Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of spatially varying wetland source signatures on the atmospheric variability of δD-CH4

We present the first spatially resolved distribution of the δD-CH4 signature of wetland methane emissions and assess its impact on atmospheric δD-CH4. The δD-CH4 signature map is derived by relating δD-H2O of precipitation to measured δD-CH4 of methane wetland emissions at a variety of wetland types and locations. This results in strong latitudinal variation in the wetland δD-CH4 source signature. When δD-CH4 is simulated in a global atmospheric model, little difference is found in global mean, inter-hemispheric difference and seasonal cycle if the spatially varying δD-CH4 source signature distribution is used instead of a globally uniform value. This is because atmospheric δD-CH4 is largely controlled by OH fractionation. However, we show that despite these small differences, using atmospheric records of δD-CH4 to infer changes in the wetland emissions distribution requires the use of the more accurate spatially varying δD-CH4 source signature. We find that models will only be sensitive to changes in emissions distribution if spatial information can be exploited through the spatially resolved source signatures. In addition, we also find that on a regional scale, at sites measuring excursions of δD-CH4 from background levels, substantial differences are simulated in atmospheric δD-CH4 if using spatially varying or uniform source signatures. This article is part of a discussion meeting issue ‘Rising methane: is warming feeding warming? (part 1)’.
The multifaceted impact of social media on risk, behavior, and negative emotions during the COVID-19 outbreak in South Korea

ABSTRACT This study examined how social media use is associated with risk perception and social distancing as preventive behavior, which in turn can elicit negative emotions. The study is based on data collected from a nationwide online panel survey conducted during the COVID-19 outbreak in South Korea. Results show that social media use directly and indirectly impacts people’s negative emotions through risk perception and social distancing. The analysis also shows that risk perception and social distancing directly influence negative emotions, which plays a mediating role in the relationship between social media use and negative emotions. The findings of the study provide important implications for effective risk and health communication and health policy during an infectious disease outbreak.
From inclusion to epistemic belonging in international environmental expertise: learning from the institutionalisation of scenarios and models in IPBES

ABSTRACT The inclusion of diverse perspectives from different disciplines, genders and locations has become a foreground concern in environmental expertise. While inclusion is increasingly accounted for in the design and evaluation of expert organisations, questions remain about the extent to which the pursuit of inclusion equates to effective participation. Building on recent scholarship on expertise in environmental sociology and public participation in environmental governance, this paper puts forward the argument that enabling inclusion in international expert organisations can be supported by facilitating epistemic belonging – a state achieved not only through mutual recognition of skilful practice amongst their expert communities (i.e. group belonging) but also the mobilisation of material resources within and beyond these organisations that enable participating experts to assert their importance, define their specialist skills and to effectively enact their epistemic practices. In this account, I trace the institutionalization of biodiversity scenarios and models in the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) to show how achieving epistemic belonging requires expert communities to actively reshape the resource environments in which they operate. This account extends current sociological perspectives on environmental expertise and offers insights for environmental expert organisations seeking to broaden their inclusion practices.
Response of Brazilian peppertree (Schinus terebinthifolia) and four mangrove species to imazamox and carfentrazone-ethyl herbicides

Abstract Mangroves are a critical component of many coastal ecosystems in Florida. Woody species, including Brazilian peppertree (Schinus terebinthifolia Raddi), have invaded thousands of hectares of mangrove habitat. The difficulty associated with ground-based management of invasive plants in mangrove communities has warranted a need to identify selective herbicides that can be applied aerially. Recent work suggests that Florida mangrove species are extremely sensitive to synthetic auxin herbicides; however, other herbicides have yet to be tested for selectivity. Greenhouse studies in 2018 and 2019 evaluated broadcast foliar applications of the acetolactate synthase inhibitor imazamox and protoporphyrinogen oxidase inhibitor carfentrazone-ethyl, both as individual treatments and in combinations, for control of S. terebinthifolia and injury to four non-target mangrove species. Across all posttreatment sample dates and species tested, there were no significant interactions between imazamox applied at 0.28 or 0.56 kg ai ha–1 in combination with carfentrazone-ethyl applied at 0 or 0.1 kg ha–1. Main effects of imazamox applied at 0.56 kg ai ha–1 and carfentrazone-ethyl applied at 0.1 kg ha–1 resulted in 99% and 97% defoliation, respectively, of Schinus terebinthifolia at 180 DAT. However, S. terebinthifolia percent survival was 56% and 44% for the same treatments. Both herbicides severely injured all four mangroves by 90 DAT and resulted in 58% to 100% defoliation across species. At 180 DAT, significant increases in percent cambium kill were also observed for all four species. Across species, mangrove survival varied, but red mangrove (Rhizophora mangle L.) survival was reduced to 6% when imazamox was applied at 0.56 kg ha–1. These results indicate both imazamox and carfentrazone-ethyl exhibit activity on S. terebinthifolia but also injure all four mangroves enough to preclude their use as selective treatments.
Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots

Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. The present study identified a total of 58,652 genes and 521 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis cv. Pachyloen) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 11,636 (54.05%) differentially expressed genes (DEGs) and 515 (98.85%) differentially expressed miRNAs (DEmiRs) were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations each between two successive stages (WTS2/TWS2_vs_WTS1/TWS1, WTS3/TWS3_vs_WTS2/TWS2, WTS4/TWS4_vs_WTS3/TWS3 and WTS5/TWS5_vs_WTS4/TWS4), and the WTTW group was composed of five between two relative stages (TWS1–5_vs_WTS1–5). Additionally, among the phytohormones, zeatin (ZT) showed more remarkable changes in concentrations than indole-3-acetic acid (IAA), gibberellic acid (GA3), and abscisic acid (ABA) throughout the five stages in the WT and the TW groups. Moreover, 118 sites were identified for 590 miRNA-mRNA pairs via degradome sequencing. The dual-luciferase reporter assay confirmed that 14 miRNAs bound to 12 targets. Fluorescence in situ hybridization (FISH) localized miR166 and miR160 in the shoot apical meristem (SAM) and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.
Transcriptomics Reveals How Minocycline-Colistin Synergy Overcomes Antibiotic Resistance in Multidrug-Resistant Klebsiella pneumoniae

Multidrug-resistant Gram-negative bacteria are a rapidly growing public health threat, and the development of novel antimicrobials has failed to keep pace with their emergence. Synergistic combinations of individually ineffective drugs present a potential solution, yet little is understood about the mechanisms of most such combinations. ABSTRACT Multidrug-resistant Gram-negative bacteria are a rapidly growing public health threat, and the development of novel antimicrobials has failed to keep pace with their emergence. Synergistic combinations of individually ineffective drugs present a potential solution, yet little is understood about the mechanisms of most such combinations. Here, we show that the combination of colistin (polymyxin E) and minocycline has a high rate of synergy against colistin-resistant and minocycline-intermediate or -resistant strains of Klebsiella pneumoniae. Furthermore, using transcriptome sequencing (RNA-Seq), we characterized the transcriptional profiles of these strains when treated with the drugs individually and in combination. We found a striking similarity between the transcriptional profiles of bacteria treated with the combination of colistin and minocycline at individually subinhibitory concentrations and those of the same isolates treated with minocycline alone. We observed a similar pattern with the combination of polymyxin B nonapeptide (a polymyxin B analogue that lacks intrinsic antimicrobial activity) and minocycline. We also found that genes involved in polymyxin resistance and peptidoglycan biosynthesis showed significant differential gene expression in the different treatment conditions, suggesting possible mechanisms for the antibacterial activity observed in the combination. These findings suggest that the synergistic activity of this combination against bacteria resistant to each drug alone involves sublethal outer membrane disruption by colistin, which permits increased intracellular accumulation of minocycline.
lon Deletion Impairs Persister Cell Resuscitation in Escherichia coli

The ATP-dependent Lon protease is one of the most studied bacterial proteases. Although deletion of lon has been frequently shown to reduce fluoroquinolone persistence, the proposed mechanisms underlying this phenomenon are highly controversial. ABSTRACT Bacterial persisters are nongrowing cells highly tolerant to bactericidal antibiotics. However, this tolerance is reversible and not mediated by heritable genetic changes. Lon, an ATP-dependent protease, has repeatedly been shown to play a critical role in fluoroquinolone persistence in Escherichia coli. Although lon deletion (Δlon) is thought to eliminate persister cells via accumulation of the cell division inhibitor protein SulA, the exact mechanism underlying this phenomenon is not yet elucidated. Here, we show that Lon is an important regulatory protein for the resuscitation of the fluoroquinolone persisters in E. coli, and lon deletion impairs the ability of persister cells to form colonies during recovery through a sulA- and ftsZ-dependent mechanism. Notably, this observed “viable but nonculturable” state of antibiotic-tolerant Δlon cells is transient, as environmental conditions, such as starvation, can restore their culturability. Our data further indicate that starvation-induced SulA degradation or expression of Lon during recovery facilitates Z-ring formation in Δlon persisters, and Z-ring architecture is important for persister resuscitation in both wild-type and Δlon strains. Our in-depth image analysis clearly shows that the ratio of cell length to number of FtsZ rings for each intact ofloxacin-treated cell predicts the probability of resuscitation and, hence, can be used as a potential biomarker for persisters. IMPORTANCE The ATP-dependent Lon protease is one of the most studied bacterial proteases. Although deletion of lon has been frequently shown to reduce fluoroquinolone persistence, the proposed mechanisms underlying this phenomenon are highly controversial. Here, we have shown that lon deletion in Escherichia coli impairs the ability of persister cells to form colonies during recovery and that this reduction of persister levels in lon-deficient cells can be transient. We also found that altered Z-ring architecture is a key biomarker in both wild-type and lon-deficient persister cells transitioning to a normal cell state. Collectively, our findings highlight the importance of differentiating persister formation mechanisms from resuscitation mechanisms and underscore the critical role of the nonculturable cell state in antibiotic tolerance.
The Synechocystis sp. PCC 6803 open reading frame slr0201 that is homologous to sdhC from Archaea codes for a [2Fe-2S] protein

A hypothetical protein encoded by Synechocystis sp. PCC 6803 open reading frame slr0201shows high sequence similarity to the C subunit of a group of unusual succinate dehydrogenases found in some archaeal species. Slr0201 was originally annotated as HdrB, the B subunit of heterodisulfide reductase, but appears to be SdhC instead. This protein was overexpressed in E. coli by cloning the PCR-derived slr0201 open reading frame into a pET16b-based expression vector. The overproduced Slr0201 accumulated predominantly in inclusion bodies with an apparent molecular mass of 33 kDa. The protein contained at least one [2Fe-2S] cluster based on UV-visible absorbance and CD spectra and EPR spectroscopy, in conjunction with stoichiometric analysis of protein-bound iron and sulfur content. Redox titration showed a midpoint potential (Em) of + 17 mV at pH 7.0, which is consistent with Slr0201 serving a role in transferring electrons between succinate and plastoquinone. Slr0201 was also overproduced in Synechocystis sp. PCC 6803 by introducing an additional, His-tagged slr0201 into the Synechocystis genome replacing psbA3, creating the slr0201+-His overexpression strain. Immunoblot analysis shows that Slr0201 is membrane-associated in the wild type. However, in the Slr0201+-His strain, immunoreaction occurred in both the membrane and soluble fractions, possibly as a consequence of processing near the N-terminus. The results obtained with Slr0201 are discussed in the light of one of the cyanobacterial SdhB subunits, which shares redox commonalities with archaeal SdhB.
Cerebrospinal fluid amyloid beta and glial fibrillary acidic protein concentrations in Huntington’s disease

Introduction Huntington’s disease (HD) is a genetic incurable lethal disease. Biomarkers are needed for objective assessment of disease progression. Evidence supports both complex protein aggregation and astrocyte activation in HD. This study assesses the 42 amino acid long amyloid beta (Aβ42) and glial fibrillary acidic protein (GFAP) as potential biomarkers in the cerebrospinal fluid (CSF) of HD mutation carriers. Methods CSF was obtained from manifest HD patients (ManHD), premanifest HD-gene-expansion carriers (PreHD) and gene-negative controls (controls). Disease Burden Score (DBS) and Total Functional Capacity (TFC) were calculated. Protein concentrations were measured by enzyme-linked immunosorbent assays (ELISA) and intergroup differences were analysed using Mann-Whitney U test. Spearman correlations were calculated to assess disease stage association. Age-adjustment was included in the statistical tests. Results The study enrolled 27 ManHD and 13 PreHD subjects. The number of controls differed in the analysis of Aβ42 and GFAP (n = 19, and 8 respectively). Aβ42 levels were higher in ManHD (mean 741 ng/l, SD 361) compared with PreHD (mean 468 ng/l, SD 184) (p = 0.025). Likewise GFAP concentration was higher in ManHD (mean 435 ng/l, SD 255) compared with both PreHD (mean 266 ng/l, SD 92.4)(p = 0.040) and controls (mean 208 ng/l, SD 83.7)(p = 0.011). GFAP correlated with DBS (r = 0.361, p = 0.028), TFC (r = − 0.463, p = 0.005), and 5-year risk of onset in PreHD (r = 0.694, p = 0.008). In contrast, there was no correlation between Aβ42 concentration and DBS, TFC or 5-year risk of onset. Conclusion CSF Aβ42 levels did not correlate with disease stage suggesting no Aβaggregation in HD. GFAP is a potential biomarker in HD with association to disease stage. Validation in larger HD cohorts and potential correlations with clinical phenotype would be of interest.
Fluctuations in Neural Complexity During Wakefulness Relate To Conscious Level and Cognition

There has been considerable recent progress in measuring conscious level using neural complexity measures. For instance, such measures can reliably distinguish healthy awake from asleep subjects and vegetative state patients. However, this line of research has never explored the dynamics of conscious level during normal wakefulness. Being able to capture meaningful differences in conscious level during wakefulness may provide a vital new insight into the nature of consciousness, by demonstrating what biological, behavioural and cognitive factors relate to such differences. Here we take advantage of a large MEG and fMRI dataset of healthy adults, to examine within-subject conscious level fluctuations during resting state and tasks, by using a range of complexity measures. We first establish the validity of this approach in both neuroimaging domains by relating neural complexity measures to pre-existing techniques for capturing transitions of consciousness from full wakefulness into drowsiness and the earliest stages of sleep, finding decreased complexity as participants become increasingly drowsy. We further demonstrate that neural complexity measures in both MEG and fMRI change both within and between tasks, and relate to performance on an executive task, with higher complexity associated with better performance and faster reaction times. This approach provides a powerful new route to further explore the cognitive and neural underpinnings of consciousness.
Assessing the optimal frequency of early parasitoid releases in an apple orchard to control Dysaphis plantaginea: a proof of concept study

Alternative measures to pesticides to control the rosy apple aphid Dysaphis plantaginea are being developed. Naturally occurring predators and parasitoids often fail to reduce aphid abundance below the economic threshold in orchards, because they are active too late after the aphid first infestation. We tested the efficiency of mass release of two parasitoid species, Aphidius matricariae and Ephedrus cerasicola, early in the season to match the presence of aphid fundatrix (sensitive stages). In this trial focusing on an organic apple orchard, three releases were done either every week or every two weeks to test the effect of the release frequency, during two consecutive years. The number of aphid colonies and aphid number per tree were monitored from late March to late May. Degree-days necessary for parasitoid emergence in the field after release were calculated. We show that a sufficient level of aphid control by parasitoids is reached during the first month of the survey, but control mostly fails during the second part of the monitoring session, for both release treatments, and compared to the neem oil control treatment. The relative effects of release frequencies were different between years probably because of interannual differences in aphid population dynamics and initial infestation in orchards. The field survey and the degree-day model suggest that parasitoid releases, at either frequency, are promising candidates for biological control of the rosy aphid, although the method still needs proper calibration. This conclusion needs to be reinforced by repeating the study in more orchards, but our case study lays the first empirical basis that will help to develop future control methods of aphids by parasitoid releases in apple orchards. We argue that releases should be done one to two weeks before first aphid detection to account for long development times of parasitoids at relatively low temperatures.
Multiple stressors and recruitment failure of long-lived endangered freshwater mussels with a complex life cycle

Multiple stressors can interactively affect the population of organisms; however, the process by which they affect recruitment efficiency remains unclear for empirical populations. Recruitment efficiency can be regulated at multiple stages of life, particularly in organisms with complex life cycles. Understanding the interactive effects of multiple stressors on recruitment efficiency and determining the bottleneck life stages is imperative for species conservation. The proportion of <20-year-old juveniles of the endangered freshwater pearl mussel Margaritifera togakushiensis, which has an obligate parasitic larval stage, was investigated in 24 rivers from eastern Hokkaido, northern Japan to reveal the influence of nutrients, fine sediment, and their combined effects on juvenile recruitment efficiency. The following indices for recruitment at adult, parasitic, and post-parasitic juvenile stages were obtained from 11 of these rivers: gravid female density, glochidia density (the number of glochidia infections per stream area), and juvenile survival rate. This study explored the bottleneck stages of recruitment efficiency and the interactive effects of the two stressors on these stages. Twenty-four population status assessments determined that the proportion of juveniles ranged from 0.00 to 0.53, and juveniles were absent from four rivers. The results showed that the parasitic and post-parasitic juvenile stages were bottlenecks for recruitment efficiency. Juvenile survival rates had a more significant positive effect on recruitment efficiency in rivers with a high glochidia density. Juvenile survival rate was decreased by the synergistic interaction of nutrients and fine sediment, although factors limiting glochidia density were not found. The nutrient concentration of rivers in the study region was well explained by the proportion of agricultural land cover and urban areas in the watersheds, but no relationship was detected between fine sediment abundance and land use. This study suggests that nutrient management at a catchment scale can be effective for re-establishing the recruitment of M. togakushiensis, particularly in rivers with a high content of fine sediments. The results also emphasise the importance of considering both parasitic and post-parasitic juvenile stages of mussels to maximise the positive effects of stressor mitigation.
Named Entity Recognition and Linking: a Portuguese and Spanish Oncological Parallel Corpus

Biomedical literature is the main mean of communication for researchers to share their findings. Since biomedical literature is composed of a large collection of text expressed in natural language, the usage of text mining tools to extract information from those texts automatically is of utmost importance. The problem is that the majority of the state-of-the-art tools were not developed to deal with other languages besides English, which in biomedical literature is even more critical since a significant part of health-related texts is written in the author’s native language. To address this issue, this work presents a deep learning NERL (Named Entity Recognition and Linking) system and a parallel corpus for the Spanish and Portuguese languages focused on the oncological domain. Both the system and the corpus are available at https://github.com/lasigeBioTM/ICERL_system-ICR_Corpus.