PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.

Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA-miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https://bioconductor.org/packages/PanomiR.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises the status of services that EMBL-EBI data resources provide to scientific communities globally. The scale, openness, rich metadata and extensive curation of EMBL-EBI added-value databases makes them particularly well-suited as training sets for deep learning, machine learning and artificial intelligence applications, a selection of which are described here. The data resources at EMBL-EBI can catalyse such developments because they offer sustainable, high-quality data, collected in some cases over decades and made openly availability to any researcher, globally. Our aim is for EMBL-EBI data resources to keep providing the foundations for tools and research insights that transform fields across the life sciences.

Control of ZIF-62 and agZIF-62 Film Thickness within Asymmetric Tubular Supports through Pressure and Dose Time Variation of Atomic Layer Deposition.

Thin-films of metal-organic frameworks (MOFs) have widespread potential applications, especially with the emergence of glass-forming MOFs, which remove the inherent issue of grain boundaries and allow coherent amorphous films to be produced. Herein, it is established that atomic layer deposition (ALD) of zinc oxide lends excellent control over the thickness and localization of resultant polycrystalline and glass zeolitic imidazole framework-62 (ZIF-62) thin-films within tubular α-alumina supports. Through the reduction of the chamber pressure and dose times during zinc oxide deposition, the resultant ZIF-62 films are reduced from 38 µm to 16 µm, while the presence of sporadic ZIF-62 (previously forming as far as 280 µm into the support) is prevented. Furthermore, the glass transformation shows a secondary reduction in film thickness from 16 to 2 µm.

Correction: Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.

[This corrects the article DOI: 10.1371/journal.pcbi.1010220.].

Clinical Use of Trabecular Bone Score: The 2023 ISCD Official Positions.

Osteoporosis can currently be diagnosed by applying the WHO classification to bone mineral density (BMD) assessed by dual-energy x-ray absorptiometry (DXA). However, skeletal factors other than BMD contribute to bone strength and fracture risk. Lumbar spine TBS, a grey-level texture measure which is derived from DXA images has been extensively studied, enhances fracture prediction independent of BMD and can be used to adjust fracture probability from FRAX® to improve risk stratification. The purpose of this International Society for Clinical Densitometry task force was to review the existing evidence and develop recommendations to assist clinicians regarding when and how to perform, report and utilize TBS. Our review concluded that TBS is most likely to alter clinical management in patients aged ≥ 40 years who are close to the pharmacologic intervention threshold by FRAX. The TBS value from L1-L4 vertebral levels, without vertebral exclusions, should be used to calculate adjusted FRAX probabilities. L1-L4 vertebral levels can be used in the presence of degenerative changes and lumbar compression fractures. It is recommended not to report TBS if extreme structural or pathological artifacts are present. Monitoring and reporting TBS change is unlikely to be helpful with the current version of the TBS algorithm. The next version of TBS software will include an adjustment based upon directly measured tissue thickness. This is expected to improve performance and address some of the technical factors that affect the current algorithm which may require modifications to these Official Positions as experience is acquired with this new algorithm.

Combating ageism in medical education with narrative medicine.

Ageism is common in medical trainees and difficult to overcome. The My Life, My Story program has been shown to be an effective tool for increasing empathy. We explored its use as an instrument for combating ageism by implementing it in a Geriatrics clerkship for fourth year medical students. During our evaluation, 151 students interviewed patients about their lives using a semi-structured question guide. Students completed the UCLA Geriatrics Attitudes Scale and the Expectations Regarding Aging Survey pre-and post-clerkship. We also facilitated 9 student debriefs and 5 faculty interviews. After completing My Life, My Story, students were more likely to disagree with "I would rather see younger patients than elderly ones" and "it's normal to be depressed when you are old". In qualitative analysis of the debriefs, we identified a key summative theme: "impact of the intervention on care teams". Within that, we describe three subthemes: an awareness of richness of the lives led by older people, their current value to society, and the social determinants of health they have faced. After participating in My Life, My Story, students' attitudes toward aging changed. A narrative medicine program using life stories can be a practical tool for addressing ageist stereotypes.

Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2.

Alzheimer's disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency <0.01) associated with AD in a region-based, whole-genome sequencing (WGS) association study (rvGWAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved association p values <10-6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden and SKAT test and replicated in case/control samples from the ADSP study reaching genome-wide significance after meta-analysis (pmeta = 4.74 × 10-8). SKAT analysis also revealed region-based association around the Discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta = 1 × 10-6). In conclusion, in a region-based rvGWAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants.

Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

[This corrects the article DOI: 10.1371/journal.pcbi.1009218.].

De novo amyloid peptides with subtle sequence variations differ in their self-assembly and nanomechanical properties.

Proteinaceous amyloids are well known for their widespread pathological roles but lately have emerged also as key components in several biological functions. The remarkable ability of amyloid fibers to form tightly packed conformations in a cross ß-sheet arrangement manifests in their robust enzymatic and structural stabilities. These characteristics of amyloids make them attractive for designing proteinaceous biomaterials for various biomedical and pharmaceutical applications. In order to design customizable and tunable amyloid nanomaterials, it is imperative to understand the sensitivity of the peptide sequence for subtle changes based on amino acid position and chemistry. Here we report our results from four rationally-designed amyloidogenic decapeptides that subtly differ in hydrophobicity and polarity at positions 5 and 6. We show that making the two positions hydrophobic renders the peptide with enhanced aggregation and material properties while introducing polar residues in position 5 dramatically changes the structure and nanomechanical properties of the fibrils formed. A charged residue at position 6, however, abrogates amyloid formation. In sum, we show that subtle changes in the sequence do not make the peptide innocuous but rather sensitive to aggregation, reflected in the biophysical and nanomechanical properties of the fibrils. We conclude that tolerance of peptide amyloid for changes in the sequence, however small they may be, should not be neglected for the effective design of customizable amyloid nanomaterials.

Oropharyngeal Dysphagia in Acute Cervical Spinal Cord Injury: A Literature Review.

Dysphagia (swallowing impairment) is a frequent complication of cervical spinal cord injury (cSCI). Recently published national guidance in the UK on rehabilitation after traumatic injury confirmed that people with cSCI are at risk for dysphagia and require early evaluation while remaining nil by mouth [National Institute for Health and Care Excellence. Rehabilitation after traumatic injury (NG211), 2022, https://www.nice.org.uk/guidance/ng21 ]. While the pathogenesis and pathophysiology of dysphagia in cSCI remains unclear, numerous risk factors have been identified in the literature. This review aims to summarize the literature on the risk factors, presentation, assessment, and management of dysphagia in patients with cSCI. A bespoke approach to dysphagia management, that accounts for the multiple system impairment in cSCI, is presented; the overarching aim of which is to support effective management of dysphagia in patients with cSCI to prevent adverse clinical consequences.

Grazing livestock move by Lévy walks: Implications for soil health and environment.

Grazing livestock plays an important role in the context of food security, agricultural sustainability and climate change. Understanding how livestock move and interact with their environment may offer new insights on how grazing practices impact soil and ecosystem functions at spatial and temporal scales where knowledge is currently limited. We characterized daily and seasonal grazing patterns using Global Positioning System (GPS) data from two grazing strategies: conventionally- and rotationally-grazed pastures. Livestock movement was consistent with the so-called Lévy walks, and could thus be simulated with Lévy-walk based probability density functions. Our newly introduced "Moovement model" links grazing patterns with soil structure and related functions by coupling animal movement and soil structure dynamics models, allowing to predict spatially-explicit changes in key soil properties. Predicted post-grazing management-specific bulk densities were consistent with field measurements and confirmed that rotational grazing produced similar disturbance as conventional grazing despite hosting higher stock densities. Harnessing information on livestock movement and its impacts in soil structure within a modelling framework can help testing and optimizing grazing strategies for ameliorating their impact on soil health and environment.

Charge and redox states modulate granulin-TDP-43 coacervation toward phase separation or aggregation.

Cytoplasmic inclusions containing aberrant proteolytic fragments of TDP-43 are associated with frontotemporal lobar degeneration (FTLD) and other related pathologies. In FTLD, TDP-43 is translocated into the cytoplasm and proteolytically cleaved to generate a prion-like domain (PrLD) containing C-terminal fragments (C25 and C35) that form toxic inclusions. Under stress, TDP-43 partitions into membraneless organelles called stress granules (SGs) by coacervating with RNA and other proteins. To study the factors that influence the dynamics between these cytoplasmic foci, we investigated the effects of cysteine-rich granulins (GRNs 1-7), which are the proteolytic products of progranulin, a protein implicated in FTLD, on TDP-43. We show that extracellular GRNs, typically generated during inflammation, internalize and colocalize with PrLD as puncta in the cytoplasm of neuroblastoma cells but show less likelihood of their presence in SGs. In addition, we show GRNs and PrLD coacervate to undergo liquid-liquid phase separation (LLPS) or form gel- or solid-like aggregates. Using charge patterning and conserved cysteines among the wild-type GRNs as guides, along with specifically engineered mutants, we discover that the negative charges on GRNs drive LLPS while the positive charges and the redox state of cysteines modulate these phase transitions. Furthermore, RNA and GRNs compete and expel one another from PrLD condensates, providing a basis for GRN's absence in SGs. Together, the results help uncover potential modulatory mechanisms by which extracellular GRNs, formed during chronic inflammatory conditions, could internalize and modulate cytoplasmic TDP-43 inclusions in proteinopathies.

Testing the effects of combining azithromycin with inhaled tobramycin for P. aeruginosa in cystic fibrosis: a randomised, controlled clinical trial.

RATIONALE: Inhaled tobramycin and oral azithromycin are common chronic therapies in people with cystic fibrosis and Pseudomonas aeruginosa airway infection. Some studies have shown that azithromycin can reduce the ability of tobramycin to kill P. aeruginosa. This trial was done to test the effects of combining azithromycin with inhaled tobramycin on clinical and microbiological outcomes in people already using inhaled tobramycin. We theorised that those randomised to placebo (no azithromycin) would have greater improvement in forced expiratory volume in one second (FEV1) and greater reduction in P. aeruginosa sputum in response to tobramycin. METHODS: A 6-week prospective, randomised, placebo-controlled, double-blind trial testing oral azithromycin versus placebo combined with clinically prescribed inhaled tobramycin in individuals with cystic fibrosis and P. aeruginosa airway infection. RESULTS: Over a 6-week period, including 4 weeks of inhaled tobramycin, the relative change in FEV1 did not statistically significantly differ between groups (azithromycin (n=56) minus placebo (n=52) difference: 3.44%; 95% CI: -0.48 to 7.35; p=0.085). Differences in secondary clinical outcomes, including patient-reported symptom scores, weight and need for additional antibiotics, did not significantly differ. Among the 29 azithromycin and 35 placebo participants providing paired sputum samples, the 6-week change in P. aeruginosa density differed in favour of the placebo group (difference: 0.75 log10 CFU/mL; 95% CI: 0.03 to 1.47; p=0.043). CONCLUSIONS: Despite having greater reduction in P. aeruginosa density in participants able to provide sputum samples, participants randomised to placebo with inhaled tobramycin did not experience significantly greater improvements in lung function or other clinical outcomes compared with those randomised to azithromycin with tobramycin.

Biophysical characteristics of lipid-induced Aß oligomers correlate to distinctive phenotypes in transgenic mice.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects cognition and memory. Recent advances have helped identify many clinical sub-types in AD. Mounting evidence point toward structural polymorphism among fibrillar aggregates of amyloid-ß (Aß) to being responsible for the phenotypes and clinical manifestations. In the emerging paradigm of polymorphism and prion-like propagation of aggregates in AD, the role of low molecular weight soluble oligomers, which are long known to be the primary toxic agents, in effecting phenotypes remains inconspicuous. In this study, we present the characterization of three soluble oligomers of Aß42, namely 14LPOs, 16LPOs, and GM1Os with discreet biophysical and biochemical properties generated using lysophosphatidyl glycerols and GM1 gangliosides. The results indicate that the oligomers share some biophysical similarities but display distinctive differences with GM1Os. Unlike the other two, GM1Os were observed to be complexed with the lipid upon isolation. It also differs mainly in detection by conformation-sensitive dyes and conformation-specific antibodies, temperature and enzymatic stability, and in the ability to propagate morphologically-distinct fibrils. GM1Os also show distinguishable biochemical behavior with pronounced neuronal toxicity. Furthermore, all the oligomers induce cerebral amyloid angiopathy (CAA) and plaque burden in transgenic AD mice, which seems to be a consistent feature among all lipid-derived oligomers, but 16LPOs and GM1Os displayed significantly higher effect than the others. These results establish a correlation between molecular features of Aß42 oligomers and their distinguishable effects in transgenic AD mice attuned by lipid characteristics, and therefore help bridge the knowledge gap in understanding how oligomer conformers could elicit AD phenotypes.

Cationic Glycopolyelectrolytes for RNA Interference in Tick Cells.

The black-legged tick (Ixodes scapularis) is the primary vector for bacteria that cause Lyme disease (Borrelia burgdorferi), where numerous glycosylated tick proteins are involved at the interface of vector-host-pathogen interactions. Reducing the expression of key tick proteins, such as selenoprotein K (SelK), through RNA interference is a promising approach to reduce pathogen transmission, but efficient delivery of nucleic acids to arthropods has proven challenging. While cationic glycopolymers have been used as nonviral gene delivery vehicles in mammalian cells, their use in arthropod or insect gene transfection has not been established. In this study, statistical acrylamide-based cationic glycopolymers with glucose or galactose pendant groups were synthesized by reversible addition-fragmentation chain transfer polymerization, and the effects of the saccharide pendant group and cationic monomer loading on polymer cytotoxicity, RNA complexation, and SelK gene knockdown in ISE6 cells were evaluated. All polymers exhibited low cytotoxicity, yet RNA/copolymer complex cell uptake and gene knockdown were highly dependent on the saccharide structure and the N:P (amino to phosphate groups) ratio.

Diketoenamine-Based Vitrimers via Thiol-ene Photopolymerization.

Likened to both thermosets and thermoplastics, vitrimers are a unique class of materials that combine remarkable stability, healability, and reprocessability. Herein, this work describes a photopolymerized thiol-ene-based vitrimer that undergoes dynamic covalent exchanges through uncatalyzed transamination of enamines derived from cyclic ß-triketones, whereby the low energy barrier for exchange facilitates reprocessing and enables rapid depolymerization. Accordingly, an alkene-functionalized ß-triketone, 5,5-dimethyl-2-(pent-4-enoyl)cyclohexane-1,3-dione, is devised which is then reacted with 1,6-diaminohexane in a stoichiometrically imbalanced fashion (≈1:0.85 primary amine:triketone). The resulting networks exhibit subambient glass transition temperature (Tg = 5.66 °C) by differential scanning calorimetry. Using a Maxwell stress-relaxation fit, the topology-freezing temperature (Tv ) is calculated to be -32 °C. Small-amplitude oscillatory shear rheological analysis enables to identify a practical critical temperature above which the vitrimer can be successfully reprocessed (Tv,eff ). Via the introduction of excess primary amines, this work can readily degrade the networks into monomeric precursors, which are in turn reacted with diamines to regenerate reprocessable networks. Photopolymerization provides unique spatiotemporal control over the network topology, thereby opening the path for further investigation of vitrimer properties. As such, this work expands the toolbox of chemical upcycling of networks and enables their wider implementation.

Synthesis and Morphology of High-Molecular-Weight Polyisobutylene-Polystyrene Block Copolymers Containing Dynamic Covalent Bonds.

Incorporating dynamic covalent bonds into block copolymers provides useful molecular level information during mechanical testing, but it is currently unknown how the incorporation of these units affects the resultant polymer morphology. High-molecular-weight polyisobutylene-b-polystyrene block copolymers containing an anthracene/maleimide dynamic covalent bond are synthesized through a combination of postpolymerization modification, reversible addition-fragmentation chain-transfer polymerization, and Diels-Alder coupling. The bulk morphologies with and without dynamic covalent bond are characterized by atomic force microscopy  and small-angle X-ray scattering, which reveal a strong dependence on annealing time and casting solvent. Morphology is largely unaffected by the inclusion of the mechanophore. The high-molecular-weight polymers synthesized allow interrogation of a large range of polymer domain sizes.

Inter-Rater Reliability and Correlation of L1 Hounsfield Unit Measurements with DXA Scores.

INTRODUCTION: While prior studies have generally reported rigorous protocols using prespecified CT scanner settings for HU measurements, the present study sought to report on the correlation between DXA and HUs recorded using several CT scanners with varying sequences, simulating measurements performed in "real-world" hospital and Emergency Department (ED) settings. METHODOLOGY: Six raters performed HU measurements of trabecular bone at the L1 vertebral body for forty consecutive patients on Phillips and General Electric (GE) abdominal CT scans obtained between 2017 and 2021. Inter-rater reliability of the HU measurements and their correlations with recorded DXA-based bone assessments were determined. Correlation coefficients were calculated for the HU measurements between scanner vendors as well as for the CT HUs with each DXA measurement. RESULTS: The ICC for L1 HUs read on the Phillips and GE scanners were 0.85 and 0.82, respectively, indicating excellent agreement. The correlation coefficient for the mean HUs on the Phillips and GE scanners was 0.92, also indicating excellent correlation. For both scanner vendors, the HU values most closely correlated with the total femur and femoral neck T-scores. CONCLUSIONS: HU values recorded on a Phillips and GE scanner both demonstrated excellent inter-rater reliability. Correlations were strongest between L1 HU values and total femur DXA T-scores. Readily available abdominal CT image data across multiple hospital settings can be utilized by providers of varying level of imaging interpretation expertise to determine vertebral body Hounsfield units that may help identify osteoporosis risk without additional radiation exposure or cost.

User perspectives on systematic data collection regarding back pain managed in general practice - a qualitative study.

BACKGROUND: Back pain is a main driver of disability and the most prevalent reason why people in Demark visit a general practitioner (GP). However, little is known about back pain management in primary care. For new strategies to be sustainable and to accommodate the recommendations for evidence-based practice, patients' perspectives are paramount to complement clinical expertise and research evidence. This study aimed to identify recommendations for systematic data collection in a nationwide cohort regarding the management of back pain in general practice from the perspectives of GPs and patients. METHOD: We applied an adapted exploratory sequential design using focus groups and individual interviews. Seven GPs and ten patients with back pain participated, and four focus groups and seventeen individual interviews were conducted. Data were analyzed using abductive reasoning. RESULTS: Both GPs and patients with back pain found that 1) recruitment to a cohort should take place through the GPs, 2) the heterogeneity of patients with back pain and their need for individualized treatment and care should be considered, and 3) data from the cohort should feed into a flowchart or guideline to illustrate a generic patient pathway and visually assist both the patient and GP to obtain an overview and, thus, structure the patient pathway. CONCLUSION: GPs and patients with back pain both considered the nationwide cohort with the overall aim to investigate back pain management as being extremely relevant in relation to improve t the patient pathway. User perspectives should be explored and integrated into health care interventions.

Cortical patterning of abnormal morphometric similarity in psychosis is associated with brain expression of schizophrenia-related genes.

Schizophrenia has been conceived as a disorder of brain connectivity, but it is unclear how this network phenotype is related to the underlying genetics. We used morphometric similarity analysis of MRI data as a marker of interareal cortical connectivity in three prior case-control studies of psychosis: in total, n = 185 cases and n = 227 controls. Psychosis was associated with globally reduced morphometric similarity in all three studies. There was also a replicable pattern of case-control differences in regional morphometric similarity, which was significantly reduced in patients in frontal and temporal cortical areas but increased in parietal cortex. Using prior brain-wide gene expression data, we found that the cortical map of case-control differences in morphometric similarity was spatially correlated with cortical expression of a weighted combination of genes enriched for neurobiologically relevant ontology terms and pathways. In addition, genes that were normally overexpressed in cortical areas with reduced morphometric similarity were significantly up-regulated in three prior post mortem studies of schizophrenia. We propose that this combined analysis of neuroimaging and transcriptional data provides insight into how previously implicated genes and proteins as well as a number of unreported genes in their topological vicinity on the protein interaction network may drive structural brain network changes mediating the genetic risk of schizophrenia.