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Traditional gene regulation models focus on protein-coding genes within the paradigm of DNA → mRNA → protein. However, recent insights have shifted this perspective, highlighting the crucial regulatory roles of noncoding regions of the genome. Protein-coding regions constitute only about 1.5% of the genome, while many noncoding RNAs (ncRNAs) are transcribed from other regulatory elements and play significant roles in regulating complex biological processes such as development, differentiation, and metabolism. This emerging understanding underscores ncRNAs as vital molecular players, necessitating advanced tools to study their dynamic expression and activity.The first three chapters of this thesis present recent advancements in metabolic labeling techniques to profile RNA expression dynamics to help elucidate novel RNA activity and dynamics. Metabolic labeling involves incorporating chemically modified nucleosides into nascent RNA, enabling detailed tracking of RNA synthesis, decay, and transient expression through pulse-chase experiments. This addresses the limitations of bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) methods, which are limited in their abilities to accurately capture RNA dynamics and cell-type-specific gene expression. The approaches outlined in this thesis provide cell-specificity to traditional metabolic labeling approaches to capture RNA activity and dynamics for a cell type of interest within complex cellular contexts. Chapter 4 explored the non-canonical regulatory roles of ncRNAs, focusing on the development of synthetic riboswitches to control mRNA translation. Riboswitches regulate gene expression through ligand-binding aptamer domains. The thesis details the creation of photoriboswitches using in vitro SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to evolve RNA aptamers that bind to photo-labile ligands. Since typical SELEX methodologies cannot efficiently ensure the selection of gene-regulating riboswit

The nitrogen (N) cycle is a familiar concept. As is the much simplified, often diagrammatic, representation commonly used to illustrate the scale, importance and interconnectedness of this global cycle that links air, water, rocks and living beings. However, in this representation, humans are often presented as a seemingly minor entity or not explicitly shown at all. This can obscure the idea that humanity is both a direct beneficiary of the nitrogen cycle (through food and resources) and an increasingly significant influence on its function. This study sought to understand how diverse Human-Nature relationships (HNR) are expressed in recent academic literature on the nitrogen cycle. A sample of peer-reviewed literature, containing explicit and inferred examples of HNR and the nitrogen cycle, was analysed using two approaches: 1) network analysis, identifying and illustrating all quantifiable links made between components of the nitrogen cycle, and 2) content analysis to understand how different kinds of terminology were being used to describe relationships between components in the cycle. The network analysis revealed diverse links between ‘human’ and ‘non-human nature’. The content analysis found some explicit use of relational terms, most commonly ‘depend*’. Both approaches highlighted strongly reciprocal links within the ‘human’ realm and the explicit centrality in which this is held across the corpus. We demonstrate the utility of combining quantitative and qualitative analysis to understand nuanced relationships in the nitrogen cycle and explore the utility this has to increase the acknowledgement and appreciation of HNR in science communication and science-policy interface work.

By combining advanced cyberinfrastructure with geospatial analysis capabilities and resources in an accessible online environment, the I-GUIDE Platform has great potential for geospatial computing focused education. However, learning occurs in different settings and contexts, both formal and informal. For I-GUIDE Platform to be successful, it should have the flexibility to support a variety of educational needs. In this paper, we argue for an expanded set of front-end building blocks to support diverse education and research use-cases, building on existing cyberGIS capabilities and Jupyter backend. We draw from experience working with the CyberGISX platform as an education tool in different learning contexts to suggest a series of front-end building blocks to best leverage the powerful combination of cyberinfrastructure and geospatial resources for flexible and adaptable educational needs.

Our increasingly connected world is faced with complex socio-environmental problems (e.g., biodiversity loss, climate change, and food insecurity). Tackling these problems requires cross- disciplinary approaches that examine the problems based on synergistic spatial and system thinking. Spatial Agent-Based Models (SABMs) represent a powerful approach to understanding complex socio-environmental systems. However, research on SABMs and associated complex problem solving face grand challenges that must be overcome to effectively unleash the power of SABMs enabled by cyber-based geographic information science and systems (cyberGIS). This paper describes four such grand challenges —reproducibility, scalability, communication, and accessibility. Resolving these challenges will enable new spatial computing frontiers to model complex socio-environmental systems at unprecedented spatiotemporal scales for tackling associated real-world problems.

BACKGROUND: Deep brain stimulation (DBS) is a promising treatment option for treatment-refractory obsessive-compulsive disorder (OCD). Several stimulation targets have been used, mostly in and around the anterior limb of the internal capsule and ventral striatum (VC/VS). However, the precise target within this region remains a matter of debate. METHODS: Here, we retrospectively studied a multicenter cohort of 82 patients that underwent DBS of the VC/VS and mapped optimal stimulation sites in this region. RESULTS: DBS sweet-spot mapping performed on a discovery set of 58 patients revealed two optimal stimulation sites associated with improvements on the Yale-Brown Obsessive-Compulsive Scale, one in the anterior limb of the internal capsule that overlapped with a previously identified OCD-DBS response tract, and one in the region of the inferior thalamic peduncle and bed nucleus of the stria terminalis. Critically, the nucleus accumbens proper and anterior commissure were associated with beneficial but suboptimal clinical improvements. Moreover, overlap with the resulting sweet- and sour-spots significantly estimated variance in outcomes in an independent cohort of 22 patients from two additional DBS centers. Finally, beyond obsessive-compulsive symptoms, stimulation of the anterior site was associated with optimal outcomes for both depression and anxiety, while the posterior site was only associated with improvements of depression. CONCLUSIONS: Our results suggest how to refine targeting of DBS in OCD and may be helpful in guiding DBS programming in existing patients.

The nitrogen (N) cycle is a familiar concept. As is the much simplified, often diagrammatic, representation commonly used to illustrate the scale, importance and interconnectedness of this global cycle that links air, water, rocks and living beings. However, in this representation, humans are often presented as a seemingly minor entity or not explicitly shown at all. This can obscure the idea that humanity is both a direct beneficiary of the nitrogen cycle (through food and resources) and an increasingly significant influence on its function. This study sought to understand how diverse Human-Nature relationships (HNR) are expressed in recent academic literature on the nitrogen cycle. A sample of peer-reviewed literature, containing explicit and inferred examples of HNR and the nitrogen cycle, was analysed using two approaches: 1) network analysis, identifying and illustrating all quantifiable links made between components of the nitrogen cycle, and 2) content analysis to understand how different kinds of terminology were being used to describe relationships between components in the cycle. The network analysis revealed diverse links between ‘human’ and ‘non-human nature’. The content analysis found some explicit use of relational terms, most commonly ‘depend*’. Both approaches highlighted strongly reciprocal links within the ‘human’ realm and the explicit centrality in which this is held across the corpus. We demonstrate the utility of combining quantitative and qualitative analysis to understand nuanced relationships in the nitrogen cycle and explore the utility this has to increase the acknowledgement and appreciation of HNR in science communication and science-policy interface work.

Frontal circuits play a critical role in motor, cognitive and affective processing, and their dysfunction may result in a variety of brain disorders. However, exactly which frontal domains mediate which (dys)functions remains largely elusive. We studied 534 deep brain stimulation electrodes implanted to treat four different brain disorders. By analyzing which connections were modulated for optimal therapeutic response across these disorders, we segregated the frontal cortex into circuits that had become dysfunctional in each of them. Dysfunctional circuits were topographically arranged from occipital to frontal, ranging from interconnections with sensorimotor cortices in dystonia, the primary motor cortex in Tourettes syndrome, the supplementary motor area in Parkinsons disease, to ventromedial prefrontal and anterior cingulate cortices in obsessive-compulsive disorder. Our findings highlight the integration of deep brain stimulation with brain connectomics as a powerful tool to explore couplings between brain structure and functional impairments in the human brain.

Light triggers numerous non-image-forming, or non-visual, biological effects. The brain correlates of these non-image-forming effects have been investigated, notably using magnetic resonance imaging and short light exposures varying in irradiance and spectral quality. However, it is not clear whether non-image-forming responses estimation may be biased by having light in sequential blocks, for example, through a potential carryover effect of one light onto the next. We reasoned that pupil light reflex was an easy readout of one of the non-image-forming effects of light that could be used to address this issue. We characterised the sustained pupil light reflex in 13-16 healthy young individuals under short light exposures during three distinct cognitive processes (executive, emotional and attentional). Light conditions pseudo-randomly alternated between monochromatic orange light (0.16 melanopic equivalent daylight illuminance lux) and polychromatic blue-enriched white light of three different levels (37, 92, 190 melanopic equivalent daylight illuminance lux). As expected, higher melanopic irradiance was associated with larger sustained pupil light reflex in each cognitive domain. This result was stable over the light sequence under higher melanopic irradiance levels compared with lower ones. Exploratory frequency-domain analyses further revealed that sustained pupil light reflex was more variable under lower melanopic irradiance levels. Importantly, sustained pupil light reflex varied across tasks independently of the light condition, pointing to a potential impact of light history and/or cognitive context on sustained pupil light reflex. Together, our results emphasise that the distinct contribution and adaptation of the different retinal photoreceptors influence the non-image-forming effects of light and therefore potentially their brain correlates.

Light has many non-image-forming functions including modulation of pupil size and stimulation of alertness and cognition. Part of these non-image-forming effects may be mediated by the brainstem locus coeruleus. The processing of sensory inputs can be associated with a transient pupil dilation that is likely driven in part by the phasic activity of the locus coeruleus. In the present study, we aimed to characterise the task-evoked pupil response associated with auditory inputs under different light levels and across two cognitive tasks. We continuously monitored the pupil of 20 young healthy participants (mean [SD] 24.05?[4.0]?years; 14 women) whilst they completed an attentional and an emotional auditory task whilst exposed to repeated 30-40-s blocks of light interleaved with darkness periods. Blocks could either consist of monochromatic orange light (0.16?melanopic equivalent daylight illuminance (EDI) lux) or blue-enriched white light of three different levels [37, 92, 190?melanopic EDI lux; 6500?K]. For the analysis, 15 and then 14 participants were included in the attentional and emotional tasks, respectively. Generalised linear mixed models showed a significant main effect of light level on the task-evoked pupil responses triggered by the attentional and emotional tasks (p?=?0.0001). The impact of light was different for the target versus non-target stimulus of the attentional task but was not different for the emotional and neutral stimulus of the emotional task. There is a smaller sustained pupil size during brighter light blocks but, a higher light level triggers a stronger task-evoked pupil response to auditory stimulation, presumably through the recruitment of the locus coeruleus.

Human cytogenetic biomonitoring (HCB) has long been used to evaluate the potential effects of work environments on the DNA integrity of workers. However, HCB studies on the genotoxic effects of occupational exposure to extremely low‐frequency electromagnetic fields (ELF‐MFs) were limited by the quality of the exposure assessment. More specifically, concerns were raised regarding the method of exposure assessment, the selection of exposure metrics, and the definition of exposure group. In this study, genotoxic effects of occupational exposure to ELF‐MFs were assessed on peripheral blood lymphocytes of 88 workers from the electrical sector using the comet and cytokinesis‐block micronucleus assay, considering workers' actual exposure over three consecutive days. Different methods were applied to define exposure groups. Overall, the summarized ELF‐MF data indicated a low exposure level in the whole study population. It also showed that relying solely on job titles might misclassify 12 workers into exposure groups. We proposed combining hierarchical agglomerative clustering on personal exposure data and job titles to define exposure groups. The final results showed that occupational MF exposure did not significantly induce more genetic damage. Other factors such as age or past smoking rather than ELF‐MF exposure could affect the cytogenetic test outcomes., SCOPUS: ar.j, info:eu-repo/semantics/published

We propose a robust method for point cloud registration that can handle both unknown scales and extreme outlier ratios. Our method, dubbed PCR-99, uses a deterministic 3-point sampling approach with two novel mechanisms that significantly boost the speed: (1) an improved ordering of the samples based on pairwise scale consistency, prioritizing the point correspondences that are more likely to be inliers, and (2) an efficient outlier rejection scheme based on triplet scale consistency, prescreening bad samples and reducing the number of hypotheses to be tested. Our evaluation shows that, up to 98% outlier ratio, the proposed method achieves comparable performance to the state of the art. At 99% outlier ratio, however, it outperforms the state of the art for both known-scale and unknown-scale problems. Especially for the latter, we observe a clear superiority in terms of robustness and speed.

In this paper, we are concerned with the micro-macro Parareal algorithm for the simulation of initial-value problems. In this algorithm, a coarse (fast) solver is applied sequentially over the time domain, and a fine (time-consuming) solver is applied as a corrector in parallel over smaller chunks of the time interval. Moreover, the coarse solver acts on a reduced state variable, which is coupled to the fine state variable through appropriate coupling operators. We first provide a contribution to the convergence analysis of the micro-macro Parareal method for multiscale linear ordinary differential equations (ODEs). Then, we extend a variant of the micro-macro Parareal algorithm for scalar stochastic differential equations (SDEs) to higher-dimensional SDEs.

In 2011 the European Society for the Study of Tourette Syndrome (ESSTS) published its first European clinical guidelines for the treatment of Tourette Syndrome (TS) with part IV on deep brain stimulation (DBS). Here, we present a revised version of these guidelines with updated recommendations based on the current literature covering the last decade as well as a survey among ESSTS experts. Currently, data from the International Tourette DBS Registry and Database, two meta-analyses, and eight randomized controlled trials (RCTs) are available. Interpretation of outcomes is limited by small sample sizes and short follow-up periods. Compared to open uncontrolled case studies, RCTs report less favorable outcomes with conflicting results. This could be related to several different aspects including methodological issues, but also substantial placebo effects. These guidelines, therefore, not only present currently available data from open and controlled studies, but also include expert knowledge. Although the overall database has increased in size since 2011, definite conclusions regarding the efficacy and tolerability of DBS in TS are still open to debate. Therefore, we continue to consider DBS for TS as an experimental treatment that should be used only in carefully selected, severely affected and otherwise treatment-resistant patients.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce marky-coco, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

info:eu-repo/semantics/published

info:eu-repo/semantics/published

Science plays a crucial role in identifying transformative change trajectories that are positive for biodiversity and human well-being. The concept of transformative change for biodiversity is receiving increased attention both within the political as well as in the scientific arena, but what transformative change entails still remains scientifically unclear. In this paper we report on a research priority exercise undertaken at the 2022 Alternet conference in which conference participants within each session were asked to jointly propose research gaps relevant to transformative change. Thirteen research priorities are identified, emphasising the need to learn from doing through transdisciplinary participatory action research, involving multiple disciplines including social sciences and building on existing research on, for example, nature-based solutions, OneHealth and climate change. The identified research priorities were later analysed under the umbrella of transformative change principles as a proxy for science to act as a lever to realise transformative change for biodiversity. Mobilising scientific research, interdisciplinarity and co-construction with stakeholders and decision-makers is a necessary step forward to make transformative progress in developing the biodiversity research agenda. In this respect, transformative action by the scientific community to develop the research agenda in an all-inclusive participatory process can be seen as a lever of transformative change for biodiversity. Such an all-inclusive participatory process for the development of a long-term biodiversity research agenda is in accordance with building on an integrated and whole-of-society approach as included in the EU Biodiversity Strategy’s aims and priorities around enabling transformative change.

Introduction The lack of evidence on patient characteristics and relational-contextual factors influencing nurse-sensitive patient outcomes of a nurse-patient relationship is a possible threat to the quality and education of the nurse-patient relationship. Aim To measure nurse-sensitive patient outcomes of the nurse-patient relationship and to explore the associations between nurse-sensitive patient outcomes and a range of patient characteristics and relational-contextual factors. Method In a multicenter cross-sectional study, 340 inpatients from 30 units in five psychiatric hospitals completed the Mental Health Nurse-Sensitive Patient Outcome Scale. Descriptive, univariate and Linear Mixed Model analyses were conducted. Results Overall, patient-reported outcomes were moderate to good. Female participants, nurse availability when needed, more nurse contact and nurse stimulation were associated with higher outcomes. Age differences were observed for some of the outcomes. Outcomes also varied across hospitals but were not related to the number of times patients were hospitalized or to their current length of stay in the hospital. Discussion The results may help nurses to become more sensitive and responsive to factors associated with nurse-sensitive patient outcomes of the nurse-patient relationship. Implications The nurse-sensitive results can support nurses in designing future nurse-patient relationships.

Science plays a crucial role in identifying transformative change trajectories that are positive for biodiversity and human well-being. The concept of transformative change for biodiversity is receiving increased attention both within the political as well as in the scientific arena, but what transformative change entails still remains scientifically unclear. In this paper we report on a research priority exercise undertaken at the 2022 Alternet conference in which conference participants within each session were asked to jointly propose research gaps relevant to transformative change. Thirteen research priorities are identified, emphasising the need to learn from doing through transdisciplinary participatory action research, involving multiple disciplines including social sciences and building on existing research on, for example, nature-based solutions, OneHealth and climate change. The identified research priorities were later analysed under the umbrella of transformative change principles as a proxy for science to act as a lever to realise transformative change for biodiversity. Mobilising scientific research, interdisciplinarity and co-construction with stakeholders and decision-makers is a necessary step forward to make transformative progress in developing the biodiversity research agenda. In this respect, transformative action by the scientific community to develop the research agenda in an all-inclusive participatory process can be seen as a lever of transformative change for biodiversity. Such an all-inclusive participatory process for the development of a long-term biodiversity research agenda is in accordance with building on an integrated and whole-of-society approach as included in the EU Biodiversity Strategy’s aims and priorities around enabling transformative change.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes

INTRODUCTION: Identifying patient-reported outcomes of the nurse-patient relationship is a priority in inpatient mental healthcare to guide clinical decision-making and quality improvement initiatives. Moreover, demonstrating nurse-sensitive patient outcomes can be a strategy to avoid further erosion of the specialism of psychiatric and/or mental health nursing. AIM/QUESTION: To measure nurse-sensitive patient outcomes of the nurse-patient relationship. METHOD: In a multicentred cross-sectional study, 296 inpatients admitted to five psychiatric hospitals completed the recently developed and validated Mental Health Nurse-Sensitive Patient Outcome-Scale (MH-NURSE-POS). The MH-NURSE-POS consists of 21 items (six-point Likert-scale) in four domains: 'growth', 'expression', 'control', and 'motivation'. RESULTS: Participants displayed moderate to good average scores for the MH-NURSE-POS total (4.42) and domain scores (≥4.09). Especially outcomes related to 'motivation' to follow and stay committed to the treatment received high average scores (≥4.60). DISCUSSION: The results demonstrate that patients perceive the nurse-patient relationship and the care given by psychiatric and/or mental health nurses as contributing to their treatment. IMPLICATIONS FOR PRACTICES: Patient-reported outcomes can guide nurses and managers to provide and organize nursing care and to build a nurse-patient relationship that has a positive impact on these outcomes. Additionally, outcomes can create nursing visibility as a profession in- and outside mental healthcare.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

The BioAgora project aims to set up a transformative Science Service for biodiversity (SSBD) within the EU, to link knowledge more effectively to policy making and implementation, so to contribute to enable the transformative changes necessary for reaching the goals of the BDS 2030. In this report we present a framework for assessing the potential of networks to contribute to transformative changes for biodiversity. Because of the setting up of the SSBD, the framework pays special attention to networks at the Science-Policy-Society Interfaces (SPSIs). The framework assumes that networks can only convincingly contribute to transformative change if they themselves work in transformative ways.

The HLA region is the major genetic risk determinant of Type 1 diabetes. How non-HLA loci contribute to the genetic risk is incompletely understood, but there are indications that at least some impact progression of asymptomatic autoimmunity. We examined whether SNPs in 7 susceptibility loci (INS, SH2B3, PTPN2, PTPN22, CTLA4, CLEC16A, and IL2RA) could improve prediction of the progression from single to multiple autoantibody positivity, and from there on to diagnosis. SNPs were genotyped in persistently autoantibody positive relatives by allelic discrimination qPCR and disease progression was studied by multivariate Cox regression analysis. In our cohort, only the CTLA4 GA genotype (rs3087243, P = 0.002) and the CLEC16A AA genotype (rs12708716, P = 0.021) were associated with accelerated progression from single to multiple autoantibody positivity, but their effects were restricted to presence of HLA-DQ2/DQ8, and IAA as first autoantibody, respectively. The interaction of CTLA4 and HLA-DQ2/DQ8 overruled the effect of DQ2/DQ8 alone. The HLA-DQ2/DQ8-mediated risk of progression to multiple autoantibodies nearly entirely depended on heterozygosity for CTLA4. The SH2B3 TT genotype (rs3184504) was protective for HLA-DQ8 positive subjects (P = 0.003). At the stage of multiple autoantibodies, only the CTLA4 GA genotype was a minor independent risk factor for progression towards clinical diabetes (P = 0.034). Our study shows that non-HLA polymorphisms impact progression of islet autoimmunity in a subgroup-, stage- and SNP-specific way, suggesting distinct mechanisms. If confirmed, these findings may help refine risk assessment, follow-up, and prevention trials in risk groups., SCOPUS: ar.j, info:eu-repo/semantics/published

We propose a micro-macro parallel-in-time Parareal method for scalar McKean-Vlasov stochastic differential equations (SDEs). In the algorithm, the fine Parareal propagator is a Monte Carlo simulation of an ensemble of particles, while an approximate ordinary differential equation (ODE) description of the mean and the variance of the particle distribution is used as a coarse Parareal propagator to achieve speedup. We analyse the convergence behaviour of our method for a linear problem and provide numerical experiments indicating the parallel weak scaling of the algorithm on a set of examples. We show that convergence typically takes place in a low number of iterations, depending on the quality of the ODE predictor. For bimodal SDEs, we avoid quality deterioration of the coarse predictor (compared to unimodal SDEs) through the usage of multiple ODEs, each describing the mean and variance of the particle distribution in locally unimodal regions of the phase space. The benefit of the proposed algorithm can be viewed through two lenses: (i) through the parallel-in-time lens, speedup is obtained through the use of a very cheap coarse integrator (an ODE moment model), and (ii) through the moment models lens, accuracy is iteratively gained through the use of parallel machinery as a corrector. In contrast to the isolated use of a moment model, the proposed method (iteratively) converges to the true distribution generated by the SDE.

Item does not contain fulltext, Objectives: Obsessive-compulsive disorder (OCD) is a psychiatric disorder with alterations of cortico-striato-thalamo-cortical loops and impaired performance monitoring. Electrophysiological markers such as conflict-related medial frontal theta (MFT) and error-related negativity (ERN) may be altered by clinically effective deep brain stimulation (DBS) of the anterior limb of the internal capsule and nucleus accumbens (ALIC/NAc). We hypothesized that ALIC/NAc DBS modulates electrophysiological performance monitoring markers. Materials and Methods: Fifteen patients (six male) with otherwise treatment-refractory OCD receiving ALIC/NAc DBS performed a flanker task with EEG recordings at three sessions: presurgery, and at follow-up with DBS on and off. We examined MFT, ERN, and task performance. Furthermore, we investigated interrelations with clinical efficacy and the explored the influence of the location of individual stimulation volumes on EEG modulations. Results: MFT and ERN were significantly attenuated by DBS with differences most pronounced between presurgery and DBS-on states. Also, we observed reaction time slowing for erroneous responses during DBS-off. Larger presurgery ERN amplitudes were associated with decreased clinical efficacy. Exploratory anatomical analyses suggested that stimulation volumes encompassing the NAc were associated with MFT modulation, whereas ALIC stimulation was associated with modulation of the ERN and clinical efficacy. Conclusion: ALIC/NAc DBS diminished MFT and ERN, demonstrating modulation of the medial frontal performance monitoring system in OCD. Furthermore, our findings encourage further studies to explore the ERN as a potential predictor for clinical efficacy.

Contains fulltext : 241592.pdf (Publisher’s version ) (Open Access), Objectives: Obsessive-compulsive disorder (OCD) is a psychiatric disorder with alterations of cortico-striato-thalamo-cortical loops and impaired performance monitoring. Electrophysiological markers such as conflict-related medial frontal theta (MFT) and error-related negativity (ERN) may be altered by clinically effective deep brain stimulation (DBS) of the anterior limb of the internal capsule and nucleus accumbens (ALIC/NAc). We hypothesized that ALIC/NAc DBS modulates electrophysiological performance monitoring markers. Materials and Methods: Fifteen patients (six male) with otherwise treatment-refractory OCD receiving ALIC/NAc DBS performed a flanker task with EEG recordings at three sessions: presurgery, and at follow-up with DBS on and off. We examined MFT, ERN, and task performance. Furthermore, we investigated interrelations with clinical efficacy and the explored the influence of the location of individual stimulation volumes on EEG modulations. Results: MFT and ERN were significantly attenuated by DBS with differences most pronounced between presurgery and DBS-on states. Also, we observed reaction time slowing for erroneous responses during DBS-off. Larger presurgery ERN amplitudes were associated with decreased clinical efficacy. Exploratory anatomical analyses suggested that stimulation volumes encompassing the NAc were associated with MFT modulation, whereas ALIC stimulation was associated with modulation of the ERN and clinical efficacy. Conclusion: ALIC/NAc DBS diminished MFT and ERN, demonstrating modulation of the medial frontal performance monitoring system in OCD. Furthermore, our findings encourage further studies to explore the ERN as a potential predictor for clinical efficacy.

In 2011 the European Society for the Study of Tourette Syndrome (ESSTS) published its first European clinical guidelines for the treatment of Tourette Syndrome (TS) with part IV on deep brain stimulation (DBS). Here, we present a revised version of these guidelines with updated recommendations based on the current literature covering the last decade as well as a survey among ESSTS experts. Currently, data from the International Tourette DBS Registry and Database, two meta-analyses, and eight randomized controlled trials (RCTs) are available. Interpretation of outcomes is limited by small sample sizes and short follow-up periods. Compared to open uncontrolled case studies, RCTs report less favorable outcomes with conflicting results. This could be related to several different aspects including methodological issues, but also substantial placebo effects. These guidelines, therefore, not only present currently available data from open and controlled studies, but also include expert knowledge. Although the overall database has increased in size since 2011, definite conclusions regarding the efficacy and tolerability of DBS in TS are still open to debate. Therefore, we continue to consider DBS for TS as an experimental treatment that should be used only in carefully selected, severely affected and otherwise treatment-resistant patients.

P66, a bifunctional integral outer membrane protein, is necessary for Borrelia burgdorferi to establish initial infection and to disseminate in mice. The integrin binding function of P66 facilitates extravasation and dissemination, but the role of its porin function during murine infection has not been investigated. A limitation to studying P66 porin function during mammalian infection has been the lack of structural information for P66. In this study, we experimentally characterized specific domains of P66 with regard to structure and function. First, we aligned the amino acid sequences of P66 from Lyme disease-causing Borrelia and relapsing fever-causing Borrelia to identify conserved and unique domains between these disease-causing clades. Then, we examined whether specific domains of P66 are exposed on the surface of the bacteria by introducing c-Myc epitope tags into each domain of interest. The c-Myc epitope tag inserted C-terminally to E33 (highly conserved domain), to T187 (integrin binding region domain and a non-conserved domain), and to E334 (non-conserved domain) were all detected on the surface of Borrelia burgdorferi. The c-Myc epitope tag inserted C-terminally to E33 and D303 in conserved domains disrupted P66 oligomerization and porin function. In a murine model of infection, the E33 and D303 mutants exhibited decreased infectivity and dissemination. Taken together, these results suggest the importance of these conserved domains, and potentially P66 porin function, in vivo.

P66, a bifunctional integral outer membrane protein, is necessary for Borrelia burgdorferi to establish initial infection and to disseminate in mice. The integrin binding function of P66 facilitates extravasation and dissemination, but the role of its porin function during murine infection has not been investigated. A limitation to studying P66 porin function during mammalian infection has been the lack of structural information for P66. In this study, we experimentally characterized specific domains of P66 with regard to structure and function. First, we aligned the amino acid sequences of P66 from Lyme disease-causing Borrelia and relapsing fever-causing Borrelia to identify conserved and unique domains between these disease-causing clades. Then, we examined whether specific domains of P66 are exposed on the surface of the bacteria by introducing c-Myc epitope tags into each domain of interest. The c-Myc epitope tag inserted C-terminally to E33 (highly conserved domain), to T187 (integrin binding region domain and a non-conserved domain), and to E334 (non-conserved domain) were all detected on the surface of Borrelia burgdorferi. The c-Myc epitope tag inserted C-terminally to E33 and D303 in conserved domains disrupted P66 oligomerization and porin function. In a murine model of infection, the E33 and D303 mutants exhibited decreased infectivity and dissemination. Taken together, these results suggest the importance of these conserved domains, and potentially P66 porin function, in vivo.

P66, a bifunctional integral outer membrane protein, is necessary for Borrelia burgdorferi to establish initial infection and to disseminate in mice. The integrin binding function of P66 facilitates extravasation and dissemination, but the role of its porin function during murine infection has not been investigated. A limitation to studying P66 porin function during mammalian infection has been the lack of structural information for P66. In this study, we experimentally characterized specific domains of P66 with regard to structure and function. First, we aligned the amino acid sequences of P66 from Lyme disease-causing Borrelia and relapsing fever-causing Borrelia to identify conserved and unique domains between these disease-causing clades. Then, we examined whether specific domains of P66 are exposed on the surface of the bacteria by introducing c-Myc epitope tags into each domain of interest. The c-Myc epitope tag inserted C-terminally to E33 (highly conserved domain), to T187 (integrin binding region domain and a non-conserved domain), and to E334 (non-conserved domain) were all detected on the surface of Borrelia burgdorferi. The c-Myc epitope tag inserted C-terminally to E33 and D303 in conserved domains disrupted P66 oligomerization and porin function. In a murine model of infection, the E33 and D303 mutants exhibited decreased infectivity and dissemination. Taken together, these results suggest the importance of these conserved domains, and potentially P66 porin function, in vivo.