dtool and dserver: A flexible ecosystem for findable data.

Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight data management tool that packages metadata with immutable data to promote accessibility, interoperability, and reproducibility. Each dataset is self-contained and does not require metadata to be stored in a centralised system. This decentralised approach means that finding datasets can be difficult. dtool's lookup server, short dserver, as defined by a REST API, makes dtool datasets findable, hence rendering the dtool ecosystem fit for a FAIR data management world. Its simplicity, modularity, accessibility and standardisation via API distinguish dtool and dserver from other solutions and enable it to serve as a common denominator for cross-disciplinary research data management. The dtool ecosystem bridges the gap between standardisation-free data management by individuals and FAIR platform solutions with rigid metadata requirements.

A Dimensional Comparison between Evolutionary Algorithm and Deep Reinforcement Learning Methodologies for Autonomous Surface Vehicles with Water Quality Sensors.

The monitoring of water resources using Autonomous Surface Vehicles with water-quality sensors has been a recent approach due to the advances in unmanned transportation technology. The Ypacaraí Lake, the biggest water resource in Paraguay, suffers from a major contamination problem because of cyanobacteria blooms. In order to supervise the blooms using these on-board sensor modules, a Non-Homogeneous Patrolling Problem (a NP-hard problem) must be solved in a feasible amount of time. A dimensionality study is addressed to compare the most common methodologies, Evolutionary Algorithm and Deep Reinforcement Learning, in different map scales and fleet sizes with changes in the environmental conditions. The results determined that Deep Q-Learning overcomes the evolutionary method in terms of sample-efficiency by 50-70% in higher resolutions. Furthermore, it reacts better than the Evolutionary Algorithm in high space-state actions. In contrast, the evolutionary approach shows a better efficiency in lower resolutions and needs fewer parameters to synthesize robust solutions. This study reveals that Deep Q-learning approaches exceed in efficiency for the Non-Homogeneous Patrolling Problem but with many hyper-parameters involved in the stability and convergence.

A Sequence Distance Graph framework for genome assembly and analysis.

The Sequence Distance Graph (SDG) framework works with genome assembly graphs and raw data from paired, linked and long reads. It includes a simple deBruijn graph module, and can import graphs using the graphical fragment assembly (GFA) format. It also maps raw reads onto graphs, and provides a Python application programming interface (API) to navigate the graph, access the mapped and raw data and perform interactive or scripted analyses. Its complete workspace can be dumped to and loaded from disk, decoupling mapping from analysis and supporting multi-stage pipelines. We present the design and implementation of the framework, and example analyses scaffolding a short read graph with long reads, and navigating paths in a heterozygous graph for a simulated parent-offspring trio dataset. SDG  is  freely  available  under  the  MIT  license  at https://github.com/bioinfologics/sdg.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research.

'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance.

Traditionally, diagnostic tools for plant pathogens were limited to the analysis of purified pathogen isolates subjected to phenotypic characterization and/or PCR-based genotypic analysis. However, these approaches detect only already known pathogenic agents, may not always recognize novel races, and can introduce bias in the results. Recent advances in next-generation sequencing technologies have provided new opportunities to integrate high-resolution genotype data into pathogen surveillance programs. Here, we describe some of the key bioinformatics analysis used in the newly developed "Field Pathogenomics" pathogen surveillance technique. This technique is based on RNA-seq data generated directly form pathogen-infected plant leaf samples collected in the field, providing a unique opportunity to characterize the pathogen population and its host directly in their natural environment. We describe two main analyses: (1) a phylogenetic analysis of the pathogen isolates that have been collected to understand how they are related to each other, and (2) a population structure analysis to provide insight into the genetic substructure within the pathogen population. This provides a high-resolution representation of pathogen population dynamics directly in the field, providing new insights into pathogen biology, population structure, and pathogenesis.

Comparación de resultados entre hernioplastia inguinal abierta con malla tipo liechtenstein y hernioplasta inguinal videolaparoscópica / Outcome Measures between Open Lichtenstein Technique and laparoscopic TAPP Repair of Inguinal Hernias

Introducción: la hernioplastía es uno de los procedimientos quirúrgicos más comunes que realiza el cirujano alrededor del mundo. En nuestra institución se realizan la hernioplastía tipo Liechtenstein (abierto) y videolaparoscópica tipo TAPP (transabdominal preperitoneal). El objetivo del estudio es comparar los resultados obtenidos utilizando ambos procedimientos. Diseño, lugar y participantes: estudio retrospectivo de 45 pacientes sometidos a uno de los dos procedimientos, durante junio-noviembre 2015, en el Hospital General Juan José Arévalo Bermejo, evaluando la prevalencia de inguinodinia crónica, hernia recidivante, complicaciones y tiempo de retorno a labores. Resultados: No se encontró diferencia, entre el grupo abierto comparado con el videolaparoscópico, en la prevalencia de inguinodinia crónica (21.4% vs 17.7%, p: 0.75), ni en el porcentaje de pacientes que consultó a la emergencia por dolor (8.5% vs 13%, p: 0.55), ni en complicaciones postoperatorias de infección, seroma, rechazo e hidrocele (19.1% vs 30.4%, p: 0.36). Las recidivas de hernia inguinal fueron más comunes en el grupo videolaparoscópico que en el abierto (17.3% vs 2.1%; p: 0.019). El tiempo promedio de retorno a labores fue de 29 días en ambos grupos (p: 1.0) Conclusión: En nuestra institución, ambos procedimientos tiene resultados comparables y probablemente, conforme aumente la experiencia de la hernioplastía videolaparoscópica, la incidencia de recidivas disminuya.

Background: Hernioplasty is one of the most common surgical procedures around the world. In our insttuton hernioplasty is performed with Lichtenstein technique (open) and laparoscopic TAPP (transabdominal preperitoneal) repair. The aim of the study is to compare clinical outcomes between both procedures. Design, Setng, and Partcipants: In this retrospectve study, 45 patents were treated with one of the techniques for hernia repair, between June and November of 2015 at the General Hospital Juan José Arévalo Bermejo. The prevalence of chronic inguinodynia, inguinal hernia recurrence, complicatons and tme to return to normal actvites were compared. Results: There is no statstcal diference between open technique compared with laparoscopic repair, in the prevalence of chronic inguinodynia (21.4% vs 17.7%, p: 0.75), nor in the percentage of patents that were atended in the emergency room for pain (8.5% vs 13%, p: 0.55), nor in postoperatve infectons, seroma formaton, rejecton or hydrocele complicatons (p: 0.36). Inguinal hernia recurrence was more common in the laparoscopic group (17.3% vs 2.1%, p: 0.019). Mean tme to return to work was 29 days in both groups (p: 1.0). Conclusions: In our insttuton both procedures have comparable results and more experience is needed to decrease hernia recurrence.