bluuebunny/crossref_metadata_2025 huggingface dataset:
Eltonian niche modelling: applying joint hierarchical niche models to ecological networks
Authors: Dehling D. Matthias , Lai Hao Ran , Stouffer Daniel B.
Published: August 2024

There is currently a dichotomy in the modelling of Grinnellian vs. Eltonian niches. Despite similar underlying data, Grinnellian niches are commonly modelled with species-distribution models (SDMs), Eltonian niches are modelled with ecological-network analysis. This separation stems from the much sparser data on species interactions, which has prevented the application of SDMs to Eltonian niches. Recently developed joint hierarchical niche models (JHNMs), however, overcome sparsity and improve predictions for individual species by considering non-independent relationships among co-occurring species. This unique ability makes JHNMs particularly suited for sparse datasets, such as ecological networks. Here, we propose to apply JHNMs to data on ecological networks, functional traits, and phylogenies to model species' Eltonian niches and exemplify the approach for frugivorous birds. Moreover, we demonstrate that JHNMs can even be used to predict interactions of species for which no empirical interaction data are available--solely based on their functional traits. This facilitates the prediction of new interactions in communities with altered composition, e.g. following climate-change induced local extinctions or species introductions. The high interpretability of our Eltonian JHNMs will provide unique insights into the mechanisms underlying species interactions and the potential impact of environmental changes and invasive species on species interactions in ecological communities.
National consensus statement on opioid agonist treatment in custodial settings
Authors: Chan Jocelyn , Cook Jon , Curtis Michael , Dunlop Adrian , Morrison Ele , Nielsen Suzanne , Winter Rebecca , Naren Thileepan
Published: August 2024

Introduction

Opioid use and dependence are prevalent among incarcerated people, contributing to elevated rates of overdose and other harms in this population. Opioid agonist treatment (OAT) has been demonstrated as an effective intervention to mitigate these risks. However, challenges to health care implementation in the custodial sector result in suboptimal and variable access to OAT in prisons nationally.

Main recommendations

Among a national multi-disciplinary expert panel, we conducted a modified Delphi study which yielded 19 recommendations to government, relevant health authorities and custodial health services. These recommendations cover five core domains: induction or continuation of OAT, OAT options and administration, transition of care to the community, special populations, organisational support. Key recommendations include prompt recognition and treatment of opioid withdrawal, active linkage to community-based OAT providers upon release, and ensuring appropriate organisational support through local protocols, adequate funding, and monitoring of key program indicators.

Changes in management as a result of this statement

This consensus statement addresses a significant gap in national policy on OAT in Australian prisons. The recommendations set forth best practice standards grounded in evidence and expert consensus. We expect that implementing these recommendations will enhance the quality, consistency, and continuity of OAT both within prison and upon release. Optimizing OAT provision is crucial for improving health outcomes and addressing overdose, which is the leading cause of death among people released from prison.
Generative artificial intelligence models in clinical infectious disease consultations: a cross-sectional analysis among specialists and resident trainees
Authors: Chiu Edwin Kwan-Yeung , Sridhar Siddharth , Wong Samson Sai-Yin , Tam Anthony Raymond , Choi Ming-Hong , Lau Alicia Wing-Tung , Wong Wai-Ching , Chiu Kelvin Hei-Yeung , Ng Yuey-Zhun , Yuen Kwok-Yung , Chung Tom Wai-Hin
Published: August 2024

Background

The potential of generative artificial intelligence (GenAI) to augment clinical consultation services in clinical microbiology and infectious diseases (ID) is being evaluated.

Methods

This cross-sectional study evaluated the performance of four GenAI chatbots (GPT-4.0, a Custom Chatbot based on GPT-4.0, Gemini Pro, and Claude 2) by analysing 40 unique clinical scenarios synthesised from real-life clinical notes. Six specialists and resident trainees from clinical microbiology or ID units conducted randomised, blinded evaluations across four key domains: factual consistency, comprehensiveness, coherence, and medical harmfulness.

Results

Analysis of 960 human evaluation entries by six clinicians, covering 160 AI-generated responses, showed that GPT-4.0 produced longer responses than Gemini Pro (p<0·001) and Claude 2 (p<0·001), averaging 577 ± 81·19 words. GPT-4.0 achieved significantly higher mean composite scores compared to Gemini Pro [mean difference (MD)=0·2313, p=0·001] and Claude 2 (MD=0·2021, p=0·006). Specifically, GPT-4.0 outperformed Gemini Pro and Claude 2 in factual consistency (Gemini Pro, p=0·02 Claude 2, p=0·02), comprehensiveness (Gemini Pro, p=0·04; Claude 2, p=0·03), and the absence of medical harm (Gemini Pro, p=0·02; Claude 2, p=0·04). Within-group comparisons showed that specialists consistently awarded higher ratings than resident trainees across all assessed domains (p<0·001) and overall composite scores (p<0·001). Specialists were 9 times more likely to recognise responses with "Fully verified facts" and 5 times more likely to consider responses as "Harmless". However, post-hoc analysis revealed that specialists may inadvertently disregard conflicting or inaccurate information in their assessments, thereby erroneously assigning higher scores.

Interpretation

Clinical experience and domain expertise of individual clinicians significantly shaped the interpretation of AI-generated responses. In our analysis, we have demonstrated disconcerting human vulnerabilities in safeguarding against potentially harmful outputs. This fallibility seemed to be most apparent among experienced specialists and domain experts, revealing an unsettling paradox in the human evaluation and oversight of advanced AI systems. Stakeholders and developers must strive to control and mitigate user-specific and cognitive biases, thereby maximising the clinical impact and utility of AI technologies in healthcare delivery.
Using VR and eye-tracking to study attention to and retention of AI-generated ads in outdoor advertising environments
Authors: Lim Sue , Cho Hee Jung , Jeon Moonsun (Sunny) , Cui Xiaoran , Schmaelzle Ralf
Published: August 2024

In contemporary urban environments, advertisements are ubiquitous, capturing the attention of individuals navigating through cityscapes. This study simulates this situation by using VR as an advertising research tool and combining it with eye-tracking to rigorously assess attention to and retention of visual advertisements. Specifically, participants drove through a virtual city with 40 AI-generated, experimentally manipulated, and randomly assigned advertisements (20 commercial, 20 health) distributed throughout. Our results confirm theoretical predictions about the link between exposure, visual attention, and incidental memory. Specifically, we found that attended ads are likely to be recalled and recognized, and concurrent task demands (counting sales signs) decreased visual attention and subsequent recall and recognition of the ads. Finally, we identify the influence of ad placement in the city as a very important but previously hard-to-study factor influencing advertising effects. This paradigm offers great flexibility for biometric advertising research and can be adapted to varying contexts, including highways, airports, and subway stations, and theoretically manipulate other variables. Moreover, considering the metaverse as a next-generation advertising environment, our work demonstrates how causal mechanisms can be identified in ways that are of equally high interest to both theoretical as well as applied advertising research.
The turbulent soundscape of intertidal oyster reefs
Authors: Volaric Martin P. , Stine Eli M. , Burtner Matthew , Andrews Steven S. , Berg Peter , Reidenbach Matthew A.
Published: August 2024

Turbulence and sound are important cues for oyster reef larval recruitment. Numerous studies have found a relationship between turbulence intensity and swimming behaviors of marine larvae, while others have documented the importance of sounds in enhancing larval recruitment to oyster reefs. However, the relationship between turbulence and the reef soundscape is not well understood. In this study we made side-by-side acoustic Doppler velocimeter turbulence measurements and hydrophone soundscape recordings over 2 intertidal oyster reefs (1 natural and 1 restored) and 1 adjacent bare mudflat as a reference. Sound pressure levels (SPL) were similar across all three sites, although SPL > 2000 Hz was highest at the restored reef, likely due to its larger area that contained a greater number of sound-producing organisms. Flow noise (FN), defined as the mean of pressure fluctuations recorded by the hydrophone atf< 100 Hz, was significantly related to mean flow speed, turbulent kinetic energy, and turbulence dissipation rate (ε), agreeing with theoretical calculations for turbulence. Our results also show a similar relationship between ε andFNto what has been previously reported for ε vs. downward larval swimming velocity (wb), with bothFNandwbdemonstrating rapid growth at ε > 0.1 cm2s-3. These results suggest that reef turbulence and sounds may attract oyster larvae in complementary and synergistic ways.
Restraint of melanoma progression by cells in the local skin environment
Authors: Ma Yilun , Tagore Mohita , Hunter Miranda V. , Huang Ting-Hsiang , Montal Emily , Weiss Joshua M. , White Richard M.
Published: August 2024

Keratinocytes, the dominant cell type in the melanoma microenvironment during tumor initiation, exhibit diverse effects on melanoma progression. Using a zebrafish model of melanoma and human cell co-cultures, we observed that keratinocytes undergo an Epithelial–Mesenchymal Transition (EMT)-like transformation in the presence of melanoma, reminiscent of their behavior during wound healing. Surprisingly, overexpression of the EMT transcription factor Twist in keratinocytes led to improved overall survival in zebrafish melanoma models, despite no change in tumor initiation rates. This survival benefit was attributed to reduced melanoma invasion, as confirmed by human cell co-culture assays. Single-cell RNA-sequencing revealed a unique melanoma cell cluster in the Twist-overexpressing condition, exhibiting a more differentiated, less invasive phenotype. Further analysis nominated homotypic jam3b-jam3b and pgrn-sort1a interactions between Twist-overexpressing keratinocytes and melanoma cells as potential mediators of the invasive restraint. Our findings suggest that EMT in the tumor microenvironment (TME) may limit melanoma invasion through altered cell-cell interactions.
Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model
Authors: Liu Wendao , Zhao Zhongming
Published: August 2024

Immune cells undergo cytokine-driven polarization in respond to diverse stimuli. This process significantly modulates their transcriptional profiles and functional states. Although single-cell RNA sequencing (scRNA-seq) has advanced our understanding of immune responses across various diseases or conditions, currently there lacks a method to systematically examine cytokine effects and immune cell polarization. To address this gap, we developed Single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization analysis. Scupa is trained on data from the Immune Dictionary, which characterizes 66 cytokine-driven polarization states across 14 immune cell types. By leveraging the cell embeddings from the Universal Cell Embeddings model, Scupa effectively identifies polarized cells in new datasets generated from different species and experimental conditions. Applications of Scupa in independent datasets demonstrated its accuracy in classifying polarized cells and further revealed distinct polarization profiles in tumor-infiltrating myeloid cells across cancers. Scupa complements conventional single-cell data analysis by providing new insights into immune cell polarization, and it holds promise for assessing molecular effects or identifying therapeutic targets in cytokine-based therapies.
Sex differences in nucleus accumbens core circuitry engaged by binge-like ethanol drinking
Authors: Chan Amy E , Anderson Justin Q , Grigsby Kolter E , Jensen Bryan E , Ryabinin Andrey E , Ozburn Angela R
Published: August 2024

Growing parity in Alcohol Use Disorder (AUD) diagnoses in men and women necessitates consideration of sex as a biological variable. In humans and rodents, the nucleus accumbens core (NAcc) regulates alcohol binge drinking, a risk factor for developing AUD. We labeled NAcc inputs with a viral retrograde tracer and quantified whole-brain c-Fos to determine the regions and NAcc inputs differentially engaged in male and female mice during binge-like ethanol drinking. We found that binge-like ethanol drinking females had 129 brain areas with greater c-Fos than males. Moreover, ethanol engaged more NAcc inputs in binge-like ethanol drinking females (as compared with males), including GABAergic and glutamatergic inputs. Relative to water controls, ethanol increased network modularity and decreased connectivity in both sexes and did so more dramatically in males. These results demonstrate that early-stage binge-like ethanol drinking engages brain regions and NAcc-inputs and alters network dynamics in a sex-specific manner.
Ankle proprioception and the relationship to rigidity in Parkinsons disease
Authors: Sertic Jacquelyn , Kang Jason , MacKinnon Colum , Konczak Juergen
Published: August 2024

INTRODUCTION: Proprioceptive mechanoreceptor afferents form the basis for the perception of body position and muscle tone regulation. Parkinsons disease (PD) is associated with proprioceptive dysfunction. Proprioceptive dysfunction at the ankle impairs balance and gait. No comprehensive data exist characterizing the extent of ankle position sense dysfunction in PD and its relationship with abnormal muscle tone. OBJECTIVES: (1) Quantify ankle position sense acuity in PD. (2) Determine the relationship between ankle position sense and muscle rigidity. METHODS: Sixteen people with mild to moderate PD and 16 age-matched controls participated. PD participants were OFF medication during testing. Using a 2-forced-choice psychophysical paradigm, a participants ankle was passively rotated to two distinct positions: a reference of 15° plantarflexion and a smaller amplitude comparison position. Subsequently, the user verbally indicated which position was perceived as more plantarflexed. From the stimulus-response data a just-noticeable-difference (JND) threshold and uncertainty area (UA) were derived as measures of ankle position sense acuity. Muscle rigidity was assessed using the MDS-UPDRS III scale (item 3.3). RESULTS: Both median JND threshold (PD: 2.1°, controls: 1.5°) and UA (PD: 1.7°, controls: 1.1°) were significantly elevated in the PD group compared to controls (p < 0.05). Seven participants with PD (44%) had thresholds above the control group maximum. JND threshold correlated positively with lower extremity rigidity (rho; = 0.50, p = 0.047). CONCLUSION: PD can lead to reduced ankle position sense acuity. Lower proprioceptive acuity tended to be associated with higher rigidity suggesting that PD broadly alters proprioceptive signal processing affecting both perception and regulation of muscle tone.
Evaluation of a Scalable Design for a Pediatric Telemedicine and Medication Delivery Service: A Prospective Cohort Study in Haiti
Authors: Klarman Molly B , Chi Xiaofei , Cajusma Youseline , Flaherty Katelyn E , Beausejour Jude Ronald , Exantus Lerby , Beau de Rochars Valery M , Baril Chantale , Becker Torben K , Gurka Matthew J , Nelson Eric J
Published: August 2024

Objective. To evaluate a scalable pediatric telemedicine and medication delivery service (TMDS) that extends early healthcare access at households to avert emergencies. Study design. A TMDS in Haiti was configured for scalability by triaging severe cases to hospital-level care, non-severe cases with higher clinical uncertainty to in-person exams at households with medication delivery, and non-severe cases with low clinical uncertainty to medication delivery alone. This design was evaluated in a prospective cohort study conducted among pediatric patients (≤10 years). Clinical and operational metrics were compared to a formative reference study in which all non-severe patients received an in-person exam. The primary outcomes were reported rates of clinical improvement/recovery and in-person care seeking at 10-days. Results: 1043 cases (41 severe; 1002 non-severe) were enrolled in the scalable TMDS mode and 19% (190) of the non-severe cases received an in-person exam. 382 cases (24 severe, 358 non-severe) were enrolled in the reference study and 94% (338) of the non-severe cases received an in-person exam. At 10-days, rates of improvement were similar for the scalable (97%, 897) and reference (95%, 329) modes. Rates of participants who sought follow-up care were 15% (138) in the scalable mode and 24% (82) in the reference mode. Conclusion: In the context of a five-fold reduction of in-person exams, participants in the scalable TMDS mode had non-inferior rates of improvement at 10-days. These findings highlight an innovative and now scalable solution to improve early access to healthcare at households without compromising safety.
Target interception in virtual reality is better for natural versus unnatural trajectory shapes and orientations
Authors: Varon Sofia , Babin Karsten , Spering Miriam , Culham Jody C
Published: August 2024

Human performance in perceptual and visuomotor tasks is enhanced when stimulus motion follows the laws of gravitational physics, including acceleration consistent with Earth's gravity, g. Here we used a manual interception task in virtual reality to investigate the effects of trajectory shape and orientation on interception timing and accuracy. Participants punched to intercept a ball moving along one of four trajectories that varied in shape (parabola or tent) and orientation (upright or inverted). We also varied the location of visual fixation such that trajectories fell entirely within the lower or upper visual field. Reaction times were faster for more natural shapes and orientations, regardless of visual field. Overall accuracy was poorer and movement time was longer for the inverted tent condition than the other three conditions, perhaps because it was imperfectly reminiscent of a bouncing ball. A detailed analysis of spatial errors revealed that interception endpoints were more likely to fall along the path of the final trajectory in upright vs. inverted conditions, suggesting stronger expectations regarding the final trajectory direction for these conditions. Taken together, these results suggest that the naturalness of the shape and orientation of a trajectory contributes to performance in a virtual interception task.
Characterization of direct Purkinje cell outputs to the brainstem
Authors: Chen Christopher H. , Yao Zhiyi , Wu Shuting , Regehr Wade G.
Published: August 2024

Purkinje cells (PCs) primarily project to cerebellar nuclei but also directly innervate the brainstem. Some PC-brainstem projections have been described previously, but most have not been thoroughly characterized. Here we use a PC-specific cre line to anatomically and electrophysiologically characterize PC projections to the brainstem. PC synapses are surprisingly widespread, with the highest densities found in the vestibular and parabrachial nuclei. However, there are pronounced regional differences in synaptic densities within both the vestibular and parabrachial nuclei. Large optogenetically-evoked PC-IPSCs are preferentially observed in subregions with the highest densities of PC synapses, suggesting that PCs selectively influence these areas and the behaviors they regulate. Unexpectedly, the pontine central gray and nearby subnuclei also contained a low density of PC synapses, and large PC-IPSCs are observed in a small fraction of cells. We combined electrophysiological recordings with immunohistochemistry to assess the molecular identities of two putative PC targets: PC synapses onto mesencephalic trigeminal neurons were not observed even though these cells are in close proximity to PC boutons. PC synapses onto locus coeruleus neurons are exceedingly rare or absent, even though previous studies concluded that PCs are a major input to these neurons. The availability of a highly selective cre line for PCs allowed us to study functional synapses, while avoiding complications that can accompany the use of viral approaches. We conclude that PCs directly innervate numerous brainstem nuclei, but only inhibit a small fraction of cells in many nuclei. This suggests that PCs target cell types with specific behavioral roles in brainstem regions.
C-C chemokine receptor 4 deficiency exacerbates early atherosclerosis in mice
Authors: Tanaka Toru , Sasaki Naoto , Krisnanda Aga , Amin Hilman Zulkifli , Ito Ken , Horibe Sayo , Matsuo Kazuhiko , Hirata Ken-ichi , Nakayama Takashi , Rikitake Yoshiyuki
Published: August 2024

Chronic inflammation via dysregulation of T cell immune responses is critically involved in the pathogenesis of atherosclerotic cardiovascular disease. Improving the balance between proinflammatory T cells and anti-inflammatory regulatory T cells (Tregs) may be an attractive approach for treating atherosclerosis. Although C-C chemokine receptor 4 (CCR4) has been shown to mediate the recruitment of T cells to inflamed tissues, its role in atherosclerosis is unclear. Here, we show that genetic deletion of CCR4 in hypercholesterolemic mice accelerates the development of early atherosclerotic lesions characterized by an inflammatory plaque phenotype. This was associated with the augmentation of proinflammatory T helper type 1 (Th1) cell responses in peripheral lymphoid tissues, para-aortic lymph nodes, and atherosclerotic aorta. Mechanistically, CCR4 deficiency in Tregs impaired their suppressive function and tended to inhibit their migration to the atherosclerotic aorta, and subsequently augmented Th1 cell-mediated immune responses through defective regulation of dendritic cell function, which accelerated aortic inflammation and atherosclerotic lesion development. Thus, we revealed a previously unrecognized role for CCR4 in controlling the early stage of atherosclerosis via Treg-dependent regulation of proinflammatory T cell responses. Our data suggest that CCR4 is an important negative regulator of atherosclerosis.
Early Inflammation and Interferon Signaling Direct Enhanced Intestinal Crypt Regeneration after Proton FLASH Radiotherapy
Authors: Lim Tristan L , Morral Clara , Verginadis Ioannis I , Kim Kyle , Luo Leo , Foley Caitlin J , Kim Michele M , Li Ning , Yoshor Benjamin , Njah Kizito , Putt Mary , Oliaei Motlagh Seyyedeh Azar , Velalopoulou Anastasia , Chowdhury Priyanka , Bicher Sandra , Goia Denisa , Lengner Christopher J , Wrana Jeffery L , Koumenis Constantinos , Minn Andy J
Published: August 2024

Ultra-high dose rate ("FLASH") radiotherapy (>40-60 Gy/s) is a promising new radiation modality currently in human clinical trials. Previous studies showed that FLASH proton radiotherapy (FR) improves toxicity of normal tissues compared to standard proton radiotherapy (SR) without compromising anti-tumor effects. Understanding this normal tissue sparing effect may offer insight into how toxicities from cancer therapy can be improved. Here, we show that compared to SR, FR resulted in improved acute weight recovery and survival in mice after whole-abdomen irradiation. Improved morbidity and mortality after FR were associated with greater proliferation of damage-induced epithelial progenitor cells followed by improved tissue regeneration. FR led to the accelerated differentiation of revival stem cells (revSCs), a rare damage-induced stem cell required for intestinal regeneration, and to qualitative and quantitative changes in activity of signaling pathways important for revSC differentiation and epithelial regeneration. Specifically, FR resulted in greater infiltration of macrophages producing TGF-β, a cytokine important for revSC induction, that was coupled to augmented TGF-β signaling in revSCs. In pericryptal fibroblasts, FR resulted in greater type I IFN (IFN-I) signaling, which directly stimulates production of FGF growth factors supporting revSC proliferation. Accordingly, the ability of FR to improve epithelial regeneration and morbidity was dependent on IFN-I signaling. In the context of SR, however, IFN-I had a detrimental effect and promoted toxicity. Thus, a tissue-level signaling network coordinated by differences in IFN-I signaling and involving stromal cells, immune cells, and revSCs underlies the ability of FLASH to improve normal tissue toxicity without compromising anti-tumor efficacy.
cytoKernel: Robust kernel embeddings for assessing differential expression of single cell data
Authors: Ghosh Tusharkanti , Baxter Ryan M , Seal Souvik , Lui Victor G , Rudra Pratyaydipta , Vu Thao , Hsieh Elena WY , Ghosh Debashis
Published: August 2024

High-throughput sequencing of single-cell data can be used to rigorously evlauate cell specification and enable intricate variations between groups or conditions. Many popular existing methods for differential expression target differences in aggregate measurements (mean, median, sum) and limit their approaches to detect only global differential changes. We present a robust method for differential expression of single-cell data using a kernel-based score test, cytoKernel. cytoKernel is specifically designed to assess the differential expression of single cell RNA sequencing and high-dimensional flow or mass cytometry data using the full probability distribution pattern. cytoKernel is based on kernel embeddings which employs the probability distributions of the single cell data, by calculating the pairwise divergence/distance between distributions of subjects. It can detect both patterns involving aggregate changes, as well as more elusive variations that are often overlooked due to the multimodal characteristics of single cell data. We performed extensive benchmarks across both simulated and real data sets from mass cytometry data and single-cell RNA sequencing. The cytoKernel procedure effectively controls the False Discovery Rate (FDR) and shows favourable performance compared to existing methods. The method is able to identify more differential patterns than existing approaches. We apply cytoKernel to assess gene expression and protein marker expression differences from cell subpopulations in various publicly available single-cell RNAseq and mass cytometry data sets. The methods described in this paper are implemented in the open-source R package cytoKernel, which is freely available from Bioconductor at \url{http://bioconductor.org/packages/cytoKernel}.
Acute systemic macrophage depletion in osteoarthritic mice alleviates pain-related behaviors and does not affect joint damage
Authors: Geraghty Terese , Ishihara Shingo , Obeidat Alia M. , Adamczyk Natalie S. , Hunter Rahel S. , Li Jun , Wang Lai , Lee Hoomin , Ko Frank C. , Malfait Anne-Marie , Miller Rachel E.
Published: August 2024

Background

Osteoarthritis (OA) is a painful degenerative joint disease and a leading source of years lived with disability globally due to inadequate treatment options. Neuroimmune interactions reportedly contribute to OA pain pathogenesis. Notably, in rodents, macrophages in the DRG are associated with onset of persistent OA pain. Our objective was to determine the effects of acute systemic macrophage depletion on pain-related behaviors and joint damage using surgical mouse models in both sexes.

Methods

We depleted CSF1R+ macrophages by treating male macrophage Fas-induced apoptosis (MaFIA) transgenic mice 8-or 16-weekspostdestabilization of the medial meniscus (DMM) with AP20187 or vehicle control (10 mg/kgi.p., 1x/day for 5 days), or treating female MaFIA mice 12 weekspostpartial meniscectomy (PMX) with AP20187 or vehicle control. We measured pain-related behaviors 1-3 days before and after depletion, and, 3-4 days after the last injection we examined joint histopathology and performed flow cytometry of the dorsal root ganglia (DRGs). In a separate cohort of male 8-week DMM mice or age-matched naïve vehicle controls, we conducted DRG bulk RNA-sequencing analyses after the 5-day vehicle or AP20187 treatment.

Results

Eight-and 16-weekspostDMM in male mice, AP20187-induced macrophage depletion resulted in attenuated mechanical allodynia and knee hyperalgesia. Female mice showed alleviation of mechanical allodynia, knee hyperalgesia, and weight bearing deficits after macrophage depletion at 12 weekspostPMX. Macrophage depletion did not affect the degree of cartilage degeneration, osteophyte width, or synovitis in either sex. Flow cytometry of the DRG revealed that macrophages and neutrophils were reduced after AP20187 treatment. In addition, in the DRG, only MHCII+ M1-like macrophages were significantly decreased, while CD163+MHCII-M2-like macrophages were not affected in both sexes. DRG bulk RNA-seq revealed thatCxcl10andIl1bwere upregulated with DMM surgery compared to naïve mice, and downregulated in DMM after acute macrophage depletion.

Conclusions

Acute systemic macrophage depletion reduced the levels of pro-inflammatory macrophages in the DRG and alleviated pain-related behaviors in established surgically induced OA in mice of both sexes, without affecting joint damage. Overall, these studies provide insight into immune cell regulation in the DRG during OA.
Metabolic engineering improves transduction efficiency and downstream vector isolation by altering the lipid composition of extracellular vesicle-enclosed AAV.
Authors: Espinoza Paula , Cheng Ming , Ng Carrie , De La Cruz Demitri , Wasson Elizabeth D , McCarthy Deirdre M , Bhide Pradeep G , Maguire Casey A , Santoscoy Miguel C
Published: August 2024

Adeno-associated viruses (AAV) are promising vectors for gene therapy due to their efficacy in vivo. However, there is room for improvement to address key limitations such as the pre-existing immunity to AAV in patients, high-dose toxicity, and relatively low efficiency for some cell types. This study introduces a metabolic engineering approach, using knockout of the enzyme phosphatidylserine synthase 1 (PTDSS1) to increase the abundance of extracellular vesicle-enclosed AAV (EV-AAV) relative to free AAV in the supernatant of producer cells, simplifying downstream purification processes. The lipid-engineered HEK293T-ΔPTDSS1 cell line achieved a 42.7-fold enrichment of EV-AAV9 compared to free AAV9 in the supernatant. The rational genetic strategy also led to a 300-fold decrease of free AAV in supernatant compared to wild-type HEK293T. The membrane-engineered EV-AAV9 (mEV-AAV9) showed unique envelope composition alterations, including cholesterol enrichment and improved transduction efficiency in human AC16 cardiomyocytes by 1.5-fold compared to conventional EV-AAV9 and by 11-fold compared to non-enveloped AAV9. Robust in-vivo transduction four weeks after intraparenchymal administration of mEV-AAV9 was observed in the murine brain. This study shows promise in the potential of lipid metabolic engineering strategies to improve the efficiency and process development of enveloped gene delivery vectors. Keywords: membrane engineering, EV-AAV, upstream, downstream.
Mispitools: An R package for comprehensive statistical methods in Kinship Inference
Authors: Marsico Franco L.
Published: August 2024

The search for missing persons is a complex process that involves the comparison of data from two entities: unidentified persons (UP), who may be alive or deceased, and missing persons (MP), whose whereabouts are unknown. Although existing tools support DNA-based kinship analyses for the search, they typically do not integrate or statistically evaluate diverse lines of evidence collected throughout the investigative process. Examples of alternative lines of evidence are pigmentation traits, biological sex, and age, among others. The packageMispitoolsfills this gap by providing comprehensive statistical methods adapted to a holistic investigation workflow.Mispitoolssystematically assesses the data from each investigative stage, computing the statistical weight of various types of evidence through a likelihood ratio (LR) approach. It also provides models for combining obtained LRs. Furthermore,Mispitoolsoffers customized visualizations and a user-friendly interface, broadening its applicability among forensic practitioners and genealogical researchers.
Crosslink Strength Governs Yielding Behavior in Dynamically Crosslinked Hydrogels
Authors: Eckman Noah , Grosskopf Abigail K. , Jiang Grace , Kamani Krutarth , Huang Michelle S. , Schmittlein Brigitte , Heilshorn Sarah C. , Rogers Simon , Appel Eric A.
Published: August 2024

Yielding of dynamically crosslinked hydrogels, or transition between a solid-like and liquid-like state, allows facile injection and utility in translational biomedical applications including delivery of therapeutic cells. Unfortunately, characterizing the time-varying nature of the transition has not been attempted, nor are there design rules for understanding the effects of yielding on encapsulated cells. Here, we unveil underlying molecular mechanisms governing the yielding transition of dynamically crosslinked gels currently being researched for use in cell therapy. We demonstrate through nonlinear rheological characterization that the network dynamics of the dynamic hydrogels dictate the speed and character of their yielding transition. Rheological testing of these materials reveals unexpected elastic strain stiffening during yielding, as well as characterizing the rapidity of the yielding transition. A slower yielding speed explains enhanced protection of directly injected cells from shear forces, highlighting the importance of mechanical characterization of all phases of yield-stress biomaterials.

Significance Statement

Many direct-injection cell therapies suffer from poor viability of injected cells due to membrane disruption by shear stresses during injection. Injectable hydrogels with dynamic crosslinks can increase viability during injection, utilizing the ability of these materials to undergo a reversible solid-to-liquid shear-rate dependent yielding transition. Much effort has been applied to understanding the yielding transition of these materials, yet design rules for connecting the character of yielding to viability of injected cells has not been established. Here, we apply rheological testing to show that faster network dynamics result in a more gradual yielding transition, affording greater protection to cells during injection. This work introduces a new rheological protocol for the development of injectable hydrogels for cell therapy.
Stabilizing microtubules aids neurite structure and disrupts syncytia formation in human cytomegalovirus-infected human forebrain neurons
Authors: Adelman Jacob W , Sukowaty Andrew T , Partridge Kaitlyn J , Gawrys Jessica E. , Terhune Scott S. , Ebert Allison D.
Published: August 2024

Human cytomegalovirus (HCMV) is a prolific human herpesvirus that infects most individuals by adulthood. While typically asymptomatic in adults, congenital infection can induce serious neurological symptoms including hearing loss, visual deficits, cognitive impairment, and microcephaly in 10-15% of cases. HCMV has been shown to infect most neural cells with our group recently demonstrating this capacity in stem cell-derived forebrain neurons. Infection of neurons induces deleterious effects on calcium dynamics and electrophysiological function paired with gross restructuring of neuronal morphology. Here, we utilize an iPSC-derived model of the human forebrain to demonstrate how HCMV infection induces syncytia, drives neurite retraction, and remodels microtubule networks to promote viral production and release. We establish that HCMV downregulates microtubule associated proteins at 14 days postinfection while simultaneously sparing other cytoskeletal elements, and this includes HCMV-driven alterations to microtubule stability. Further, we pharmacologically modulate microtubule dynamics using paclitaxel (stabilize) and colchicine (destabilize) to examine the effects on neurite structure, syncytial morphology, assembly compartment formation, and viral release. With paclitaxel, we found improvement of neurite outgrowth with a corresponding disruption to HCMV-induced syncytia formation and Golgi network disruptions but with limited impact on viral titers. Together, these data suggest that HCMV infection-induced disruption of microtubules in human cortical neurons can be partially mitigated with microtubule stabilization, suggesting a potential avenue for future neuroprotective therapeutic exploration.

IMPORTANCE

Infection by human cytomegalovirus (HCMV) continues to cause significant damage to human health. In the absence of a vaccine, vertical transmission from mother to fetus can result in profound neurological damage impacting quality of life. These studies focus on understanding the impact of HCMV infection on forebrain cortical neurons derived from iPSCs. We show that infection results in loss of neurite extension accompanied by cell-to-cell fusion. These pathogenic changes involve HCMV infection-mediated disruption to the microtubule network. Upon addition of the microtubule stabilization agent paclitaxel, the structural damage was limited, but infection still progressed to produce infectious particles. This work is part of our continued efforts to define putative strategies to limit HCMV-induced neurological damage.
Evidence of persistent hyperphagia following a dietary weight-loss intervention in mice
Authors: Heyward Frankie D , Rosen Evan D
Published: August 2024

This study sought to determine whether the drive to regain weight following weight loss was truly long-lived in mice. We generated a model of reduced dietary obesity (ReDO) whereby male mice with diet-induced obesity (DIO) mice were calorically restricted until weight matched to control mice, and then after a 24-hour food assessment period were pair-fed relative to control mice. We subsequently generated ReDO mice that, after CR, were pair-fed relative to control mice for 0, 8, or 28 days, or chronically. Body weight, food intake, and select metabolic parameters were measured, along with whole hypothalamic Pomc gene expression. ReDO mice in both experiments exhibited hyperphagia following CR, while a persistent form of hyperphagia was detected in ReDO_8d and ReDO_28d mice relative to control and chronically pair-fed mice. 4-week initial weight gain on a high-fat diet was predictive of the degree of weight regain across ReDO_8d and ReDO_28d mice. In summary, this study showcases the perdurance of weight loss-associated hyperphagia and introduces a prognostic tool for identifying mice that are prone towards weight regain, while setting the stage for future inquiries into the neurobiological basis of persistent hunger following weight loss owed to a dietary intervention in mice.
A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)
Authors: Hookway Caroline , Borensztejn Antoine , Harris Leigh K. , Carlson Sara , Dalgin Gokhan , Mishra Suraj , Nivedita Nivedita , Adams Ellen M. , Barszczewski Tiffany , Dixon Julie C. , Edmonds Jacqueline H. , Ehlers Erik A. , Ferrante Alexandra J. , Fuqua Margaret A. , Garrison Philip , Gopalan Janani , Gregor Benjamin W. , Hedayati Maxwell J. , Klein Kyle N. , Leveille Chantelle L. , Meharry Sean L. , Morris Haley S. , Nadarajan Gouthamrajan , Oluoch Sandra A. , Parent Serge E. , Phan Amber , Roberts Brock , Sanchez Emmanuel E. , Sluzewski M. Filip , Snyder Lev S. , Thirstrup Derek J. , Thottam John Paul , Torvi Julia R. , Turman Gaea , Viana Matheus P. , Wilhelm Lyndsay , Wijesooriya Chamari S. , Yao Jie , Theriot Julie A. , Rafelski Susanne M. , Gunawardane Ruwanthi N.
Published: August 2024

The epithelial to mesenchymal transition (EMT) is a widely studied but poorly defined state change due to the variety of ways in which it has been characterized in cells. There is a need for reproducible cell model systems that enable the integration and comparison of different types of measured observations of cells across many distinct cellular contexts. We present human induced pluripotent stem (hiPS) cells as such a model system by demonstrating its utility through a comparative analysis of hiPS cell-EMT in 2D and 3D cell culture geometries. We developed live-imaging-based assays to directly compare examples of changes in cell function (via migration timing), molecular components (via expression of marker proteins), organization (via reorganization of cell junctions), and environment (via dynamics of basement membrane) in the same experimental system. The EMT-related changes we measured occurred earlier in 2D colonies than in 3D lumenoids, likely due to differences in the basement membrane environments associated with 2D vs. 3D initial hiPS cell culture geometries. We have made the 449 60-hour-long 3D time-lapse movies and the associated tools used for analysis and visualization open-source and easily accessible as a resource for future work in this field.
Measuring the effects of age on contrast suppression
Authors: Scott Martin T.W. , Wade Alex R , Baseler Heidi A
Published: August 2024

The apparent contrast of a suprathreshold central stimulus can be reduced by a surrounding stimulus - a phenomenon known as surround suppression. When stimuli are presented at the fovea, this effect reportedly increases in strength with age. The underlying mechanism proposed for this age dependence, a change in the balance of inhibition and excitation in cortex, makes this phenomenon potentially interesting as a biomarker of neurological dysfunction. Here, we attempt to repeat these measurements, but we use stimuli designed to control for untuned overlay masking, a different form of suppression thought to be of pre-cortical origin. We measured contrast matching thresholds in twenty younger (< 30) and seventeen older (>60) observers. Across all observers, we find weak suppression that has little or no orientation tuning and, importantly, no dependence on age. Our findings contradict those from earlier studies and suggest that effects relating to age may be dependent on the temporal parameters of this stimulus, and could arise from effects on other pre-cortical mechanisms.
Reconstituted high-density lipoproteins rescue diabetes-impaired endothelial cell metabolic reprograming and angiogenic responses to hypoxia
Authors: Primer Khalia Rose , Tan Joanne T.M. , Sandeman Lauren , Nankivell Victoria , Stretton Liam George , Solly Emma , Psaltis Peter James , Bursill Christina A
Published: August 2024

Objective: Impaired angiogenic responses to ischemia underlie diabetic vascular complications. Reconstituted high-density lipoproteins (rHDL) have proangiogenic effects in diabetes. The pyruvate dehydrogenase kinase 4 (PDK4)/pyruvate dehydrogenase complex (PDC) axis is an oxygen-conserving mechanism that preserves EC functions in hypoxia. We aimed to determine the role of the PDK4/PDC axis in angiogenesis, the effect of diabetes on its regulation in response to ischemia, and in the proangiogenic properties of rHDL. Approach and Results: In a murine wound healing model, PDK4 and pPDC were elevated early (24h) post induction of wound ischemia in non-diabetic wounds, which did not occur in diabetic mice. Topical rHDL rescued this impairment, enhancing PDK4 (68%, P<0.05) and pPDC (165%, P<0.01) in diabetic wounds. In parallel, wound neovascularization (62%, P<0.05) and closure (154%, P<0.0001) were increased in diabetic rHDL-treated wounds. In vitro, PDK4 and pPDC levels were increased in ECs exposed to hypoxia (65%, 70% respectively, P<0.05). High glucose did not elicit a further step-wise induction in PDK4/pPDC, with aberrant increases in mitochondrial respiration (19%, P<0.05), coupled with impaired EC angiogenic functions. Importantly, rHDL increased PDK4 and pPDC two-fold, returning mitochondrial respiration and EC angiogenic functions to normal glucose levels. In vitro, PDK4 siRNA knockdown attenuated the proangiogenic effects of rHDL. In vivo PDK4 inhibition ameliorated topical rHDL-mediated increases in wound angiogenesis and closure. Using chromatin immunoprecipitation, rHDL increased forkhead box O1 (FOXO1) binding to the PDK4 promoter and suppressed FOXO1 phosphorylation, presenting FOXO1 as a mechanism for the induction of PDK4 by rHDL. Conclusion: The PDK4/PDC axis response to ischemia is impaired in diabetes and important for the proangiogenic effects of rHDL.
Epigenetic Activation of the EBV Protein Kinase Determines Antiviral Drug Response in Central Nervous System Lymphoma
Authors: Weigel Christoph , Klimaszewski Haley L , Addissie Selamawit , Schlotter Sarah , Tounkara Fode , Dugan James P , Haverkos Bradley M , Villagomez Lynda , Lustberg Mark , Porcu Pierluigi , Voorhees Timothy , Caligiuri Michael A , Bumgardner Ginny , Oakes Christopher C , Baiocchi Robert A
Published: August 2024

Epstein-Barr virus (EBV)-associated central nervous system lymphoproliferative diseases (CNSL) are aggressive clinical conditions with poor prognosis. We have reported that durable responses in patients with primary CNS post-transplant lymphoproliferative disease (PTLD) were associated with detection of two ganciclovir (GCV)/zidovudine (AZT) viral drug target proteins, the EBV kinases BGLF4 and BXLF1 in CNSL biopsies. These are associated with lytic EBV and the mechanism for expression in latently infected EBV+ CNSL has been unknown. By carrying out RNA expression analysis in CNSL tissue biopsies (n=12), we confirmed expression of LMP1, BXLF1, and BGLF4, but not BZLF1, pointing to an incomplete lytic EBV program. Biopsies from systemic PTLD (n=24) were used for comparison and showed significantly less expression of BGLF4. By quantifying DNA methylation in EBV gene promoters we showed significantly decreased promoter methylation at BGLF4 in CNSL versus systemic PTLD (p=0.0006). Luciferase reporter analysis of the BGLF4 upstream sequence revealed 3 regions of promoter activity and 5ˈ RACE in n=4 EBV-infected cell lines and n=5 CNSL biopsy samples identified transcription start sites at these promoters. We identified DNA methylation loss at single CpG dinucleotides which were specifically demethylated in CNSL, while surrounding EBV methylation remained high. Lastly, TET knockout and expression of TET1/2-suppressive mutant IDH1 in a latent HEK293 EBV model indicated that active demethylation is necessary for activity of BGLF4 promoters. We detail the epigenetic basis of BGLF4 expression in CNSL via locus-specific promoter activation that may hold value for determination of antiviral drug sensitivity.