavone metabolite equol might play roles.Methods: Cox proportional hazard regression models were performed in 4781 children (2152 girls and 2629 boys) aged 6-8 years old from the Chinese Adolescent Cohort Study for whom a food frequency questionnaire at baseline and information about potential confounders were available. Anthropometry and pubertal status including age at Tanner stage 2 for breast development (B2) or age at the initiation of gonadal growth (G2), and age at menarche (M) or voice break (VB) were assessed annually. Equol excretion was determined by urine samples from 1311 participants.Results: Among girls and boys, higher soy intake was associated with later puberty timing (hazard ratio (HR)-B2: 0.88 (95% CI, 0.80-0.96), p=0.02; HR-M, 0.87 (0.77-0.94), p=0.01; HR-G2, 0.91 (0.82-0.98), p=0.013; HR-VB, 0.90 (0.82-0.9), p=0.02), independent of prepubertal body fatness and fibre intake. These associations were more pronounced among children with a high urinary equol level (pfor-interaction ≤ 0.04) or with a high cereal fibre intake (pfor-interaction ≤ 0.06). Intake of dietary fibre or its subtype was not prospectively associated with puberty onset after adjusting for dietary soy intake (p≥0.06).Conclusion: Higher childhood soy intake is prospectively associated with later puberty timing in both Chinese girls and boys, independent of prepubertal body fatness, and the association is particularly pronounced among individuals with a higher urinary equol level. [ABSTRACT FROM AUTHOR]

• Economic development may drive academic construction safety research. • There has been an increase in construction safety research conducted by developing countries in recent years, probably due to an improvement in their economic performance. • Authors' keywords evidenced the popularity of research on safety management and climate. • There is a new interdisciplinary research trend where construction safety combines with digitalization technologies, with the largest number involving deep learning. The construction industry contributes significantly to economic development worldwide, yet it is one of the most hazardous industries where numerous accidents and fatalities happen every year. Little research to date has shed light on the impact of economic development on construction safety research. In this paper, we conduct an analysis of construction safety articles published in the 21st century via a bibliometrics approach. We have analysed: (1) construction safety in developed and developing countries; (2) the major organisations that have conducted construction safety research; (3) authors and territories of the research and (4) topics in construction safety and future research directions. The largest number of published construction safety documents were published by scholars from the US and China; the total number of published articles by these two countries was 1,125, at 56% of the 2000 articles that were published. Both countries showed high levels of research collaboration. While our results suggest that economic development may drive academic construction safety research, there has been an increase in construction safety research conducted by developing countries in recent years, probably due to an improvement in their economic development. While authors' keywords evidenced the popularity of research on safety management and climate, the network analysis on all keywords, i.e. keywords given by Web of Science and authors, suggest that construction safety research focused on three areas: construction safety management, the relationship between people and construction safety, and the protection and health of workers' impact on construction safety. We found that there is a new interdisciplinary research trend where construction safety combines with digital technologies, with the largest number involving deep learning. Other trends focus on machine learning, Building Information Modelling, and visualisation. [ABSTRACT FROM AUTHOR]

Metallothionein (MTs) can be used in the prevention and treatment of tumors and diabetes due to its antioxidant properties. However, it is necessary to solve its non-transmembrane properties and further improve its antioxidant activity, increase its fluorescence visualization and enhance its stability to meet practical applications in the biomedical field. Here, we report the preparation of a novel metallothionein-AuNP composite material with high transmembrane ability, fluorescence visualization, antioxidant activity, and stability by genetic modification (introducing transduction peptide TAT, fluorescence tag GFP and increasing sulfydryl groups) and immobilization technology (covalently bonding with AuNPs). The transmembrane activity of modified proteins was verified by immunofluorescence. Increasing the sulfhydryl content within a certain range can enhance the antioxidant activity of the protein. In addition, GFP were used to further simplify the imaging of the metallothionein-AuNP composite in cells. XPS results indicated that AuNPs can immobilize metallothionein through Au S covalent bonds. TGA characterization and degradation experiments showed that thermal and degradation stability of the immobilized material was significantly improved. This work provides new ideas to construct metallothionein composites with high transmembrane ability, antioxidant activity, fluorescence visualization and stability to meet novel applications in the biomedical field. [Display omitted] • TAT- Sh MT3 was obtained by long primer PCR. • TAT- Sh MT3 has about 30 % increase in antioxidant capacity compared to TAT- Sh MT. • TAT- Sh MT3-GFP was obtained by SOE-PCR. • TAT- Sh MT3-GFP + AuNPs was obtained Au S covalent bond. • TAT-ShMT3-GFP + AuNPs has higher stability compared to TAT- Sh MT3-GFP. [ABSTRACT FROM AUTHOR]

Nurudea zhengii Ren was identified by aphid morphological characteristics as well as the gall shape and host plant species, and placed in the tribe Fordini (Hemiptera, Aphididae, Eriosomatinae). Here, its whole genome was firstly sequenced by a genome-skimming method and its mitochondrial genome (mitogenome) was assembled to examine its genetic variation and phylogenetic position. The complete mitogenome of Nurudea zhengii is 15,392 bp in length, and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs and one D-loop region. The gene order follows the mitogenomes of the other Rhus gall aphids, and similarly has an AT bias with the content of 83.9%. The majority strand is A-skewed and C-skewed, and shows opposite skewness for G-skewed in the minority strands. The ratios of nonsynonymous to synonymous substitution rates of protein-coding genes are lower than one except for ATP8, which indicated that ATP8 was undergoing positive selection. Phylogenetic analysis among the Rhus gall aphids based on 13 protein-coding genes and two rRNA genes showed that N. zhengii was sister to N. shiraii, and then clustered with N. yanoniella as a group with high support value. The two species, N. shiraii and N. yanoniella, share the same host plant Rhus chinensis, while the host of N. zhengii is R. hypoleuca. However, the phylogenetic relationship indicated that the taxa sharing the same host plant were not absolutely clustered as the closest taxa at least at species level. [ABSTRACT FROM AUTHOR]

Abstract: Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van’t Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. [Copyright &y& Elsevier]

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured. [Copyright &y& Elsevier]

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide’s backbone. The dihedral angles determining the chain’s configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain’s configuration is determined by its radius of gyration.A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 A˚ with an optimised hydrophobic term in the fitness function. [Copyright &y& Elsevier]

In areas such as drug development, clinical diagnosis and biotechnology research, acquiring details about the kinetic parameters of enzymes is crucial. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. We demonstrate that a Bayesian approach (the use of prior knowledge) can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment.Developing the use of Bayesian Utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of KM and/or the kinetic model.We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. [Copyright &y& Elsevier]

Background: Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results: We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions: Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species. [ABSTRACT FROM AUTHOR]

Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation‐sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance. [ABSTRACT FROM AUTHOR]

Abstract Under rapid Arctic warming, the vast amount of labile organic carbon stored in Arctic permafrost soils poses a potentially huge threat. Thawing permafrost will release hundreds of billion tons of soil carbon into the atmosphere in the form of CO 2 and CH 4 that would further intensify global warming and bring more challenges to human society. In this study, we use the PInc-PanTher model to estimate carbon emissions from thawing permafrost in the circum-Arctic during 2010–2100 followed by the PAGE09 integrated assessment model to evaluate the net economic losses caused by these permafrost carbon emissions. Our results show that in terms of net present value (NPV), the release of CO 2 and CH 4 from circum-Arctic permafrost will generate estimated net economic losses of US$2.5 trillion (5–95% range: 0.3–11.2 US$ trillion) under the RCP4.5-SPP1 scenario and US$12.7 trillion (5–95% range: 1.6–41.8 US$ trillion) under the RCP8.5-SPP3 scenario between 2010 and 2100, which contribute ~4.9% and ~6.4% respectively of net economic losses of global carbon emissions. Graphical abstract Unlabelled Image Highlights • Circum-Arctic permafrost carbon stock will lose 21–92 Pg in 2010–2100. • Economic losses of permafrost emissions will reach US$2.5–12.7 trillion by 2100. • A multi-model integrated assessment model is used. [ABSTRACT FROM AUTHOR]

Bacterial RNA polymerase (RNAP) is an effective target for antibacterial treatment. In order to search new potential targets in RNAP of Mycobacterium , we detected adaptive selections of RNAP related genes in 13 strains of Mycobacterium by phylogenetic analysis. We first collected sequences of 17 genes including rpoA, rpoB, rpoC, rpoZ, and sigma factor A-M. Then maximum likelihood trees were constructed, followed by positive selection detection. We found that sigG shows positive selection along the clade ( M. tuberculosis , M. bovis ), suggesting its important evolutionary role and its potential to be a new antibacterial target. Moreover, the regions near 933Cys and 935His on the rpoB subunit of M. tuberculosis showed significant positive selection, which could also be a new attractive target for anti-tuberculosis drugs. [ABSTRACT FROM AUTHOR]

Humans are exposed to disinfection by-products through oral, inhalation, and dermal routes, during bathing and swimming, potentially causing skin lesions, asthma, and bladder cancer. Nuclear factor E2-related factor 2 (NRF2) is a master regulator of the adaptive antioxidant response via the antioxidant reaction elements (ARE) orchestrating the transcription of a large group of antioxidant and detoxification genes. Here we used an immortalized human keratinocyte model HaCaT cells to investigate NRF2-ARE as a responder and protector in the acute cytotoxicity of seven haloacetonitriles (HANs), including chloroacetonitrile (CAN), bromoacetonitrile (BAN), iodoacetonitrile (IAN), bromochloroacetonitrile (BCAN), dichloroacetonitrile (DCAN), dibromoacetonitrile (DBAN), and trichloroacetonitrile (TCAN) found in drinking water and swimming pools. The rank order of cytotoxicity among the HANs tested was IAN ≈ BAN ˃ DBAN ˃ BCAN ˃ CAN ˃ TCAN ˃ DCAN based on their LC 50. The HANs induced intracellular reactive oxygen species accumulation and activated cellular antioxidant responses in concentration- and time-dependent fashions, showing elevated NRF2 protein levels and ARE activity, induction of antioxidant genes, and increased glutathione levels. Additionally, knockdown of NRF2 by lentiviral shRNAs sensitized the HaCaT cells to HANs-induced cytotoxicity, emphasizing a protective role of NRF2 against the cytotoxicity of HANs. These results indicate that HANs cause oxidative stress and activate NRF2-ARE-mediated antioxidant response, which in turn protects the cells from HANs-induced cytotoxicity, highlighting that NRF2-ARE activity could be a sensitive indicator to identify and characterize the oxidative stress induced by HANs and other environmental pollutants. [Display omitted] • Haloacetonitriles cause acute cytotoxicity and oxidative stress in HaCaT cells. • Haloacetonitriles induce NRF2-ARE-mediated antioxidant response in HaCaT cells. • NRF2 protects human keratinocytes from HANs-induced acute cell damage. • NRF2-ARE activity is an indicator for the oxidative stress caused by haloacetonitriles. [ABSTRACT FROM AUTHOR]

Comprehensive enrichment of contaminants in drinking water is an essential step for accurately determining exposure levels of contaminants and testing their biological effects. Traditional methods using a single absorbent for enriching contaminants in water might not be adequate for complicated matrices with different physical-chemical profiles. To examine this hypothesis, we used an integrated enrichment system that had three sequential stages-XAD-2 resin, poly (styrene–divinylbenzene) and activated charcoal to capture organic pollutants and disinfection by-products (DBPs) from drinking water in Shanghai. Un-adsorbed Organic Compounds in Eluates (UOCEs) named UOCEs-A, -B, and-C following each adsorption stage were determined by gas chromatography-mass spectrometry to evaluate adsorption efficiency of the enrichment system. Meanwhile, biological effects such as cytotoxicity, effects on reactive oxygen species (ROS) generation and glutathione (GSH) depletion were determined in human LO2 cells to identify potential adverse effects on exposure to low dose contaminants. We found that poly-styrene–divinylbenzene (PS-DVB) and activated charcoal (AC) could still partly collect UOCEs-A and-B that the upper adsorption column incompletely captured, and that potential carcinogens like 2-naphthamine were present in all eluates. UOCEs-A at (1–4000), UOCEs-B at (1000–4000), and UOCEs-C at (2400–4000) folds of the actual concentrations had significant cytotoxicity to LO2 cells. Additionally, ROS and GSH change in cells treated with UOCEs indicated the potential for long-term effects of exposure to some mixtures of contaminants such as DBPs at low doses. These results suggested that an enriching system with a single adsorbent would underestimate the exposure level of pollutants and the biological effects of organic pollutants from drinking water. Effective methods for pollutants' enrichment and capture of drinking water should be given priority in future studies on accurate evaluation of biological effects exposed to mixed pollutants via drinking water. [Display omitted] • Capacity of enriched pollutants from water by a single adsorbent is limited. • 69.5% of target chemicals are efficiently enriched by series of adsorption. • Unabsorbed organic compounds in eluate are cytotoxic and impact cell viability. • Low concentrations unabsorbed chemicals in eluate alter the ROS and GSH of cells. • Single sorbent underestimated exposures and effects of drinking-water pollutants. [ABSTRACT FROM AUTHOR]

Nitrosamine by-products in drinking water are designated as probable human carcinogens by the IARC, but the health effects of simultaneous exposure to multiple nitrosamines in drinking water remain unknown. Genotoxicity assays were used to assess the effects of both individual and mixed nitrosamines in finished drinking water produced by a large water treatment plant in Shanghai, China. Cytotoxicity and genotoxicity were measured at 1, 10-, 100- and 1000-fold actual concentrations by the Ames test, Comet assay, γ -H2AX assay, and the cytokinesis-block micronuclei assay; oxidative stress and the Nrf2 pathway were also assessed. Nitrosamines detected in drinking water included NDMA (36.45 ng/L), NDPA (44.68 ng/L), and NEMA (37.27 ng/L). Treatment with a mixture of the three nitrosamines at 1000-fold actual drinking-water concentration induced a doubling of revertants in Salmonella typhimurium strain TA100, DNA and chromosome damage in HepG2 cells, while 1–1000-fold concentrations of compounds applied singly lacked these effects. Treatment with 100- and 1000-fold concentrations increased ROS, GSH, and MDA and decreased SOD activity. Thus, nitrosamine mixtures showed greater genotoxic potential than that of the individual compounds. N -Acetylcysteine protected against the nitrosamine-induced chromosome damage, and Nrf2 pathway activation suggested that oxidative stress played pivotal roles in the genotoxic property of the nitrosamine mixtures. [Display omitted] • Nitrosamines (NAms) like NDMA, NDPA & NEMA, were found in finished drinking water. • Mixed vs single NAms increased genotoxic potential, even at low concentrations. • Oxidative stress and NRF2 pathway activation played key roles in genotoxic effects. • NDMA, the priority NAms compound, was the main risk component for carcinogenesis. [ABSTRACT FROM AUTHOR]

Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). However, there are still inconsistent standards of gene panels using next-generation sequencing and poor correlation between the TMB genes, immune cell infiltrating, and prognosis. We applied text-mining technology to construct specific TMB-associated gene panels cross various cancer types. As a case exploration, Pearson's correlation between TMB genes and immune cell infiltrating was further analyzed in colorectal cancer. We then performed LASSO Cox regression to construct a prognosis predictive model and calculated the risk score of each sample for receiver operating characteristic (ROC) analysis. The results showed that the assessment of TMB gene panels performed well with fewer than 500 genes, highly mutated genes, and the inclusion of synonymous mutations and immune regulatory and drug-target genes. Moreover, the analysis of TMB differentially expressed genes (DEGs) suggested that JAKMIP1 was strongly correlated with the gene expression level of CD8+ T cell markers in colorectal cancer. Additionally, the prognosis predictive model based on 19 TMB DEGs reached AUCs of 0.836, 0.818, and 0.787 in 1-, 3-, and 5-year OS models, respectively (C-index: 0.810). In summary, the gene panel performed well and TMB DEGs showed great potential value in immune cell infiltration and in predicting survival. [ABSTRACT FROM AUTHOR]

• Applies both social network analysis and sentiment analysis in construction safety research. • Provides insights to opinion leaders and Twitter users when they share construction safety knowledge via Twitter. • Investigates social structure of "construction safety"- related twitter networks and the opinion leaders. • Sentiment valence exhibits a positive correlation between favorites and retweets. Many studies show that unsafe behavior is the main cause of construction accidents. Safety education and training are effective means to minimise people's unsafe behaviors. Apart from traditional face-to-face construction knowledge sharing, social media is a good tool because it is convenient, efficient, and widely used. We applied both social network analysis and sentiment analysis to investigate knowledge sharing on Twitter. Our study is a novel attempt to understand social structure of "construction safety"- related twitter networks and the opinion leaders. We selected and analyzed 6561 tweets of three users' networks on Twitter – "construction safety", "construction health" and "construction accident". We found that three networks had low density and many isolated vertices, which showed that users did not actively interact with each other. The opinion leaders in this study were mostly organizations or government agencies. The top one is "cif_ireland", the Irish construction industry's representative body, the Construction Industry Federation. 3200 Tweets of the top opinion leader were analyzed through graph metrics calculation, cluster analysis, sentiment analysis, and correlation analysis. The opinion leader used Twitter as a medium to disseminate the latest safety news. Thus, we may use Twitter to stimulate people's interest on construction safety topics, share construction safety knowledge, opinions and ideas. Besides, our results showed that sentiment valence had no correlation with number of favorites or retweets. Nevertheless, there was a positive correlation between favorites and retweets. [ABSTRACT FROM AUTHOR]

Background: The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. Principal Findings/Significance: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer. [ABSTRACT FROM AUTHOR]