bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral and genetic markers of susceptibility to escalate fentanyl intake
Authors: Keady Jack , Charnigo Richard , Shaykin Jakob D. , Prantzalos Emily R. , Xia Mengfan , Denehy Emily , Bumgardner Cody , Miller Justin , Ortinski Pavel , Bardo Michael T. , Turner Jill R.
Published: December 2024

Background

The “loss of control” over drug consumption, present in opioid use disorder (OUD) and known as escalation of intake, is well-established in preclinical rodent models. However, little is known about how antecedent behavioral characteristics, such as valuation of hedonic reinforcers prior to drug use, may impact the trajectory of fentanyl intake over time. Moreover, it is unclear if distinct escalation phenotypes may be driven by genetic markers predictive of OUD susceptibility.

Methods

Male and female Sprague-Dawley rats (n=63) were trained in a sucrose reinforcement task using a progressive ratio schedule. Individual differences in responsivity to sucrose were hypothesized to predict escalation of fentanyl intake. Rats underwent daily 1-h acquisition sessions for i.v. fentanyl self-administration (2.5 µg/kg; FR1) for 7 days, followed by 21 6-h escalation sessions, then tissue from prefrontal cortex was collected for RNA sequencing and qPCR. Latent growth curve and group-based trajectory modeling were used, respectively, to evaluate the association between sucrose reinforcement and fentanyl self-administration and to identify whether distinct escalation phenotypes can be linked to gene expression patterns.

Results

Sucrose breakpoints were not predictive of fentanyl acquisition nor change during escalation, but did predict fentanyl intake on the first day of extended access to fentanyl. Permutation analyses did not identify associations between behavior and single gene expression when evaluated overall, or between our ascertained phenotypes. However, weighted genome correlation network analysis (WGCNA) and gene set enrichment analysis (GSEA) determined several gene modules linked to escalated fentanyl intake, including genes coding for voltage-gated potassium channels, calcium channels, and genes involved in excitatory synaptic signaling. Transcription factor analyses identified EZH2 and JARID2 as potential transcriptional regulators associated with escalated fentanyl intake. Genome-wide association study (GWAS) term categories were also generated and positively associated with terms relating to substance use disorders.

Discussion

Escalation of opioid intake is largely distinct from motivation for natural reward, such as sucrose. Further, the gene networks associated with fentanyl escalation suggest that engagement of select molecular pathways distinguish individuals with “addiction prone” behavioral endophenotypes, potentially representing druggable targets for opioid use disorder. Our extended in silico identification of SNPs and transcription factors associated with the “addiction prone” high escalating rats highlights the importance of integrating findings from translational preclinical models. Through a precision medicine approach, our results may aid in the development of patient-centered treatment options for those with OUD.
Neural mechanisms underlying the effects of cognitive fatigue on physical effort-based choice
Authors: Dryzer Michael , Chib Vikram S
Published: December 2024

Fatigue is a state of exhaustion that influences our willingness to engage in effortful tasks. While both physical and cognitive exertion can cause fatigue, there is a limited understanding of how fatigue in one exertion domain (e.g., cognitive) affects decisions to exert in another (e.g., physical). We use functional magnetic resonance imaging (fMRI) to measure brain activity while human participants make decisions to exert prospective physical effort before and after engaging in a cognitively fatiguing working memory task. Using computational modeling of choice behavior, we show that fatiguing cognitive exertion increases participants’ subjective costs of physical effort compared to a baseline rested state. We describe how signals related to fatiguing cognitive exertion in the dorsolateral prefrontal cortex influence physical effort value computations instantiated by the insula, thereby increasing an individual’s subjective valuation of prospective physical effort while cognitively fatigued. Our results support the idea of a general fatigue signal that integrates exertion-specific information to guide effort-based choice.
Using paralogs for phylogenetic inference mitigates the effects of long-branch attraction
Authors: Smith Megan L. , Hahn Matthew W.
Published: December 2024

Abstract

Traditionally, the inference of species trees has relied on orthologs, or genes related through speciation events, to the exclusion of paralogs, or genes related through duplication events. This has led to a focus on using only gene families with a single gene-copy per species, as these families are likely to be composed of orthologs. However, recent work has demonstrated that phylogenetic inference using paralogs is accurate and allows researchers to take advantage of more data. Here, we investigate a case in which using larger gene families actually increases accuracy compared to using single-copy genes alone. Long-branch attraction is a phenomenon in which taxa with long branches may be incorrectly inferred as sister taxa due to homoplasy. The most common solution to long-branch attraction is to increase taxon sampling to break up long branches. Sampling additional taxa is not always feasible, perhaps due to extinction or access to high-quality DNA. We propose the use of larger gene families with additional gene copies to break up long branches. Using simulations, we demonstrate that using larger gene families mitigates the impacts of long-branch attraction across large regions of parameter space. We also analyze data from Chelicerates, with a focus on assessing support for a sister relationship between scorpions and pseudoscorpions. Previous work has suggested that the failure to recover this relationship is due to long-branch attraction between pseudoscorpions and other lineages. Using data from larger gene families increases support for a clade uniting scorpions and pseudoscorpions, further highlighting the potential utility of these gene families in phylogenetic inference.
Goal-Directed Learning in Cortical Organoids
Authors: Robbins Ash , Schweiger Hunter E. , Hernandez Sebastian , Spaeth Alex , Voitiuk Kateryna , Parks David F. , van der Molen Tjitse , Geng Jinghui , Sharf Tal , Mostajo-Radji Mohammed A. , Haussler David , Teodorescu Mircea
Published: December 2024

Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise asin vitromodels of brain development and function. Although sensory input is vital to neurodevelopmentin vivo, few studies have explored the effect of meaningful input toin vitroneural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as ‘Cartpole’) and evaluate learning through high-frequency training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanismsin vitroopens new possibilities for therapeutic interventions and biological computation.
CrossLabFit: A Novel Framework for Integrating Qualitative and Quantitative Data Across Multiple Labs for Model Calibration
Authors: Blanco-Rodriguez Rodolfo , Miura Tanya A. , Hernandez-Vargas Esteban
Published: December 2024

The integration of computational models with experimental data is a cornerstone for gaining insight into biomedical applications. However, parameter fitting procedures often require a vast availability and frequency of data that are challenging to obtain from a single source.

Here, we present a novel methodology “CrossLabFit” designed to integrate qualitative data from multiple laboratories, overcoming the constraints of single-lab data collection. Our approach harmonizes disparate qualitative assessments—ranging from different experimental labs to categorical observations—into a unified framework for parameter estimation. By using machine learning algorithms, these qualitative constraints are represented as dynamic “qualitative windows” that capture significant trends to which models must adhere. For numerical implementation, we developed a GPU-accelerated version of differential evolution to navigate in the cost function that integrated quantitative and qualitative data.

We validate our approach across a series of case studies, demonstrating significant improvements in model accuracy and parameter identifiability. This work opens a new paradigm for collaborative science, enabling a methodological road to combine and compare findings between studies to improve our understanding of biological systems and beyond.
Simulating big mechanically-active culture systems (BigMACS) using paired biomechanics-histology FEA modelling to derive mechanobiology design relationships
Authors: Schoenborn Sabrina , Yuan Mingyang , Fell Cody A. , Liu Chuanhai , Fletcher David F. , Priola Selene , Chan Hon Fai , Woodruff Mia , Li Zhiyong , Toh Yi-Chin , Allenby Mark C.
Published: December 2024

Big mechanically-active culture systems (BigMACS) are promising to stimulate, control, and pattern cell and tissue behaviours with less soluble factor requirements, however, it remains challenging to predict if and how distributed mechanical forces impact single-cell behaviours to pattern tissue. In this study, we introduce a centimetre, tissue-scale, finite element analysis (FEA) framework able to correlate sub-cellular quantitative histology with centimetre-scale biomechanics. Our framework is relevant to diverse bigMACS; media perfusion, tensile-stress, magnetic, and pneumatic tissue culture platforms. We apply our framework to understand how the design and operation of a multi-axial soft robotic bioreactor can spatially control mesenchymal stem cell (MSC) proliferation, orientation, differentiation to smooth muscle, and extracellular vascular matrix deposition. We find MSC proliferation and matrix deposition correlate positively with mechanical stimulation but cannot be locally patterned by soft robot mechanical stimulation within a centimetre scale tissue. In contrast, local stress distribution was able to locally pattern MSC orientation and differentiation to smooth muscle phenotypes, where MSCs aligned perpendicular to principal stress direction and expressed increased α-SMA with increasing 3D Von Mises Stresses from 0 to 15 kPa. Altogether, our new biomechanical-histological simulation framework is a promising technique to derive the future mechanical design equations to control cell behaviours and engineer patterned tissue generation.
Global multi-omics analysis of exerkines in progressive treadmill-exercised rodents
Authors: Taha Hash Brown
Published: December 2024

Exercise is widely recognized for its comprehensive physiological benefits, attributed largely to the secretion of signaling molecules known as exerkines. These molecules, originating from various tissues like muscles, brain, and liver, facilitate inter-organ communication and enhance metabolic health, immune function, and tissue repair. However, the responsiveness of multiple tissues and exerkines to the same exercise regimen remains poorly understood. To address this issue and elucidate patterns of time-dependent, intensity-related and sex-dimorphic tissue and exerkine responsiveness, we leveraged the publicly available Molecular Transducers of Physical Activity Consortium (MoTrPAC) dataset. Male and female Fischer 344 rats aged 6 months underwent a progressive treadmill training protocol designed to emulate human endurance exercise. Blood (cells and plasma) and 18 solid tissues such as adipose, skeletal muscle and brain were collected and multi-omics analyses, including proteomics and transcriptomics were performed on them. We examined the distribution of 26 known and 2 speculative exerkines across 2 biofluids and 18 solid tissues. Our analysis reveals that brown adipose tissue (BAT), the adrenal gland, and white adipose tissue (WAT) are the most responsive to exercise-induced changes. Fractalkine was the most responsive exerkine, followed by prosaposin (speculative), cathepsin B, and FNDC5/irisin, platelet factor 4, Clusterin and SPARC. Additionally, we found distinct patterns in the responsiveness of tissues and exerkines based on the duration and intensity of exercise, with notable differences between male and female rodents. Future research should investigate whether our findings on tissue exerkine responsiveness vary with age and disease status, and determine if these findings can be extrapolated to human populations.
SevereGBA1variants drive the GBA-PD clinical phenotype: implications for counselling and clinical trials
Authors: Menozzi Elisa , Del Pozo Sara Lucas , Macnaughtan Jane , Mezabrovschi Roxana , Koletsi Sofia , Mitrotti Pierfrancesco , Gallo Luca , Calabrese Rosaria , Toffoli Marco , Loefflad Nadine , Valzania Franco , Cavallieri Francesco , Fioravanti Valentina , Yalkic Selen , Limbachiya Naomi , Blandini Fabio , Avenali Micol , Schapira Anthony HV
Published: December 2024

Background

Variants in theGBA1gene are the commonest genetic risk factor for Parkinson disease (PD). Genotype- phenotype correlations exist but with conflicting data, particularly in the cognitive domain.

Objectives

Comparing clinical phenotypes in a multicentre, international cohort incorporating GBA-PD and idiopathic PD (iPD) patients.

Methods

Patients underwent a comprehensive assessment of motor and non-motor functions. Two-group (GBA- PD vs iPD) and multiple-group comparisons (iPD, risk, mild, and severe variant GBA-PD) were performed.

Results

Three hundred eleven PD patients were recruited: 183 iPD, 39 severe GBA-PD, 24 mild GBA-PD, 55 risk GBA-PD, and 10 patients carrying variants of unknown significance. Groups were matched for sex, education, disease duration and medications. Mild and severe GBA-PD were younger and developed PD earlier. Severe GBA-PD had worse depression, cognitive impairment, hyposmia, and motor complications.

Conclusions

Only severe variant GBA-PD have a distinctive, more severe clinical profile.
HP1 binding creates a local barrier against transcription activation and persists during chromatin decondensation
Authors: Weinmann Robin , Udupa Arjun , Nickels Jan Fabio , Frank Lukas , Knotz Caroline , Rippe Karsten
Published: December 2024

Mouse pericentric repeats form transcriptionally silent and compacted domains known as chromocenters. These prototypic heterochromatin compartments are marked by heterochromatin protein 1 (HP1). However, its contributions to chromocenter structure and function remain debated. We investigated the role of HP1α by recruiting the activators VP16, p65, and VPR to mouse fibroblast chromocenters and analyzed its silencing activity with a transcription reporter. Upon chromocenter decondensation and transcription activation, interactions of HP1α with chromatin and H3K9 trimethylation remained stable, suggesting stoichiometric binding rather than higher-order assembly. HP1α-mediated repression required promoter-proximal binding and effectively suppressed VP16-triggered activation but not the stronger activation by VPR. These observations are explained by a 1D lattice binding model, which conceptualizes chromocenters as arrays of repeat units that can independently switch between silenced and activated states. Our findings provide a quantitative framework that explains how chromocenter organization responds to transcriptional activation while maintaining local heterochromatin features.

GRAPHICAL ABSTRACT

HIGHLIGHTS

HP1α represses transcription at mouse chromocenters and an ectopic reporter when competing with transcriptional activators VP16, p65 and VPR

HP1α repression requires promoter-proximal binding and effectively counteracts the weak activator VP16

The strong activator VPR overcomes HP1α-mediated repression while HP1α remains bound to chromatin

HP1α binding and H3K9me3 persist during chromocenter decondensation and transcriptional activation

A 1D lattice binding model explains how independent repeat units transition between silenced and activated states without requiring phase separation
A haplotype-resolved chromosomal reference genome for the porcini mushroomBoletus edulis
Authors: Lamartinière Etienne Brejon , Tremble Keaton , Dentinger Bryn T.M. , Dasmahapatra Kanchon K. , Hoffman Joseph I.
Published: December 2024

Haplotype-resolved chromosomal reference genomes are increasingly available for many fungi, offering insights into the evolution of pathogenic and symbiotic lifestyles. However, these resources remain scarce for ectomycorrhizal fungi (EMF), which play crucial roles in forest ecosystems. Here, we used a combination of chromatin conformation capture (Hi-C) and PacBio sequencing to construct a haplotype-resolved chromosomal genome assembly forBoletus edulis, an emerging model for EMF research and a prized edible fungus. Our new reference assembly, “BolEdBiel_h2”, derives from a sporocarp sampled in Bielefeld, Germany. The genome assembly spans 41.8 Mb, with a scaffold N50 of 4.1 Mb, and includes 11 chromosome-level scaffolds, achieving near telomere-to-telomere coverage across multiple chromosomes. We annotated 15,406 genes, with a Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 96.2%. Key genomic features such as mating loci, CAZymes, and effector proteins, were mapped across the assembly. As a first application of this new genomic resource, we mapped whole genome resequencing data from 49 genets to investigate the population structure and genetic diversity of the European lineage ofB. edulis. We identified five distinct genetic clusters and found that high-latitude populations from Iceland and Fennoscandia exhibited greater nucleotide diversity than populations from the United Kingdom and central Europe. Additionally, we discovered a 0.4 Mb inversion on chromosome three and identified several regions of locally elevated nucleotide diversity, which may represent candidates for ecological adaptation. This genomic resource will facilitate a deeper understanding of this ecologically and commercially important wild fungus.
Histone H3 tail modifications required for meiosis inSaccharomyces cerevisiae
Authors: Prichard Amy , Johansson Marnie , Kirkpatrick David T. , Clarke Duncan J.
Published: December 2024

Histone tail phosphorylation has diverse effects on a myriad of cellular processes, including cell division, and is highly conserved throughout eukaryotes. Histone H3 phosphorylation at threonine 3 (H3T3) during mitosis occurs at the inner centromeres and is required for proper biorientation of chromosomes on the mitotic spindle. While H3T3 is also phosphorylated during meiosis, a possible role for this modification has not been tested. Here, we asked if H3T3 phosphorylation (H3T3ph) is important for meiotic division by quantifying sporulation efficiency and spore viability inSaccharomyces cerevisiaemutants with a T3A amino acid substitution. The T3A substitution resulted in greatly reduced sporulation efficiency and reduced spore viability. Analysis of two other H3 tail mutants, K4A and S10A, revealed different effects on sporulation efficiency and spore viability compared to the T3A mutant, suggesting that these phenotypes are due to failures in distinct functions. To determine if the spindle checkpoint promotes spore viability of the T3A mutant, theMAD2gene required for the spindle assembly checkpoint was deleted to abolish spindle assembly checkpoint function. This resulted in a severe reduction in spore viability following meiosis. Altogether, the data reveal a critical function for histone H3 threonine 3 that requires monitoring by the spindle checkpoint to ensure successful completion of meiosis.
Extracorporeal shock wave therapy for erectile dysfunction: rethinking study design, implementation, and analysis
Authors: Desai Janak , Huyghe Eric , Maffulli Gayle D. , Nussbaum-Krammer Carmen , Tittelmeier Jessica , Schmitz Christoph
Published: December 2024

Introduction

Extracorporeal shock wave therapy (ESWT) for erectile dysfunction (ED) presents a challenging paradox. While numerous clinical studies, systematic reviews, and meta-analyses have been published, indicating a substantial body of evidence supporting the efficacy and safety of ESWT, significant questions remain. Notably, the American Urological Association (AUA) continues to classify ESWT for ED as investigational (Evidence Level: Grade C), suggesting that the true therapeutic effect o f ESWT may differ considerably from current estimates. This review aims to critically assess the evidence and propose strategies to address this unresolved discrepancy.

Data sources

We systematically searched two electronic databases (PubMed and Ovid/Embase) and published systematic reviews on ESWT for ED and compiled a systematic literature review and meta-analysis based on 87 relevant studies.

Areas of agreement

There is clear evidence that ESWT for ED is effective and can therefore be a valuable treatment modality in the management of ED.

Areas of controversy

Current assessments of ESWT for ED as investigational by, e.g., the AUA may not stem from a lack of clinical studies, insufficient related basic science, or an inadequate number of systematic reviews and meta-analyses. Instead, the deficits lie in the area of the scientific quality of the clinical studies published to date.

Growing points

We hypothesize that this unfortunate situation will only change if the following aspects will be rigorously considered in future clinical studies on ESWT for ED: adequate characterization and reporting of extracorporeal shock waves, appropriate handling of missing data and intercurrent events, and comprehensive classification of ESWT in the overall context of the available treatment options for ED.

Areas for developing research

We are convinced that the consistent implementation of these aspects will significantly contribute to establishing ESWT as the first truly regenerative therapy in the management of ED. This overall aim justifies the corresponding efforts, for the benefit of our patients.
ACCURACY OF COMPUTER-ASSISTED DETECTION IN SCREENING PEOPLE WITH DIABETES MELLITUS FOR ACTIVE TUBERCULOSIS: A SYSTEMATIC REVIEW
Authors: Reagan Emoru Daniel , Mrema Lucy Elauteri , Ntinginya Nyanda Elias , Biraro Irene Andia , van Crevel Reinout , Critchley Julia A
Published: December 2024

Objectives

Diabetes mellitus (DM) significantly increases the risk of tuberculosis (TB), and active TB screening of people with DM has been advocated. This systematic review aimed to evaluate the accuracy of computer-assisted detection (CAD) for identifying pulmonary TB among people living with DM.

Methods

Medline, Embase, Scopus, Global Health and Web of science were searched from January 2010 to May 2024 supplemented with grey literature (Conference abstracts, Trial registries,MedRxiv.org). Studies evaluating CAD accuracy for identifying TB in populations living with diabetes were included. Two researchers independently assessed titles, abstracts, full texts, extracted data and assessed the risk of bias. Due to heterogeneity and a limited number of studies, a descriptive analysis was performed instead of statistical pooling. Forest plot and Summary Receiver Operating Curves (SROC) were generated using RevMan 5.4.

Results

Five eligible studies, all conducted in Asia between 2013 and 2023 were identified, including a total of 1879 individuals of whom 391 were diagnosed with TB. Four different Computer Assisted Detection (CAD) software algorithms were used. Sensitivities ranged from 0.73 (95%CI: 0.61-0.83) to 1.00 (95%CI:0.59-1.00), while specificities ranged from 0.60 (95%CI:0.53-0.67) to 0.88 (95%CI: 0.84-0.91). Area Under the receiver Operating Curve (AUC) values varied from 0.7 (95%CI: 0.68-0.75) to 0.9(95%CI: 0.91-0.96). False positive rates ranged from 0.24% to 30.5%, while false negative rates were 0-3.2%. The risk of bias assessment of the five studies was generally good to excellent.

Conclusions

CAD tools show promise in screening people living with diabetes for active TB, but data are scarce, and performance varies across settings.
Return-to-work for People Living with Long COVID: A Scoping Review of Interventions and Recommendations
Authors: Nagra Gagan , Ezeugwu Victor E. , Bostick Geoff P. , Branton Erin , Dennett Liz , Drake Kevin , Durand-Moreau Quentin , Guptill Christine , Hall Mark , Ho Chester , Hung Pam , Khan Aiza , Lam Grace Y. , Nowrouzi-Kia Behdin , Gross Douglas
Published: December 2024

Introduction

Long COVID affects individuals’ labour market participation in many ways. While some cannot work at all, others may return to work (RTW) in a limited capacity. Determining what rehabilitation or related strategies are safe and effective for facilitating RTW is necessary.

Objectives

To synthesize evidence on RTW interventions for people living with Long COVID and to identify ‘promising’ interventions for enhancing work ability and RTW.

Methods

We followed Arksey & O’Malley’s methodology and the PRISMA extension for scoping reviews. Five electronic bibliographic databases and grey literature were searched. The included various study designs, such as randomized controlled trials (RCT), quasi-experimental designs, and observational studies. Two reviewers conducted screening and data extraction, with disagreements resolved through consensus. Intervention studies were categorized as promising (statistically significant RTW outcomes or ≥ 50% RTW), somewhat promising (20% to < 50% RTW), or not promising (non-statistically significant RTW outcomes or < 20% RTW).

Results

Eleven recommendations and eleven intervention studies were identified. Of the intervention studies, 6 were cohort studies, 3 quasi-experimental studies, 1 RCT and 1 case report. Promising interventions included multimodal and interdisciplinary work-focused rehabilitation (1 article), psychoeducation, pacing, and breathing strategies (2 articles), shifting focus from symptom monitoring to optimizing functional outcomes (1 article), and enhanced external CounterPulsation (EECP) inflatable pressure to improve blood flow (1 article).

Conclusion

Many uncertainties remain regarding which RTW interventions are effective or the optimal characteristics of these interventions.
Accelerating the pace and accuracy of systematic reviews using AI: a validation study
Authors: Zhan Jiada , Suvada Kara , Xu Muwu , Tian Wenya , Cara Kelly C. , Wallace Taylor C. , Ali Mohammed K.
Published: December 2024

Background

Artificial intelligence (AI) can greatly enhance efficiency in systematic literature reviews and meta-analyses, but its accuracy in screening titles/abstracts and full-text articles is uncertain.

Objectives

This study evaluated the performance metrics (sensitivity, specificity) of a GPT-4 AI program, Review Copilot, against human decisions (gold standard) in screening titles/abstracts and full-text articles from four published systematic reviews/meta-analyses.

Research Design

Participant data from four already-published systematic literature reviews were used for this validation study. This was a study comparing Review Copilot to human decision-making (gold standard) in screening titles/abstracts and full-text articles for systematic reviews/meta-analyses. The four studies that were used in this study included observational studies and randomized control trials. Review Copilot operates on the OpenAI, GPT-4 server. We examined the performance metrics of Review Copilot to include and exclude titles/abstracts and full-text articles as compared to human decisions in four systematic reviews/meta-analyses. Sensitivity, specificity, and balanced accuracy of title/abstract and full-text screening were compared between Review Copilot and human decisions.

Results

Review Copilot’s sensitivity and specificity for title/abstract screening were 99.2% and 83.6%, respectively, and 97.6% and 47.4% for full-text screening. The average agreement between two runs was 95.4%, with a kappa statistic of 0.83. Review Copilot screened in one-quarter of the time compared to humans.

Conclusions

AI use in systematic reviews and meta-analyses is inevitable. Health researchers must understand these technologies’ strengths and limitations to ethically leverage them for research efficiency and evidence-based decision-making in health.
Using routinely-collected, linked data to measure and monitor health system performance in Australia: development of an indicator of continuity of primary health care
Authors: Welsh Jennifer , Soga Kay , Robinson Rachel Freeman , Butler Danielle , Eddowes Rachael , Yazidjoglou Amelia , Douglas Angus , Douglas Kirsty , Lazarevic Nina , Law Hsei-Di , Joshy Grace , Trevenar Sue , Tsheten Tsheten , Webster Adrian , Frost Michael , Cropper Bernice , Dykgraaf Sally Hall , Phillips Christine , Banks Emily , Korda Rosemary J
Published: December 2024

Objective

To examine a potential new Australian health system indicator—continuity of care (CoC) in general practice—derived from whole-of-population linked administrative data.

Methods

Using data from Census 2016 and 2021 and the Medicare Benefits Schedule, available via the Person-Level Integrated Data Asset (PLIDA), we examined an indicator of CoC in general practice, the Usual Provider Index (UPI), over eight overlapping 2-year periods (2016-17 to 2022-23), and the 2-year period following the introduction of universal telehealth in April 2020). We measured population coverage of the UPI, sociodemographic- and health-related variation in high COC (UPI≥0.7), and changes in CoC over time.

Results

Population coverage of the UPI was high (>75%); higher for groups with greater healthcare needs, including older people and people with chronic conditions. Coverage decreased with increasing remoteness. In 2022-23, 36% of those with a UPI score had high CoC; proportions with high CoC were greater for older people, those born overseas, not proficient in English, and with health conditions, but lower for people living in more remote areas. Prior to 2020, 32-33% of the population had high CoC, increasing to 39% in the 2-year period directly following the introduction of universal telehealth.

Conclusion

When derived from whole-of population linked administrative data, the UPI is a suitable indicator of CoC for people with varying healthcare needs, and across different settings. Using new national data assets, the UPI could be included in routine health system reporting as one indicator of quality of care.

Online Short Summary

What is known?

Health system performance monitoring aims to facilitate health system planning and improvement. Whole-of-population linked administrative data may be used to extend current health system indicators in Australia.

What this paper adds?

We examined a potential new indicator—continuity of care within general practice—by assessing coverage and sensitivity to differences between groups and over time. Coverage was high, those with greater healthcare need had higher continuity, and continuity increased after the introduction of telehealth.

What are the implications?

New national data assets can be used to derive health system indicators, enhancing insight into Australian healthcare.
Selective Targeting of a Defined Subpopulation of Corticospinal Neurons using a Novel Klhl14-Cre Mouse Line Enables Molecular and Anatomical Investigations through Development into Maturity
Authors: Lustig Jake , Lammers Alexander , Kaiser Julia , Patel Payal , Raghu Aidan , Conner James M. , Nguyen Phong , Azim Eiman , Sahni Vibhu
Published: December 2024

The corticospinal tract (CST) facilitates skilled, precise movements, which necessitates that subcerebral projection neurons (SCPN) establish segmentally specific connectivity with brainstem and spinal circuits. Developmental molecular delineation enables prospective identification of corticospinal neurons (CSN) projecting to thoraco-lumbar spinal segments; however, it remains unclear whether other SCPN subpopulations in developing sensorimotor cortex can be prospectively identified in this manner. Such molecular tools could enable investigations of SCPN circuitry with precision and specificity. During development, Kelch-like 14 (Klhl14) is specifically expressed by a specific SCPN subpopulation, CSNBC-lat, that reside in lateral sensorimotor cortex with axonal projections exclusively to bulbar-cervical targets. In this study, we generated Klhl14-T2A-Cre knock-in mice to investigate SCPN that areKlhl14+during development into maturity. Using conditional anterograde and retrograde labeling, we find that Klhl14-Cre is specifically expressed by CSNBC-latonly at specific developmental time points. We establish conditional viral labeling in Klhl14-T2A-Cre mice as a new approach to reliably investigate CSNBC-lataxon targeting and confirm that this identifies known molecular regulators of CSN axon targeting. Therefore, Klhl14-T2A-Cre mice can be used as a novel tool for identifying molecular regulators of CST axon guidance in a relatively high-throughput mannerin vivo. Finally, we demonstrate that intersectional viral labeling enables precise targeting of only Klhl14-Cre+ CSNBC-latin the adult central nervous system. Together, our results establish that developmental molecular delineation of SCPN subpopulations can be used to selectively and specifically investigate their development, as well as anatomical and functional organization into maturity.

Significance Statement

The cortex connects to brainstem and spinal targets through subcerebral projection neurons (SCPN), which exhibit molecular diversity during development based on their neocortical location and axonal targets. We generated a novel Klhl14-Cre mouse line to utilize this developmental delineation and drive Cre expression in a specific SCPN subpopulation. This developmental specificity enabled investigation of 1) areal locations of Klhl14+ SCPN in mature cortex, 2) their axonal collateralization at maturity, and 3) which genes can control their axon targeting. Using intersectional tools, we can also selectively label these neurons in the adult CNS. Therefore, developmental molecular delineation of SCPN not only provides prospective identification but also enables molecular analysis during development, as well as anatomical and functional investigations in adulthood.
Intrinsic multiplication rate variation of Plasmodium falciparum in clinical isolates prior to elimination in Malaysia
Authors: Stewart Lindsay B. , Lantero Escolar Elena , Philpott James , Cox-Singh Janet , Singh Balbir , Conway David J.
Published: December 2024

Replication rates and virulence of pathogens are hypothesised to evolve in response to varying intensity of transmission and competition among genotypes. Under exponential growth conditions in culture, clinical isolates of the malaria parasitePlasmodium falciparumhave variable intrinsic multiplication rates, but comparisons of samples from different areas are needed. To analyse parasites from an area of low endemicity, Malaysian clinical isolates cryopreserved prior to malaria elimination were studied. The mean and range ofP. falciparummultiplication rates in Malaysian isolates was no less than that seen among isolates from more highly endemic populations in Africa, which does not support a hypothesis of adaptation to prevailing levels of infection endemicity. Moreover, the distribution of multiplication rates was similar between isolates with single parasite genotypes and those containing multiple genotypes, which does not support a hypothesis of facultative adjustment to competing parasites. Based on clinical isolates, the findings indicate that parasites may not evolve lower multiplication rates under conditions of reduced transmission, and that the virulence potential is likely to be undiminished in pre-elimination settings. This encourages efforts to eliminate endemic infection completely, as has been achieved at the national level in Malaysia.
Spatially resolved rewiring of mitochondria-lipid droplet interactions in hepatic lipid homeostasis
Authors: Kang Sun Woo Sophie , Brown Lauryn A , Miller Colin B , Barrows Katherine M , Golino Jihye L , Cultraro Constance M , Feliciano Daniel , Cornelius-Muwanuzi Mercedes B. , Tran Andy D , Kruhlak Michael , Lobanov Alexei , Cam Maggie , Porat-Shliom Natalie
Published: December 2024

Hepatic lipid accumulation, or Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD), is a significant risk factor for liver cancer. Despite the rising incidence of MASLD, the underlying mechanisms of steatosis and lipotoxicity remain poorly understood. Interestingly, lipid accumulation also occurs during fasting, driven by the mobilization of adipose tissue-derived fatty acids into the liver. However, how hepatocytes adapt to increased lipid flux during nutrient deprivation and what occurs differently in MASLD is not known. To investigate the differences in lipid handling in response to nutrient deficiency and excess, we developed a novel single-cell tissue imaging (scPhenomics) technique coupled with spatial proteomics. Our investigation revealed extensive remodeling of lipid droplet (LD) and mitochondrial topology in response to dietary conditions. Notably, fasted mice exhibited extensive mitochondria-LD interactions, which were rarely observed in Western Diet (WD)-fed mice. Spatial proteomics showed an increase in PLIN5 expression, a known mediator of LD-mitochondria interaction, in response to fasting. To examine the functional role of mitochondria-LD interaction on lipid handling, we overexpressed PLIN5 variants. We found that the phosphorylation state of PLIN5 impacts its capacity to form mitochondria-LD contact sites. PLIN5 S155A promoted extensive organelle interactions, triglyceride (TG) synthesis, and LD expansion in mice fed a control diet. Conversely, PLIN5 S155E expressing cells had fewer LDs and contact sites and contained less TG. Wild-type (WT) PLIN5 overexpression in WD-fed mice reduced steatosis and improved redox state despite continued WD consumption. These findings highlight the importance of organelle interactions in lipid metabolism, revealing a critical mechanism by which hepatocytes maintain homeostasis during metabolic stress. Our study underscores the potential utility of targeting mitochondria-LD interactions for therapeutic intervention.
Counting rare Wolbachia endosymbionts using digital droplet PCR
Authors: Njogu Alphaxand K , Logozzo Francesca , Conner William R. , Shropshire J. Dylan
Published: December 2024

Wolbachia is the most widespread animal-associated intracellular microbe, living within the cells of over half of insect species. Since they can suppress pathogen replication and spread rapidly through insect populations, Wolbachia is at the vanguard of public health initiatives to control mosquito-borne diseases. Wolbachia's abilities to block pathogens and spread quickly are closely linked to their abundance in host tissues. The most common method for counting Wolbachia is quantitative polymerase chain reaction (qPCR), yet qPCR can be insufficient to count rare Wolbachia, necessitating tissue pooling and consequently compromising individual-level resolution of Wolbachia dynamics. Digital droplet PCR (ddPCR) offers superior sensitivity, enabling the detection of rare targets and eliminating the need for sample pooling. Here, we report three ddPCR assays to measure total Wolbachia abundance, Wolbachia abundance adjusted for DNA extraction efficiency, and Wolbachia density relative to host genome copies. Using Drosophila melanogaster with wMel Wolbachia as a model, we show these ddPCR assays can reliably detect as few as 7 to 12 Wolbachia gene copies in a 20 μL reaction. The designed oligos are homologous to sequences from at least 106 Wolbachia strains across Supergroup A and 53 host species from the Drosophila, Scaptomyza, and Zaprionus genera, suggesting broad utility. These highly sensitive ddPCR assays are expected to significantly advance Wolbachia-host interactions research by enabling the collection of molecular data from individual insect tissues. Their ability to detect rare Wolbachia will be especially valuable in applied and natural field settings where pooling samples could obscure important variation.
Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate
Authors: Velando Félix , Xing Jiawei , Genova Roberta , Cerna-Vargas Jean Paul , Santiago Raquel Vázquez- , Matilla Miguel A. , Zhulin Igor B. , Krell Tino
Published: December 2024

Plant pathogens and plant-associated bacteria contain about twice as many chemoreceptors as the bacterial average, indicating that chemotaxis is particularly important for bacteria-plant interactions. However, information on the corresponding chemoreceptors is limited. In this study, we identified the chemoreceptor PacP from the phytopathogenPectobacterium atrosepticum, which exclusively recognized C3 phosphorylated compounds at its sCache ligand binding domain, mediating chemoattraction. Using a motif of PacP amino acid residues involved in ligand binding, we identified a chemoreceptor family, termed sCache_PC3, that was specific for C3 phosphorylated compounds. Isothermal titration calorimetry studies revealed that family members preferentially bound glycerol 3-phosphate, a key plant signaling molecule. Additionally, family members recognized glycerol 2-phosphate and glycolysis intermediates glyceraldehyde 3-phosphate, dihydroxyacetone phosphate and 3-phosphoglycerate. This study presents the first evidence of chemoreceptors that bind phosphorylated compounds. We show that the sCache_PC3 family has evolved from an ancestral sCache domain that respond primarily to Krebs cycle intermediates. Members of the sCache_PC3 family were mainly found in bacteria that interact with plants, including many important plant pathogens such asBrenneria, Dickeya, Musicola, Pectobacterium,andHerbaspirillum. Glycerol 3-phosphate is a signal molecule that is excreted by plants in response to stress and infection. Chemotaxis towards this molecule may thus be a means for bacteria to localize stressed plants and move to infection sites. This study lays the groundwork for investigating the functional importance of chemotaxis to phosphorylated C3 compounds in plant-bacteria interactions and virulence.

Significance statement

The bacterial lifestyle has shaped the evolution of signal transduction systems, and the number and type of chemoreceptors varies greatly between bacteria occupying various ecological niches. Our understanding of the relationship between lifestyle and chemoreceptor function is limited and the discovery of a chemoreceptor family in plant-associated bacteria that primarily responds to an important plant signal molecule is a significant advancement, allowing for further studies to determine its physiological relevance. The lack of knowledge about signals recognized by bacterial receptors is currently a major challenge in microbiology. This study illustrates the potential of combining experimental ligand screening with computational ligand prediction to identify signals recognized by uncharacterized receptors.
Enhancer lncRNA LOC730338 limits the innate immune response against lymphoma cells, inhibiting ADAR2-dependent alternative transcription
Authors: Cascione Luciano , Guidetti Francesca , Ramnarayanan Sunandini , Rinaldi Andrea , Spriano Filippo , Zadro Alex , Tarantelli Chiara , Munz Nicolas , Arribas Alberto J. , Johnson Rory , Bertoni Francesco , Napoli Sara
Published: December 2024

Chronic antigenic stimulation is central to marginal zone lymphoma (MZL) development. While the pharmacological inhibition of the B-cell receptor (BCR) signaling is initially effective, secondary resistance frequently develops. We conducted a CRISPR interference (CRISPRi) screen investigating enhancer-associated long non-coding RNAs (elncRNAs) in MZL cells to identify transcripts crucial to shape their dependence on BCR pathway activation. We identified LOC730338, an elncRNA associated with A-to-I RNA editing, which we renamed ADARreg. Silencing ADARreg re-sensitized tumor cells to BCR pathway inhibition by modulating ADAR2 nuclear translocation and altering intronic RNA editing. The process preferentially affected genes that enhance immune responses, such as STING, IRF3, and p65. ADARreg knockdown also increased lymphoma cell sensitivity to NK cell-mediated cytotoxicity. Our results indicate that targeting elncRNAs like ADARreg represents a potential strategy to overcome drug resistance in lymphoma, also opening new therapeutic opportunities for immunotherapy.
Activation of the ChvG-ChvI pathway promotes multiple survival strategies during cell wall stress inAgrobacterium tumefaciens
Authors: Bouchier Jacob M. , Knebel Emily , Amstutz Jennifer , Torrens Gabriel , Santiago-Collazo Gustavo , McCurry Carli , Weisberg Alexandra J. , Cava Felipe , Brown Pamela J.B.
Published: December 2024

Agrobacterium tumefaciensshifts from a free-living soil bacterium to a plant-invading state upon encountering the plant root microenvironment. The acid-induced two- component sensor system ChvG-ChvI drives this shift and triggers a complex transcriptional program that promotes host invasion and survival against host immune defenses. Remarkably, ChvG-ChvI is also activated under cell wall stress conditions suggesting that the transcriptional response may have a broader function. Here, we find that blocking cell wall synthesis either genetically or chemically leads to ChvG-ChvI activation. Mutations in key cell wall synthesis or outer membrane proteins, such as PBP1a, FtsW, and AopA1, suppress ChvG-ChvI activation suggesting that providing structural integrity is a primary function of the ChvG-ChvI regulon. Here, we investigated regulon components for this function. First, the exopolysaccharide succinoglycan confers tolerance to multiple β-lactam antibiotics targeting different enzymes by forming a protective barrier around the cells. Next, a Class D β-lactamase is expressed which may contribute to the high level of β-lactam resistance inA. tumefaciens. Finally, outer membrane remodeling compensates for the accumulation of cell wall damage by providing structural integrity. Overall, we expand our understanding of mechanisms driving ChvG-ChvI activation and β-lactam resistance in a bacterial plant pathogen.

Significance Statements.

Activation of the ChvG-ChvI two component system promotes survival when the bacterial cell walls are damaged by a variety of genetic or chemical approaches

The ChvG-ChvI dependent production of the exopolysaccharide succinoglycan, β-lactamase Cbl activity, and outer membrane proteome remodeling all contribute to survival in the presence of β-lactam antibiotics

Improved understanding of bacterial stress responses that promote antibiotic tolerance and resistance has the potential to inform development of novel drug targets