LiPheStream - A 18-month high spatiotemporal resolution point cloud time series of Boreal trees from Finland.

In the present paper, we introduce a high-resolution spatiotemporal point cloud time series, acquired using a LiDAR sensor mounted 30 metres above ground on a flux observation tower monitoring a boreal forest. The dataset comprises a 18-month long (April 2020 - September 2021) time series with an average interval of 3.5 days between observations.

The effect of hydrogen bonding on the π depletion and the π-π stacking interaction.

Non-covalent interactions such as hydrogen bonding and π-π stacking are essential types of interactions governing molecular self-assembly. The π-π stacking ability of aromatic rings depends on the electron density of the π orbitals, which is affected by the electron-withdrawing or electron-donating properties of the substituents. We have here studied the effect of hydrogen bonding on the strength of the π-π stacking interactions by calculating the binding energies at the explicitly correlated Møller-Plesset (MP2-F12) perturbation theory level using polarized triple- quality basis sets.

Value of Pharmacogenetic Testing Assessed with Real-World Drug Utilization and Genotype Data.

Implementation of pharmacogenetic testing in clinical care has been slow and with few exceptions is hindered by the lack of real-world evidence on how to best target testing. In this retrospective register-based study, we analyzed a nationwide cohort of 1,425,000 patients discharged from internal medicine or surgical wards and a cohort of 2,178 university hospital patients for purchases and prescriptions of pharmacogenetically actionable drugs. Pharmacogenetic variants were obtained from whole genome genotype data for a subset (n = 930) of the university hospital patients.

Attractive acceptor-acceptor interactions in self-complementary quadruple hydrogen bonds for molecular self-assembly.

Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its driving forces. A potent method is to exploit self-complementary hydrogen bonding, where a molecule interacts with its own copy by suitable positions of hydrogen-bond donor (D) and acceptor (A) groups.

Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.

Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging.

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth.

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing.

Synthesis and Evaluation of a Set of 6-Deoxy-6-thio-carboranyl d-Glucoconjugates Shed Light on the Substrate Specificity of the GLUT1 Transporter.

Glucose- and sodium-dependent glucose transporters (GLUTs and SGLTs) play vital roles in human biology. Of the 14 GLUTs and 12 SGLTs, the GLUT1 transporter has gained the most widespread recognition because GLUT1 is overexpressed in several cancers and is a clinically valid therapeutic target. We have been pursuing a GLUT1-targeting approach in boron neutron capture therapy (BNCT).

Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.

Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations.

Human exposome assessment platform.

The Human Exposome Assessment Platform (HEAP) is a research resource for the integrated and efficient management and analysis of human exposome data. The project will provide the complete workflow for obtaining exposome actionable knowledge from population-based cohorts. HEAP is a state-of-the-science service composed of computational resources from partner institutions, accessed through a software framework that provides the world's fastest Hadoop platform for data warehousing and applied artificial intelligence (AI).

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard.

Exploring the Biochemical Foundations of a Successful GLUT1-Targeting Strategy to BNCT: Chemical Synthesis and Evaluation of the Entire Positional Isomer Library of -Carboranylmethyl-Bearing Glucoconjugates.

Boron neutron capture therapy (BNCT) is a noninvasive binary therapeutic modality applicable to the treatment of cancers. While BNCT offers a tumor-targeting selectivity that is difficult to match by other means, the last obstacles preventing the full harness of this potential come in the form of the suboptimal boron delivery strategies presently used in the clinics. To address these challenges, we have developed delivery agents that target the glucose transporter GLUT1.

Modelling aerosol transport and virus exposure with numerical simulations in relation to SARS-CoV-2 transmission by inhalation indoors.

We provide research findings on the physics of aerosol and droplet dispersion relevant to the hypothesized aerosol transmission of SARS-CoV-2 during the current pandemic. We utilize physics-based modeling at different levels of complexity, along with previous literature on coronaviruses, to investigate the possibility of airborne transmission. The previous literature, our 0D-3D simulations by various physics-based models, and theoretical calculations, indicate that the typical size range of speech and cough originated droplets ( ) allows lingering in the air for ) so that they could be inhaled.

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR's framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses.

3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.

With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images. In particular, we focussed here on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons.

Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.

Orchestrating differential data access for translational research: a pilot implementation.

Background: Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data.

Recommendations on e-infrastructures for next-generation sequencing.

With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations based on the collective experiences from participants in the EU COST Action SeqAhead for the tasks of data preprocessing, upstream processing, data delivery, and downstream analysis, as well as long-term storage and archiving. We cover demands on computational and storage resources, networks, software stacks, automation of analysis, education, and also discuss emerging trends in the field.

Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops.

There is a clear demand for hands-on bioinformatics training. The development of bioinformatics workshop content is both time-consuming and expensive. Therefore, enabling trainers to develop bioinformatics workshops in a way that facilitates reuse is becoming increasingly important.

Individual FEV1 Trajectories Can Be Identified from a COPD Cohort.

Objective: We aim to make use of clinical spirometry data in order to identify individual COPD-patients with divergent trajectories of lung function over time.

Study Design And Setting: Hospital-based COPD cohort (N = 607) was followed on average 4.6 years.

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences.

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments.

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners.