State of Amphibia 2020: Five years of amphibian research, diversity and resources

Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, taking stock of our current understanding of amphibians is imperative. Focusing on 2016–2020, we assessed trends in amphibian publishing, conservation research, systematics, and community resources. We show that while research and data availability are increasing rapidly, information is not evenly distributed across research fields, clades, or geographic regions, leading to substantial knowledge gaps. A complete review of amphibian NCBI resources indicates that genomic data are poised for rapid expansion, but amphibian genomes pose significant challenges. A review of recent conservation literature and cataloged threats on 1,261 species highlight the need to address land use change and disease using adaptive management strategies. We underscore the importance of database integration for advancing amphibian research and conservation and suggest other understudied or imperiled clades would benefit from similar assessments.

The Roman Hinterland Project: Integrating Archaeological Field Surveys around Rome and Beyond

This article presents the background to and prospects for a new initiative in archaeological field survey and database integration. The Roman Hinterland Project combines data from the Tiber Valley Project, Roman Suburbium Project, and the Pontine Region Project into a single database, which the authors believe to be one of the most complete repositories of data for the hinterland of a major ancient metropolis, covering nearly 2000 years of history. The logic of combining these databases in the context of studying the Roman landscape is explained and illustrated with analyses that show their capacity to contribute to major debates in Roman economy, demography, and the longue durée of the human condition in a globalizing world.

The mining and construction of a knowledge base for gene-disease association in mitochondrial diseases

Mitochondrial diseases are a group of heterogeneous genetic metabolic diseases caused by mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) gene mutations. Mining the gene-disease association of mitochondrial diseases is helpful for understanding the pathogenesis of mitochondrial diseases, for carrying out early clinical diagnosis for related diseases, and for formulating better treatment strategies for mitochondrial diseases. This project researched the relationship between genes and mitochondrial diseases, combined the Malacards, Genecards, and MITOMAP disease databases to mine the knowledge on mitochondrial diseases and genes, used database integration and the sequencing method of the phenolyzer tool to integrate disease-related genes from different databases, and sorted the disease-related candidate genes. Finally, we screened 531 mitochondrial related diseases, extracted 26,723 genes directly or indirectly related to mitochondria, collected 24,602 variant sites on 1474 genes, and established a mitochondrial disease knowledge base (MitDisease) with a core of genes, diseases, and variants. This knowledge base is helpful for clinicians who want to combine the results of gene testing for diagnosis, to understand the occurrence and development of mitochondrial diseases, and to develop corresponding treatment methods.

SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures

In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glycan fragments which contain underdetermined linkages, and a database search for glycans drawn on the canvas. This tool provides an easy editing feature for various glycan structures in just a few steps using template structures and pop-up windows which allow users to select specific information for each structure element. This tool has a unique feature for selecting possible attachment sites, which is defined in the Symbol Nomenclature for Glycans (SNFG). In addition, this tool can input and output glycans in WURCS and GlycoCT formats, which are the most commonly-used text formats for glycan structures.

Integrative Bioinformatics Analysis Reveals That Infarct-Mediated Overexpression of Potential miR-662/CREB1 Pathway-Induced Neuropeptide VIP Is Associated with the Risk of Atrial Fibrillation: A Correlation Analysis between Myocardial Electrophysiology and Neuroendocrine

Background. Neuropeptide levels are closely associated with the development and maintenance of atrial fibrillation (AF) after myocardial infarction (MI). This study was aimed at investigating the regulatory network that affects neuropeptide expression through transcription factor modulation. Methods. We downloaded three datasets from the GEO database, and after performing differential and crosstabulation analyses, we screened out differentially expressed (DE) miRNAs and DEmRNAs coexpressed in AF and MI and performed DEmiRNA–DEmRNA pairing prediction; from which, we constructed a regulatory network. Subsequently, the hsa-miR-662-CREB1-VIP axis was obtained, and the role of CREB1 and VIP in the development of AF after MI was further revealed by single-cell analysis and prediction model construction. Results. In this study, eight DEmRNAs and four miRNAs were screened. hsa-miR-662 was identified by database integration analysis to regulate the transcription factor CREB1, a potential transcriptional regulator in VIP. CREB1 and VIP are mainly enriched in pathways of energy metabolism, ion channels, and myocardial contraction. CREB1 and VIP were identified as biomarkers of the onset and prognosis of MI and AF. Conclusions. In this study, the miR-662/CREB1/VIP regulatory pathway was constructed through integrated analysis of datasets, thus providing new ideas to study the mechanisms of AF development.

Automated Access Communication System

Automated Access Communication System is concerned with the development of a system that is simple and easy to use yet a powerful web application for sharing, managing and controlling enterprise documents on intranet/internet in a secure manner within the particular organization. It enables the communication between all the departments of the company through online. The development of this new system contains the following activities, which try to automate the entire process keeping in the view of database integration approach.

Productividad D E Lechuga (Lactuca Sativ A L .) En Acuaponía E Hidroponía

El cambio de uso del suelo con fines agrícolas bajo esquemas de manejo agrícola y uso del agua poco eficientes, originan suelos infértiles. Para el cultivo de hortalizas se estudian técnicas que produzcan altos rendimientos con los menores costos económicos y ambientales. Los objetivos del estudio fueron estimar y comparar el rendimiento de la lechuga (Lactuca sativa L.) en los sistemas productivos acuapónico (SA) e hidropónico (SH). La metodología comprendió dos etapas: el establecimiento de los sistemas productivos tipo Nutrition Film Technique (NFT) y el monitoreo del desarrollo del cultivo en ambos sistemas. Las bases de datos y el tratamiento estadístico se realizaron en el programa Excel de Windows Versión 10. La prueba t de student con un nivel de significancia de 0.05 indicó el peso promedio de las lechugas: 0.056 kg (± 0.005 kg) en el SA, y 0.097 kg (± 0.007 kg) en el SH. El SH generó mayor rendimiento (1.847 kg/m2) que el SA (1.080 kg/m2); lo que se atribuyó a que el SH contó con los nutrientes necesarios desde el inicio del cultivo, por la aplicación de fertilizante. La temperatura alta influyó en el comportamiento de los peces del SA, ya que provocaron menor consumo alimenticio y de aporte de desechos orgánicos al agua que, promovieron una baja cantidad de nutrientes y afectaron la producción y el rendimiento del cultivo. Se recomiendan la generación de conocimiento para complementar los resultados obtenidos, como el gasto hídrico y su comparación con los sistemas de cultivo de lechuga tradicionales. Land use change for agriculture under poor farm management and inefficient water use, produces infertile soils. For green vegetable farming, there are some techniques for the achievement of high crop yields with the lowest economic and environmental costs. The study objectives were to estimate and compare lettuce yields (Lactuca sativa L.) in aquaponic (SA) and hydroponic (SH) production systems. Methodology encompassed two stages: the establishing of a Nutrition Film Technique (NFT) productive system and the monitoring of the crop growing in both systems. Database integration and statistical analyses were performed using Windows Excel version 10. Average lettuce weight using t-test (significance level of 0.05) were 0.056 kg (± 0.005 kg) in SA, y 0.097 kg (± 0.007 kg) in SH. SH reached higher yields (1.847 kg/m2) than SA (1.080 kg/m2); likely due to the fact that SH had all needed nutrients since the beginning of the crop, by applying fertilizer. High temperature influenced fish behavior in SA, observing lower food consumption and organic waste supply to the water, releasing low nutrient load that affected crop production and yield. More studies are recommended in order to deepen the outcomes, such as those including water flow and the comparison with conventional lettuce crop systems.