Reliability of evidence-review methods in restoration ecology.

In restoration science, evidence reviews play a crucial role in summarizing research findings in practice and policy. However, if unreliable or inappropriate methods are used to review evidence, decisions based on these reviews may not accurately reflect the available evidence base. To assess the current value of restoration reviews, we examined a sample of meta-analyses and narrative syntheses (n = 91) with the Collaboration for Environmental Evidence Synthesis Assessment Tool (CEESAT), which uses detailed criteria to assesses the method of policy-relevant evidence synthesis according to elements important for objectivity, transparency, and comprehensiveness. Overall, reviews scored low based on this standard: median score 16 out of 39, modal score 15, and mean 16.6. Meta-analyses scored higher than narrative syntheses (median 17 vs. 5, respectively), although there were some outlier narrative syntheses that had high scores, suggesting that quantitative synthesis does not solely reflect the reliability of a review. In general, criteria spanning the more fundamental review stages (i.e., searching for studies and including studies) received low scores for both synthesis types. Conversely, criteria comprising the later stages of the review (i.e., critical appraisal, data extraction, and data synthesis) were generally well described in meta-analyses; thus, these criteria achieved the highest individual CEESAT scores. We argue that restoration ecology is well positioned to advance so-called evidence-based restoration, but review authors should elucidate their conceptual understanding of evidence syntheses and recognize that conducting reliable reviews demands the same methodological rigor and reporting standards used in primary research. Given the potential of evidence reviews to inform management, policy, and research, it is of vital importance that the overall methodological reliability of restoration reviews be improved.

Confiabilidad de los Métodos de Revisión de Evidencias en la Ecología de Restauración Resumen Para las ciencias de la restauración, las revisiones de evidencias juegan un papel muy importante en la síntesis de los hallazgos de las investigaciones en la práctica y en las políticas. Sin embargo, si se usan métodos poco fiables o inapropiados para revisar las evidencias, las decisiones que se tomen con base en estas revisiones pueden no reflejar acertadamente la base disponible de evidencias. Para analizar el valor actual de las revisiones de restauraciones examinamos una muestra de metaanálisis y síntesis narrativas (n = 91) con la Herramienta para la Síntesis de Análisis de la Colaboración para la Evidencia Ambiental (CEESAT), la cual usa criterios detallados para analizar el método de síntesis de evidencias relevantes para las políticas de acuerdo con los elementos importantes para la objetividad, transparencia y exhaustividad. En general, las revisiones tuvieron puntajes bajos con base en este estándar (puntaje medio: 16 de 39, puntaje modal: 15, media: 16.6). Los metaanálisis tuvieron un puntaje más alto que las síntesis narrativas (mediana: 17 vs 5, respectivamente), aunque hubo algunas síntesis narrativas atípicas que tuvieron puntajes altos, lo que sugiere que la síntesis cuantitativa no refleja por sí sola la confiabilidad de una revisión. En suma, los criterios que abarcaron las etapas de revisión más fundamentales (es decir, buscar estudios e incluir estudios) recibieron puntajes bajos para ambos tipos de síntesis. Al contrario, los criterios que comprendieron las etapas tardías de la revisión (es decir, la valoración crítica, la extracción de datos y la síntesis de los datos) estuvieron generalmente bien descritos en los metaanálisis; por lo tanto, estos criterios alcanzaron los puntajes CEESAT individuales más altos. Argumentamos que la ecología de restauración se encuentra bien posicionada para adelantar la llamada restauración basada en evidencias, pero los autores de las revisiones deberían aclarar su entendimiento conceptual de la síntesis de evidencias y reconocer que la realización de revisiones confiables requiere el mismo rigor metodológico y los mismos estándares de reporte usados en la investigación primaria. Dado el potencial que tienen las revisiones de evidencias para orientar el manejo, las políticas y la investigación, es de vital importancia que se mejore la confiabilidad metodológica generalizada de las revisiones de restauración.

visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level.

BACKGROUND: Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understanding of the ligand-receptor recognition process is of fundamental importance since these methods are a major step towards ligand prediction, target identification, lead discovery, and more. This article presents visGReMLIN, a web server that couples a graph mining-based strategy to detect motifs at the protein-ligand interface with an interactive platform to visually explore and interpret these motifs in the context of protein-ligand interfaces. RESULTS: To illustrate the potential of visGReMLIN, we conducted two cases in which our strategy was compared with previous experimentally and computationally determined results. visGReMLIN allowed us to detect patterns previously documented in the literature in a totally visual manner. In addition, we found some motifs that we believe are relevant to protein-ligand interactions in the analyzed datasets. CONCLUSIONS: We aimed to build a visual analytics-oriented web server to detect and visualize common motifs at the protein-ligand interface. visGReMLIN motifs can support users in gaining insights on the key atoms/residues responsible for protein-ligand interactions in a dataset of complexes.

Convergence and divergence in science and practice of urban and rural forest restoration.

Forest restoration has never been higher on policymakers' agendas. Complex and multi-dimensional arrangements across the urban-rural continuum challenge restorationists and require integrative approaches to strengthen environmental protection and increase restoration outcomes. It remains unclear if urban and rural forest restoration are moving towards or away from each other in practice and research, and whether comparing research outcomes can help stakeholders to gain a clearer understanding of the interconnectedness between the two fields. This study aims to identify the challenges and opportunities for enhancing forest restoration in both urban and rural systems by reviewing the scientific evidence, engaging with key stakeholders and using an urban-rural forest restoration framework. Using the Society for Ecological Restoration's International Principles as discussion topics, we highlight aspects of convergence and divergence between the two fields to broaden our understanding of forest restoration and promote integrative management approaches to address future forest conditions. Our findings reveal that urban and rural forest restoration have convergent and divergent aspects. We emphasise the importance of tailoring goals and objectives to specific contexts and the need to design different institutions and incentives based on the social and ecological needs and goals of stakeholders in different regions. Additionally, we discuss the challenges of achieving high levels of ecological restoration and the need to go beyond traditional ecology to plan, implement, monitor, and adaptively manage restored forests. We suggest that rivers and watersheds could serve as a common ground linking rural and urban landscapes and that forest restoration could interact with other environmental protection measures. We note the potential for expanding the creative vision associated with increasing tree-containing environments in cities to generate more diverse and resilient forest restoration outcomes in rural settings. This study underscores the value of integrative management approaches in addressing future forest conditions across the urban-rural continuum. Our framework provides valuable insights for policymakers, researchers, and decision-makers to advance the field of forest restoration and address the challenges of restoration across the urban-rural continuum. The rural-urban interface serves as a convergence point for forest restoration, and both urban and rural fields can benefit from each other's expertise.