The Natural Products Atlas 3.0: extending the database of microbially derived natural products.

The Natural Products Atlas is a database of microbially derived natural products that contains structures, producing organism taxonomy, biosynthetic and chemical ontology classifications, grouping by compound classes and cross-links to a suite of other natural product-related data resources. The database is supported by a web server that includes functionality to browse the collection, search the database using both chemical structures and text/numerical terms and visualize the chemical diversity it contains using interactive dashboards. In the current database release, we have curated 1347 papers, increasing the number of compounds to 36 545.

Digitally augmented, parent-led CBT versus treatment as usual for child anxiety problems in child mental health services in England and Northern Ireland: a pragmatic, non-inferiority, clinical effectiveness and cost-effectiveness randomised controlled trial.

Background: Anxiety problems are common in children, yet few affected children access evidence-based treatment. Digitally augmented psychological therapies bring potential to increase availability of effective help for children with mental health problems. This study aimed to establish whether therapist-supported, digitally augmented, parent-led cognitive behavioural therapy (CBT) could increase the efficiency of treatment without compromising clinical effectiveness and acceptability.

The diagnostic power of salivary electrolytes for Sjögren's disease: a systematic literature review and meta-analysis.

Objectives: To perform a systematic review and meta-analysis to determine the power of salivary electrolytes for the diagnosis of Sjögren's disease (SjD).

Methods: A literature search was conducted (last search March 2023) using PubMed and Web of Science and completed with a manual search. Articles were screened for reports of human salivary ion concentrations, comparing SjD patients with healthy controls and/or sicca patients.

A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data.

Nuclear magnetic resonance (NMR) data are rarely deposited in open databases, leading to loss of critical scientific knowledge. Existing data reporting methods (images, tables, lists of values) contain less information than raw data and are poorly standardized. Together, these issues limit FAIR (findable, accessible, interoperable, reusable) access to these data, which in turn creates barriers for compound dereplication and the development of new data-driven discovery tools.

Artificial intelligence for natural product drug discovery.

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature.

Use and efficacy of dry-mouth interventions in Sjögren's disease patients and possible association with perceived oral dryness and patients' discomfort.

Objectives: Sjögren's disease (SjD) patients use various interventions to relief their oral dryness. However, the use and efficacy of these interventions have only partially been evaluated. The present study aims to investigate whether there is an association between the perceived oral dryness and discomfort of SjD patients and their use of specific interventions.

Implementation of exergaming for people with dementia: facilitators, barriers, and recommendations.

Objectives: To identify facilitators, barriers, and formulate recommendations for the implementation of exergames for people with dementia (PWD) in day-care centers (DCCs).

Methods: Within a randomized controlled trial into the effectiveness of exergaming, 73 PWD with their informal caregivers (IC) from 11 DCCs in the Netherlands and two exergame providers participated in a process evaluation. This was a mixed-methods study using focus groups, semi-structured interviews, the Measurement Instrument for Determinants of Innovations, forms for DCC staff, and a short satisfaction questionnaire.

Observation of high-energy neutrinos from the Galactic plane.

The origin of high-energy cosmic rays, atomic nuclei that continuously impact Earth's atmosphere, is unknown. Because of deflection by interstellar magnetic fields, cosmic rays produced within the Milky Way arrive at Earth from random directions. However, cosmic rays interact with matter near their sources and during propagation, which produces high-energy neutrinos.

Effective root responses to salinity stress include maintained cell expansion and carbon allocation.

Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S.

Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting.

Spectral matching of MS fragmentation spectra has become a popular method for characterizing natural products libraries but identification remains challenging due to differences in MS fragmentation properties between instruments and the low coverage of current spectral reference libraries. To address this bottleneck we present Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) which matches chemical similarity grouping in the Natural Products Atlas to grouping of mass spectrometry features from molecular networking. This approach assigns compound families to molecular networking subnetworks without the need for experimental or calculated reference spectra.

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC.

Strong Constraints on Neutrino Nonstandard Interactions from TeV-Scale ν_{μ} Disappearance at IceCube.

We report a search for nonstandard neutrino interactions (NSI) using eight years of TeV-scale atmospheric muon neutrino data from the IceCube Neutrino Observatory. By reconstructing incident energies and zenith angles for atmospheric neutrino events, this analysis presents unified confidence intervals for the NSI parameter ε_{μτ}. The best-fit value is consistent with no NSI at a p value of 25.

Candidate Tidal Disruption Event AT2019fdr Coincident with a High-Energy Neutrino.

The origins of the high-energy cosmic neutrino flux remain largely unknown. Recently, one high-energy neutrino was associated with a tidal disruption event (TDE). Here we present AT2019fdr, an exceptionally luminous TDE candidate, coincident with another high-energy neutrino.

NP Analyst: An Open Online Platform for Compound Activity Mapping.

Few tools exist in natural products discovery to integrate biological screening and untargeted mass spectrometry data at the library scale. Previously, we reported Compound Activity Mapping as a strategy for predicting compound bioactivity profiles directly from primary screening results on extract libraries. We now present NP Analyst, an open online platform for Compound Activity Mapping that accepts bioassay data of almost any type, and is compatible with mass spectrometry data from major instrument manufacturers via the mzML format.

Search for Relativistic Magnetic Monopoles with Eight Years of IceCube Data.

We present an all-sky 90% confidence level upper limit on the cosmic flux of relativistic magnetic monopoles using 2886 days of IceCube data. The analysis was optimized for monopole speeds between 0.750c and 0.

An isotopic labeling approach linking natural products with biosynthetic gene clusters.

Major advances in genome sequencing and large-scale biosynthetic gene cluster (BGC) analysis have prompted an age of natural product discovery driven by genome mining. Still, connecting molecules to their cognate BGCs is a substantial bottleneck for this approach. We have developed a mass-spectrometry-based parallel stable isotope labeling platform, termed IsoAnalyst, which assists in associating metabolite stable isotope labeling patterns with BGC structure prediction to connect natural products to their corresponding BGCs.

NP-MRD: the Natural Products Magnetic Resonance Database.

The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the 'gold standard' for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics).

The Natural Products Atlas 2.0: a database of microbially-derived natural products.

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019.

Cost-effectiveness of exergaming compared to regular day-care activities in dementia: Results of a randomised controlled trial in The Netherlands.

The growing number of people living with dementia will result in increased costs of dementia worldwide. The e-Health intervention 'Exergaming' may improve health and quality of life of people with dementia, but the cost-effectiveness is unknown. We assessed the cost-effectiveness of exergaming compared to regular activities from a societal perspective in day-care centres (DCC) for people with dementia and their informal caregivers (IC) alongside a cluster randomised controlled trial.

Automated Scoring of Tablet-Administered Expressive Language Tests.

Speech and language impairments are common pediatric conditions, with as many as 10% of children experiencing one or both at some point during development. Expressive language disorders in particular often go undiagnosed, underscoring the immediate need for assessments of expressive language that can be administered and scored reliably and objectively. In this paper, we present a set of highly accurate computational models for automatically scoring several common expressive language tasks.

A Pseudo-Value Approach to Analyze the Semantic Similarity of the Speech of Children With and Without Autism Spectrum Disorder.

Conversational impairments are well known among people with autism spectrum disorder (ASD), but their measurement requires time-consuming manual annotation of language samples. Natural language processing (NLP) has shown promise in identifying semantic difficulties when compared to clinician-annotated reference transcripts. Our goal was to develop a novel measure of lexico-semantic similarity - based on recent work in natural language processing (NLP) and recent applications of pseudo-value analysis - which could be applied to transcripts of children's conversational language, without recourse to some ground-truth reference document.